diff options
| author | Marius Bakke <mbakke@fastmail.com> | 2018-11-20 01:14:12 +0100 |
|---|---|---|
| committer | Marius Bakke <mbakke@fastmail.com> | 2018-11-20 01:14:12 +0100 |
| commit | 4f70db97a040b35f125484ce8885766ca5807dd4 (patch) | |
| tree | 30274f4a57e4a149127125fb6df626dd1d9f9cf0 /gnu/packages | |
| parent | 2d546858b139e5fcf2cbdf9958a17fd98803ac4c (diff) | |
| parent | 9acfe275adf1bc27483ba58c6d86a84ba20aa08f (diff) | |
| download | guix-4f70db97a040b35f125484ce8885766ca5807dd4.tar.gz | |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages')
33 files changed, 3618 insertions, 1017 deletions
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 45a3da1713..eea23bd621 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Andreas Enge <andreas@enge.fr> +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr> ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org> @@ -179,7 +179,7 @@ PARI is also available as a C library to allow for faster computations.") (define-public gp2c (package (name "gp2c") - (version "0.0.11") + (version "0.0.11pl1") (source (origin (method url-fetch) (uri (string-append @@ -187,7 +187,7 @@ PARI is also available as a C library to allow for faster computations.") version ".tar.gz")) (sha256 (base32 - "1z69xj2dpd8yyi8108rz26c50xpv0k2j8qnk0bzy1c5lw3pd1adm")))) + "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (inputs `(("pari-gp" ,pari-gp))) @@ -210,6 +210,36 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.") (license license:gpl2) (home-page "https://pari.math.u-bordeaux.fr/"))) +(define-public cmh + (package + (name "cmh") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://gforge.inria.fr/frs/download.php/33497/cmh-" + version ".tar.gz")) + (sha256 + (base32 + "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p")))) + (build-system gnu-build-system) + (inputs + `(("gmp" ,gmp) + ("mpfr" ,mpfr) + ("mpc" ,mpc) + ("mpfrcx" ,mpfrcx) + ("fplll" ,fplll) + ("pari-gp" ,pari-gp))) + (synopsis "Igusa class polynomial computations") + (description + "The CMH software computes Igusa (genus 2) class polynomials, which +parameterize the CM points in the moduli space of 2-dimensional abelian +varieties, i.e. Jacobians of hyperelliptic curves. +It can also be used to compute theta constants at arbitrary +precision.") + (license license:gpl3+) + (home-page "http://cmh.gforge.inria.fr/"))) + (define-public giac-xcas (package (name "giac-xcas") diff --git a/gnu/packages/antivirus.scm b/gnu/packages/antivirus.scm new file mode 100644 index 0000000000..95749761bd --- /dev/null +++ b/gnu/packages/antivirus.scm @@ -0,0 +1,156 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2018 Christopher Baines <mail@cbaines.net> +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. + +(define-module (gnu packages antivirus) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix build-system gnu) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix utils) + #:use-module (gnu packages) + #:use-module (gnu packages autotools) + #:use-module (gnu packages bison) + #:use-module (gnu packages check) + #:use-module (gnu packages compression) + #:use-module (gnu packages curl) + #:use-module (gnu packages cyrus-sasl) + #:use-module (gnu packages flex) + #:use-module (gnu packages llvm) + #:use-module (gnu packages multiprecision) + #:use-module (gnu packages ncurses) + #:use-module (gnu packages pcre) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages tls) + #:use-module (gnu packages web) + #:use-module (gnu packages xml)) + +(define-public clamav + (package + (name "clamav") + (version "0.100.2") + (source (origin + (method url-fetch) + (uri (string-append "https://www.clamav.net/downloads/production/" + "clamav-" version ".tar.gz")) + (sha256 + (base32 + "1mkd41sxbjkfjinpx5b9kb85q529gj2s3d0klysssqhysh64ybja")) + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file-recursively + '("win32" ;unnecessary + "libclamav/c++/llvm" ;use system llvm + "libclamunrar")))) ;non-free license + (patches + (search-patches "clamav-system-tomsfastmath.patch" + "clamav-config-llvm-libs.patch")))) + (build-system gnu-build-system) + (native-inputs + `(("bison" ,bison) + ("check" ,check) ;for tests + ("flex" ,flex) + ("pkg-config" ,pkg-config) + ;; The tomsfastmath patch touches configure.ac and Makefile.am + ("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("bzip2" ,bzip2) + ("libcurl" ,curl) + ("libjson" ,json-c) + ("libltdl" ,libltdl) + ("libmspack" ,libmspack) + ("llvm" ,llvm-3.6) ;requires <3.7, for JIT/verifier + ("ncurses" ,ncurses) + ("openssl" ,libressl) + ("pcre" ,pcre "bin") ;for pcre-config + ("sasl" ,cyrus-sasl) ;for linking curl with libtool + ("tomsfastmath" ,tomsfastmath) + ("xml" ,libxml2) + ("zlib" ,zlib))) + (arguments + `(#:configure-flags + (let-syntax ((with (syntax-rules () + ((_ name) + (string-append "--with-" name "=" + (assoc-ref %build-inputs name)))))) + (list "--disable-unrar" + "--enable-llvm" + "--with-system-llvm" + "--with-system-libmspack" + "--without-included-ltdl" + (with "xml") + (with "openssl") + (with "libjson") + (with "pcre") + (with "zlib") + (with "libcurl") + ;; For sanity, specifying --enable-* flags turns + ;; "support unavailable" warnings into errors. + "--enable-bzip2" + "--enable-check" + "--sysconfdir=/etc/clamav" + ;; Default database directory needs to be writeable + "--with-dbdir=/var/db/clamav")) + ;; install sample .conf files to %output/etc rather than /etc/clamav + #:make-flags (list (string-append "sysconfdir=" %output "/etc")) + #:phases (modify-phases %standard-phases + (add-after 'unpack 'reconf + (lambda _ (zero? (system* "autoreconf" "-vfi")))) + (add-before 'configure 'patch-llvm-config + (lambda _ + (substitute* '("libclamav/c++/detect.cpp" + "libclamav/c++/ClamBCRTChecks.cpp" + "libclamav/c++/bytecode2llvm.cpp") + (("llvm/Config/config.h") "llvm/Config/llvm-config.h")) + ;; `llvm-config --libfiles` inappropriately lists lib*.a + ;; libraries, rather than the lib*.so's that our llvm + ;; contains. They're used only for listing extra build + ;; dependencies, so ignore them until that's fixed. + (substitute* "libclamav/c++/Makefile.in" + (("@LLVMCONFIG_LIBFILES@") "")) + #t)) + (add-before 'check 'skip-clamd-tests + ;; XXX: The check?_clamd tests fail inside the build + ;; chroot, but pass outside. + (lambda _ + (substitute* "unit_tests/Makefile" + (("check2_clamd.sh.*check4_clamd.sh") "")) + #t))))) + (home-page "https://www.clamav.net") + (synopsis "Antivirus engine") + (description + "Clam AntiVirus is an anti-virus toolkit, designed especially for e-mail +scanning on mail gateways. It provides a number of utilities including a +flexible and scalable multi-threaded daemon, a command line scanner, and +advanced tool for automatic database updates. The core of the package is an +anti-virus engine available in the form of a shared library.") + (license (list license:gpl2+ ;ClamAV itself + license:lgpl2.1 ;libclamav/mspack.[ch] + license:public-domain ;libclamav/7z/*, libclamav/rijndael.[ch], etc... + (package-license bzip2) ;modified bzip2 source in libclamav/nsis + license:bsd-2 ;several files in libclamav + license:bsd-3 ;libclamav/{regex,qsort.c,swf.[ch] + license:ncsa ;libclamav/c++/PointerTracking.cpp + license:zlib ;libclamav/inf*.h + license:x11 ;libclamav/lzw + (license:non-copyleft "libclamav/strlcat.c") ;"OpenBSD" license + license:asl2.0 ;libclamav/yara* + license:expat)))) ;shared/getopt.[ch] diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 2e1b0467c3..7883834d18 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org> ;;; Copyright © 2018 Brett Gilio <brettg@posteo.net> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -427,6 +428,46 @@ and editing digital audio. It features digital effects and spectrum analysis tools.") (license license:gpl2+))) +(define-public autotalent + (package + (name "autotalent") + (version "0.2") + (source (origin + (method url-fetch) + (uri (string-append "http://tombaran.info/autotalent-" + version ".tar.gz")) + (sha256 + (base32 + "1n04qm66f14195ly6gsy3ra7v2j7zad5n19d8dwfmh0qs6h9hphh")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + ;; no configure script + (delete 'configure) + (add-before 'install 'prepare-target-directory + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa")) + #t)) + (add-after 'unpack 'override-target-directory + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("/usr/lib64/ladspa") + (string-append (assoc-ref outputs "out") "/lib/ladspa"))) + #t))))) + (inputs + `(("ladspa" ,ladspa))) + (home-page "http://tombaran.info/autotalent.html") + (synopsis "Pitch-correction LADSPA audio plugin") + (description + "Autotalent is a LADSPA plugin for real-time pitch-correction. Among its +controls are allowable notes, strength of correction, LFO for vibrato and +formant warp.") + ;; All code except the FFT routine is licensed under GPLv2+. + ;; The FFT routine is under BSD-3. + (license (list license:gpl2+)))) + (define-public azr3 (package (name "azr3") @@ -514,6 +555,47 @@ tools (analyzer, mono/stereo tools, crossovers).") ;; The plugins are released under LGPLv2.1+ (license (list license:lgpl2.1+ license:gpl2+)))) +(define-public caps-plugins-lv2 + (package + (name "caps-plugins-lv2") + (version "0.9.24") ; version that has been ported. + (source + (origin + ;; The Github project hasn't tagged a release. + (method git-fetch) + (uri (git-reference + ;; Actually https://github.com/moddevices/caps-lv2.git, but it's + ;; missing fixes for newer glibc, so using the origin of a pull + ;; request regarding this issue: + (url "https://github.com/jujudusud/caps-lv2.git") + (commit "9c9478b7fbd8f9714f552ebe2a6866398b0babfb"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1idfnazin3cca41zw1a8vwgnxjnkrap7bxxjamjqvgpmvydgcam1")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + ;; no configure script + (delete 'configure) + (add-after 'unpack 'override-target-directory + (lambda* (#:key outputs #:allow-other-keys) + (substitute* (find-files "plugins" "Makefile") + (("/usr/local")(assoc-ref outputs "out"))) + #t))))) + (inputs + `(("lv2" ,lv2))) + ;; home-page of the original LADSPA version: http://quitte.de/dsp/caps.html + (home-page "https://github.com/moddevices/caps-lv2") + (synopsis "LV2 port of the CAPS audio plugin colection") + (description + "LV2 port of CAPS, a collection of audio plugins comprising basic virtual +guitar amplification and a small range of classic effects, signal processors and +generators of mostly elementary and occasionally exotic nature.") + (license license:gpl3+))) + (define-public espeak (package (name "espeak") @@ -1045,7 +1127,7 @@ follower.") (define-public fluidsynth (package (name "fluidsynth") - (version "2.0.1") + (version "2.0.2") (source (origin (method git-fetch) (uri (git-reference @@ -1054,7 +1136,7 @@ follower.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1mqyym5qkh8xd1rqj3yhfxbw5dxjcrljb6nkfqzvcarlv4h6rjn7")))) + "02vs5sfsyh1dl7wlcvgs4w3x0qcmsl7vi000qgp99ynwh3wjb274")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no check target @@ -1193,7 +1275,7 @@ PS, and DAB+.") `(list (string-append "prefix=" (assoc-ref %outputs "out")) "world")))) (native-inputs - `(("llvm" ,llvm-3.8-with-rtti) + `(("llvm" ,llvm-3.8) ("which" ,which) ("xxd" ,xxd) ("ctags" ,emacs-minimal) ; for ctags @@ -3522,3 +3604,37 @@ using ALSA, MPD, PulseAudio, or a FIFO buffer as its input.") (synopsis "Pro-quality GM soundfont") (description "Fluid-3 is Frank Wen's pro-quality GM soundfont.") (license license:expat)))) + +(define-public libfdk + (let ((commit "2326faaf8f2cdf2c3a9108ccdaf1d7551aec543e") + (revision "0")) + (package + (name "libfdk") + ;; The latest upstream revision, with many bug fixes. + (version (git-version "0.1.6" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mstorsjo/fdk-aac") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0yy6ndd9d61bwl283vl1r5kva2a4acc0f4r9g0sza156f2abr9ws")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (home-page "https://github.com/mstorsjo/fdk-aac") + (synopsis "Fraunhofer FDK AAC library") + (description "FDK is a library for encoding and decoding Advanced Audio +Coding (AAC) format audio, developed by Fraunhofer IIS, and included as part of +Android. It supports several Audio Object Types including MPEG-2 and MPEG-4 AAC +LC, HE-AAC (AAC LC + SBR), HE-AACv2 (LC + SBR + PS) as well AAC-LD (low delay) +and AAC-ELD (enhanced low delay) for real-time communication. The encoding +library supports sample rates up to 96 kHz and up to eight channels (7.1 +surround).") + (license (license:fsf-free "https://github.com/mstorsjo/fdk-aac/blob/master/NOTICE" + "https://www.gnu.org/licenses/license-list.html#fdk"))))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 28b6cd318b..b913d5647d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7380,13 +7380,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1xqpgngd8by0yn627v9kz26a03v5a1lhcfwlnx2i0ivplk9bd40s")))) + "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -9748,14 +9748,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0nnlydpklmv9kwlk3gkjgabx7l6y4gav3imq98w8wskb1fhm50c0")))) + "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -10223,14 +10223,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1js05dcv1dj4g2vj7lzlg0rgjcjlk2irdr9rxqpwxmivm8nbvf36")))) + "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -11166,7 +11166,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (define-public sambamba (package (name "sambamba") - (version "0.6.7-10-g223fa20") + (version "0.6.8") (source (origin (method git-fetch) @@ -11176,7 +11176,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn")))) + "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there is no test target @@ -11187,9 +11187,10 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (add-after 'unpack 'fix-ldc-version (lambda _ (substitute* "gen_ldc_version_info.py" - (("/usr/bin/env.*") (which "python"))) + (("/usr/bin/env.*") (which "python3"))) (substitute* "Makefile" - (("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) + ;; We use ldc2 instead of ldmd2 to compile sambamba. + (("\\$\\(shell which ldmd2\\)") (which "ldc2"))) #t)) (add-after 'unpack 'place-biod-and-undead (lambda* (#:key inputs #:allow-other-keys) @@ -11201,21 +11202,21 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (substitute* "Makefile" (("htslib/libhts.a lz4/lib/liblz4.a") "-L-lhts -L-llz4") - ((" htslib-static lz4-static") "")) + ((" lz4-static htslib-static") "")) #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) (mkdir-p bin) - (install-file "build/sambamba" bin) + (install-file "bin/sambamba" bin) #t)))))) (native-inputs `(("ldc" ,ldc) ("rdmd" ,rdmd) - ("python" ,python2-minimal) + ("python" ,python-minimal) ("biod" - ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6")) + ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e")) (origin (method git-fetch) (uri (git-reference @@ -11226,20 +11227,20 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") "-checkout")) (sha256 (base32 - "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37"))))) + "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426"))))) ("undead" - ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89")) + ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d")) (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dlang/undeaD.git") + (url "https://github.com/biod/undeaD.git") (commit commit))) (file-name (string-append "undead-" (string-take commit 9) "-checkout")) (sha256 (base32 - "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138"))))))) + "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d"))))))) (inputs `(("lz4" ,lz4) ("htslib" ,htslib-for-sambamba))) @@ -14376,3 +14377,77 @@ both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.") (license (list license:gpl3 ;filtlong license:asl2.0))))) ;histogram.py + +(define-public nanopolish + ;; The recommended way to install is to clone the git repository + ;; <https://github.com/jts/nanopolish#installing-a-particular-release>. + ;; Also, the differences between release and current version seem to be + ;; significant. + (let ((commit "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d") + (revision "1")) + (package + (name "nanopolish") + (version (git-version "0.10.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jts/nanopolish.git") + (commit commit) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc") + #:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-eigen + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CPATH" + (string-append (assoc-ref inputs "eigen") + "/include/eigen3")) + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (scripts (string-append out "/share/nanopolish/scripts"))) + + (install-file "nanopolish" bin) + (for-each (lambda (file) (install-file file scripts)) + (find-files "scripts" ".*")) + #t))) + (add-after 'install 'wrap-programs + (lambda* (#:key outputs #:allow-other-keys) + (for-each (lambda (file) + (wrap-program file `("PYTHONPATH" ":" prefix (,path)))) + (find-files "/share/nanopolish/scripts" "\\.py")) + (for-each (lambda (file) + (wrap-program file `("PERL5LIB" ":" prefix (,path)))) + (find-files "/share/nanopolish/scripts" "\\.pl")) + #t))))) + (inputs + `(("eigen" ,eigen) + ("hdf5" ,hdf5) + ("htslib" ,htslib) + ("perl" ,perl) + ("python" ,python) + ("python-biopython" ,python-biopython) + ("python-numpy" ,python-numpy) + ("python-pysam" ,python-pysam) + ("python-scikit-learn" , python-scikit-learn) + ("python-scipy" ,python-scipy) + ("zlib" ,zlib))) + (home-page "https://github.com/jts/nanopolish") + (synopsis "Signal-level analysis of Oxford Nanopore sequencing data") + (description + "This package analyses the Oxford Nanopore sequencing data at signal-level. +Nanopolish can calculate an improved consensus sequence for a draft genome +assembly, detect base modifications, call SNPs (Single nucleotide +polymorphisms) and indels with respect to a reference genome and more.") + (license license:expat)))) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 8038c18326..d6e38bb0b8 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages bison) #:use-module (gnu packages cdrom) #:use-module (gnu packages check) + #:use-module (gnu packages compression) #:use-module (gnu packages cross-base) #:use-module (gnu packages disk) #:use-module (gnu packages firmware) @@ -361,7 +362,7 @@ tree binary files. These are board description files used by Linux and BSD.") (define u-boot (package (name "u-boot") - (version "2018.09") + (version "2018.11") (source (origin (method url-fetch) (uri (string-append @@ -369,12 +370,13 @@ tree binary files. These are board description files used by Linux and BSD.") "u-boot-" version ".tar.bz2")) (sha256 (base32 - "0s122kyz1svvs2yjzj4j9qravl3ra4vn0fjqgski7rlczqyg56w3")))) + "0znkwljfwwn4y7j20pzz4ilqw8znphrfxns0x1lwdzh3xbr96z3k")))) (native-inputs `(("bc" ,bc) ("bison" ,bison) ("dtc" ,dtc) ("flex" ,flex) + ("lz4" ,lz4) ("openssl" ,openssl) ("python-2" ,python-2) ("python2-coverage" ,python2-coverage) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6ce9bdd16f..f08a204fb8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1593,14 +1593,14 @@ the Kaplan-Meier and Aalen-Johansen methods.") (define-public r-dimred (package (name "r-dimred") - (version "0.1.0") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 - "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v")))) + "0ssy2qriiy6zdawriqcbl67qiq68ipml3frq7aqlq70r2fqyyw48")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs `(("r-drr" ,r-drr))) @@ -1864,14 +1864,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "1vqh3pxs4n1azhnd1lzg91vasya6g323kllhbrw177j7kdxqyimy")))) + "0bwijw4427v2k5z3qci2kyr5dyzql8b3lvf88rwy16p741jckjsn")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -4450,14 +4450,14 @@ and adds the annotation to the plot.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.1.9") + (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "0rvfgii2gxarra7d33n6c63ky0mivxxyx35acsrn94xkbd8mbcsj")))) + "0rkpcjb1x7lvhj68aam5airbi534jqyiq12x5xk40a25iifhghq6")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -6725,14 +6725,14 @@ detection, parallelism through BLAS and parallel user templates.") (define-public r-sjstats (package (name "r-sjstats") - (version "0.17.1") + (version "0.17.2") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 - "0s9b0xr8gmcm0kh48jkwk8ns0lqknd8kpys4f7czf0xwzmcx2n1z")))) + "0c7g35vn7r9rylhp0gj1yfslg7jybwrhpqpp7vdcd90xfccih24r")))) (build-system r-build-system) (propagated-inputs `(("r-bayesplot" ,r-bayesplot) @@ -6803,14 +6803,14 @@ differentiation.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "00l02g7yssqxmcmbrzk2wsj3i9ywd0xsy0rmbfh57q1qi76a1wq1")))) + "070c3fxmzajq2fy816s5pfqdyjlnzkabj97z7fcsva4h5rnqi9d6")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) @@ -7499,14 +7499,14 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.3") + (version "1.30.4") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 (base32 - "0mfvx1xzsgiag9p42kdyqg8fvajyakrdy3z2smhdlaawzbi0qmax")))) + "0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiocManager/") diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 3e32998a9f..ce1add3915 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -3659,7 +3659,11 @@ after buffer changes.") version ".tar")) (sha256 (base32 - "108wgxg7fb4byaiasgvbxv2hq7b00biq9f0mh9hy6vw4160y5w24")))) + "108wgxg7fb4byaiasgvbxv2hq7b00biq9f0mh9hy6vw4160y5w24")) + (patches + ;; Patch awaiting inclusion upstream (see: + ;; https://github.com/realgud/realgud/pull/226). + (search-patches "emacs-realgud-fix-configure-ac.patch")))) (build-system emacs-build-system) (arguments `(#:tests? #t diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 1f73025db7..34a015bdf7 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -397,7 +397,7 @@ support.") (define-public tiled (package (name "tiled") - (version "1.2.0") + (version "1.2.1") (source (origin (method git-fetch) (uri (git-reference @@ -406,7 +406,7 @@ support.") (file-name (git-file-name name version)) (sha256 (base32 - "1rra48hlkcgqxwxi802fb182p1q0723c9hhfvkd5inz9467idd4c")))) + "1dl06k2p0r7l20ghxcq5sn7j0jl2l8q4m27vmfs2qfgvldjll2h3")))) (build-system gnu-build-system) (inputs `(("qtbase" ,qtbase) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 3679aa09c6..bc5d3d581b 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5606,8 +5606,8 @@ quotation from a collection of quotes.") (lambda* (#:key outputs inputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (data (assoc-ref inputs "xonotic-data"))) - (copy-recursively (string-append data "/share/xonotic") - (string-append out "/share/xonotic")) + (symlink (string-append data "/share/xonotic") + (string-append out "/share/xonotic")) #t))) (add-after 'install-binaries 'wrap-binaries (lambda* (#:key outputs inputs #:allow-other-keys) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index 03c8b497b8..851a31447b 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -259,7 +259,8 @@ also known as DXTn or DXTC) for Mesa.") ("libxvmc" ,libxvmc) ,@(match (%current-system) ((or "x86_64-linux" "i686-linux") - `(("llvm" ,llvm))) + ;; FIXME: Change to 'llvm' in the next rebuild cycle. + `(("llvm" ,llvm-without-rtti))) (_ `())) ("makedepend" ,makedepend) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index f3eb2dcd36..022ac5ee24 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -2286,8 +2286,8 @@ Guile.") ;; There has not been any release yet. (define-public guile-newt - (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83") - (revision "1")) + (let ((commit "a73889c57b0572347f7641facdb1bcf08922feff") + (revision "2")) (package (name "guile-newt") (version (string-append "0-" revision "." (string-take commit 9))) @@ -2299,7 +2299,7 @@ Guile.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0ww7jbdsmjlsxm60ym6cb5s5kc4ljz8bn4y2lvcqnap0aihqfk10")))) + "0k37vir22r2sq121lyy74grfai4643s7kr55z01k4j0bh27i06c3")))) (build-system gnu-build-system) (arguments '(#:make-flags diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 11e1b1539b..5503e5dd19 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -900,7 +900,7 @@ language bindings to VIGRA.") (define-public libwebp (package (name "libwebp") - (version "1.0.0") + (version "1.0.1") (source (origin ;; No tarballs are provided for >0.6.1. @@ -911,7 +911,7 @@ language bindings to VIGRA.") (file-name (git-file-name name version)) (sha256 (base32 - "1w8jzdbr1s4238ygyrlxryycss3f2z6d9amxdq8m82nl3l6skar4")))) + "09l4pq4k2acglkmwr96arn79rssl54sv7vrdrgsxqlg7v8c882zh")))) (build-system gnu-build-system) (inputs `(("freeglut" ,freeglut) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 51baade8fd..97d36c72d3 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1988,151 +1988,6 @@ new Date();")) `(("java-junit" ,java-junit) ,@(package-inputs ant/java8))))) -(define-public clojure - (let* ((remove-archives '(begin - (for-each delete-file - (find-files "." ".*\\.(jar|zip)")) - #t)) - (submodule (lambda (prefix version hash) - (origin - (method url-fetch) - (uri (string-append "https://github.com/clojure/" - prefix version ".tar.gz")) - (sha256 (base32 hash)) - (modules '((guix build utils))) - (snippet remove-archives))))) - (package - (name "clojure") - (version "1.9.0") - (source - (origin - (method url-fetch) - (uri - (string-append "https://github.com/clojure/clojure/archive/clojure-" - version ".tar.gz")) - (sha256 - (base32 "0xjbzcw45z32vsn9pifp7ndysjzqswp5ig0jkjpivigh2ckkdzha")) - (modules '((guix build utils))) - (snippet remove-archives))) - (build-system ant-build-system) - (arguments - `(#:modules ((guix build ant-build-system) - (guix build utils) - (ice-9 ftw) - (ice-9 regex) - (srfi srfi-1) - (srfi srfi-26)) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (for-each - (lambda (name) - (mkdir-p name) - (with-directory-excursion name - (invoke "tar" - ;; Use xz for repacked tarball. - "--xz" - "--extract" - "--verbose" - "--file" (assoc-ref inputs name) - "--strip-components=1")) - (copy-recursively (string-append name "/src/main/clojure/") - "src/clj/")) - '("core-specs-alpha-src" - "data-generators-src" - "spec-alpha-src" - "test-check-src" - "test-generative-src" - "tools-namespace-src")) - #t)) - (add-after 'unpack 'fix-manifest-classpath - (lambda _ - (substitute* "build.xml" - (("<attribute name=\"Class-Path\" value=\".\"/>") "")) - #t)) - ;; The javadoc target is not built by default. - (add-after 'build 'build-doc - (lambda _ - (invoke "ant" "javadoc"))) - ;; Needed since no install target is provided. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((java-dir (string-append (assoc-ref outputs "out") - "/share/java/"))) - ;; Install versioned to avoid collisions. - (install-file (string-append "clojure-" ,version ".jar") - java-dir) - #t))) - ;; Needed since no install-doc target is provided. - (add-after 'install 'install-doc - (lambda* (#:key outputs #:allow-other-keys) - (let ((doc-dir (string-append (assoc-ref outputs "out") - "/share/doc/clojure-" - ,version "/"))) - (copy-recursively "doc/clojure" doc-dir) - (copy-recursively "target/javadoc/" - (string-append doc-dir "javadoc/")) - (for-each (cut install-file <> doc-dir) - (filter (cut string-match - ".*\\.(html|markdown|md|txt)" - <>) - (scandir "./"))) - #t)))))) - ;; The native-inputs below are needed to run the tests. - (native-inputs - `(("core-specs-alpha-src" - ,(submodule "core.specs.alpha/archive/core.specs.alpha-" - "0.1.24" - "0v2a0svf1ar2y42ajxwsjr7zmm5j7pp2zwrd2jh3k7xzd1p9x1fv")) - ("data-generators-src" - ,(submodule "data.generators/archive/data.generators-" - "0.1.2" - "0kki093jp4ckwxzfnw8ylflrfqs8b1i1wi9iapmwcsy328dmgzp1")) - ("spec-alpha-src" - ,(submodule "spec.alpha/archive/spec.alpha-" - "0.1.143" - "00alf0347licdn773w2jarpllyrbl52qz4d8mw61anjksacxylzz")) - ("test-check-src" - ,(submodule "test.check/archive/test.check-" - "0.9.0" - "0p0mnyhr442bzkz0s4k5ra3i6l5lc7kp6ajaqkkyh4c2k5yck1md")) - ("test-generative-src" - ,(submodule "test.generative/archive/test.generative-" - "0.5.2" - "1pjafy1i7yblc7ixmcpfq1lfbyf3jaljvkgrajn70sws9xs7a9f8")) - ("tools-namespace-src" - ,(submodule "tools.namespace/archive/tools.namespace-" - "0.2.11" - "10baak8v0hnwz2hr33bavshm7y49mmn9zsyyms1dwjz45p5ymhy0")))) - (home-page "https://clojure.org/") - (synopsis "Lisp dialect running on the JVM") - (description "Clojure is a dynamic, general-purpose programming language, -combining the approachability and interactive development of a scripting -language with an efficient and robust infrastructure for multithreaded -programming. Clojure is a compiled language, yet remains completely dynamic -– every feature supported by Clojure is supported at runtime. Clojure -provides easy access to the Java frameworks, with optional type hints and type -inference, to ensure that calls to Java can avoid reflection. - -Clojure is a dialect of Lisp, and shares with Lisp the code-as-data philosophy -and a powerful macro system. Clojure is predominantly a functional programming -language, and features a rich set of immutable, persistent data structures. -When mutable state is needed, Clojure offers a software transactional memory -system and reactive Agent system that ensure clean, correct, multithreaded -designs.") - ;; Clojure is licensed under EPL1.0 - ;; ASM bytecode manipulation library is licensed under BSD-3 - ;; Guava Murmur3 hash implementation is licensed under APL2.0 - ;; src/clj/repl.clj is licensed under CPL1.0 - ;; - ;; See readme.html or readme.txt for details. - (license (list license:epl1.0 - license:bsd-3 - license:asl2.0 - license:cpl1.0))))) - (define-public javacc-4 (package (name "javacc") diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index bdad1602b9..661b7ed2ca 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -400,8 +400,8 @@ It has been modified to remove all non-free binary blobs.") ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.19.1") -(define %linux-libre-hash "12mrrgg2ih4jiylpy45q5nsd8afj3nya0klr543s0mcga88v9527") +(define %linux-libre-version "4.19.2") +(define %linux-libre-hash "1yh4ll9qh4wmf9r62ksyic57g1iy1b84qbv855l545ilk12znbmj") (define %linux-libre-4.19-patches (list %boot-logo-patch @@ -423,8 +423,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-4.19-patches #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.80") -(define %linux-libre-4.14-hash "0h4hi5lqizdx5nk0f3immbcv2n7p5jh26m80v4x6bw4wi5b44fra") +(define %linux-libre-4.14-version "4.14.81") +(define %linux-libre-4.14-hash "0vxs8k7ka8aqnn1fcr88bhr07wa5jg83pq1rcjby9k422mbv254q") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version @@ -433,8 +433,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.136" - "1kk6px1jcwbgkpfmf9pdklk6kz90h5l8fvdqwmvnk4bz6b2xrrfp" + (make-linux-libre "4.9.137" + "1d8313r2k0qr4x7nqlnbwn5lzfc7dz6w8sfg47jml1q38c2fyjf2" %intel-compatible-systems #:configuration-file kernel-config)) @@ -3188,7 +3188,7 @@ is flexible, efficient and uses a modular implementation.") (define-public fuse-exfat (package (name "fuse-exfat") - (version "1.2.8") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append @@ -3196,7 +3196,7 @@ is flexible, efficient and uses a modular implementation.") version "/" name "-" version ".tar.gz")) (sha256 (base32 - "1jwnxw0bg9v5ij8xvbg4xpjr50nykq8a1lmc2xkblz204rq7wd8z")))) + "1lz00q8g4590mrdqmf13ba1s9zrqq645ymgm5p9y99ad0qv22r87")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 9fb25a15a2..6849cdd2bf 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Benjamin Slade <slade@jnanam.net> +;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -34,6 +35,8 @@ #:use-module (guix hg-download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system ant) + #:use-module (guix build-system clojure) #:use-module (guix build-system asdf) #:use-module (guix build-system trivial) #:use-module (gnu packages admin) @@ -530,8 +533,12 @@ statistical profiler, a code coverage tool, and many other extensions.") (install-file kernel libdir) (install-file heap libdir) - (let ((dirs '("lib" "library" "examples" "contrib" - "tools" "objc-bridge"))) + (let ((dirs '("lib" "library" "examples" "tools" "objc-bridge" + ,(match (%current-system) + ("x86_64-linux" + "x86-headers64") + ("i686-linux" + "x86-headers"))))) (for-each copy-recursively dirs (map (cut string-append libdir <>) dirs))) @@ -559,6 +566,119 @@ interface.") (license (list license:lgpl2.1 license:clarified-artistic)))) ;TRIVIAL-LDAP package +(define-public clojure + (let* ((lib (lambda (prefix version hash) + (origin (method url-fetch) + (uri (string-append "https://github.com/clojure/" + prefix version ".tar.gz")) + (sha256 (base32 hash))))) + ;; The libraries below are needed to run the tests. + (libraries + `(("core-specs-alpha-src" + ,(lib "core.specs.alpha/archive/core.specs.alpha-" + "0.1.24" + "0v2a0svf1ar2y42ajxwsjr7zmm5j7pp2zwrd2jh3k7xzd1p9x1fv")) + ("data-generators-src" + ,(lib "data.generators/archive/data.generators-" + "0.1.2" + "0kki093jp4ckwxzfnw8ylflrfqs8b1i1wi9iapmwcsy328dmgzp1")) + ("spec-alpha-src" + ,(lib "spec.alpha/archive/spec.alpha-" + "0.1.143" + "00alf0347licdn773w2jarpllyrbl52qz4d8mw61anjksacxylzz")) + ("test-check-src" + ,(lib "test.check/archive/test.check-" + "0.9.0" + "0p0mnyhr442bzkz0s4k5ra3i6l5lc7kp6ajaqkkyh4c2k5yck1md")) + ("test-generative-src" + ,(lib "test.generative/archive/test.generative-" + "0.5.2" + "1pjafy1i7yblc7ixmcpfq1lfbyf3jaljvkgrajn70sws9xs7a9f8")) + ("tools-namespace-src" + ,(lib "tools.namespace/archive/tools.namespace-" + "0.2.11" + "10baak8v0hnwz2hr33bavshm7y49mmn9zsyyms1dwjz45p5ymhy0")))) + (library-names (match libraries + (((library-name _) ...) + library-name)))) + + (package + (name "clojure") + (version "1.9.0") + (source + (origin + (method url-fetch) + (uri + (string-append "https://github.com/clojure/clojure/archive/clojure-" + version ".tar.gz")) + (sha256 + (base32 "0xjbzcw45z32vsn9pifp7ndysjzqswp5ig0jkjpivigh2ckkdzha")))) + (build-system ant-build-system) + (arguments + `(#:imported-modules ((guix build clojure-utils) + (guix build guile-build-system) + ,@%ant-build-system-modules) + #:modules ((guix build ant-build-system) + (guix build clojure-utils) + (guix build java-utils) + (guix build utils) + (srfi srfi-26)) + #:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-library-sources + (lambda* (#:key inputs #:allow-other-keys) + (define (extract-library name) + (mkdir-p name) + (with-directory-excursion name + (invoke "tar" + "--extract" + "--verbose" + "--file" (assoc-ref inputs name) + "--strip-components=1")) + (copy-recursively (string-append name "/src/main/clojure/") + "src/clj/")) + (for-each extract-library ',library-names) + #t)) + (add-after 'unpack-library-sources 'fix-manifest-classpath + (lambda _ + (substitute* "build.xml" + (("<attribute name=\"Class-Path\" value=\".\"/>") "")) + #t)) + (add-after 'build 'build-javadoc ant-build-javadoc) + (replace 'install (install-jars "./")) + (add-after 'install-license-files 'install-doc + (cut install-doc #:doc-dirs '("doc/clojure/") <...>)) + (add-after 'install-doc 'install-javadoc + (install-javadoc "target/javadoc/"))))) + (native-inputs libraries) + (home-page "https://clojure.org/") + (synopsis "Lisp dialect running on the JVM") + (description "Clojure is a dynamic, general-purpose programming language, +combining the approachability and interactive development of a scripting +language with an efficient and robust infrastructure for multithreaded +programming. Clojure is a compiled language, yet remains completely dynamic +– every feature supported by Clojure is supported at runtime. Clojure +provides easy access to the Java frameworks, with optional type hints and type +inference, to ensure that calls to Java can avoid reflection. + +Clojure is a dialect of Lisp, and shares with Lisp the code-as-data philosophy +and a powerful macro system. Clojure is predominantly a functional programming +language, and features a rich set of immutable, persistent data structures. +When mutable state is needed, Clojure offers a software transactional memory +system and reactive Agent system that ensure clean, correct, multithreaded +designs.") + ;; Clojure is licensed under EPL1.0 + ;; ASM bytecode manipulation library is licensed under BSD-3 + ;; Guava Murmur3 hash implementation is licensed under APL2.0 + ;; src/clj/repl.clj is licensed under CPL1.0 + + ;; See readme.html or readme.txt for details. + (license (list license:epl1.0 + license:bsd-3 + license:asl2.0 + license:cpl1.0))))) + (define-public femtolisp (let ((commit "68c5b1225572ecf2c52baf62f928063e5a30511b") (revision "1")) @@ -1488,6 +1608,158 @@ compressor. It works on data produced by @code{parse-js} to generate a ("sbcl-cl-uglify-js" ,sbcl-cl-uglify-js))) (synopsis "JavaScript compressor"))) +(define-public clojure-algo-generic + (package + (name "clojure-algo-generic") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri + (string-append "https://github.com/clojure/algo.generic/archive" + "/algo.generic-" version ".tar.gz")) + (sha256 + (base32 "12w9681i545gp1af4576z1qbixwps1j13c16fmcc7zsb0bd1zr7w")))) + (build-system clojure-build-system) + (arguments + '(#:source-dirs '("src/main/clojure/") + #:test-dirs '("src/test/clojure/") + #:doc-dirs '())) + (synopsis "Generic versions of common functions") + (description + "Generic versions of commonly used functions, implemented as multimethods +that can be implemented for any data type.") + (home-page "https://github.com/clojure/algo.generic") + (license license:epl1.0))) + +(define-public clojure-algo-monads + (package + (name "clojure-algo-monads") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri + (string-append "https://github.com/clojure/algo.monads/archive" + "/algo.monads-" version ".tar.gz")) + (sha256 + (base32 "14gbvfgmrda990h45yn7zag83vp1kdkz4f4yzmyvkr0sjihlgdmq")))) + (build-system clojure-build-system) + (arguments + '(#:source-dirs '("src/main/clojure/") + #:test-dirs '("src/test/clojure/") + #:doc-dirs '())) + (native-inputs + `(("clojure-tools-macro" ,clojure-tools-macro))) + (synopsis + "Monad Macros and Definitions") + (description + "This library contains the most commonly used monads as well as macros for +defining and using monads and useful monadic functions.") + (home-page "https://github.com/clojure/algo.monads") + (license license:epl1.0))) + +(define-public clojure-core-match + (let ((commit "1837ffbd4a150e8f3953b2d9ed5cf4a4ad3720a7") + (revision "1")) ; this is the 1st commit buildable with clojure 1.9 + (package + (name "clojure-core-match") + (version (git-version "0.3.0-alpha5" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/clojure/core.match.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04bdlp5dgkrqzrz0lw3mfwmygj2218qnm1cz3dkb9wy4m0238s4d")))) + (build-system clojure-build-system) + (arguments + '(#:source-dirs '("src/main/clojure") + #:test-dirs '("src/test/clojure") + #:doc-dirs '())) + (synopsis "Optimized pattern matching for Clojure") + (description + "An optimized pattern matching library for Clojure. +It supports Clojure 1.5.1 and later as well as ClojureScript.") + (home-page "https://github.com/clojure/core.match") + (license license:epl1.0)))) + +(define-public clojure-instaparse + (let ((commit "dcfffad5b065e750f0f5835f017cdd8188b8ca2e") + (version "1.4.9")) ; upstream forget to tag this release + (package + (name "clojure-instaparse") + (version version) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Engelberg/instaparse.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "002mrgin4z3dqy88r1lak7smd0m7x8d22vmliw0m6w6mh5pa17lk")))) + (build-system clojure-build-system) + (arguments + '(#:doc-dirs '("docs/"))) + (synopsis "No grammar left behind") + (description + "Instaparse aims to be the simplest way to build parsers in Clojure. + +@itemize +@item Turns @emph{standard EBNF or ABNF notation} for context-free grammars +into an executable parser that takes a string as an input and produces a parse +tree for that string. + +@item @dfn{No Grammar Left Behind}: Works for @emph{any} context-free grammar, +including @emph{left-recursive}, @emph{right-recursive}, and @emph{ambiguous} +grammars. + +@item Extends the power of context-free grammars with PEG-like syntax for +lookahead and negative lookahead. + +@item Supports both of Clojure's most popular tree formats (hiccup and enlive) +as output targets + +@item Detailed reporting of parse errors. + +@item Optionally produces lazy sequence of all parses (especially useful for +diagnosing and debugging ambiguous grammars). + +@item ``Total parsing'' mode where leftover string is embedded in the parse +tree. + +@item Optional combinator library for building grammars programmatically. + +@item Performant. +@end itemize") + (home-page "https://github.com/Engelberg/instaparse") + (license license:epl1.0)))) + +(define-public clojure-tools-macro + (package + (name "clojure-tools-macro") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri + (string-append "https://github.com/clojure/tools.macro/archive" + "/tools.macro-" version ".tar.gz")) + (sha256 + (base32 "0fs64a0g63xx6g7sj6vrsqknhl90s0isf6k053nw8vv5prfzc7v6")))) + (build-system clojure-build-system) + (arguments + '(#:source-dirs '("src/main/clojure/") + #:test-dirs '("src/test/clojure/") + #:doc-dirs '())) + (synopsis "Utilities for macro writers") + (description "Tools for writing macros.") + (home-page "https://github.com/clojure/tools.macro") + (license license:epl1.0))) + (define-public confusion-mdl (let* ((commit "12a055581fc262225272df43287dae48281900f5")) (package diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index f57e263449..0d3bff9476 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2016 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2014, 2016, 2018 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> @@ -66,6 +66,7 @@ "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE" "-DBUILD_SHARED_LIBS:BOOL=TRUE" "-DLLVM_ENABLE_FFI:BOOL=TRUE" + "-DLLVM_REQUIRES_RTTI=1" ; For some third-party utilities "-DLLVM_INSTALL_UTILS=ON") ; Needed for rustc. ;; Don't use '-g' during the build, to save space. @@ -91,6 +92,26 @@ languages is in development. The compiler infrastructure includes mirror sets of programming tools as well as libraries with equivalent functionality.") (license license:ncsa))) +;; FIXME: This package is here to prevent many rebuilds on x86_64 and i686 +;; from commit fc9dbf41311d99d0fd8befc789ea7c0e35911890. Update users of +;; this in the next rebuild cycle. +(define-public llvm-without-rtti + (package + (inherit llvm) + (arguments + `(#:configure-flags '("-DCMAKE_SKIP_BUILD_RPATH=FALSE" + "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE" + "-DBUILD_SHARED_LIBS:BOOL=TRUE" + "-DLLVM_ENABLE_FFI:BOOL=TRUE" + "-DLLVM_INSTALL_UTILS=ON") + #:build-type "Release" + #:phases (modify-phases %standard-phases + (add-before 'build 'shared-lib-workaround + (lambda _ + (setenv "LD_LIBRARY_PATH" + (string-append (getcwd) "/lib")) + #t))))))) + (define* (clang-runtime-from-llvm llvm hash #:optional (patches '())) (package @@ -281,18 +302,6 @@ code analysis tools.") (base32 "1ybmnid4pw2hxn12ax5qa5kl1ldfns0njg8533y3mzslvd5cx0kf")))))) -;; This is for Faust 2 -(define-public llvm-3.8-with-rtti - (package (inherit llvm-3.8) - (name "llvm-with-rtti") - (arguments - (substitute-keyword-arguments (package-arguments llvm) - ((#:configure-flags flags) - `(append '("-DCMAKE_SKIP_BUILD_RPATH=FALSE" - "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE" - "-DLLVM_REQUIRES_RTTI=1") - ,flags)))))) - (define-public clang-runtime-3.8 (clang-runtime-from-llvm llvm-3.8 diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 990a6c771a..09c525ff20 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org> ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com> +;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> ;;; ;;; This file is part of GNU Guix. ;;; @@ -300,7 +301,9 @@ networks) based on simulation of (stochastic) flow in graphs.") "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110")))) (build-system ocaml-build-system) (arguments - `(#:phases + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:phases (modify-phases %standard-phases (add-before 'configure 'patch-paths (lambda _ diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm index 58e26d82ff..b640884933 100644 --- a/gnu/packages/man.scm +++ b/gnu/packages/man.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2012, 2014, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014 David Thompson <dthompson2@worcester.edu> ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Alex Kost <alezost@gmail.com> @@ -216,6 +216,18 @@ Linux kernel and C library interfaces employed by user-space programs.") automatically.") (license gpl3+))) +(define-public help2man/latest + (package + (inherit help2man) + (version "1.47.8") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnu/help2man/help2man-" + version ".tar.xz")) + (sha256 + (base32 + "1p5830h88cx0zn0snwaj0vpph81xicpsirfwlxmcgjrlmn0nm3sj")))))) + (define-public txt2man (package (name "txt2man") diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3e1fe7c2c1..7dc8b62a47 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -28,6 +28,7 @@ ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> +;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1808,6 +1809,41 @@ scientific applications modeled by partial differential equations.") ,@(delete "--with-mpi=0" ,cf))))) (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) +(define-public python-petsc4py + (package + (name "python-petsc4py") + (version "3.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "petsc4py" version)) + (sha256 + (base32 + "1f8zd1ac9irsgkyqmzq30d9kl10fy1nh6zk312dhs43g449fkkhc")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda _ + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("petsc" ,petsc-openmpi) + ("python-numpy" ,python-numpy))) + (home-page "https://bitbucket.org/petsc/petsc4py/") + (synopsis "Python bindings for PETSc") + (description "PETSc, the Portable, Extensible Toolkit for +Scientific Computation, is a suite of data structures and routines for +the scalable (parallel) solution of scientific applications modeled by +partial differential equations. It employs the MPI standard for all +message-passing communication. @code{petsc4py} provides Python +bindings to almost all functions of PETSc.") + (license license:bsd-3))) + (define-public python-kiwisolver (package (name "python-kiwisolver") @@ -1939,6 +1975,43 @@ arising after the discretization of partial differential equations.") ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) +(define-public python-slepc4py + (package + (name "python-slepc4py") + (version "3.9.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "slepc4py" version)) + (sha256 + (base32 + "02xr0vndgibgkz3rgprqk05n3mk5mpgqw550sr4681vcsgz4zvb7")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda _ + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + ;; Define path to SLEPc installation. + (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) + #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("python-numpy" ,python-numpy) + ("python-petsc4py" ,python-petsc4py) + ("slepc" ,slepc-openmpi))) + (home-page "https://bitbucket.org/slepc/slepc4py/") + (synopsis "Python bindings for SLEPc") + (description "SLEPc, the Scalable Library for Eigenvalue Problem +Computations, is based on PETSc, the Portable, Extensible Toolkit for +Scientific Computation. It employs the MPI standard for all +message-passing communication. @code{slepc4py} provides Python +bindings to almost all functions of SLEPc.") + (license license:bsd-3))) + (define-public mumps (package (name "mumps") @@ -2716,6 +2789,18 @@ to BMP, JPEG or PNG image formats.") (lambda _ (chmod "src/maxima" #o555) #t)) + (replace 'check + (lambda _ + ;; This is derived from the testing code in the "debian/rules" file + ;; of Debian's Maxima package. + ;; If Maxima can successfully run this, the binary to be installed + ;; should be fine. + (zero? + (system + (string-append "./maxima-local " + "--lisp=gcl " + "--batch-string=\"run_testsuite();\" " + "| grep -q \"No unexpected errors found\""))))) ;; Make sure the doc and emacs files are found in the ;; standard location. Also configure maxima to find gnuplot ;; without having it on the PATH. @@ -3861,15 +3946,15 @@ as equations, scalars, vectors, and matrices.") (define-public z3 (package (name "z3") - (version "4.5.0") + (version "4.8.1") + (home-page "https://github.com/Z3Prover/z3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/Z3Prover/z3/archive/z3-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "z3-" version)))) (sha256 (base32 - "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf")))) + "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -3898,43 +3983,57 @@ as equations, scalars, vectors, and matrices.") (synopsis "Theorem prover") (description "Z3 is a theorem prover and @dfn{satisfiability modulo theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.") - (home-page "https://github.com/Z3Prover/z3") (license license:expat))) (define-public cubicle (package (name "cubicle") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (string-append "http://cubicle.lri.fr/cubicle-" version ".tar.gz")) (sha256 (base32 - "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h")))) + "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q")))) (build-system gnu-build-system) (native-inputs - `(("ocaml" ,ocaml) + `(("automake" ,automake) + ("ocaml" ,ocaml) ("which" ,(@@ (gnu packages base) which)))) (propagated-inputs - `(("z3" ,z3))) + `(("ocaml-num" ,ocaml-num) + ("z3" ,z3))) (arguments `(#:configure-flags (list "--with-z3") + #:make-flags (list "QUIET=") #:tests? #f #:phases (modify-phases %standard-phases (add-before 'configure 'configure-for-release (lambda _ (substitute* "Makefile.in" - (("SVNREV=") "#SVNREV=")))) + (("SVNREV=") "#SVNREV=")) + #t)) (add-before 'configure 'fix-/bin/sh (lambda _ (substitute* "configure" - (("/bin/sh") (which "sh"))))) + (("-/bin/sh") (string-append "-" (which "sh")))) + #t)) (add-before 'configure 'fix-smt-z3wrapper.ml (lambda _ (substitute* "Makefile.in" - (("\\\\n") ""))))))) + (("\\\\n") "")) + #t)) + (add-before 'configure 'fix-ocaml-num + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile.in" + (("= \\$\\(FUNCTORYLIB\\)") + (string-append "= -I " + (assoc-ref inputs "ocaml-num") + "/lib/ocaml/site-lib" + " $(FUNCTORYLIB)"))) + #t))))) (home-page "http://cubicle.lri.fr/") (synopsis "Model checker for array-based systems") (description "Cubicle is a model checker for verifying safety properties diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm index fc8aadef29..f08a7f5f88 100644 --- a/gnu/packages/mpi.scm +++ b/gnu/packages/mpi.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2017 Dave Love <fx@gnu.org> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,6 +30,7 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages gcc) #:use-module (gnu packages linux) @@ -263,3 +265,43 @@ only provides @code{MPI_THREAD_FUNNELED}."))) ;; in the build environment than the package wants while testing. (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes") #t)) + +(define-public python-mpi4py + (package + (name "python-mpi4py") + (version "3.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mpi4py" version)) + (sha256 + (base32 + "1mzgd26dfv4vwbci8gq77ss9f0x26i9aqzq9b9vs9ndxhlnv0mxl")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'pre-check + (lambda _ + ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init() + ;; failed --> Returned "Unreachable"' in chroot environment). + (substitute* "test/test_spawn.py" + (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)") + "unittest.skipMPI('openmpi')")) + #t))))) + (inputs + `(("openmpi" ,openmpi))) + (home-page "https://bitbucket.org/mpi4py/mpi4py/") + (synopsis "Python bindings for the Message Passing Interface standard") + (description "MPI for Python (mpi4py) provides bindings of the Message +Passing Interface (MPI) standard for the Python programming language, allowing +any Python program to exploit multiple processors. + +mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an +object oriented interface which closely follows MPI-2 C++ bindings. It +supports point-to-point and collective communications of any picklable Python +object as well as optimized communications of Python objects (such as NumPy +arrays) that expose a buffer interface.") + (license bsd-3))) diff --git a/gnu/packages/multiprecision.scm b/gnu/packages/multiprecision.scm index 4f5eac16b9..71e1efcd8c 100644 --- a/gnu/packages/multiprecision.scm +++ b/gnu/packages/multiprecision.scm @@ -26,6 +26,7 @@ (define-module (gnu packages multiprecision) #:use-module (guix licenses) #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages m4) #:use-module (gnu packages gcc) #:use-module (guix packages) @@ -225,3 +226,68 @@ minor changes to the source code. In most cases only a few type statements and (for Fortran-90 programs) read/write statements need to be changed. PSLQ and numerical quadrature programs are included.") (license bsd-3))) + +(define-public tomsfastmath + (package + (name "tomsfastmath") + (version "0.13.0") + (synopsis "Large integer arithmetic library") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/libtom/tomsfastmath/" + "releases/download/v" version "/" + "tfm-" (version-major+minor version) ".tar.bz2")) + (sha256 + (base32 + "01rlsvp6lskk2a0gfdi24ak5h8vdwi6kqbvbwjnmb92r0zrfdvwd")) + (patches (search-patches "tomsfastmath-constness.patch")))) + (build-system gnu-build-system) + (native-inputs + `(("libtool" ,libtool))) + (arguments + `(#:make-flags (list "-f" "makefile.shared" + (string-append "LIBPATH=" %output "/lib") + (string-append "INCPATH=" %output "/include") + "GROUP=root" "USER=root" + "CC=gcc") + #:phases + (modify-phases %standard-phases + (delete 'configure) ;no configuration + (replace 'check + (lambda* (#:key make-flags #:allow-other-keys) + (and (zero? (apply system* "make" + "stest" "test_standalone" + make-flags)) + (zero? (system* "./stest")) + (zero? (system* "./test"))))) + (add-before 'install 'install-nogroup + (lambda _ + ;; Let permissions inherit from the current process + (substitute* "makefile.shared" + (("-g \\$\\(GROUP\\) -o \\$\\(USER\\)") "")) + #t)) + (add-after 'install 'install-doc + (lambda* (#:key outputs #:allow-other-keys) + (let ((docdir (string-append (assoc-ref outputs "out") + "/share/doc/tomsfastmath"))) + (install-file "doc/tfm.pdf" docdir) + #t))) + (add-after 'install 'install-pc + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (pc-dir (string-append out "/lib/pkgconfig"))) + (call-with-output-file "tomsfastmath.pc" + (lambda (port) + (format port "~ +Name: TomsFastMath +Description: ~a +Version: ~a +Libs: -L~a/lib -ltfm~%" + ,synopsis ,version out))) + (install-file "tomsfastmath.pc" pc-dir) + #t)))))) + (home-page "http://www.libtom.org/TomsFastMath/") + (description "TomsFastMath is a large integer library written in portable +ISO C. It is a port of LibTomMath with optional support for inline assembler +multiplies.") + (license public-domain))) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 6b55e84fed..e1323582a2 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il> -;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu> +;;; Copyright © 2016-2018 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Peter Kreye <kreyepr@gmail.com> @@ -120,7 +120,7 @@ "/lib/ocaml/site-lib")) #:phases (modify-phases %standard-phases (delete 'configure)))) -(define-public ocaml +(define-public ocaml-4.02 (package (name "ocaml") (version "4.02.3") @@ -145,7 +145,8 @@ (files (list "lib/ocaml" "lib/ocaml/site-lib"))) (search-path-specification (variable "CAML_LD_LIBRARY_PATH") - (files (list "lib/ocaml/site-lib/stubslibs"))))) + (files (list "lib/ocaml/site-lib/stubslibs" + "lib/ocaml/site-lib/stublibs"))))) (native-inputs `(("perl" ,perl) ("pkg-config" ,pkg-config))) @@ -228,7 +229,7 @@ functional, imperative and object-oriented styles of programming.") (define-public ocaml-4.01 (package - (inherit ocaml) + (inherit ocaml-4.02) (version "4.01.0") (source (origin (method url-fetch) @@ -240,7 +241,7 @@ functional, imperative and object-oriented styles of programming.") (base32 "03d7ida94s1gpr3gadf4jyhmh5rrszd5s4m4z59daaib25rvfyv7")))) (arguments - (substitute-keyword-arguments (package-arguments ocaml) + (substitute-keyword-arguments (package-arguments ocaml-4.02) ((#:phases phases) `(modify-phases ,phases (replace 'build @@ -256,10 +257,78 @@ functional, imperative and object-oriented styles of programming.") (string-append "TOPDIR=" (getcwd) "/..")))))))))))) +(define-public ocaml-4.07 + (package + (inherit ocaml-4.02) + (version "4.07.0") + (source (origin + (method url-fetch) + (uri (string-append + "http://caml.inria.fr/pub/distrib/ocaml-" + (version-major+minor version) + "/ocaml-" version ".tar.xz")) + (sha256 + (base32 + "03wzkzv6w4rdiiva20g5amz0n4x75swpjl8d80468p6zm8hgfnzl")))) + (arguments + (substitute-keyword-arguments (package-arguments ocaml-4.02) + ((#:phases phases) + `(modify-phases ,phases + (delete 'prepare-socket-test) + (replace 'check + (lambda _ + (with-directory-excursion "testsuite" + (invoke "make" "all")) + #t)))))))) + +(define-public ocaml ocaml-4.07) + +(define-public ocamlbuild + (package + (name "ocamlbuild") + (version "0.13.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ocaml/ocamlbuild/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1320cfkixs1xlng5av04pa5qjb3ynvi2kl3k1ngqzg5fpi29b0vr")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:tests? #f; tests require findlib + #:make-flags + (list (string-append "OCAMLBUILD_PREFIX=" (assoc-ref %outputs "out")) + (string-append "OCAMLBUILD_BINDIR=" (assoc-ref %outputs "out") + "/bin") + (string-append "OCAMLBUILD_LIBDIR=" (assoc-ref %outputs "out") + "/lib/ocaml/site-lib") + (string-append "OCAMLBUILD_MANDIR=" (assoc-ref %outputs "out") + "/share/man")) + #:phases + (modify-phases %standard-phases + (delete 'bootstrap) + (delete 'configure) + (add-before 'build 'findlib-environment + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (setenv "OCAMLFIND_DESTDIR" (string-append out "/lib/ocaml/site-lib")) + (setenv "OCAMLFIND_LDCONF" "ignore") + #t)))))) + (native-inputs + `(("ocaml" ,ocaml))) + (home-page "https://github.com/ocaml/ocamlbuild") + (synopsis "OCaml build tool") + (description "OCamlbuild is a generic build tool, that has built-in rules + for building OCaml library and programs.") + (license license:lgpl2.1+))) + (define-public opam (package (name "opam") - (version "1.2.2") + (version "2.0.0") (source (origin (method url-fetch) ;; Use the '-full' version, which includes all the dependencies. @@ -271,7 +340,7 @@ functional, imperative and object-oriented styles of programming.") ) (sha256 (base32 - "004gwn6rbpcb53y3rpb3v23vk39rp2xmf0liyd5iy12ij8bigrhm")))) + "09gdpxiqmyr6z78l85d7pwhiwrycdi2xi1b2mafqr1sk9z5lzbcx")))) (build-system gnu-build-system) (arguments '(;; Sometimes, 'make -jX' would fail right after ./configure with @@ -321,7 +390,7 @@ Git-friendly development workflow.") ;; The 'LICENSE' file waives some requirements compared to LGPLv3. (license license:lgpl3))) -(define-public camlp4 +(define-public camlp4-4.02 (package (name "camlp4") (version "4.02+6") @@ -334,9 +403,9 @@ Git-friendly development workflow.") "0icdfzhsbgf89925gc8gl3fm8z2xzszzlib0v9dj5wyzkyv3a342")) (file-name (string-append name "-" version ".tar.gz")))) (build-system gnu-build-system) - (native-inputs `(("ocaml" ,ocaml) + (native-inputs `(("ocaml" ,ocaml-4.02) ("which" ,which))) - (inputs `(("ocaml" ,ocaml))) + (inputs `(("ocaml" ,ocaml-4.02))) (arguments '(#:tests? #f ;no documented test target ;; a race-condition will lead byte and native targets to mkdir _build @@ -377,17 +446,42 @@ syntax of OCaml.") ;; against the library to be released under any terms. (license license:lgpl2.0))) +(define-public camlp4-4.07 + (package + (inherit camlp4-4.02) + (name "camlp4") + (version "4.07+1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ocaml/camlp4/archive/" + version ".tar.gz")) + (sha256 + (base32 + "143hhxv1i6aq413z0i1pynrjcfl2g5gnh5r3863v6h9z0riqknzc")) + (file-name (string-append name "-" version ".tar.gz")))) + (properties + `((ocaml4.02-variant . ,(delay camlp4-4.02)))) + (native-inputs + `(("ocaml" ,ocaml-4.07) + ("ocamlbuild" ,ocamlbuild) + ("which" ,which))) + (inputs + `(("ocaml" ,ocaml-4.07))))) + +(define-public camlp4 camlp4-4.07) + (define-public camlp5 (package (name "camlp5") - (version "6.14") + (version "7.06") (source (origin (method url-fetch) - (uri (string-append "http://camlp5.gforge.inria.fr/distrib/src/" - name "-" version ".tgz")) + (uri (string-append "https://github.com/camlp5/camlp5/archive/rel" + (string-delete #\. version) ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1ql04iyvclpyy9805kpddc4ndjb5d0qg4shhi2fc6bixi49fvy89")))) + "08kr0h2rq3jh3kzqh5f6pr589bqw3y76z8k59ad2kdh50fjgp8xy")))) (build-system gnu-build-system) (inputs `(("ocaml" ,ocaml))) @@ -404,6 +498,11 @@ syntax of OCaml.") (invoke "./configure" "--prefix" out "--mandir" mandir)))) + (add-before 'build 'fix-/bin-references + (lambda _ + (substitute* "config/Makefile" + (("/bin/rm") "rm")) + #t)) (replace 'build (lambda _ (invoke "make" "-j" (number->string @@ -427,17 +526,19 @@ concrete syntax of the language (Quotations, Syntax Extensions).") (define-public hevea (package (name "hevea") - (version "2.28") + (version "2.32") (source (origin (method url-fetch) (uri (string-append "http://hevea.inria.fr/old/" name "-" version ".tar.gz")) (sha256 (base32 - "14fns13wlnpiv9i05841kvi3cq4b9v2sw5x3ff6ziws28q701qnd")))) + "1s4yqphfcr1pf5mcj5c84mvmd107k525iiym5jdwsxz0ka0ccmfy")))) (build-system gnu-build-system) (inputs `(("ocaml" ,ocaml))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild))) (arguments `(#:tests? #f ; no test suite #:make-flags (list (string-append "PREFIX=" %output)) @@ -455,6 +556,50 @@ concrete syntax of the language (Quotations, Syntax Extensions).") written in Objective Caml.") (license license:qpl))) +(define-public ocaml-num + (package + (name "ocaml-num") + (version "1.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ocaml/num/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1xlkd0svc0mgq5s7nrm2rjrsvg15i9wxqkc1kvwjp6sv8vv8bb04")))) + (build-system ocaml-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'fix-makefile + (lambda* (#:key outputs #:allow-other-keys) + ;; This package supposes we install to the same directory as + ;; the ocaml package. + (substitute* "src/META" + (("\"\\^\"") (string-append "\"" (assoc-ref outputs "out") + "/lib/ocaml/site-lib\""))) + (substitute* "src/Makefile" + (("\\) \\$\\(STDLIBDIR\\)") + (string-append ") " (assoc-ref outputs "out") + "/lib/ocaml/site-lib"))) + #t)) + (add-after 'install 'fix-stubslib + (lambda* (#:key outputs #:allow-other-keys) + (format #t "~a~%" (find-files "." ".*.so")) + (let ((stubdir (string-append (assoc-ref outputs "out") + "/lib/ocaml/site-lib"))) + (mkdir-p stubdir) + (install-file "src/dllnums.so" stubdir)) + #t))))) + (home-page "https://github.com/ocaml/num") + (synopsis "Arbitrary-precision integer and rational arithmetic") + (description "OCaml-Num contains the legacy Num library for +arbitrary-precision integer and rational arithmetic that used to be part of +the OCaml core distribution.") + (license license:lgpl2.1+))); with linking exception + (define-public coq (package (name "coq") @@ -478,7 +623,8 @@ written in Objective Caml.") (inputs `(("lablgtk" ,lablgtk) ("python" ,python-2) - ("camlp5" ,camlp5))) + ("camlp5" ,camlp5) + ("ocaml-num" ,ocaml-num))) (arguments `(#:phases (modify-phases %standard-phases @@ -598,7 +744,7 @@ provers.") (define-public emacs-tuareg (package (name "emacs-tuareg") - (version "2.0.10") + (version "2.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/ocaml/tuareg/archive/" @@ -606,7 +752,7 @@ provers.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1r2smclcs63n74lcyckbp90j09wyjdngn816cqzfkw54iwh3hd7q")))) + "1ynpfc170f9jqx49biji9npfkvfpflbm29xf24wc7fnxxayr49ig")))) (build-system gnu-build-system) (native-inputs `(("emacs" ,emacs-minimal) ("opam" ,opam))) @@ -650,6 +796,8 @@ Emacs.") (build-system gnu-build-system) (inputs `(("ocaml" ,ocaml))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild))) (arguments `(#:parallel-build? #f ; Parallel build causes failure #:tests? #f ; No check target @@ -660,6 +808,8 @@ Emacs.") (let ((out (assoc-ref outputs "out"))) (setenv "PREFIX" out)) #t))))) + (properties + `((ocaml4.02-variant . ,(delay ocaml4.02-menhir)))) (home-page "http://gallium.inria.fr/~fpottier/menhir") (synopsis "Parser generator") (description "Menhir is a parser generator. It turns high-level grammar @@ -671,17 +821,26 @@ Knuth’s LR(1) parser construction technique.") ;; are QPL licensed. (license (list license:gpl2+ license:qpl)))) +(define-public ocaml4.02-menhir + (package + (inherit ocaml-menhir) + (name "ocaml4.02-menhir") + (inputs `(("ocaml" ,ocaml-4.02))) + (native-inputs '()))) + (define-public lablgtk (package (name "lablgtk") - (version "2.18.5") + (version "2.18.6") (source (origin (method url-fetch) - (uri (ocaml-forge-uri name version 1627)) + (uri (ocaml-forge-uri name version 1726)) (sha256 (base32 - "0cyj6sfdvzx8hw7553lhgwc0krlgvlza0ph3dk9gsxy047dm3wib")))) + "1y38fdvswy6hmppm65qvgdk4pb3ghhnvz7n4ialf46340r1s5p2d")))) (build-system gnu-build-system) + (properties + `((ocaml4.02-variant . ,(delay ocaml4.02-lablgtk)))) (native-inputs `(("camlp4" ,camlp4) ("ocaml" ,ocaml) @@ -732,6 +891,23 @@ libglade (and it an generate OCaml code from .glade files), libpanel, librsvg and quartz.") (license license:lgpl2.1))) +(define-public ocaml4.02-lablgtk + (package + (inherit lablgtk) + (name "ocaml4.02-lablgtk") + (version "2.18.5") + (source (origin + (method url-fetch) + (uri (ocaml-forge-uri name version 1627)) + (sha256 + (base32 + "0cyj6sfdvzx8hw7553lhgwc0krlgvlza0ph3dk9gsxy047dm3wib")))) + (native-inputs + `(("camlp4" ,camlp4-4.02) + ("ocaml" ,ocaml-4.02) + ("findlib" ,ocaml4.02-findlib) + ("pkg-config" ,pkg-config))))) + (define-public unison (package (name "unison") @@ -792,12 +968,13 @@ libpanel, librsvg and quartz.") (outputs '("out" "doc")) ; 1.9 MiB of documentation (native-inputs - `(("ocaml" ,ocaml) + `(("ocaml" ,ocaml-4.02) ;; For documentation ("ghostscript" ,ghostscript) ("texlive" ,texlive) ("hevea" ,hevea) - ("lynx" ,lynx))) + ("lynx" ,lynx) + ("which" ,which))) (arguments `(#:parallel-build? #f #:parallel-tests? #f @@ -827,6 +1004,14 @@ libpanel, librsvg and quartz.") (let ((doc (string-append (assoc-ref outputs "doc") "/share/doc/unison"))) (mkdir-p doc) + ;; This is a workaround to prevent a build failure. Running + ;; make docs somehow allows it to pass, but the generated + ;; documentation is not pretty. + (catch #t + (lambda _ + (invoke "make" "docs" + "TEXDIRECTIVES=\\\\draftfalse")) + (lambda _ #t)) ;; This file needs write-permissions, because it's ;; overwritten by 'docs' during documentation generation. (chmod "src/strings.ml" #o600) @@ -856,14 +1041,14 @@ to the other.") (define-public ocaml-findlib (package (name "ocaml-findlib") - (version "1.7.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (string-append "http://download.camlcity.org/download/" "findlib" "-" version ".tar.gz")) (sha256 (base32 - "12xx8si1qv3xz90qsrpazjjk4lc1989fzm97rsmc4diwla7n15ni")))) + "1b97zqjdriqd2ikgh4rmqajgxwdwn013riji5j53y3xvcmnpsyrb")))) (build-system gnu-build-system) (native-inputs `(("camlp4" ,camlp4) @@ -912,6 +1097,15 @@ compilation and linkage, there are new frontends of the various OCaml compilers that can directly deal with packages.") (license license:x11))) +(define-public ocaml4.02-findlib + (package + (inherit ocaml-findlib) + (name "ocaml4.02-findlib") + (native-inputs + `(("camlp4" ,camlp4-4.02) + ("m4" ,m4) + ("ocaml" ,ocaml-4.02))))) + (define-public ocaml4.01-findlib (package (inherit ocaml-findlib) @@ -933,7 +1127,8 @@ compilers that can directly deal with packages.") "03ifp9hjcxg4m5j190iy373jcn4039d3vy10kmd8p4lfciwzwc1f")))) (build-system ocaml-build-system) (native-inputs - `(("libxml2" ,libxml2))) ; for xmllint + `(("libxml2" ,libxml2) ; for xmllint + ("ocamlbuild" ,ocamlbuild))) (arguments `(#:phases (modify-phases %standard-phases @@ -947,6 +1142,9 @@ other XUnit testing frameworks.") (define-public ocaml4.01-ounit (package-with-ocaml4.01 ocaml-ounit)) +(define-public ocaml4.02-ounit + (package-with-ocaml4.02 ocaml-ounit)) + (define-public camlzip (package (name "camlzip") @@ -1007,19 +1205,23 @@ files in these formats.") (base32 "0syh72jk9s0qwjmmfrkqchaj98m020ii082jn38pwnmb6v3p02wk"))))))) +(define-public ocaml4.02-camlzip + (package-with-ocaml4.02 camlzip)) + (define-public ocamlmod (package (name "ocamlmod") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) - (uri (ocaml-forge-uri name version 1544)) + (uri (ocaml-forge-uri name version 1702)) (sha256 (base32 - "1w0w8lfyymvk300dv13gvhrddpcyknvyp4g2yvq2vaw7khkhjs9g")))) + "0cgp9qqrq7ayyhddrmqmq1affvfqcn722qiakjq4dkywvp67h4aa")))) (build-system ocaml-build-system) (native-inputs - `(("ounit" ,ocaml-ounit))) + `(("ounit" ,ocaml-ounit) + ("ocamlbuild" ,ocamlbuild))) (arguments `(#:phases (modify-phases %standard-phases @@ -1030,6 +1232,9 @@ files in these formats.") (description "Generate modules from OCaml source files.") (license license:lgpl2.1+))) ; with an exception +(define-public ocaml4.02-ocamlmod + (package-with-ocaml4.02 ocamlmod)) + (define-public ocaml-zarith (package (name "ocaml-zarith") @@ -1060,6 +1265,9 @@ over big integers. Small integers are represented as Caml unboxed integers, for speed and space economy.") (license license:lgpl2.1+))) ; with an exception +(define-public ocaml4.02-zarith + (package-with-ocaml4.02 ocaml-zarith)) + (define-public ocaml-frontc (package (name "ocaml-frontc") @@ -1073,7 +1281,9 @@ for speed and space economy.") "16dz153s92dgbw1rrfwbhscy73did87kfmjwyh3qpvs748h1sc4g")))) (build-system ocaml-build-system) (arguments - `(#:phases + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:phases (modify-phases %standard-phases (delete 'configure) (add-after 'install 'install-meta @@ -1116,7 +1326,8 @@ GNU CC attributes. It provides also a C pretty printer as an example of use.") "1zs1pg5cb1iry554v3cdmmiglsrwmsqa9x8zxmzb118fnk5d3ha6")))) (build-system ocaml-build-system) (native-inputs - `(("ounit" ,ocaml-ounit))) + `(("ounit" ,ocaml-ounit) + ("ocamlbuild" ,ocamlbuild))) (home-page "https://github.com/c-cube/qcheck") (synopsis "QuickCheck inspired property-based testing for OCaml") (description "QuickCheck inspired property-based testing for OCaml. This @@ -1125,6 +1336,9 @@ generated instances of the type. It provides combinators for generating instances and printing them.") (license license:lgpl3+))) +(define-public ocaml4.02-qcheck + (package-with-ocaml4.02 ocaml-qcheck)) + (define-public ocaml-qtest (package (name "ocaml-qtest") @@ -1139,7 +1353,7 @@ instances and printing them.") "1ff4if64mc9c7wmhjdgnlnh6k6a713piqzr4043zzj4s5pw7smxk")))) (build-system ocaml-build-system) (native-inputs - `(("findlib" ,ocaml-findlib))) + `(("ocamlbuild" ,ocamlbuild))) (propagated-inputs `(("ounit" ,ocaml-ounit) ("qcheck" ,ocaml-qcheck))) @@ -1161,6 +1375,9 @@ to use -- to sophisticated random generation of test cases.") (define-public ocaml4.01-qtest (package-with-ocaml4.01 ocaml-qtest)) +(define-public ocaml4.02-qtest + (package-with-ocaml4.02 ocaml-qtest)) + (define-public ocaml-stringext (package (name "ocaml-stringext") @@ -1175,7 +1392,8 @@ to use -- to sophisticated random generation of test cases.") "19g6lfn03iki9f8h91hi0yiqn0b3wkxyq08b3y23wgv6jw6mssfh")))) (build-system ocaml-build-system) (native-inputs - `(("qtest" ,ocaml-qtest))) + `(("ocamlbuild" ,ocamlbuild) + ("qtest" ,ocaml-qtest))) (home-page "https://github.com/rgrinberg/stringext") (synopsis "Extra string functions for OCaml") (description "Provides a single module named Stringext that provides a grab @@ -1185,17 +1403,21 @@ full_split, cut, rcut, etc..") ;; where it says `mit'. (license license:expat))) +(define-public ocaml4.02-stringext + (package-with-ocaml4.02 ocaml-stringext)) (define-public ocaml-bisect (package (name "ocaml-bisect") - (version "1.3") + (version "1.3.1") (source (origin (method url-fetch) - (uri (ocaml-forge-uri "bisect" version 1051)) + (uri (string-append "https://github.com/gasche/bisect/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0kcg2rh0qlkfpbv3nhcb75n62b04gbrz0zasq15ynln91zd5qrg0")) + "0p67fppk5ifb63b00kxwrb1xg75hrqhknng3bsdyw3gxxqyjlpmx")) (patches (search-patches "ocaml-bisect-fix-camlp4-in-another-directory.patch")))) @@ -1203,6 +1425,7 @@ full_split, cut, rcut, etc..") (native-inputs `(("camlp4" ,camlp4) ("libxml2" ,libxml2) + ("ocamlbuild" ,ocamlbuild) ("which" ,which))) (propagated-inputs `(("camlp4" ,camlp4))) @@ -1215,9 +1438,11 @@ full_split, cut, rcut, etc..") #:phases (modify-phases %standard-phases (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "./configure" "-prefix" - (assoc-ref outputs "out")))))))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (invoke "./configure" "-prefix" (assoc-ref outputs "out") + "-ocaml-prefix" (assoc-ref inputs "ocaml") + "-camlp4-prefix" (assoc-ref inputs "camlp4")) + #t))))) (home-page "http://bisect.x9c.fr") (synopsis "Code coverage tool for the OCaml language") (description "Bisect is a code coverage tool for the OCaml language. It is @@ -1225,46 +1450,260 @@ a camlp4-based tool that allows to instrument your application before running tests. After application execution, it is possible to generate a report in HTML format that is the replica of the application source code annotated with code coverage information.") - (properties `((ocaml4.01-variant . ,(delay ocaml4.01-bisect)))) + (properties + `((ocaml4.01-variant . ,(delay ocaml4.01-bisect)) + (ocaml4.02-variant . ,(delay ocaml4.02-bisect)))) (license license:gpl3+))) (define-public ocaml4.01-bisect (let ((base (package-with-ocaml4.01 (strip-ocaml4.01-variant ocaml-bisect)))) (package (inherit base) + (version "1.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/gasche/bisect/archive/" + version ".tar.gz")) + (file-name (string-append "ocaml-bisect-" version ".tar.gz")) + (sha256 + (base32 + "1ip49jqf0kkbrqf8qspmfjbg9ap9fhvjkg718myzix88dg5rv8d4")))) (arguments `(#:ocaml ,ocaml-4.01 - ;; Camlp4 is included with OCaml 4.01, so do not include it as a - ;; separate input. - ,@(strip-keyword-arguments '(#:make-flags) (package-arguments base)))) + ,@(substitute-keyword-arguments (package-arguments ocaml-bisect) + ((#:make-flags flags) + `(list "all")) + ((#:phases phases) + `(modify-phases ,phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (invoke "./configure" + "-ocaml-prefix" (assoc-ref inputs "ocaml")) + #t))))))) (native-inputs `(,@(alist-delete "camlp4" (package-native-inputs base)))) (propagated-inputs `(,@(alist-delete "camlp4" (package-propagated-inputs base))))))) +(define-public ocaml4.02-bisect + (let ((base (package-with-ocaml4.02 (strip-ocaml4.02-variant ocaml-bisect)))) + (package + (inherit base) + (native-inputs + `(("camlp4" ,camlp4-4.02) + ("libxml2" ,libxml2) + ("which" ,which))) + (propagated-inputs + `(("camlp4" ,camlp4-4.02)))))) + +(define-public dune + (package + (name "dune") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ocaml/dune/releases/" + "download/" version "/dune-" version ".tbz")) + (sha256 + (base32 + "00c5dbm4hkdapc2i7pg07b2lj8sv6ly38qr7zid58cdmbmzq21z9")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f; require odoc + #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (invoke "./configure") + #t))))) + (home-page "https://github.com/ocaml/dune") + (synopsis "OCaml build system") + (description "Dune is a build system that was designed to simplify the +release of Jane Street packages. It reads metadata from @file{dune} files +following a very simple s-expression syntax.") + (license license:expat))) + +(define-public ocaml-migrate-parsetree + (package + (name "ocaml-migrate-parsetree") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ocaml-ppx/" + "ocaml-migrate-parsetree/releases/download/v" + version "/ocaml-migrate-parsetree-" + version ".tbz")) + (sha256 + (base32 + "01zjp1q4hryqaxv4apkjd868fycz2kf887r6lkb6x2a545h1lh7f")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "jbuilder" "build" "@install") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "jbuilder" "install" + "--prefix" (assoc-ref outputs "out")) + #t))))) + (propagated-inputs + `(("ocamlbuild" ,ocamlbuild) + ("ocaml-result" ,ocaml-result))) + (native-inputs + `(("dune" ,dune))) + (home-page "https://github.com/ocaml-ppx/ocaml-migrate-parsetree") + (synopsis "OCaml parsetree convertor") + (description "This library converts between parsetrees of different OCaml +versions. For each version, there is a snapshot of the parsetree and conversion +functions to the next and/or previous version.") + (license license:lgpl2.1+))) + +(define-public ocaml-ppx-tools-versioned + (package + (name "ocaml-ppx-tools-versioned") + (version "5.2.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ocaml-ppx/" + "ppx_tools_versioned/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1x2xfjpkzbcz4rza1d7gh3ipliw6jqfcklbsln82v3561qgkqgmh")))) + (build-system ocaml-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "dune" "build" "@install") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "dune" "install" + "--prefix" (assoc-ref outputs "out")) + #t))))) + (native-inputs + `(("dune" ,dune))) + (propagated-inputs + `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree))) + (home-page "https://github.com/let-def/ppx_tools_versioned") + (synopsis "Variant of ppx_tools") + (description "This package is a variant of ppx_tools based on +ocaml-migrate-parsetree") + (license license:expat))) + +(define-public ocaml-ppx-tools-versioned + (package + (name "ocaml-ppx-tools-versioned") + (version "5.2.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ocaml-ppx/" + "ppx_tools_versioned/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1x2xfjpkzbcz4rza1d7gh3ipliw6jqfcklbsln82v3561qgkqgmh")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "dune" "build" "@install") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "dune" "install" + "--prefix" (assoc-ref outputs "out")) + #t))))) + (native-inputs + `(("dune" ,dune))) + (propagated-inputs + `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree))) + (home-page "https://github.com/let-def/ppx_tools_versioned") + (synopsis "Variant of ppx_tools") + (description "This package is a variant of ppx_tools based on +ocaml-migrate-parsetree") + (license license:expat))) + (define-public ocaml-bitstring (package (name "ocaml-bitstring") - (version "2.1.1") + (version "3.1.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/xguerin/bitstring" - "/archive/v" version ".tar.gz")) + (uri (string-append "https://bitbucket.org/thanatonauts/bitstring/" + "get/v" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0vy8ibrxccii1jbsk5q6yh1kxjigqvi7lhhcmizvd5gfhf7mfyc8")) - (patches (search-patches "ocaml-bitstring-fix-configure.patch")))) + "15jjk2pq1vx311gl49s5ag6x5y0654x35w75z07g7kr2q334hqps")))) (build-system ocaml-build-system) (native-inputs `(("camlp4" ,camlp4) ("time" ,time) ("autoconf" ,autoconf) ("automake" ,automake) - ("bisect" ,ocaml-bisect))) + ("bisect" ,ocaml-bisect) + ("dune" ,dune))) (propagated-inputs - `(("camlp4" ,camlp4))) + `(("camlp4" ,camlp4) + ("ocaml-ppx-tools-versioned" ,ocaml-ppx-tools-versioned))) (arguments - `(#:configure-flags + `(#:tests? #f; Tests fail to build + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "jbuilder" "build" "@install") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "dune" "install" + "--prefix" (assoc-ref outputs "out")) + #t))))) + (properties + `((ocaml4.02-variant . ,(delay ocaml4.02-bitstring)))) + (home-page "https://github.com/xguerin/bitstring") + (synopsis "Bitstrings and bitstring matching for OCaml") + (description "Adds Erlang-style bitstrings and matching over bitstrings as +a syntax extension and library for OCaml. You can use this module to both parse +and generate binary formats, files and protocols. Bitstring handling is added +as primitives to the language, making it exceptionally simple to use and very +powerful.") + (license license:isc))) + +(define-public ocaml4.02-bitstring + (let ((base (package-with-ocaml4.02 (strip-ocaml4.02-variant ocaml-bitstring)))) + (package + (inherit base) + (version "2.1.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/xguerin/bitstring" + "/archive/v" version ".tar.gz")) + (file-name (string-append "ocaml-bitstring-" version ".tar.gz")) + (sha256 + (base32 + "0vy8ibrxccii1jbsk5q6yh1kxjigqvi7lhhcmizvd5gfhf7mfyc8")) + (patches (search-patches "ocaml-bitstring-fix-configure.patch")))) + (arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:configure-flags (list "CAMLP4OF=camlp4of" "--enable-coverage") #:make-flags (list (string-append "BISECTLIB=" @@ -1280,14 +1719,6 @@ coverage information.") "$(BISECTLIB)/bisect")) #:phases (modify-phases %standard-phases - (add-before 'configure 'fix-configure - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "Makefile.in" - (("@abs_top_builddir@") - (string-append "@abs_top_builddir@:" (getenv "LIBRARY_PATH")))) - (substitute* "configure" - (("-/bin/sh") (string-append "-" (assoc-ref inputs "bash") - "/bin/sh"))))) (add-after 'install 'link-lib (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -1297,15 +1728,24 @@ coverage information.") "/lib/ocaml/site-lib/bitstring"))) (mkdir-p stubs) (symlink (string-append lib "/dllbitstring.so") - (string-append stubs "/dllbitstring.so")))))))) - (home-page "https://github.com/xguerin/bitstring") - (synopsis "Bitstrings and bitstring matching for OCaml") - (description "Adds Erlang-style bitstrings and matching over bitstrings as -a syntax extension and library for OCaml. You can use this module to both parse -and generate binary formats, files and protocols. Bitstring handling is added -as primitives to the language, making it exceptionally simple to use and very -powerful.") - (license license:isc))) + (string-append stubs "/dllbitstring.so"))) + #t)) + (add-before 'configure 'fix-configure + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile.in" + (("@abs_top_builddir@") + (string-append "@abs_top_builddir@:" (getenv "LIBRARY_PATH")))) + (substitute* "configure" + (("-/bin/sh") (string-append "-" (assoc-ref inputs "bash") + "/bin/sh")))))))) + (native-inputs + `(("camlp4" ,camlp4-4.02) + ("time" ,time) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("bisect" ,ocaml4.02-bisect))) + (propagated-inputs + `(("camlp4" ,camlp4-4.02)))))) (define-public ocaml-result (package @@ -1331,6 +1771,9 @@ powerful.") staying compatible with older version of OCaml should use the Result module defined in this library.") (license license:bsd-3))) + +(define-public ocaml4.02-result + (package-with-ocaml4.02 ocaml-result)) (define-public ocaml-topkg (package @@ -1345,7 +1788,8 @@ defined in this library.") "18rrh6fmf708z7dd30amljmcgaypj3kk49jrmrj68r4wnw8004j8")))) (build-system ocaml-build-system) (native-inputs - `(("opam" ,opam))) + `(("opam" ,opam) + ("ocamlbuild" ,ocamlbuild))) (propagated-inputs `(("result" ,ocaml-result))) (arguments @@ -1361,6 +1805,9 @@ provides an API to describe the files a package installs in a given build configuration and to specify information about the package's distribution, creation and publication procedures.") (license license:isc))) + +(define-public ocaml4.02-topkg + (package-with-ocaml4.02 ocaml-topkg)) (define-public ocaml-rresult (package @@ -1375,7 +1822,8 @@ creation and publication procedures.") "1xxycxhdhaq8p9vhwi93s2mlxjwgm44fcxybx5vghzgbankz9yhm")))) (build-system ocaml-build-system) (native-inputs - `(("opam" ,opam))) + `(("opam" ,opam) + ("ocamlbuild" ,ocamlbuild))) (propagated-inputs `(("topkg" ,ocaml-topkg))) (arguments @@ -1392,6 +1840,9 @@ to operate on the result type available from OCaml 4.03 in the standard library.") (license license:isc))) +(define-public ocaml4.02-rresult + (package-with-ocaml4.02 ocaml-rresult)) + (define-public ocaml-sqlite3 (package (name "ocaml-sqlite3") @@ -1407,7 +1858,8 @@ library.") "14c1nir7c6bivajg0vyx853y7la7r5d25g1v5hjb2wfi73r15p1m")))) (build-system ocaml-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("ocamlbuild" ,ocamlbuild) + ("pkg-config" ,pkg-config))) (inputs `(("sqlite" ,sqlite))) (home-page "https://mmottl.github.io/sqlite3-ocaml") @@ -1424,6 +1876,9 @@ coexistence with the old (version 2) SQLite and its OCaml wrapper (define-public ocaml4.01-sqlite3 (package-with-ocaml4.01 ocaml-sqlite3)) +(define-public ocaml4.02-sqlite3 + (package-with-ocaml4.02 ocaml-sqlite3)) + (define-public ocaml-csv (package (name "ocaml-csv") @@ -1439,6 +1894,8 @@ coexistence with the old (version 2) SQLite and its OCaml wrapper (base32 "0rv7x843vn6scxj87hzl01yqrl26rc27lr8s7z6rp9vs745g05zj")))) (build-system ocaml-build-system) + (native-inputs + `(("ocamlbuild" ,ocamlbuild))) (home-page "https://github.com/Chris00/ocaml-csv") (synopsis "Pure OCaml functions to read and write CSV") (description @@ -1451,6 +1908,9 @@ manipulate such data.") (define-public ocaml4.01-csv (package-with-ocaml4.01 ocaml-csv)) +(define-public ocaml4.02-csv + (package-with-ocaml4.02 ocaml-csv)) + (define-public ocaml-mtime (package (name "ocaml-mtime") @@ -1464,7 +1924,8 @@ manipulate such data.") "1hfx4ny2dkw6jf3jppz0640dafl5xgn8r2si9kpwzhmibal8qrah")))) (build-system ocaml-build-system) (native-inputs - `(("opam" ,opam))) + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) (propagated-inputs `(("topkg" ,ocaml-topkg))) (arguments @@ -1480,6 +1941,9 @@ manipulate such data.") spans without being subject to operating system calendar time adjustments.") (license license:isc))) +(define-public ocaml4.02-mtime + (package-with-ocaml4.02 ocaml-mtime)) + (define-public ocaml-cmdliner (package (name "ocaml-cmdliner") @@ -1493,7 +1957,8 @@ spans without being subject to operating system calendar time adjustments.") "0hdxlkgiwjml9dpaa80282a8350if7mc1m6yz2mrd7gci3fszykx")))) (build-system ocaml-build-system) (native-inputs - `(("opam" ,opam))) + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) (arguments `(#:tests? #f #:build-flags '("native=true" "native-dynlink=true") @@ -1510,6 +1975,9 @@ generation. It supports programs with single or multiple commands and respects most of the POSIX and GNU conventions.") (license license:bsd-3))) +(define-public ocaml4.02-cmdliner + (package-with-ocaml4.02 ocaml-cmdliner)) + (define-public ocaml-fmt (package (name "ocaml-fmt") @@ -1522,10 +1990,13 @@ most of the POSIX and GNU conventions.") (sha256 (base32 "16y7ibndnairb53j8a6qgipyqwjxncn4pl9jiw5bxjfjm59108px")))) (build-system ocaml-build-system) - (native-inputs `(("opam" ,opam) - ("topkg" ,ocaml-topkg))) - (propagated-inputs `(("result" ,ocaml-result) - ("cmdliner" ,ocaml-cmdliner))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam) + ("topkg" ,ocaml-topkg))) + (propagated-inputs + `(("result" ,ocaml-result) + ("cmdliner" ,ocaml-cmdliner))) (arguments `(#:tests? #f #:build-flags (list "build" "--with-base-unix" "true" "--with-cmdliner" "true") @@ -1538,6 +2009,9 @@ most of the POSIX and GNU conventions.") functions.") (license license:isc))) +(define-public ocaml4.02-fmt + (package-with-ocaml4.02 ocaml-fmt)) + (define-public ocaml-astring (package (name "ocaml-astring") @@ -1550,13 +2024,16 @@ functions.") (sha256 (base32 "0ixjwc3plrljvj24za3l9gy0w30lsbggp8yh02lwrzw61ls4cri0")))) (build-system ocaml-build-system) - (native-inputs `(("opam" ,opam) - ("topkg" ,ocaml-topkg))) - (arguments `(#:tests? #f - #:build-flags (list "build") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam) + ("topkg" ,ocaml-topkg))) + (arguments + `(#:tests? #f + #:build-flags (list "build") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) (home-page "http://erratique.ch/software/astring") (synopsis "Alternative String module for OCaml") (description "Astring exposes an alternative String module for OCaml. This @@ -1568,6 +2045,9 @@ adds a few missing functions and fully exploits OCaml's newfound string immutability.") (license license:isc))) +(define-public ocaml4.02-astring + (package-with-ocaml4.02 ocaml-astring)) + (define-public ocaml-alcotest (package (name "ocaml-alcotest") @@ -1580,15 +2060,19 @@ immutability.") (base32 "0g5lzk0gpfx4q8hyhr460gr4lab5wakfxsmhfwvb3yinxwzs95gc")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:build-flags (list "build") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs `(("opam" ,opam) - ("topkg" ,ocaml-topkg))) - (propagated-inputs `(("fmt" ,ocaml-fmt) - ("astring" ,ocaml-astring))) + (arguments + `(#:tests? #f + #:build-flags (list "build") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam) + ("topkg" ,ocaml-topkg))) + (propagated-inputs + `(("fmt" ,ocaml-fmt) + ("astring" ,ocaml-astring))) (home-page "https://github.com/mirage/alcotest") (synopsis "Lightweight OCaml test framework") (description "Alcotest exposes simple interface to perform unit tests. It @@ -1599,25 +2083,44 @@ displayed at the end of the run (with the full logs ready to inspect), with a simple (yet expressive) query language to select the tests to run.") (license license:isc))) +(define-public ocaml4.02-alcotest + (package-with-ocaml4.02 ocaml-alcotest)) + (define-public ocaml-ppx-tools (package (name "ocaml-ppx-tools") - (version "5.0+4.02.0") + (version "5.1+4.06.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/alainfrisch/ppx_tools/archive/" version ".tar.gz")) (sha256 (base32 - "0rjg4rngi8k9873z4zq95zn9hj8qyw1vcrf11y15aqasfpqq16rc")))) + "0mncpy9v2mcjgnj7s2vqpp2b1ixv54djicfx66ic9wny9d202gj1")))) (build-system ocaml-build-system) - (arguments `(#:phases (modify-phases %standard-phases (delete 'configure)) - #:tests? #f)) + (arguments + `(#:phases (modify-phases %standard-phases (delete 'configure)) + #:tests? #f)) + (properties + `((ocaml4.02-variant . ,(delay ocaml4.02-ppx-tools)))) (home-page "https://github.com/alainfrisch/ppx_tools") (synopsis "Tools for authors of ppx rewriters and other syntactic tools") (description "Tools for authors of ppx rewriters and other syntactic tools.") (license license:expat))) +(define-public ocaml4.02-ppx-tools + (let ((base (package-with-ocaml4.02 (strip-ocaml4.02-variant ocaml-ppx-tools)))) + (package + (inherit base) + (version "5.0+4.02.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/alainfrisch/ppx_tools/archive/" + version ".tar.gz")) + (sha256 (base32 + "0rjg4rngi8k9873z4zq95zn9hj8qyw1vcrf11y15aqasfpqq16rc"))))))) + (define-public ocaml-react (package (name "ocaml-react") @@ -1630,12 +2133,15 @@ simple (yet expressive) query language to select the tests to run.") (sha256 (base32 "0knhgbngphv5sp1yskfd97crf169qhpc0igr6w7vqw0q36lswyl8")))) (build-system ocaml-build-system) - (native-inputs `(("opam" ,opam))) - (arguments `(#:tests? #f - #:build-flags (list "native=true" "native-dynlink=true") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) + (arguments + `(#:tests? #f + #:build-flags (list "native=true" "native-dynlink=true") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) (home-page "http://erratique.ch/software/react") (synopsis "Declarative events and signals for OCaml") (description "React is an OCaml module for functional reactive programming @@ -1644,6 +2150,9 @@ events and signals. React doesn't define any primitive event or signal, it lets the client choose the concrete timeline.") (license license:bsd-3))) +(define-public ocaml4.02-react + (package-with-ocaml4.02 ocaml-react)) + (define-public ocaml-ssl (package (name "ocaml-ssl") @@ -1658,20 +2167,23 @@ lets the client choose the concrete timeline.") (sha256 (base32 "0fviq8xhp3qk7pmkl7knchywsipxgb7p0z489hj8qnf2sx8xzdmy")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:make-flags (list "OCAMLFIND_LDCONF=ignore") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'bootstrap - (lambda* (#:key #:allow-other-keys) - (system* "sh" "bootstrap") - (substitute* "src/OCamlMakefile" - (("/bin/sh") (which "bash"))) - (substitute* "configure" - (("/bin/sh") (which "bash")))))))) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("which" ,which))) + (arguments + `(#:tests? #f + #:make-flags (list "OCAMLFIND_LDCONF=ignore") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'bootstrap + (lambda* (#:key #:allow-other-keys) + (system* "sh" "bootstrap") + (substitute* "src/OCamlMakefile" + (("/bin/sh") (which "bash"))) + (substitute* "configure" + (("/bin/sh") (which "bash"))) + #t))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("which" ,which))) (propagated-inputs `(("openssl" ,openssl))) (home-page "https://github.com/savonet/ocaml-ssl/") (synopsis "OCaml bindings for OpenSSL") @@ -1680,10 +2192,13 @@ lets the client choose the concrete timeline.") through Transport Layer Security (@dfn{TLS}) encrypted connections.") (license license:lgpl2.1))) +(define-public ocaml4.02-ssl + (package-with-ocaml4.02 ocaml-ssl)) + (define-public ocaml-lwt (package (name "ocaml-lwt") - (version "2.6.0") + (version "4.1.0") (source (origin (method url-fetch) @@ -1691,35 +2206,37 @@ through Transport Layer Security (@dfn{TLS}) encrypted connections.") ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1gbw0g8a5a4b16diqrmlhc8ilnikrm4w3jjm1zq310maqg8z0zxz")))) + "0mhh019bjkg5xfvpy1pxs4xdxb759fyydmgb6l4j0qww1qgr8klp")))) (build-system ocaml-build-system) (arguments - `(#:configure-flags - (list "--enable-ssl" "--enable-glib" "--enable-react" - "--enable-ppx") + `(#:tests? #f; require lwt_ppx #:phases (modify-phases %standard-phases - (add-before 'configure 'disable-some-checks - (lambda* (#:key #:allow-other-keys) - (substitute* "tests/unix/main.ml" - (("Test_mcast.suite;") "")))) - (add-after 'install 'link-stubs + (replace 'configure + (lambda _ + (invoke "ocaml" "src/util/configure.ml" "-use-libev" "true") + #t)) + (replace 'build + (lambda _ + (invoke "jbuilder" "build" "@install") + #t)) + (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (stubs (string-append out "/lib/ocaml/site-lib/stubslibs")) - (lib (string-append out "/lib/ocaml/site-lib/lwt"))) - (mkdir-p stubs) - (symlink (string-append lib "/dlllwt-glib_stubs.so") - (string-append stubs "/dlllwt-glib_stubs.so")) - (symlink (string-append lib "/dlllwt-unix_stubs.so") - (string-append stubs "/dlllwt-unix_stubs.so")))))))) - (native-inputs `(("pkg-config" ,pkg-config) - ("ppx-tools" ,ocaml-ppx-tools))) - (inputs `(("libev" ,libev) - ("glib" ,glib))) - (propagated-inputs `(("result" ,ocaml-result) - ("ocaml-ssl" ,ocaml-ssl) - ("ocaml-react" ,ocaml-react))) + (invoke "jbuilder" "install" "--prefix" (assoc-ref outputs "out")) + #t))))) + (native-inputs + `(("dune" ,dune) + ("ocaml-cppo" ,ocaml-cppo) + ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + ("pkg-config" ,pkg-config) + ("ppx-tools-versioned" ,ocaml-ppx-tools-versioned))) + (inputs + `(("libev" ,libev) + ("glib" ,glib))) + (propagated-inputs + `(("result" ,ocaml-result) + ("ocaml-ssl" ,ocaml-ssl) + ("ocaml-react" ,ocaml-react))) (home-page "https://github.com/ocsigen/lwt") (synopsis "Cooperative threads and I/O in monadic style") (description "Lwt provides typed, composable cooperative threads. These @@ -1728,6 +2245,48 @@ process. Also, in many cases, Lwt threads can interact without the need for locks or other synchronization primitives.") (license license:lgpl2.1))) +(define-public ocaml4.02-lwt + (package-with-ocaml4.02 ocaml-lwt)) + +(define-public ocaml-lwt-log + (package + (name "ocaml-lwt-log") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/aantron/lwt_log/archive/" version + ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 (base32 + "1lr62j2266pbsi54xmzsfvl2z7fi7smhak7fp1ybl8hssxwi6in2")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f; require lwt_ppx + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "jbuilder" "build" "@install") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "jbuilder" "install" "--prefix" (assoc-ref outputs "out")) + #t))))) + (native-inputs + `(("dune" ,dune))) + (propagated-inputs + `(("lwt" ,ocaml-lwt))) + (home-page "https://github.com/aantron/lwt_log") + (synopsis "Logging library") + (description "This package provides a deprecated logging component for +ocaml lwt.") + (license license:lgpl2.1))) + +(define-public ocaml4.02-lwt-log + (package-with-ocaml4.02 ocaml-lwt-log)) + (define-public ocaml-logs (package (name "ocaml-logs") @@ -1740,18 +2299,22 @@ locks or other synchronization primitives.") (base32 "1khbn7jqpid83zn8rvyh1x1sirls7zc878zj4fz985m5xlsfy853")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:build-flags (list "build" "--with-js_of_ocaml" "false") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs `(("opam" ,opam))) - (propagated-inputs `(("fmt" ,ocaml-fmt) - ("lwt" ,ocaml-lwt) - ("mtime" ,ocaml-mtime) - ("result" ,ocaml-result) - ("cmdliner" ,ocaml-cmdliner) - ("topkg" ,ocaml-topkg))) + (arguments + `(#:tests? #f + #:build-flags (list "build" "--with-js_of_ocaml" "false") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) + (propagated-inputs + `(("fmt" ,ocaml-fmt) + ("lwt" ,ocaml-lwt) + ("mtime" ,ocaml-mtime) + ("result" ,ocaml-result) + ("cmdliner" ,ocaml-cmdliner) + ("topkg" ,ocaml-topkg))) (home-page "http://erratique.ch/software/logs") (synopsis "Logging infrastructure for OCaml") (description "Logs provides a logging infrastructure for OCaml. Logging is @@ -1759,6 +2322,9 @@ performed on sources whose reporting level can be set independently. Log message report is decoupled from logging and is handled by a reporter.") (license license:isc))) +(define-public ocaml4.02-logs + (package-with-ocaml4.02 ocaml-logs)) + (define-public ocaml-fpath (package (name "ocaml-fpath") @@ -1771,14 +2337,18 @@ message report is decoupled from logging and is handled by a reporter.") (base32 "05134ij27xjl6gaqsc65yl19vfj6cjxq3mbm9bf4mija8grdpn6g")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:build-flags (list "build") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs `(("opam" ,opam))) - (propagated-inputs `(("topkg" ,ocaml-topkg) - ("astring" ,ocaml-astring))) + (arguments + `(#:tests? #f + #:build-flags (list "build") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) + (propagated-inputs + `(("topkg" ,ocaml-topkg) + ("astring" ,ocaml-astring))) (home-page "http://erratique.ch/software/fpath") (synopsis "File system paths for OCaml") (description "Fpath is an OCaml module for handling file system paths with @@ -1786,6 +2356,9 @@ POSIX or Windows conventions. Fpath processes paths without accessing the file system and is independent from any system library.") (license license:isc))) +(define-public ocaml4.02-fpath + (package-with-ocaml4.02 ocaml-fpath)) + (define-public ocaml-bos (package (name "ocaml-bos") @@ -1798,18 +2371,22 @@ file system and is independent from any system library.") (base32 "1ly66lysk4w6mdy4k1n3ynlpfpq7lw4wshcpzgx58v6x613w5s7q")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:build-flags (list "build") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs `(("opam" ,opam))) - (propagated-inputs `(("topkg" ,ocaml-topkg) - ("astring" ,ocaml-astring) - ("fmt" ,ocaml-fmt) - ("fpath" ,ocaml-fpath) - ("logs" ,ocaml-logs) - ("rresult" ,ocaml-rresult))) + (arguments + `(#:tests? #f + #:build-flags (list "build") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) + (propagated-inputs + `(("topkg" ,ocaml-topkg) + ("astring" ,ocaml-astring) + ("fmt" ,ocaml-fmt) + ("fpath" ,ocaml-fpath) + ("logs" ,ocaml-logs) + ("rresult" ,ocaml-rresult))) (home-page "http://erratique.ch/software/bos") (synopsis "Basic OS interaction for OCaml") (description "Bos provides support for basic and robust interaction with @@ -1818,26 +2395,31 @@ environment, parse command line arguments, interact with the file system and run command line programs.") (license license:isc))) +(define-public ocaml4.02-bos + (package-with-ocaml4.02 ocaml-bos)) + (define-public ocaml-xmlm (package (name "ocaml-xmlm") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "http://erratique.ch/software/xmlm/releases/" "xmlm-" version ".tbz")) (sha256 (base32 - "1jywcrwn5z3gkgvicr004cxmdaqfmq8wh72f81jqz56iyn5024nh")))) + "1rrdxg5kh9zaqmgapy9bhdqyxbbvxxib3bdfg1vhw4rrkp1z0x8n")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (replace 'build - (lambda* (#:key #:allow-other-keys) - (zero? (system* "pkg/build" "true"))))))) - (native-inputs `(("opam" ,opam))) + (arguments + `(#:tests? #f + #:build-flags (list "build") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("ocaml-topkg" ,ocaml-topkg) + ("opam" ,opam))) (home-page "http://erratique.ch/software/xmlm") (synopsis "Streaming XML codec for OCaml") (description "Xmlm is a streaming codec to decode and encode the XML data @@ -1848,32 +2430,41 @@ representation of the data.") (define-public ocaml4.01-xmlm (package-with-ocaml4.01 ocaml-xmlm)) +(define-public ocaml4.02-xmlm + (package-with-ocaml4.02 ocaml-xmlm)) + (define-public ocaml-ulex (package (name "ocaml-ulex") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) - (uri (string-append "http://www.cduce.org/download/ulex-" + (uri (string-append "https://github.com/whitequark/ulex/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0fjlkwps14adfgxdrbb4yg65fhyimplvjjs1xqj5np197cig67x0")))) + "16gnbhqs6y2v89vw4igzvxdf2g8ybh5643636824aldcv8sscac0")))) (build-system ocaml-build-system) - (arguments `(#:phases (modify-phases %standard-phases (delete 'configure)) - #:tests? #f - #:make-flags - (list "all.opt" - (string-append "OCAMLBUILD=ocamlbuild -byte-plugin " - "-cflags -I," - (assoc-ref %build-inputs "camlp4") - "/lib/ocaml/site-lib/camlp4")))) - (native-inputs `(("camlp4" ,camlp4))) + (arguments + `(#:phases (modify-phases %standard-phases (delete 'configure)) + #:tests? #f + #:make-flags + (list "all.opt" + (string-append "OCAMLBUILD=ocamlbuild -byte-plugin " + "-cflags -I," (assoc-ref %build-inputs "camlp4") + "/lib/ocaml/site-lib/camlp4")))) + (native-inputs + `(("camlp4" ,camlp4) + ("ocamlbuild" ,ocamlbuild))) (home-page "http://www.cduce.org/download.html#side") (synopsis "Lexer generator for Unicode and OCaml") (description "Lexer generator for Unicode and OCaml.") (license license:expat))) +(define-public ocaml4.02-ulex + (package-with-ocaml4.02 ocaml-ulex)) + (define-public ocaml-uchar (package (name "ocaml-uchar") @@ -1886,39 +2477,49 @@ representation of the data.") (sha256 (base32 "0ficw1x7ymbd6m8hqw3w1aycwm1hbwd6bad3c5pspwnzh3qlikhi")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:build-flags (list "native=true" "native-dynlink=true") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs `(("opam" ,opam))) + (arguments + `(#:tests? #f + #:build-flags (list "native=true" "native-dynlink=true") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) (home-page "https://github.com/ocaml/uchar") (synopsis "Compatibility library for OCaml's Uchar module") (description "The uchar package provides a compatibility library for the `Uchar` module introduced in OCaml 4.03.") (license license:lgpl2.1))) +(define-public ocaml4.02-uchar + (package-with-ocaml4.02 ocaml-uchar)) + (define-public ocaml-uutf (package (name "ocaml-uutf") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (string-append "http://erratique.ch/software/uutf/releases/" "uutf-" version ".tbz")) (sha256 (base32 - "08i0cw02cxw4mi2rs01v9xi307qshs6fnd1dlqyb52kcxzblpp37")))) + "1gp96dcggq7s84934vimxh89caaxa77lqiff1yywbwkilkkjcfqj")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:build-flags (list "build") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs `(("opam" ,opam) - ("topkg" ,ocaml-topkg))) - (propagated-inputs `(("uchar" ,ocaml-uchar) - ("cmdliner" ,ocaml-cmdliner))) + (arguments + `(#:tests? #f + #:build-flags (list "build") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam) + ("topkg" ,ocaml-topkg))) + (propagated-inputs + `(("uchar" ,ocaml-uchar) + ("cmdliner" ,ocaml-cmdliner))) (home-page "http://erratique.ch/software/uutf") (synopsis "Non-blocking streaming Unicode codec for OCaml") (description "Uutf is a non-blocking streaming codec to decode and encode @@ -1930,27 +2531,34 @@ Functions are also provided to fold over the characters of UTF encoded OCaml string values and to directly encode characters in OCaml Buffer.t values.") (license license:isc))) +(define-public ocaml4.02-uutf + (package-with-ocaml4.02 ocaml-uutf)) + (define-public ocaml-jsonm (package (name "ocaml-jsonm") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (string-append "http://erratique.ch/software/jsonm/releases/" "jsonm-" version ".tbz")) (sha256 (base32 - "1v3ln6d965lplj28snjdqdqablpp1kx8bw2cfx0m6i157mqyln62")))) + "1176dcmxb11fnw49b7yysvkjh0kpzx4s48lmdn5psq9vshp5c29w")))) (build-system ocaml-build-system) - (arguments `(#:tests? #f - #:build-flags (list "build") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs `(("opam" ,opam) - ("topkg" ,ocaml-topkg))) - (propagated-inputs `(("uutf" ,ocaml-uutf) - ("cmdliner" ,ocaml-cmdliner))) + (arguments + `(#:tests? #f + #:build-flags (list "build") + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam) + ("topkg" ,ocaml-topkg))) + (propagated-inputs + `(("uutf" ,ocaml-uutf) + ("cmdliner" ,ocaml-cmdliner))) (home-page "http://erratique.ch/software/jsonm") (synopsis "Non-blocking streaming JSON codec for OCaml") (description "Jsonm is a non-blocking streaming codec to decode and encode @@ -1958,25 +2566,30 @@ the JSON data format. It can process JSON text without blocking on IO and without a complete in-memory representation of the data.") (license license:isc))) +(define-public ocaml4.02-jsonm + (package-with-ocaml4.02 ocaml-jsonm)) + (define-public ocaml-ocurl (package (name "ocaml-ocurl") - (version "0.7.9") + (version "0.8.2") (source (origin (method url-fetch) (uri (string-append "http://ygrek.org.ua/p/release/ocurl/ocurl-" version ".tar.gz")) (sha256 (base32 - "0pm6nm33wi0p9h765k6zb94ljpknryam4qd1hmb2rsk2y0y1181n")))) + "1ax3xdlzgb1zg7d0wr9nwgmh6a45a764m0wk8p6mx07ad94hz0q9")))) (build-system ocaml-build-system) - (arguments `(#:phases - (modify-phases %standard-phases - (add-before 'configure 'fix-/bin/sh - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "configure" - (("-/bin/sh") (string-append "-" (which "bash"))))))))) - (native-inputs `(("pkg-config" ,pkg-config))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'fix-/bin/sh + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "configure" + (("-/bin/sh") (string-append "-" (which "bash"))))))))) + (native-inputs + `(("pkg-config" ,pkg-config))) (inputs `(("curl" ,curl))) (home-page "http://ocurl.forge.ocamlcore.org/") (synopsis "OCaml bindings for libcurl") @@ -1984,6 +2597,9 @@ without a complete in-memory representation of the data.") multitude of other network protocols (FTP/SMTP/RTSP/etc).") (license license:isc))) +(define-public ocaml4.02-ocurl + (package-with-ocaml4.02 ocaml-ocurl)) + (define-public ocaml-base64 (package (name "ocaml-base64") @@ -2005,6 +2621,7 @@ multitude of other network protocols (FTP/SMTP/RTSP/etc).") (delete 'configure)))) (native-inputs `(("topkg" ,ocaml-topkg) + ("ocamlbuild" ,ocamlbuild) ("opam" ,opam) ("rresult" ,ocaml-rresult) ("bos" ,ocaml-bos) @@ -2016,6 +2633,9 @@ that represent binary data in an ASCII string format by translating it into a radix-64 representation. It is specified in RFC 4648.") (license license:isc))) +(define-public ocaml4.02-base64 + (package-with-ocaml4.02 ocaml-base64)) + (define-public ocamlify (package (name "ocamlify") @@ -2029,7 +2649,9 @@ radix-64 representation. It is specified in RFC 4648.") (build-system ocaml-build-system) ; tests are done during build (arguments - `(#:phases + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:phases (modify-phases %standard-phases (delete 'check)))) (home-page "https://forge.ocamlcore.org/projects/ocamlify") @@ -2043,14 +2665,14 @@ OCaml code.") (define-public omake (package (name "omake") - (version "0.10.1") + (version "0.10.3") (source (origin (method url-fetch) (uri (string-append "http://download.camlcity.org/download/" "omake-" version ".tar.gz")) (sha256 (base32 - "093ansbppms90hiqvzar2a46fj8gm9iwnf8gn38s6piyp70lrbsj")) + "07bdg1h5i7qnlv9xq81ad5hfypl10hxm771h4rjyl5cn8plhfcgz")) (patches (search-patches "omake-fix-non-determinism.patch")))) (build-system ocaml-build-system) (arguments @@ -2063,6 +2685,8 @@ OCaml code.") (lambda* (#:key outputs #:allow-other-keys) (substitute* "mk/osconfig_unix.mk" (("CC = cc") "CC = gcc"))))))) + (properties + `((ocaml4.02-variant . ,(delay ocaml4.02-omake)))) (native-inputs `(("hevea" ,hevea))) (home-page "http://projects.camlcity.org/projects/omake.html") (synopsis "Build system designed for scalability and portability") @@ -2084,28 +2708,66 @@ many additional enhancements, including: license:gpl2)))) ; OMake itself, with ocaml linking exception ; see LICENSE.OMake +(define-public ocaml4.02-omake + (let ((base (package-with-ocaml4.02 (strip-ocaml4.02-variant omake)))) + (package + (inherit base) + (version "0.10.2") + (source (origin + (method url-fetch) + (uri (string-append "http://download.camlcity.org/download/" + "omake-" version ".tar.gz")) + (sha256 + (base32 + "1znnlkpz89hk44byvnl1pr92ym6hwfyyw2qm9clq446r6l2z4m64")) + (patches (search-patches "omake-fix-non-determinism.patch"))))))) + (define-public ocaml-batteries (package (name "ocaml-batteries") - (version "2.5.3") + (version "2.9.0") (source (origin (method url-fetch) - (uri (ocaml-forge-uri "batteries" version 1650)) + (uri (string-append "https://github.com/ocaml-batteries-team/" + "batteries-included/releases/download/v" + version "/batteries-" version ".tar.gz")) (sha256 (base32 - "1a97w3x2l1jr5x9kj5gqm1x6b0q9fjqdcsvls7arnl3bvzgsia0n")))) + "0lkdmv2my5hirkswmci2cch341n6wkkj2q8apjhs83sg6528caxi")))) (build-system ocaml-build-system) (native-inputs - `(("qtest" ,ocaml-qtest) + `(("ocamlbuild" ,ocamlbuild) + ("qtest" ,ocaml-qtest) ("bisect" ,ocaml-bisect) ("ounit" ,ocaml-ounit))) + (propagated-inputs + `(("ocaml-num" ,ocaml-num))) (arguments `(#:phases (modify-phases %standard-phases (delete 'check) ; tests are run by the build phase (replace 'build - (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "ocaml" "setup.ml" "-build"))))))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((files + (map (lambda (str) + (substring str 0 (- (string-length str) 1))) + (append + (find-files "src" ".*.mliv") + (find-files "src" ".*.mlv") + (find-files "src" ".*.mlp"))))) + (apply invoke "ocamlbuild" "-no-links" "-use-ocamlfind" "-I" "num" + "-lflag" "-dllpath-all" files) + (for-each (lambda (file) + (copy-file (string-append "_build/" file) file)) + files)) + (invoke "ocamlbuild" "-no-links" "-use-ocamlfind" "-I" "num" + "-lflag" "-dllpath-all" "build/mkconf.byte") + (copy-file "_build/build/mkconf.byte" "build/mkconf.byte") + (invoke "make" "all") + #t))))) + (properties + `((ocaml4.01-variant . ,(delay ocaml4.01-batteries)) + (ocaml4.02-variant . ,(delay ocaml4.02-batteries)))) (home-page "http://batteries.forge.ocamlcore.org/") (synopsis "Development platform for the OCaml programming language") (description "Define a standard set of libraries which may be expected on @@ -2113,8 +2775,24 @@ every compliant installation of OCaml and organize these libraries into a hierarchy of modules.") (license license:lgpl2.1+))) +(define-public ocaml4.02-batteries + (let ((base (package-with-ocaml4.02 (strip-ocaml4.02-variant ocaml-batteries)))) + (package + (inherit base) + (version "2.5.3") + (source (origin + (method url-fetch) + (uri (ocaml-forge-uri "batteries" version 1650)) + (sha256 + (base32 + "1a97w3x2l1jr5x9kj5gqm1x6b0q9fjqdcsvls7arnl3bvzgsia0n")))) + (propagated-inputs '())))) + (define-public ocaml4.01-batteries - (package-with-ocaml4.01 ocaml-batteries)) + (let ((base (package-with-ocaml4.01 (strip-ocaml4.01-variant ocaml4.02-batteries)))) + (package + (inherit base) + (name "ocaml4.01-batteries")))) (define-public ocaml-pcre (package @@ -2139,9 +2817,11 @@ hierarchy of modules.") (lib (string-append out "/lib/ocaml/site-lib/pcre"))) (mkdir-p stubs) (symlink (string-append lib "/dllpcre_stubs.so") - (string-append stubs "/dllpcre_stubs.so")))))))) + (string-append stubs "/dllpcre_stubs.so"))) + #t))))) (native-inputs `(("batteries" ,ocaml-batteries) + ("ocamlbuild" ,ocamlbuild) ("pcre:bin" ,pcre "bin"))) (propagated-inputs `(("pcre" ,pcre))) (home-page "https://mmottl.github.io/pcre-ocaml") @@ -2151,19 +2831,26 @@ matching and substitution, similar to the functionality offered by the Perl language.") (license license:lgpl2.1+))); with the OCaml link exception +(define-public ocaml4.02-pcre + (package-with-ocaml4.02 ocaml-pcre)) + (define-public ocaml-expect (package (name "ocaml-expect") - (version "0.0.5") + (version "0.0.6") (source (origin (method url-fetch) - (uri (ocaml-forge-uri name version 1372)) + (uri (ocaml-forge-uri name version 1736)) (sha256 (base32 - "07xq8w2x2vffc32z7vk6y14jwbfb1cw0m2lm1jzi60hnr1dvg8by")))) + "098qvg9d4yrqzr5ax291y3whrpax0m3sx4gi6is0mblc96r9yqk0")))) + (arguments + `(#:tests? #f)) (build-system ocaml-build-system) (native-inputs - `(("ocaml-pcre" ,ocaml-pcre) + `(("ocamlbuild" ,ocamlbuild) + ("ocaml-num" ,ocaml-num) + ("ocaml-pcre" ,ocaml-pcre) ("ounit" ,ocaml-ounit))) (propagated-inputs `(("batteries" ,ocaml-batteries))) (home-page "https://forge.ocamlcore.org/projects/ocaml-expect/") @@ -2172,18 +2859,22 @@ language.") can match the question using a regular expression or a timeout.") (license license:lgpl2.1+))) ; with the OCaml static compilation exception -(define-public ocaml-fileutils +(define-public ocaml4.02-fileutils (package - (name "ocaml-fileutils") - (version "0.5.1") + (name "ocaml4.02-fileutils") + (version "0.5.3") (source (origin (method url-fetch) - (uri (ocaml-forge-uri name version 1651)) + (uri (ocaml-forge-uri name version 1728)) (sha256 (base32 - "0g6zx2rcvacklxyli19ixcf6ich9ipxsps4k3jz98f5zlaab0a7g")))) + "1rc4cqlvdhbs55i85zfbfhz938fsy4fj6kwlkfm3ra7bpwn8bmpd")))) (build-system ocaml-build-system) - (native-inputs `(("ounit" ,ocaml-ounit))) + (arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib)) + (native-inputs + `(("ounit" ,ocaml4.02-ounit))) (home-page "http://ocaml-fileutils.forge.ocamlcore.org") (synopsis "Pure OCaml functions to manipulate real file and filename") (description "Library to provide pure OCaml functions to manipulate real @@ -2193,20 +2884,20 @@ file (POSIX like) and filename.") (define-public ocaml-oasis (package (name "ocaml-oasis") - (version "0.4.8") + (version "0.4.11") (source (origin (method url-fetch) - (uri (ocaml-forge-uri name version 1669)) + (uri (ocaml-forge-uri name version 1757)) (sha256 (base32 - "1ln7vc7ip6s5xbi20mhnn087xi4a2m5vqawx0703qqnfkzhmslqy")) + "0bn13mzfa98dq3y0jwzzndl55mnywaxv693z6f1rlvpdykp3vdqq")) (modules '((guix build utils))) (snippet '(begin (substitute* "test/test-main/Test.ml" ;; most of these tests fail because ld cannot find crti.o, but according ;; to the log file, the environment variables {LD_,}LIBRARY_PATH - ;; are set correctly whene LD_LIBRARY_PATH is defined beforhand. + ;; are set correctly when LD_LIBRARY_PATH is defined beforhand. (("TestBaseCompat.tests;") "") (("TestExamples.tests;") "") (("TestFull.tests;") "") @@ -2216,17 +2907,12 @@ file (POSIX like) and filename.") (("TestPluginOMake.tests;") "")) #t)))) (build-system ocaml-build-system) + (arguments + `(#:tests? #f)) (native-inputs - `(("ocamlify" ,ocamlify) - ("ocamlmod" ,ocamlmod) - ("ounit" ,ocaml-ounit) - ("omake" ,omake) - ("ocaml-expect" ,ocaml-expect) - ("ocaml-pcre" ,ocaml-pcre) - ("ocaml-fileutils" ,ocaml-fileutils) - ("camlp4" ,camlp4) - ("texlive" ,texlive) - ("pkg-config" ,pkg-config))) + `(("ocamlbuild" ,ocamlbuild) + ("ocamlify" ,ocamlify) + ("ocamlmod" ,ocamlmod))) (home-page "https://oasis.forge.ocamlcore.org") (synopsis "Integrates a configure, build, install system in OCaml projects") (description "OASIS is a tool to integrate a configure, build and install @@ -2234,6 +2920,9 @@ system in your OCaml projects. It helps to create standard entry points in your build system and allows external tools to analyse your project easily.") (license license:lgpl2.1+))) ; with ocaml static compilation exception +(define-public ocaml4.02-oasis + (package-with-ocaml4.02 ocaml-oasis)) + (define-public ocaml-js-build-tools (package (name "ocaml-js-build-tools") @@ -2242,6 +2931,7 @@ build system and allows external tools to analyse your project easily.") "0r8z4fz8iy5y6hkdlkpwf6rk4qigcr3dzyv35585xgg2ahf12zy6")) (native-inputs `(("oasis" ,ocaml-oasis) + ("ocamlbuild" ,ocamlbuild) ("opam" ,opam))) (build-system ocaml-build-system) (arguments janestreet-arguments) @@ -2256,17 +2946,23 @@ from the oasis build log @end enumerate") (license license:asl2.0))) -(define-public ocaml-bin-prot +(define-public ocaml4.02-js-build-tools + (package-with-ocaml4.02 ocaml-js-build-tools)) + +(define-public ocaml4.02-bin-prot (package - (name "ocaml-bin-prot") + (name "ocaml4.02-bin-prot") (version "113.33.03") (source (janestreet-origin "bin_prot" version "1ws8c017z8nbj3vw92ndvjk9011f71rmp3llncbv8r5fc76wqv3l")) + (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) - (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/bin_prot/") (synopsis "Binary protocol generator") (description "This library contains functionality for reading and writing @@ -2277,17 +2973,20 @@ protocol is also heavily optimized for size, making it ideal for long-term storage of large amounts of data.") (license license:asl2.0))) -(define-public ocaml-fieldslib +(define-public ocaml4.02-fieldslib (package - (name "ocaml-fieldslib") + (name "ocaml4.02-fieldslib") (version "113.33.03") (source (janestreet-origin "fieldslib" version "1rm3bn54bzk2hlq8f3w067ak8s772w4a8f78i3yh79vxfzq8ncvv")) + (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) - (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/fieldslib/") (synopsis "Syntax extension to record fields") (description "Syntax extension to define first class values representing @@ -2295,18 +2994,21 @@ record fields, to get and set record fields, iterate and fold over all fields of a record and create new record values.") (license license:asl2.0))) -(define-public ocaml-ppx-core +(define-public ocaml4.02-ppx-core (package - (name "ocaml-ppx-core") + (name "ocaml4.02-ppx-core") (version "113.33.03") (source (janestreet-origin "ppx_core" version "0f69l4czhgssnhb5ds2j9dbqjyz8dp1y3i3x0i4h6pxnms20zbxa")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) - (inputs `(("ppx-tools" ,ocaml-ppx-tools))) - (arguments janestreet-arguments) + (inputs `(("ppx-tools" ,ocaml4.02-ppx-tools))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_core/") (synopsis "Standard library for ppx rewriters") (description "Ppx_core is a standard library for OCaml AST transformers. @@ -2319,20 +3021,23 @@ It contains: @end enumerate") (license license:asl2.0))) -(define-public ocaml-ppx-optcomp +(define-public ocaml4.02-ppx-optcomp (package - (name "ocaml-ppx-optcomp") + (name "ocaml4.02-ppx-optcomp") (version "113.33.03") (source (janestreet-origin "ppx_optcomp" version "13an8p2r7sd0d5lv54mlzrxdni47408bwqi3bjcx4m6005170q30")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_optcomp/") (synopsis "Optional compilation for OCaml") (description "Ppx_optcomp stands for Optional Compilation. It is a tool @@ -2340,21 +3045,24 @@ used to handle optional compilations of pieces of code depending of the word size, the version of the compiler, ...") (license license:asl2.0))) -(define-public ocaml-ppx-driver +(define-public ocaml4.02-ppx-driver (package - (name "ocaml-ppx-driver") + (name "ocaml4.02-ppx-driver") (version "113.33.03") (source (janestreet-origin "ppx_driver" version "011zzr45897j49b7iiybb29k7pspcx36mlnp7nh6pxb8b0ga76fh")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam) - ("ppx-optcomp" ,ocaml-ppx-optcomp))) + ("ppx-optcomp" ,ocaml4.02-ppx-optcomp))) (propagated-inputs - `(("ppx-optcomp" ,ocaml-ppx-optcomp) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-optcomp" ,ocaml4.02-ppx-optcomp) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_driver/") (synopsis "Feature-full driver for OCaml AST transformers") (description "A driver is an executable created from a set of OCaml AST @@ -2372,21 +3080,33 @@ provide a tool that can be used to: (define-public ocaml-cppo (package (name "ocaml-cppo") - (version "1.4.1") + (version "1.6.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/mjambon/cppo/archive/v" version ".tar.gz")) (sha256 (base32 - "02gma6nw09vfnd6h7bl3n70lwz7m9z2svplxyfh6h5bf4lqgqzjv")) + "1dkm3d5h6h56y937gcdk2wixlpzl59vv5pmiafglr89p20kf7gqf")) (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) (arguments - `(#:phases (modify-phases %standard-phases (delete 'configure)) - #:make-flags (list (string-append "BINDIR=" - (assoc-ref %outputs "out") "/bin")) + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "dune" "build" "@install" "--profile" "release") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "dune" "install" + "--prefix" (assoc-ref outputs "out")) + #t))) #:tests? #f)) + (native-inputs + `(("dune" ,dune) + ("ocamlbuild" ,ocamlbuild))) (home-page "https://github.com/mjambon/cppo") (synopsis "Equivalent of the C preprocessor for OCaml programs") (description "Cppo is an equivalent of the C preprocessor for OCaml @@ -2399,11 +3119,14 @@ programs. It allows the definition of simple macros and file inclusion. Cpp oi @end enumerate") (license license:bsd-3))) +(define-public ocaml4.02-cppo + (package-with-ocaml4.02 ocaml-cppo)) + ;; this package is not reproducible. This is related to temporary filenames ;; such as findlib_initxxxxx where xxxxx is random. -(define-public ocaml-ppx-deriving +(define-public ocaml4.02-ppx-deriving (package - (name "ocaml-ppx-deriving") + (name "ocaml4.02-ppx-deriving") (version "4.1") (source (origin @@ -2415,15 +3138,17 @@ programs. It allows the definition of simple macros and file inclusion. Cpp oi (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) - ("cppo" ,ocaml-cppo) - ("ounit" ,ocaml-ounit) + `(("js-build-tools" ,ocaml4.02-js-build-tools) + ("cppo" ,ocaml4.02-cppo) + ("ounit" ,ocaml4.02-ounit) ("opam" ,opam))) (propagated-inputs - `(("result" ,ocaml-result) - ("ppx-tools" ,ocaml-ppx-tools))) + `(("result" ,ocaml4.02-result) + ("ppx-tools" ,ocaml4.02-ppx-tools))) (arguments - `(#:phases + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:phases (modify-phases %standard-phases (delete 'configure) (add-before 'install 'fix-environment @@ -2438,90 +3163,100 @@ programs. It allows the definition of simple macros and file inclusion. Cpp oi code based on type definitions, and a set of useful plugins for common tasks.") (license license:expat))) -(define-public ocaml-ppx-type-conv +(define-public ocaml4.02-ppx-type-conv (package - (name "ocaml-ppx-type-conv") + (name "ocaml4.02-ppx-type-conv") (version "113.33.03") (source (janestreet-origin "ppx_type_conv" version "1sp602ads2f250nv4d4rgw54d14k7flyhb4w8ff084f657hhmxv2")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-deriving" ,ocaml-ppx-deriving) - ("ppx-tools" ,ocaml-ppx-tools) - ("result" ,ocaml-result) - ("ppx-core" ,ocaml-ppx-core) - ("ppx-driver" ,ocaml-ppx-driver))) - (arguments janestreet-arguments) + `(("ppx-deriving" ,ocaml4.02-ppx-deriving) + ("ppx-core" ,ocaml4.02-ppx-core) + ("ppx-driver" ,ocaml4.02-ppx-driver))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_type_conv/") (synopsis "Support Library for type-driven code generators") (description "The type_conv library factors out functionality needed by different preprocessors that generate code from type specifications.") (license license:asl2.0))) -(define-public ocaml-ppx-inline-test +(define-public ocaml4.02-ppx-inline-test (package - (name "ocaml-ppx-inline-test") + (name "ocaml4.02-ppx-inline-test") (version "113.33.03") (source (janestreet-origin "ppx_inline_test" version "0859ni43fl39dd5g6cxfhq0prxmx59bd2bfq8jafp593ba4q0icq")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam) - ("ppx-core" ,ocaml-ppx-core))) + ("ppx-core" ,ocaml4.02-ppx-core))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_inline_test/") (synopsis "Syntax extension for writing in-line tests in ocaml code") (description "Syntax extension for writing in-line tests in ocaml code.") (license license:asl2.0))) -(define-public ocaml-ppx-bench +(define-public ocaml4.02-ppx-bench (package - (name "ocaml-ppx-bench") + (name "ocaml4.02-ppx-bench") (version "113.33.03") (source (janestreet-origin "ppx_bench" version "1hky3y17qpb925rymf97wv54di9gaqdmkix7wpkjw14qzl512b68")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam) - ("ppx-core" ,ocaml-ppx-core))) + ("ppx-core" ,ocaml4.02-ppx-core))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-inline-test" ,ocaml-ppx-inline-test) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-inline-test" ,ocaml4.02-ppx-inline-test) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_bench/") (synopsis "Syntax extension for writing in-line benchmarks in ocaml code") (description "Syntax extension for writing in-line benchmarks in ocaml code.") (license license:asl2.0))) -(define-public ocaml-ppx-compare +(define-public ocaml4.02-ppx-compare (package - (name "ocaml-ppx-compare") + (name "ocaml4.02-ppx-compare") (version "113.33.03") (source (janestreet-origin "ppx_compare" version "0bfhi33kq9l4q6zzc6svki2csracz5j4731c3npcy6cs73jynn0z")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam) - ("ppx-core" ,ocaml-ppx-core))) + ("ppx-core" ,ocaml4.02-ppx-core))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core) - ("ppx-type-conv" ,ocaml-ppx-type-conv))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_compare/") (synopsis "Generation of comparison functions from types") (description "Generation of fast comparison functions from type expressions @@ -2532,94 +3267,109 @@ flexibility by allowing you to override them for a specific type and more safety by making sure that you only compare comparable values.") (license license:asl2.0))) -(define-public ocaml-sexplib +(define-public ocaml4.02-sexplib (package - (name "ocaml-sexplib") + (name "ocaml4.02-sexplib") (version "113.33.03") (source (janestreet-origin "sexplib" version "1ffjmj8if9lyv965cgn2ld1xv7g52qsr8mqflbm515ck1i8l2ima")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/sexplib/") (synopsis "Library for serializing OCaml values to and from S-expressions") (description "Sexplib contains functionality for parsing and pretty-printing s-expressions.") (license license:asl2.0))) -(define-public ocaml-typerep +(define-public ocaml4.02-typerep (package - (name "ocaml-typerep") + (name "ocaml4.02-typerep") (version "113.33.03") (source (janestreet-origin "typerep" version "1b9v5bmi824a9d4sx0f40ixq0yfcbiqxafg4a1jx95xg9199zafy")) + (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) - (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/typerep/") (synopsis "Typerep is a library for runtime types") (description "Typerep is a library for runtime types.") (license license:asl2.0))) -(define-public ocaml-variantslib +(define-public ocaml4.02-variantslib (package - (name "ocaml-variantslib") + (name "ocaml4.02-variantslib") (version "113.33.03") (source (janestreet-origin "variantslib" version "05vp799vl38fvl98ga5miwbzh09cnnpapi6q6gdvwyqi6w7s919n")) + (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) - (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/variantslib") (synopsis "OCaml variants as first class values") (description "OCaml variants as first class values.") (license license:asl2.0))) -(define-public ocaml-ppx-sexp-conv +(define-public ocaml4.02-ppx-sexp-conv (package - (name "ocaml-ppx-sexp-conv") + (name "ocaml4.02-ppx-sexp-conv") (version "113.33.03") (source (janestreet-origin "ppx_sexp_conv" version "1rbj6d5dl625gdxih34xcrdvikci6h8i2dl9x3wraa4qrgishiw7")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam) - ("ppx-core" ,ocaml-ppx-core))) + ("ppx-core" ,ocaml4.02-ppx-core))) (propagated-inputs - `(("sexplib" ,ocaml-sexplib) - ("ppx-core" ,ocaml-ppx-core) - ("ppx-type-conv" ,ocaml-ppx-type-conv) - ("ppx-tools" ,ocaml-ppx-tools))) - (arguments janestreet-arguments) + `(("sexplib" ,ocaml4.02-sexplib) + ("ppx-core" ,ocaml4.02-ppx-core) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv) + ("ppx-tools" ,ocaml4.02-ppx-tools))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_sexp_conv") (synopsis "Generation of S-expression conversion functions from type definitions") (description "Generation of S-expression conversion functions from type definitions.") (license license:asl2.0))) -(define-public ocaml-ppx-variants-conv +(define-public ocaml4.02-ppx-variants-conv (package - (name "ocaml-ppx-variants-conv") + (name "ocaml4.02-ppx-variants-conv") (version "113.33.03") (source (janestreet-origin "ppx_variants_conv" version "0vnn2l1118cj72413d3f7frlw6yc09l8f64jlzkzbgb9bxpalx34")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-core" ,ocaml-ppx-core) - ("variantslib" ,ocaml-variantslib) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-type-conv" ,ocaml-ppx-type-conv))) - (arguments janestreet-arguments) + `(("ppx-core" ,ocaml4.02-ppx-core) + ("variantslib" ,ocaml4.02-variantslib) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_variants_conv") (synopsis "Generation of accessor and iteration functions for ocaml variant types") @@ -2627,65 +3377,74 @@ types") variant types.") (license license:asl2.0))) -(define-public ocaml-ppx-here +(define-public ocaml4.02-ppx-here (package - (name "ocaml-ppx-here") + (name "ocaml4.02-ppx-here") (version "113.33.03") (source (janestreet-origin "ppx_here" version "1ay8lfxi0qg3ib2zkwh4h0vqk3gjmxaz572gzab0bbxyqn3z86v7")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_here") (synopsis "Expands [%here] into its location") (description "Expands [%here] into its location.") (license license:asl2.0))) -(define-public ocaml-ppx-assert +(define-public ocaml4.02-ppx-assert (package - (name "ocaml-ppx-assert") + (name "ocaml4.02-ppx-assert") (version "113.33.03") (source (janestreet-origin "ppx_assert" version "1k5kxmqkibp5fk25pgz81f3c1r4mgvb5byzf6bnmxd24y60wn46p")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-compare" ,ocaml-ppx-compare) - ("ppx-core" ,ocaml-ppx-core) - ("ppx-driver" ,ocaml-ppx-driver) - ("ppx-sexp-conv" ,ocaml-ppx-sexp-conv) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-type-conv" ,ocaml-ppx-type-conv) - ("ppx-sexplib" ,ocaml-sexplib) - ("ppx-here" ,ocaml-ppx-here))) - (arguments janestreet-arguments) + `(("ppx-compare" ,ocaml4.02-ppx-compare) + ("ppx-core" ,ocaml4.02-ppx-core) + ("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-sexp-conv" ,ocaml4.02-ppx-sexp-conv) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv) + ("ppx-sexplib" ,ocaml4.02-sexplib) + ("ppx-here" ,ocaml4.02-ppx-here))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_assert") (synopsis "Assert-like extension nodes that raise useful errors on failure") (description "Assert-like extension nodes that raise useful errors on failure.") (license license:asl2.0))) -(define-public ocaml-ppx-enumerate +(define-public ocaml4.02-ppx-enumerate (package - (name "ocaml-ppx-enumerate") + (name "ocaml4.02-ppx-enumerate") (version "113.33.03") (source (janestreet-origin "ppx_enumerate" version "15g7yfv9wg2h9r6k6q1zrhygmsl4xrfn25mrb0i4czjjivzmxjh4")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-tools" ,ocaml-ppx-tools) - ("ppx-type-conv" ,ocaml-ppx-type-conv) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_enumerate") (synopsis "Generate a list containing all values of a finite type") (description "Ppx_enumerate is a ppx rewriter which generates a definition @@ -2693,174 +3452,198 @@ for the list of all values of a type (for a type which only has finitely many values).") (license license:asl2.0))) -(define-public ocaml-ppx-let +(define-public ocaml4.02-ppx-let (package - (name "ocaml-ppx-let") + (name "ocaml4.02-ppx-let") (version "113.33.03") (source (janestreet-origin "ppx_let" version "0gd6d3gdaqfwjcs7gaw1qxc30i584q6a86ndaj1bx1q63xqd6yx9")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_let") (synopsis "Monadic let-bindings") (description "A ppx rewriter for monadic and applicative let bindings, match expressions, and if expressions.") (license license:asl2.0))) -(define-public ocaml-ppx-typerep-conv +(define-public ocaml4.02-ppx-typerep-conv (package - (name "ocaml-ppx-typerep-conv") + (name "ocaml4.02-ppx-typerep-conv") (version "113.33.03") (source (janestreet-origin "ppx_typerep_conv" version "0g0xqm9s1b2jjvxb8yp69281q2s3bwz6sibn10fvgcdawpa0rmrg")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-tools" ,ocaml-ppx-tools) - ("ppx-type-conv" ,ocaml-ppx-type-conv) - ("ppx-core" ,ocaml-ppx-core) - ("typerep" ,ocaml-typerep))) - (arguments janestreet-arguments) + `(("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv) + ("ppx-core" ,ocaml4.02-ppx-core) + ("typerep" ,ocaml4.02-typerep))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_typerep_conv") (synopsis "Generation of runtime types from type declarations") (description "Automatic generation of runtime types from type definitions.") (license license:asl2.0))) -(define-public ocaml-ppx-sexp-value +(define-public ocaml4.02-ppx-sexp-value (package - (name "ocaml-ppx-sexp-value") + (name "ocaml4.02-ppx-sexp-value") (version "113.33.03") (source (janestreet-origin "ppx_sexp_value" version "0m3ag23mbqm0i2pv1dzilfks15ipa5q60mf57a0cd3p0pvarq10g")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-here" ,ocaml-ppx-here) - ("ppx-sexp-conv" ,ocaml-ppx-sexp-conv) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-here" ,ocaml4.02-ppx-here) + ("ppx-sexp-conv" ,ocaml4.02-ppx-sexp-conv) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_sexp_value/") (synopsis "Simplify building s-expressions from ocaml values") (description "A ppx rewriter that simplifies building s-expressions from ocaml values.") (license license:asl2.0))) -(define-public ocaml-ppx-pipebang +(define-public ocaml4.02-ppx-pipebang (package - (name "ocaml-ppx-pipebang") + (name "ocaml4.02-ppx-pipebang") (version "113.33.03") (source (janestreet-origin "ppx_pipebang" version "1965c7hymp26ncmjs0pfxi2s5jlj60z2c9b194lgcwxqiav56pcw")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_pipebang/") (synopsis "Inline reverse application operators `|>` and `|!`") (description "A ppx rewriter that inlines reverse application operators @code{|>} and @code{|!}.") (license license:asl2.0))) -(define-public ocaml-ppx-bin-prot +(define-public ocaml4.02-ppx-bin-prot (package - (name "ocaml-ppx-bin-prot") + (name "ocaml4.02-ppx-bin-prot") (version "113.33.03") (source (janestreet-origin "ppx_bin_prot" version "173kjv36giik11zgfvsbzwfbpr66dm2pcha9vf990jgzh8hqz39h")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("bin-prot" ,ocaml-bin-prot) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-type-conv" ,ocaml-ppx-type-conv) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("bin-prot" ,ocaml4.02-bin-prot) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_bin_prot/") (synopsis "Generation of bin_prot readers and writers from types") (description "Generation of binary serialization and deserialization functions from type definitions.") (license license:asl2.0))) -(define-public ocaml-ppx-fail +(define-public ocaml4.02-ppx-fail (package - (name "ocaml-ppx-fail") + (name "ocaml4.02-ppx-fail") (version "113.33.03") (source (janestreet-origin "ppx_fail" version "1dwgad0f05gqp5rnwf9dcasidpfi7q3mrpazsw3a2vijjblbhjgn")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-here" ,ocaml-ppx-here) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-here" ,ocaml4.02-ppx-here) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_fail/") (synopsis "Add location to calls to failwiths") (description "Syntax extension that makes [failwiths] always include a position.") (license license:asl2.0))) -(define-public ocaml-ppx-custom-printf +(define-public ocaml4.02-ppx-custom-printf (package - (name "ocaml-ppx-custom-printf") + (name "ocaml4.02-ppx-custom-printf") (version "113.33.03") (source (janestreet-origin "ppx_custom_printf" version "11jlx0n87g2j1vyyp343dibx7lvvwig5j5q0nq0b80kbsq0k6yr8")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-sexp-conv" ,ocaml-ppx-sexp-conv) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core) - ("ppx-driver" ,ocaml-ppx-driver))) - (arguments janestreet-arguments) + `(("ppx-sexp-conv" ,ocaml4.02-ppx-sexp-conv) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core) + ("ppx-driver" ,ocaml4.02-ppx-driver))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_custom_printf/") (synopsis "Printf-style format-strings for user-defined string conversion") (description "Extensions to printf-style format-strings for user-defined string conversion.") (license license:asl2.0))) -(define-public ocaml-ppx-sexp-message +(define-public ocaml4.02-ppx-sexp-message (package - (name "ocaml-ppx-sexp-message") + (name "ocaml4.02-ppx-sexp-message") (version "113.33.03") (source (janestreet-origin "ppx_sexp_message" version "084w1l3gnyw4ri9vbn7bv9b2xkw1520qczfxpxdarfivdrz8xr68")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-driver" ,ocaml-ppx-driver) - ("ppx-here" ,ocaml-ppx-here) - ("ppx-sexp-conv" ,ocaml-ppx-sexp-conv) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core))) - (arguments janestreet-arguments) + `(("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-here" ,ocaml4.02-ppx-here) + ("ppx-sexp-conv" ,ocaml4.02-ppx-sexp-conv) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_sexp_message/") (synopsis "A ppx rewriter for easy construction of s-expressions") (description "Ppx_sexp_message aims to ease the creation of s-expressions @@ -2869,23 +3652,26 @@ where one needs to construct a s-expression based on various element of the context such as function arguments.") (license license:asl2.0))) -(define-public ocaml-ppx-fields-conv +(define-public ocaml4.02-ppx-fields-conv (package - (name "ocaml-ppx-fields-conv") + (name "ocaml4.02-ppx-fields-conv") (version "113.33.03") (source (janestreet-origin "ppx_fields_conv" version "1vzbdz27g5qhhfs7wx6rjf979q4xyssxqbmp6sc1sxknbghslbdv")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam) - ("ppx-core" ,ocaml-ppx-core))) + ("ppx-core" ,ocaml4.02-ppx-core))) (propagated-inputs - `(("fieldslib" ,ocaml-fieldslib) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-core" ,ocaml-ppx-core) - ("ppx-type-conv" ,ocaml-ppx-type-conv))) - (arguments janestreet-arguments) + `(("fieldslib" ,ocaml4.02-fieldslib) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-core" ,ocaml4.02-ppx-core) + ("ppx-type-conv" ,ocaml4.02-ppx-type-conv))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_fields_conv/") (synopsis "Generation of accessor and iteration functions for ocaml records") (description "Ppx_fields_conv is a ppx rewriter that can be used to define @@ -2894,10 +3680,59 @@ and set record fields, iterate and fold over all fields of a record and create new record values.") (license license:asl2.0))) +(define-public ocaml-seq + (package + (name "ocaml-seq") + (version "0.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/c-cube/seq/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02lb2d9i12bxrz2ba5wygk2bycan316skqlyri0597q7j9210g8r")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((install-dir (string-append (assoc-ref outputs "out") + "/lib/ocaml/site-lib/seq"))) + (mkdir-p install-dir) + (with-output-to-file (string-append install-dir "/META") + (lambda _ + (display "name=\"seq\" +version=\"[distributed with ocaml]\" +description=\"dummy package for compatibility\" +requires=\"\""))) + #t)))))) + (properties + `((ocaml4.02-variant . ,(delay ocaml4.02-seq)))) + (home-page "https://github.com/c-cube/seq") + (synopsis "OCaml's standard iterator type") + (description "This package is a compatibility package for OCaml's +standard iterator type starting from 4.07.") + (license license:lgpl2.1+))) + +(define-public ocaml4.02-seq + (let ((base (package-with-ocaml4.02 (strip-ocaml4.02-variant ocaml-seq)))) + (package + (inherit base) + (arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:tests? #f; no tests + #:phases (modify-phases %standard-phases (delete 'configure))))))) + (define-public ocaml-re (package (name "ocaml-re") - (version "1.7.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/ocaml/ocaml-re//archive/" @@ -2905,9 +3740,27 @@ new record values.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1s3rcr76cgm4p1xmaazc58arkg2lz3zfcp1icm00m6s5ccnkh67b")))) + "1pdb0mr6z5ax6szblr3f5lbdnqq9grm97cmsfjmdma60yrx2rqhd")))) (build-system ocaml-build-system) - (native-inputs `(("ounit" ,ocaml-ounit))) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "dune" "build" "@install" "--profile" "release") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "dune" "install" + "--prefix" (assoc-ref outputs "out")) + #t))))) + (propagated-inputs + `(("ocaml-seq" ,ocaml-seq))) + (native-inputs + `(("dune" ,dune) + ("ounit" ,ocaml-ounit))) (home-page "https://github.com/ocaml/ocaml-re/") (synopsis "Regular expression library for OCaml") (description "Pure OCaml regular expressions with: @@ -2920,32 +3773,38 @@ new record values.") @end enumerate") (license license:expat))) -(define-public ocaml-ppx-expect +(define-public ocaml4.02-re + (package-with-ocaml4.02 ocaml-re)) + +(define-public ocaml4.02-ppx-expect (package - (name "ocaml-ppx-expect") + (name "ocaml4.02-ppx-expect") (version "113.33.03") (source (janestreet-origin "ppx_expect" version "03sbs4s5i8l9syr45v25f5hzy7msd2b47k2a9wsq9m43d4imgkrc")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("fieldslib" ,ocaml-fieldslib) - ("ppx-tools" ,ocaml-ppx-tools) - ("ppx-assert" ,ocaml-ppx-assert) - ("ppx-compare" ,ocaml-ppx-compare) - ("ppx-core" ,ocaml-ppx-core) - ("ppx-custom-printf" ,ocaml-ppx-custom-printf) - ("ppx-driver" ,ocaml-ppx-driver) - ("ppx-fields-conv" ,ocaml-ppx-fields-conv) - ("ppx-inline-test" ,ocaml-ppx-inline-test) - ("ppx-sexp-conv" ,ocaml-ppx-sexp-conv) - ("ppx-variants-conv" ,ocaml-ppx-variants-conv) - ("re" ,ocaml-re) - ("sexplib" ,ocaml-sexplib) - ("variantslib" ,ocaml-variantslib))) - (arguments janestreet-arguments) + `(("fieldslib" ,ocaml4.02-fieldslib) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("ppx-assert" ,ocaml4.02-ppx-assert) + ("ppx-compare" ,ocaml4.02-ppx-compare) + ("ppx-core" ,ocaml4.02-ppx-core) + ("ppx-custom-printf" ,ocaml4.02-ppx-custom-printf) + ("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-fields-conv" ,ocaml4.02-ppx-fields-conv) + ("ppx-inline-test" ,ocaml4.02-ppx-inline-test) + ("ppx-sexp-conv" ,ocaml4.02-ppx-sexp-conv) + ("ppx-variants-conv" ,ocaml4.02-ppx-variants-conv) + ("re" ,ocaml4.02-re) + ("sexplib" ,ocaml4.02-sexplib) + ("variantslib" ,ocaml4.02-variantslib))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_expect/") (synopsis "Cram like framework for OCaml") (description "Expect-test is a framework for writing tests in OCaml, similar @@ -2955,66 +3814,72 @@ output-generating code, interleaved with %expect extension expressions to denote the expected output.") (license license:asl2.0))) -(define-public ocaml-ppx-jane +(define-public ocaml4.02-ppx-jane (package - (name "ocaml-ppx-jane") + (name "ocaml4.02-ppx-jane") (version "113.33.03") (source (janestreet-origin "ppx_jane" version "0bjxkhmzgm6x9dcvjwybbccn34khbvyyjimcbaja30fp6qcqk5yl")) (build-system ocaml-build-system) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) + `(("js-build-tools" ,ocaml4.02-js-build-tools) ("opam" ,opam))) (propagated-inputs - `(("ppx-assert" ,ocaml-ppx-assert) - ("ppx-bench" ,ocaml-ppx-bench) - ("ppx-bin-prot" ,ocaml-ppx-bin-prot) - ("ppx-compare" ,ocaml-ppx-compare) - ("ppx-custom-printf" ,ocaml-ppx-custom-printf) - ("ppx-deriving" ,ocaml-ppx-deriving) - ("ppx-enumerate" ,ocaml-ppx-enumerate) - ("ppx-expect" ,ocaml-ppx-expect) - ("ppx-fail" ,ocaml-ppx-fail) - ("ppx-fields-conv" ,ocaml-ppx-fields-conv) - ("ppx-here" ,ocaml-ppx-here) - ("ppx-inline-test" ,ocaml-ppx-inline-test) - ("ppx-let" ,ocaml-ppx-let) - ("ppx-pipebang" ,ocaml-ppx-pipebang) - ("ppx-sexp-conv" ,ocaml-ppx-sexp-conv) - ("ppx-sexp-message" ,ocaml-ppx-sexp-message) - ("ppx-sexp-value" ,ocaml-ppx-sexp-value) - ("ppx-typerep-conv" ,ocaml-ppx-typerep-conv) - ("ppx-variants-conv" ,ocaml-ppx-variants-conv))) - (arguments janestreet-arguments) + `(("ppx-assert" ,ocaml4.02-ppx-assert) + ("ppx-bench" ,ocaml4.02-ppx-bench) + ("ppx-bin-prot" ,ocaml4.02-ppx-bin-prot) + ("ppx-compare" ,ocaml4.02-ppx-compare) + ("ppx-custom-printf" ,ocaml4.02-ppx-custom-printf) + ("ppx-deriving" ,ocaml4.02-ppx-deriving) + ("ppx-enumerate" ,ocaml4.02-ppx-enumerate) + ("ppx-expect" ,ocaml4.02-ppx-expect) + ("ppx-fail" ,ocaml4.02-ppx-fail) + ("ppx-fields-conv" ,ocaml4.02-ppx-fields-conv) + ("ppx-here" ,ocaml4.02-ppx-here) + ("ppx-inline-test" ,ocaml4.02-ppx-inline-test) + ("ppx-let" ,ocaml4.02-ppx-let) + ("ppx-pipebang" ,ocaml4.02-ppx-pipebang) + ("ppx-sexp-conv" ,ocaml4.02-ppx-sexp-conv) + ("ppx-sexp-message" ,ocaml4.02-ppx-sexp-message) + ("ppx-sexp-value" ,ocaml4.02-ppx-sexp-value) + ("ppx-typerep-conv" ,ocaml4.02-ppx-typerep-conv) + ("ppx-variants-conv" ,ocaml4.02-ppx-variants-conv))) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/ppx_jane/") (synopsis "Standard Jane Street ppx rewriters") (description "Ppx_jane is a ppx_driver including all standard ppx rewriters.") (license license:asl2.0))) -(define-public ocaml-core-kernel +(define-public ocaml4.02-core-kernel (package - (name "ocaml-core-kernel") + (name "ocaml4.02-core-kernel") (version "113.33.03") (source (janestreet-origin "core_kernel" version "0fl23jrwivixawhxinbwaw9cabqnzn7fini7dxpxjjvkxdc8ip5y")) (native-inputs - `(("js-build-tools" ,ocaml-js-build-tools) - ("ppx-jane" ,ocaml-ppx-jane) + `(("js-build-tools" ,ocaml4.02-js-build-tools) + ("ppx-jane" ,ocaml4.02-ppx-jane) ("opam" ,opam))) (propagated-inputs - `(("bin_prot" ,ocaml-bin-prot) - ("ppx-assert" ,ocaml-ppx-assert) - ("ppx-bench" ,ocaml-ppx-bench) - ("ppx-driver" ,ocaml-ppx-driver) - ("ppx-expect" ,ocaml-ppx-expect) - ("ppx-inline-test" ,ocaml-ppx-inline-test) - ("typerep" ,ocaml-typerep) - ("sexplib" ,ocaml-sexplib) - ("variantslib" ,ocaml-variantslib) - ("result" ,ocaml-result) - ("fieldslib" ,ocaml-fieldslib))) + `(("bin_prot" ,ocaml4.02-bin-prot) + ("ppx-assert" ,ocaml4.02-ppx-assert) + ("ppx-bench" ,ocaml4.02-ppx-bench) + ("ppx-driver" ,ocaml4.02-ppx-driver) + ("ppx-expect" ,ocaml4.02-ppx-expect) + ("ppx-inline-test" ,ocaml4.02-ppx-inline-test) + ("typerep" ,ocaml4.02-typerep) + ("sexplib" ,ocaml4.02-sexplib) + ("variantslib" ,ocaml4.02-variantslib) + ("result" ,ocaml4.02-result) + ("fieldslib" ,ocaml4.02-fieldslib))) (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/core_kernel/") (synopsis "Portable standard library for OCaml") (description "Core is an alternative to the OCaml standard library. @@ -3023,127 +3888,145 @@ Core_kernel is the system-independent part of Core. It is aimed for cases when the full Core is not available, such as in Javascript.") (license license:asl2.0))) -(define-public ocaml-async-kernel +(define-public ocaml4.02-async-kernel (package - (name "ocaml-async-kernel") + (name "ocaml4.02-async-kernel") (version "113.33.03") (source (janestreet-origin "async_kernel" version "04bjsaa23j831r09r38x6xx9nhryvp0z5ihickvhxqa4fb2snyvd")) (native-inputs `(("oasis" ,ocaml-oasis) - ("js-build-tools" ,ocaml-js-build-tools) - ("ppx-jane" ,ocaml-ppx-jane) + ("js-build-tools" ,ocaml4.02-js-build-tools) + ("ppx-jane" ,ocaml4.02-ppx-jane) ("opam" ,opam))) (propagated-inputs - `(("core-kernel" ,ocaml-core-kernel))) + `(("core-kernel" ,ocaml4.02-core-kernel))) (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/async_kernel/") (synopsis "Monadic concurrency library") (description "Async-kernel is a library for concurrent programming in OCaml.") (license license:asl2.0))) -(define-public ocaml-async-rpc-kernel +(define-public ocaml4.02-async-rpc-kernel (package - (name "ocaml-async-rpc-kernel") + (name "ocaml4.02-async-rpc-kernel") (version "113.33.03") (source (janestreet-origin "async_rpc_kernel" version "0y97h9pkb00v7jpf87m8cbb0ffkclj9g26ph6sq97q8dpisnkjwh")) (native-inputs `(("oasis" ,ocaml-oasis) - ("js-build-tools" ,ocaml-js-build-tools) - ("ppx-jane" ,ocaml-ppx-jane) + ("js-build-tools" ,ocaml4.02-js-build-tools) + ("ppx-jane" ,ocaml4.02-ppx-jane) ("opam" ,opam))) (propagated-inputs - `(("async-kernel" ,ocaml-async-kernel))) + `(("async-kernel" ,ocaml4.02-async-kernel))) (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/async_rpc_kernel/") (synopsis "Platform-independent core of the Async RPC library") (description "Async_rpc_kernel is the platform-independent core of the Async RPC library.") (license license:asl2.0))) -(define-public ocaml-core +(define-public ocaml4.02-core (package - (name "ocaml-core") + (name "ocaml4.02-core") (version "113.33.03") (source (janestreet-origin "core" version "1znll157qg56g9d3247fjibv1hxv3r9wxgr4nhy19j2vzdh6a268")) (native-inputs `(("oasis" ,ocaml-oasis) - ("js-build-tools" ,ocaml-js-build-tools) - ("ppx-jane" ,ocaml-ppx-jane) + ("js-build-tools" ,ocaml4.02-js-build-tools) + ("ppx-jane" ,ocaml4.02-ppx-jane) ("opam" ,opam))) (propagated-inputs - `(("core-kernel" ,ocaml-core-kernel))) + `(("core-kernel" ,ocaml4.02-core-kernel))) (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/core/") (synopsis "Alternative to OCaml's standard library") (description "The Core suite of libraries is an alternative to OCaml's standard library that was developed by Jane Street.") (license license:asl2.0))) -(define-public ocaml-async-unix +(define-public ocaml4.02-async-unix (package - (name "ocaml-async-unix") + (name "ocaml4.02-async-unix") (version "113.33.03") (source (janestreet-origin "async_unix" version "1fwl0lfrizllcfjk8hk8m7lsz9ha2jg6qgk4gssfyz377qvpcq4h")) (native-inputs `(("oasis" ,ocaml-oasis) - ("js-build-tools" ,ocaml-js-build-tools) - ("ppx-jane" ,ocaml-ppx-jane) + ("js-build-tools" ,ocaml4.02-js-build-tools) + ("ppx-jane" ,ocaml4.02-ppx-jane) ("opam" ,opam))) (propagated-inputs - `(("async-kernel" ,ocaml-async-kernel) - ("core" ,ocaml-core))) + `(("async-kernel" ,ocaml4.02-async-kernel) + ("core" ,ocaml4.02-core))) (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/async_unix") (synopsis "Asynchronous execution library for Unix") (description "Async_unix is an asynchronous execution library for Unix.") (license license:asl2.0))) -(define-public ocaml-async-extra +(define-public ocaml4.02-async-extra (package - (name "ocaml-async-extra") + (name "ocaml4.02-async-extra") (version "113.33.03") (source (janestreet-origin "async_extra" version "1si8jgiq5xh5sl9f2b7f9p17p7zx5h1pg557x2cxywi2x7pxqg4f")) (native-inputs `(("oasis" ,ocaml-oasis) - ("js-build-tools" ,ocaml-js-build-tools) - ("ppx-jane" ,ocaml-ppx-jane) + ("js-build-tools" ,ocaml4.02-js-build-tools) + ("ppx-jane" ,ocaml4.02-ppx-jane) ("opam" ,opam))) (propagated-inputs - `(("async-rpc-kernel" ,ocaml-async-rpc-kernel) - ("async-unix" ,ocaml-async-unix) - ("core" ,ocaml-core))) + `(("async-rpc-kernel" ,ocaml4.02-async-rpc-kernel) + ("async-unix" ,ocaml4.02-async-unix) + ("core" ,ocaml4.02-core))) (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/async_extra") (synopsis "Extra functionnalities for the async library") (description "Async_extra provides additional functionnalities for the async library.") (license license:asl2.0))) -(define-public ocaml-async +(define-public ocaml4.02-async (package - (name "ocaml-async") + (name "ocaml4.02-async") (version "113.33.03") (source (janestreet-origin "async" version "0210fyhcs12kpmmd26015bgivkfd2wqkyn3c5wd7688d0f872y25")) (native-inputs `(("oasis" ,ocaml-oasis) - ("js-build-tools" ,ocaml-js-build-tools) - ("ppx-jane" ,ocaml-ppx-jane) + ("js-build-tools" ,ocaml4.02-js-build-tools) + ("ppx-jane" ,ocaml4.02-ppx-jane) ("opam" ,opam))) (propagated-inputs - `(("async-extra" ,ocaml-async-extra))) + `(("async-extra" ,ocaml4.02-async-extra))) (build-system ocaml-build-system) - (arguments janestreet-arguments) + (arguments + (ensure-keyword-arguments janestreet-arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib))) (home-page "https://github.com/janestreet/async") (synopsis "Monadic concurrency library") (description "Async is a library for concurrent programming in OCaml.") @@ -3162,7 +4045,9 @@ async library.") "0hwj09rnzjs0m0kazz5h2mgs6p95j0zlga8cda5srnzqmzhniwkn")) (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) - (native-inputs `(("cppo" ,ocaml-cppo))) + (native-inputs + `(("cppo" ,ocaml-cppo) + ("ocamlbuild" ,ocamlbuild))) (home-page "https://github.com/OCamlPro/ocplib-endian") (synopsis "Optimised functions to read and write int16/32/64 from strings and bigarrays") @@ -3172,9 +4057,12 @@ strings, bytes and bigstring (Bigarrys of chars), and provides submodules for big- and little-endian, with their unsafe counter-parts.") (license license:lgpl2.1))) -(define-public ocaml-cstruct +(define-public ocaml4.02-ocplib-endian + (package-with-ocaml4.02 ocaml-ocplib-endian)) + +(define-public ocaml4.02-cstruct (package - (name "ocaml-cstruct") + (name "ocaml4.02-cstruct") (version "2.3.1") (source (origin (method url-fetch) @@ -3186,7 +4074,9 @@ big- and little-endian, with their unsafe counter-parts.") (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) (arguments - `(#:configure-flags + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:configure-flags (list "--enable-lwt" "--enable-async") #:phases (modify-phases %standard-phases @@ -3199,14 +4089,14 @@ big- and little-endian, with their unsafe counter-parts.") (symlink (string-append lib "/dllcstruct_stubs.so") (string-append stubs "/dllcstruct_stubs.so")))))))) (native-inputs - `(("ounit" ,ocaml-ounit) - ("ppx-tools" ,ocaml-ppx-tools) - ("camlp4" ,camlp4))) + `(("ounit" ,ocaml4.02-ounit) + ("ppx-tools" ,ocaml4.02-ppx-tools) + ("camlp4" ,camlp4-4.02))) (propagated-inputs - `(("ocplib-endian" ,ocaml-ocplib-endian) - ("lwt" ,ocaml-lwt) - ("async" ,ocaml-async) - ("sexplib" ,ocaml-sexplib))) + `(("ocplib-endian" ,ocaml4.02-ocplib-endian) + ("lwt" ,ocaml4.02-lwt) + ("async" ,ocaml4.02-async) + ("sexplib" ,ocaml4.02-sexplib))) (home-page "https://github.com/mirage/ocaml-cstruct") (synopsis "Access C structures via a camlp4 extension") (description "Cstruct is a library and syntax extension to make it easier @@ -3214,9 +4104,9 @@ to access C-like structures directly from OCaml. It supports both reading and writing to these structures, and they are accessed via the Bigarray module.") (license license:isc))) -(define-public ocaml-hex +(define-public ocaml4.02-hex (package - (name "ocaml-hex") + (name "ocaml4.02-hex") (version "1.0.0") (source (origin (method url-fetch) @@ -3227,15 +4117,19 @@ writing to these structures, and they are accessed via the Bigarray module.") "0s63g0b8gfv2xm6fv6xg7bva8h76b5pcjb0zw3f8cygs0lq9072v")) (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) - (propagated-inputs `(("cstruct" ,ocaml-cstruct))) + (arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib)) + (propagated-inputs + `(("cstruct" ,ocaml4.02-cstruct))) (home-page "https://github.com/mirage/ocaml-hex/") (synopsis "Minimal library providing hexadecimal converters") (description "Hex is a minimal library providing hexadecimal converters.") (license license:isc))) -(define-public ocaml-ezjsonm +(define-public ocaml4.02-ezjsonm (package - (name "ocaml-ezjsonm") + (name "ocaml4.02-ezjsonm") (version "0.4.3") (source (origin (method url-fetch) @@ -3247,14 +4141,16 @@ writing to these structures, and they are accessed via the Bigarray module.") (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) (native-inputs - `(("alcotest" ,ocaml-alcotest))) + `(("alcotest" ,ocaml4.02-alcotest))) (propagated-inputs - `(("hex" ,ocaml-hex) - ("jsonm" ,ocaml-jsonm) - ("lwt" ,ocaml-lwt) - ("sexplib" ,ocaml-sexplib))) + `(("hex" ,ocaml4.02-hex) + ("jsonm" ,ocaml4.02-jsonm) + ("lwt" ,ocaml4.02-lwt) + ("sexplib" ,ocaml4.02-sexplib))) (arguments - `(#:configure-flags (list "--enable-lwt"))) + `(#:configure-flags (list "--enable-lwt") + #:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib)) (home-page "https://github.com/mirage/ezjsonm/") (synopsis "Read and write JSON data") (description "Ezjsonm provides more convenient (but far less flexible) input @@ -3263,9 +4159,9 @@ the need to write signal code, which is useful for quick scripts that manipulate JSON.") (license license:isc))) -(define-public ocaml-uri +(define-public ocaml4.02-uri (package - (name "ocaml-uri") + (name "ocaml4.02-uri") (version "1.9.2") (source (origin (method url-fetch) @@ -3276,14 +4172,17 @@ JSON.") "02bzrag79prx261rxf9mlak749pwf4flpfl8p012x1xznv9m0clc")) (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) + (arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib)) (native-inputs - `(("ounit" ,ocaml-ounit))) + `(("ounit" ,ocaml4.02-ounit))) (propagated-inputs - `(("ppx-sexp-conv" ,ocaml-ppx-sexp-conv) - ("re" ,ocaml-re) - ("ppx-deriving" ,ocaml-ppx-deriving) - ("sexplib" ,ocaml-sexplib) - ("stringext" ,ocaml-stringext))) + `(("ppx-sexp-conv" ,ocaml4.02-ppx-sexp-conv) + ("re" ,ocaml4.02-re) + ("ppx-deriving" ,ocaml4.02-ppx-deriving) + ("sexplib" ,ocaml4.02-sexplib) + ("stringext" ,ocaml4.02-stringext))) (home-page "https://github.com/mirage/ocaml-uri") (synopsis "RFC3986 URI/URL parsing library") (description "OCaml-uri is a library for parsing URI/URL in the RFC3986 format.") @@ -3312,6 +4211,9 @@ JSON.") Format module of the OCaml standard library.") (license license:bsd-3))) +(define-public ocaml4.02-easy-format + (package-with-ocaml4.02 ocaml-easy-format)) + (define-public optcomp (package (name "optcomp") @@ -3326,13 +4228,15 @@ Format module of the OCaml standard library.") (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) (arguments - `(#:use-make? #t + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:use-make? #t #:make-flags (list (string-append "BUILDFLAGS=\"-cflags -I," (assoc-ref %build-inputs "camlp4") "/lib/ocaml/site-lib/camlp4/Camlp4Parsers\"")))) - (native-inputs `(("camlp4" ,camlp4))) - (propagated-inputs `(("camlp4" ,camlp4))) + (native-inputs `(("camlp4" ,camlp4-4.02))) + (propagated-inputs `(("camlp4" ,camlp4-4.02))) (home-page "https://github.com/diml/optcomp") (synopsis "Optional compilation for OCaml") (description "Optcomp provides an optional compilation facility with @@ -3342,14 +4246,14 @@ cpp-like directives.") (define-public ocaml-piqilib (package (name "ocaml-piqilib") - (version "0.6.13") + (version "0.6.14") (source (origin (method url-fetch) (uri (string-append "https://github.com/alavrik/piqi/archive/v" version ".tar.gz")) (sha256 (base32 - "1whqr2bb3gds2zmrzqnv8vqka9928w4lx6mi6g244kmbwb2h8d8l")) + "1ssccnwqzfyf7syfq2fv4zyhwayxwd75rhq9y28mvq1w6qbww4l7")) (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) (arguments @@ -3365,14 +4269,17 @@ cpp-like directives.") (let ((out (assoc-ref outputs "out"))) (substitute* "make/OCamlMakefile" (("/bin/sh") (which "bash"))) - (zero? (system* "./configure" "--prefix" out "--ocaml-libdir" - (string-append out "/lib/ocaml/site-lib")))))) + (invoke "./configure" "--prefix" out "--ocaml-libdir" + (string-append out "/lib/ocaml/site-lib"))) + #t)) (add-after 'build 'build-ocaml (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "make" "ocaml")))) + (invoke "make" "ocaml") + #t)) (add-after 'install 'install-ocaml (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "make" "ocaml-install")))) + (invoke "make" "ocaml-install") + #t)) (add-after 'install-ocaml 'link-stubs (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -3388,15 +4295,18 @@ cpp-like directives.") (propagated-inputs `(("xmlm" ,ocaml-xmlm) ("ulex" ,ocaml-ulex) - ("optcomp" ,optcomp) ("easy-format" ,ocaml-easy-format) ("base64" ,ocaml-base64))) + (home-page "http://www.cduce.org/download.html#side") (home-page "http://piqi.org") (synopsis "Data serialization and conversion library") (description "Piqilib is the common library used by the piqi command-line tool and piqi-ocaml.") (license license:asl2.0))) +(define-public ocaml4.02-piqilib + (package-with-ocaml4.02 ocaml-piqilib)) + (define-public ocaml-uuidm (package (name "ocaml-uuidm") @@ -3416,7 +4326,8 @@ tool and piqi-ocaml.") (modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("opam" ,opam))) + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam))) (propagated-inputs `(("cmdliner" ,ocaml-cmdliner) ("topkg" ,ocaml-topkg))) @@ -3427,21 +4338,24 @@ unique identifiers (UUIDs) version 3, 5 (named based with MD5, SHA-1 hashing) and 4 (random based) according to RFC 4122.") (license license:isc))) +(define-public ocaml4.02-uuidm + (package-with-ocaml4.02 ocaml-uuidm)) + (define-public ocaml-graph (package (name "ocaml-graph") - (version "1.8.7") + (version "1.8.8") (source (origin (method url-fetch) (uri (string-append "http://ocamlgraph.lri.fr/download/" "ocamlgraph-" version ".tar.gz")) (sha256 (base32 - "1845r537swjil2fcj7lgbibc2zybfwqqasrd2s7bncajs83cl1nz")) - (patches (search-patches "ocaml-graph-honor-source-date-epoch.patch")))) + "0m9g16wrrr86gw4fz2fazrh8nkqms0n863w7ndcvrmyafgxvxsnr")))) (build-system ocaml-build-system) (arguments `(#:install-target "install-findlib" + #:tests? #f #:phases (modify-phases %standard-phases (add-before 'configure 'set-shell @@ -3454,10 +4368,13 @@ and 4 (random based) according to RFC 4122.") (description "OCamlgraph is a generic graph library for OCaml.") (license license:lgpl2.1))) +(define-public ocaml4.02-graph + (package-with-ocaml4.02 ocaml-graph)) + (define-public ocaml-piqi (package (name "ocaml-piqi") - (version "0.7.5") + (version "0.7.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/alavrik/piqi-ocaml/" @@ -3465,7 +4382,7 @@ and 4 (random based) according to RFC 4122.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0ngz6y8i98i5v2ma8nk6mc83pdsmf2z0ks7m3xi6clfg3zqbddrv")))) + "0da0v2v28aj65b0cwpvvmcqyrfvz94pp3j5zgfdr1jrl5s37c21g")))) (build-system ocaml-build-system) (arguments `(#:make-flags @@ -3477,9 +4394,13 @@ and 4 (random based) according to RFC 4122.") (delete 'configure)))) (native-inputs `(("which" ,which) + ("camlp4" ,camlp4) ("protobuf" ,protobuf))) ; for tests (propagated-inputs - `(("piqilib" ,ocaml-piqilib))) + `(("num" ,ocaml-num) + ("piqilib" ,ocaml-piqilib))) + (properties + `((ocaml4.02-variant . ,(delay ocaml4.02-piqi)))) (home-page "https://github.com/alavrik/piqi-ocaml") (synopsis "Protocol serialization system for OCaml") (description "Piqi is a multi-format data serialization system for OCaml. @@ -3487,67 +4408,73 @@ It provides a uniform interface for serializing OCaml data structures to JSON, XML and Protocol Buffers formats.") (license license:asl2.0))) +(define-public ocaml4.02-piqi + (let ((base (package-with-ocaml4.02 (strip-ocaml4.02-variant ocaml-piqi)))) + (package + (inherit base) + (propagated-inputs + `(("piqilib" ,ocaml4.02-piqilib)))))) + (define-public bap (package (name "bap") - (version "1.1.0") + (version "1.3.0") (home-page "https://github.com/BinaryAnalysisPlatform/bap") (source (origin (method url-fetch) (uri (string-append home-page "/archive/v" version ".tar.gz")) (sha256 (base32 - "1ms95m4j1qrmy7zqmsn2izh7gq68lnmssl7chyhk977kd3sxj66m")) + "0v95v9mp7mg8fj25ry0w7566zd9xp6cs8nnqj4l38q54fb1hfav9")) (file-name (string-append name "-" version ".tar.gz")))) (build-system ocaml-build-system) (native-inputs - `(("oasis" ,ocaml-oasis) + `(("oasis" ,ocaml4.02-oasis) ("clang" ,clang-3.8) - ("ounit" ,ocaml-ounit))) + ("ounit" ,ocaml4.02-ounit))) (propagated-inputs - `(("core-kernel" ,ocaml-core-kernel) - ("ppx-driver" ,ocaml-ppx-driver) - ("uri" ,ocaml-uri) + `(("core-kernel" ,ocaml4.02-core-kernel) + ("ppx-driver" ,ocaml4.02-ppx-driver) + ("bin-prot" ,ocaml4.02-bin-prot) + ("uri" ,ocaml4.02-uri) ("llvm" ,llvm-3.8) ("gmp" ,gmp) ("clang-runtime" ,clang-runtime) - ("fileutils" ,ocaml-fileutils) - ("cmdliner" ,ocaml-cmdliner) - ("zarith" ,ocaml-zarith) - ("uuidm" ,ocaml-uuidm) - ("camlzip" ,camlzip) + ("fileutils" ,ocaml4.02-fileutils) + ("cmdliner" ,ocaml4.02-cmdliner) + ("zarith" ,ocaml4.02-zarith) + ("uuidm" ,ocaml4.02-uuidm) + ("camlzip" ,ocaml4.02-camlzip) ("frontc" ,ocaml-frontc) - ("ezjsonm" ,ocaml-ezjsonm) - ("ocurl" ,ocaml-ocurl) - ("piqi" ,ocaml-piqi) - ("ocamlgraph" ,ocaml-graph) - ("bitstring" ,ocaml-bitstring) - ("ppx-jane" ,ocaml-ppx-jane) - ("re" ,ocaml-re))) + ("ezjsonm" ,ocaml4.02-ezjsonm) + ("ocurl" ,ocaml4.02-ocurl) + ("piqi" ,ocaml4.02-piqi) + ("ocamlgraph" ,ocaml4.02-graph) + ("bitstring" ,ocaml4.02-bitstring) + ("ppx-jane" ,ocaml4.02-ppx-jane) + ("re" ,ocaml4.02-re))) (inputs `(("llvm" ,llvm-3.8))) (arguments - `(#:use-make? #t + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:use-make? #t #:phases (modify-phases %standard-phases (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "./configure" "--prefix" - (assoc-ref outputs "out") - "--libdir" - (string-append - (assoc-ref outputs "out") - "/lib/ocaml/site-lib") - "--with-llvm-version=3.8" - "--with-llvm-config=llvm-config" - "--enable-everything")))) - (add-after 'install 'link-stubs - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (stubs (string-append out "/lib/ocaml/site-lib/stubslibs")) - (lib (string-append out "/lib/ocaml/site-lib/bap-plugin-llvm"))) - (mkdir-p stubs) - (symlink (string-append lib "/dllllvm_plugin_stubs.so") - (string-append stubs "/dllllvm_plugin_stubs.so")))))))) + (lambda* (#:key outputs inputs #:allow-other-keys) + (invoke "./configure" "--prefix" + (assoc-ref outputs "out") + "--libdir" + (string-append + (assoc-ref outputs "out") + "/lib/ocaml/site-lib") + "--with-llvm-version=3.8" + "--with-llvm-config=llvm-config" + "--enable-everything") + (substitute* "plugins/objdump/objdump_main.ml" + (("Re_perl") "Re.Perl")) + (substitute* "oasis/objdump" + (("re.pcre") "re.pcre, re.perl"))))))) (synopsis "Binary Analysis Platform") (description "Binary Analysis Platform is a framework for writing program analysis tools, that target binary files. The framework consists of a plethora @@ -3558,23 +4485,33 @@ the plugins facilitate extensibility, and the frontends serve as entry points.") (define-public ocaml-camomile (package (name "ocaml-camomile") - (version "0.8.5") + (version "1.0.1") (home-page "https://github.com/yoriyuki/Camomile") (source (origin (method url-fetch) - (uri (string-append home-page "/releases/download/rel-" version - "/camomile-" version ".tar.bz2")) + (uri (string-append home-page "/releases/download/" version + "/camomile-" version ".tbz")) (sha256 (base32 - "003ikpvpaliy5hblhckfmln34zqz0mk3y2m1fqvbjngh3h2np045")))) + "01ssjrqz41jvrqh27jxnh9cx7ywi9b5sgsykd00i7z9nrcwhlfy2")))) (build-system ocaml-build-system) - (native-inputs `(("camlp4" ,camlp4))) + (native-inputs + `(("camlp4" ,camlp4) + ("dune" ,dune))) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'configure 'fix-bin/sh + (delete 'configure) + (replace 'build (lambda _ - (setenv "CONFIG_SHELL" (which "bash"))))))) + (invoke "dune" "build" "@install" "--profile" "release") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "dune" "install" + "--prefix" (assoc-ref outputs "out")) + #t))) + #:tests? #f)) (synopsis "Comprehensive Unicode library") (description "Camomile is a Unicode library for OCaml. Camomile provides Unicode character type, UTF-8, UTF-16, UTF-32 strings, conversion to/from about @@ -3583,6 +4520,9 @@ library is currently designed for Unicode Standard 3.2.") ;; with an exception for linked libraries to use a different license (license license:lgpl2.0+))) +(define-public ocaml4.02-camomile + (package-with-ocaml4.02 ocaml-camomile)) + (define-public ocaml-jbuilder (package (name "ocaml-jbuilder") @@ -3595,10 +4535,12 @@ library is currently designed for Unicode Standard 3.2.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0gcy52y0mkg450yxwszp3lww303a1154566r8jb4hh5l61dh4dwj")))) + "1cy07pwvbrlysszs938yd74yyvvbgkffpb82qrjph77zf0h2gdi7")))) (build-system ocaml-build-system) (arguments - `(#:phases + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:phases (modify-phases %standard-phases (replace 'configure (lambda* (#:key outputs #:allow-other-keys) @@ -3606,7 +4548,7 @@ library is currently designed for Unicode Standard 3.2.") (setenv "PREFIX" out)) #t))))) (native-inputs - `(("menhir" ,ocaml-menhir))) + `(("menhir" ,ocaml4.02-menhir))) (propagated-inputs `(("opam" ,opam))) (home-page "https://github.com/janestreet/jbuilder") @@ -3654,10 +4596,13 @@ to write text editors, edition widgets, readlines, etc. You just have to connect an engine to your inputs and rendering functions to get an editor.") (license license:bsd-3))) +(define-public ocaml4.02-zed + (package-with-ocaml4.02 ocaml-zed)) + (define-public ocaml-lambda-term (package (name "ocaml-lambda-term") - (version "1.11") + (version "1.13") (source (origin (method url-fetch) @@ -3665,26 +4610,27 @@ connect an engine to your inputs and rendering functions to get an editor.") version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "10lx1jqgmmfwwlv64di4a8nia9l53v7179z70n9fx6aq5l7r8nba")))) + (base32 "1hy5ryagqclgdm9lzh1qil5mrynlypv7mn6qm858hdcnmz9zzn0l")))) (build-system ocaml-build-system) (arguments - `(#:test-target "test" - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) - ;; currently, ocaml-lwt is an old version of lwt from before lwt.react - ;; was split into a separate module called lwt_react - (add-before 'build 'use-old-lwt-react-name + (replace 'build (lambda _ - (substitute* "src/jbuild" (("lwt_react") "lwt.react")))) + (invoke "dune" "build" "@install" "--profile" "release") + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (zero? (system* "jbuilder" "install" "--prefix" out)))))))) + (invoke "dune" "install" + "--prefix" (assoc-ref outputs "out")) + #t))) + #:tests? #f)) (native-inputs - `(("jbuilder" ,ocaml-jbuilder))) + `(("dune" ,dune))) (propagated-inputs `(("lwt" ,ocaml-lwt) + ("lwt-log" ,ocaml-lwt-log) ("zed" ,ocaml-zed))) (home-page "https://github.com/diml/lambda-term") (synopsis "Terminal manipulation library for OCaml") @@ -3696,18 +4642,21 @@ manipulation than, for example, ncurses, by providing a native OCaml interface instead of bindings to a C library.") (license license:bsd-3))) +(define-public ocaml4.02-lambda-term + (package-with-ocaml4.02 ocaml-lambda-term)) + (define-public ocaml-utop (package (name "ocaml-utop") - (version "2.0.2") + (version "2.2.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/diml/utop/archive/" + (uri (string-append "https://github.com/ocaml-community/utop/archive/" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0rglznh4prcix8spi3f060jz2gngk7x8vkd291fxs10b88aqcpxf")))) + "1414snwmqaxs1x8wbpjf6fn3jsl01hq0phrr7639xmb5vh15mgd4")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -3761,6 +4710,8 @@ sensitive completion, colors, and more.") #:phases (modify-phases %standard-phases (delete 'configure)))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild))) (inputs `(("topkg" ,ocaml-topkg) ("opam" ,opam))) @@ -3773,7 +4724,7 @@ long and size_t whose sizes depend on the host platform.") (define-public ocaml-ctypes (package (name "ocaml-ctypes") - (version "0.13.1") + (version "0.14.0") (home-page "https://github.com/ocamllabs/ocaml-ctypes") (source (origin (method url-fetch) @@ -3781,10 +4732,11 @@ long and size_t whose sizes depend on the host platform.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "17w0pr5k0zjcjns4y9n36rjpfl35zhvp3h8ggqs9lz12qhshdk2m")))) + "0zrsd42q2nciyg9375g2kydqax6ay299rhyfgms59qiw7d9ylyp9")))) (build-system ocaml-build-system) (arguments - `(#:make-flags + `(#:tests? #f; require an old lwt + #:make-flags (list (string-append "INSTALL_HEADERS = $(wildcard $($(PROJECT).dir)/*.h)")) #:phases (modify-phases %standard-phases @@ -3832,7 +4784,8 @@ without writing or generating any C!") `(("topkg" ,ocaml-topkg) ("opam" ,opam))) (native-inputs - `(("astring" ,ocaml-astring))) + `(("astring" ,ocaml-astring) + ("ocamlbuild" ,ocamlbuild))) (synopsis "OCamlbuild plugin for C stubs") (description "Ocb-stubblr is about ten lines of code that you need to repeat over, over, over and over again if you are using ocamlbuild to build @@ -3860,7 +4813,8 @@ OCaml projects that contain C stubs.") (modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("opam" ,opam) + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam) ("pkg-config" ,pkg-config))) (inputs `(("topkg" ,ocaml-topkg) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index fe784ffaa1..471a08b799 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -343,7 +343,8 @@ the Nix package manager.") (replace 'install (lambda* (#:key outputs #:allow-other-keys) (invoke "make" "install-binPROGRAMS" - "install-nodist_pkglibexecSCRIPTS") + "install-nodist_pkglibexecSCRIPTS" + "install-nodist_libexecSCRIPTS") ;guix-authenticate ;; We need to tell 'guix-daemon' which 'guix' command to use. ;; Here we use a questionable hack where we hard-code root's @@ -568,13 +569,13 @@ transactions from C or Python.") (define-public diffoscope (package (name "diffoscope") - (version "104") + (version "105") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "0vnfhnvqvdwgh1sh2lmwad8jk2vjvq76p5xm3pfgxdik2yblmvqd")))) + "0bqkwvrvlvybqfi73qv1k5xic2qzw5lv20imqadf1wc4l8vc0vq3")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/patches/clamav-config-llvm-libs.patch b/gnu/packages/patches/clamav-config-llvm-libs.patch new file mode 100644 index 0000000000..054264ee2e --- /dev/null +++ b/gnu/packages/patches/clamav-config-llvm-libs.patch @@ -0,0 +1,14 @@ +Our llvm does not contain a single top-level library, so consult llvm-config +for the libraries that need to be linked against. + +--- clamav-0.100.2/libclamav/c++/configure.ac 2018-09-19 14:29:07.000000000 -0500 ++++ clamav-0.100.2/libclamav/c++/configure.ac 2018-10-06 21:45:09.377249158 -0500 +@@ -105,7 +105,7 @@ + + if test "x$llvm_linking" = "xdynamic"; then + AC_SUBST(LLVMCONFIG_LDFLAGS, [`$llvmconfig --ldflags`]) +- AC_SUBST(LLVMCONFIG_LIBS, [-lLLVM-$llvmver]) ++ AC_SUBST(LLVMCONFIG_LIBS, [`$llvmconfig --libs $llvmcomp`]) + AC_SUBST(LLVMCONFIG_LIBFILES, []) + else + if test $llvmver_test -ge 350; then diff --git a/gnu/packages/patches/clamav-system-tomsfastmath.patch b/gnu/packages/patches/clamav-system-tomsfastmath.patch new file mode 100644 index 0000000000..07ab79f3f7 --- /dev/null +++ b/gnu/packages/patches/clamav-system-tomsfastmath.patch @@ -0,0 +1,102 @@ +From 756ff89526b5ffaa7a4f49b1bbecf2ecbd6f85f9 Mon Sep 17 00:00:00 2001 +From: Andreas Cadhalpun <Andreas.Cadhalpun@googlemail.com> +Date: Wed, 11 Mar 2015 20:03:15 +0100 +Subject: add support for system tomsfastmath + +Patch-Name: add-support-for-system-tomsfastmath.patch +--- + configure.ac | 2 ++ + libclamav/Makefile.am | 10 ++++++++-- + libclamav/bignum.h | 6 +++++- + libclamav/xdp.c | 2 +- + m4/reorganization/libs/tomsfastmath.m4 | 12 ++++++++++++ + 5 files changed, 28 insertions(+), 4 deletions(-) + create mode 100644 m4/reorganization/libs/tomsfastmath.m4 + +--- a/configure.ac ++++ b/configure.ac +@@ -82,6 +82,7 @@ m4_include([m4/reorganization/libs/xml.m + m4_include([m4/reorganization/libs/openssl.m4]) + m4_include([m4/reorganization/libs/json.m4]) + m4_include([m4/reorganization/libs/pcre.m4]) ++m4_include([m4/reorganization/libs/tomsfastmath.m4]) + + AM_MAINTAINER_MODE + m4_include([m4/reorganization/libs/libz.m4]) +@@ -285,6 +286,7 @@ else + fi + CL_MSG_STATUS([yara ],[$enable_yara],[$enable_yara]) + CL_MSG_STATUS([fts ],[yes],[$lfs_fts_msg]) ++CL_MSG_STATUS([tomsfastmath],[yes],[$tomsfastmath_msg]) + + + # Yep, downgrading the compiler avoids the bug too: +--- a/libclamav/Makefile.am ++++ b/libclamav/Makefile.am +@@ -496,8 +496,10 @@ libclamav_la_SOURCES += yara_arena.c \ + yara_clam.h + endif + +-libclamav_la_SOURCES += bignum.h\ +- bignum_fast.h\ ++libclamav_la_SOURCES += bignum.h ++ ++if !SYSTEM_TOMSFASTMATH ++libclamav_la_SOURCES += bignum_fast.h\ + tomsfastmath/addsub/fp_add.c\ + tomsfastmath/addsub/fp_add_d.c\ + tomsfastmath/addsub/fp_addmod.c\ +@@ -579,6 +581,10 @@ libclamav_la_SOURCES += bignum.h\ + tomsfastmath/sqr/fp_sqr_comba_generic.c\ + tomsfastmath/sqr/fp_sqr_comba_small_set.c\ + tomsfastmath/sqr/fp_sqrmod.c ++else ++libclamav_la_CFLAGS += $(TOMSFASTMATH_CFLAGS) ++libclamav_la_LIBADD += $(TOMSFASTMATH_LIBS) ++endif + + .PHONY: version.h.tmp + version.c: version.h +--- a/libclamav/bignum.h ++++ b/libclamav/bignum.h +@@ -1,9 +1,13 @@ + #ifndef BIGNUM_H_ + #define BIGNUM_H_ + ++#if HAVE_SYSTEM_TOMSFASTMATH ++#include <tfm.h> ++#else + #define TFM_CHECK +- + #include "bignum_fast.h" ++#endif ++ + typedef fp_int mp_int; + #define mp_cmp fp_cmp + #define mp_toradix_n(a,b,c,d) fp_toradix_n(a,b,c,d) +--- a/libclamav/xdp.c ++++ b/libclamav/xdp.c +@@ -57,7 +57,7 @@ + #include "scanners.h" + #include "conv.h" + #include "xdp.h" +-#include "bignum_fast.h" ++#include "bignum.h" + #include "filetypes.h" + + static char *dump_xdp(cli_ctx *ctx, const char *start, size_t sz); +--- /dev/null ++++ b/m4/reorganization/libs/tomsfastmath.m4 +@@ -0,0 +1,12 @@ ++dnl Check for system tomsfastmath ++PKG_CHECK_MODULES([TOMSFASTMATH], [tomsfastmath], [have_system_tomsfastmath=yes], [have_system_tomsfastmath=no]) ++ ++AM_CONDITIONAL([SYSTEM_TOMSFASTMATH], [test "x$have_system_tomsfastmath" = "xyes"]) ++ ++if test "x$have_system_tomsfastmath" = "xyes"; then ++ AC_DEFINE([HAVE_SYSTEM_TOMSFASTMATH], [1], [link against system-wide tomsfastmath library]) ++ tomsfastmath_msg="External, $TOMSFASTMATH_CFLAGS $TOMSFASTMATH_LIBS" ++else ++ AC_DEFINE([HAVE_SYSTEM_TOMSFASTMATH], [0], [don't link against system-wide tomsfastmath library]) ++ tomsfastmath_msg="Internal" ++fi diff --git a/gnu/packages/patches/emacs-realgud-fix-configure-ac.patch b/gnu/packages/patches/emacs-realgud-fix-configure-ac.patch new file mode 100644 index 0000000000..8165857c87 --- /dev/null +++ b/gnu/packages/patches/emacs-realgud-fix-configure-ac.patch @@ -0,0 +1,27 @@ +From a293690f29407ac54a218d6d20c2142e1a0319d1 Mon Sep 17 00:00:00 2001 +From: Maxim Cournoyer <maxim.cournoyer@gmail.com> +Date: Wed, 31 Oct 2018 00:08:34 -0400 +Subject: [PATCH] configure.ac: Fix NO_CHECK_EMACS_PACKAGES elisp. + +Remove the extraneous trailing parenthesis. +--- + configure.ac | 3 +-- + 1 file changed, 1 insertion(+), 2 deletions(-) + +diff --git a/configure.ac b/configure.ac +index de0d932..69bcea7 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -25,8 +25,7 @@ AC_MSG_NOTICE("Checking prerequiste packages") + $EMACS -batch -q --no-site-file -eval \ + '(dolist (package + (quote (cl-lib loc-changes load-relative test-simple))) +- (require package)) +- )' ++ (require package))' + fi + if test $? -ne 0 ; then + AC_MSG_ERROR([Can't continue until above error is corrected.]) +-- +2.19.0 + diff --git a/gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch b/gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch index 2056b42356..fd9a4c9401 100644 --- a/gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch +++ b/gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch @@ -1,16 +1,28 @@ -From 26cac62fe0154cf65c06faaee10805531e9dade8 Mon Sep 17 00:00:00 2001 +From bc3b353cb2f26cf10aa5c5caebddf6d3d5b1e318 Mon Sep 17 00:00:00 2001 From: Julien Lepiller <julien@lepiller.eu> -Date: Wed, 14 Dec 2016 14:14:59 +0100 +Date: Fri, 21 Sep 2018 22:31:29 +0200 Subject: [PATCH] fix camlp4 in another directory --- - Makefile | 11 ++++++----- - configure | 13 ++++++++++++- - myocamlbuild.ml | 2 +- - 3 files changed, 19 insertions(+), 7 deletions(-) + Makefile | 11 ++++++----- + configure | 13 ++++++++++++- + tests/Makefile | 2 +- + tests/camlp4-comments/Makefile | 2 +- + tests/camlp4-exclude-file/Makefile | 2 +- + tests/camlp4-exclude/Makefile | 2 +- + tests/camlp4-instrument-fast/Makefile | 2 +- + tests/camlp4-instrument/Makefile | 2 +- + tests/combine-expr/Makefile | 2 +- + tests/ppx-comments/Makefile | 2 +- + tests/ppx-exclude-file/Makefile | 2 +- + tests/ppx-exclude/Makefile | 2 +- + tests/ppx-instrument-fast/Makefile | 2 +- + tests/ppx-instrument/Makefile | 2 +- + tests/report/Makefile | 2 +- + 15 files changed, 31 insertions(+), 19 deletions(-) diff --git a/Makefile b/Makefile -index 4a8ce17..d94a6d5 100644 +index b0980ee..6697922 100644 --- a/Makefile +++ b/Makefile @@ -25,7 +25,7 @@ PATH_BUILD=$(PATH_BASE)/_build @@ -19,12 +31,12 @@ index 4a8ce17..d94a6d5 100644 PATH_TESTS=$(PATH_BASE)/tests -PATH_INSTALL=$(PATH_OCAML_PREFIX)/lib/ocaml/bisect +PATH_INSTALL=$(PREFIX)/lib/ocaml/bisect - - + + # DEFINITIONS @@ -33,7 +33,8 @@ PATH_INSTALL=$(PATH_OCAML_PREFIX)/lib/ocaml/bisect PROJECT_NAME=bisect - OCAMLBUILD=$(PATH_OCAML_PREFIX)/bin/ocamlbuild + OCAMLBUILD=ocamlbuild OCAMLBUILD_ENV=WARNINGS=$(WARNINGS) PATH_OCAML_PREFIX=$(PATH_OCAML_PREFIX) -OCAMLBUILD_FLAGS=-classic-display -no-links +CAMLP4_INCLUDE=$(shell test -z $(CAMLP4_LIBDIR) || echo "-cflags -I,$(CAMLP4_LIBDIR)") @@ -33,22 +45,22 @@ index 4a8ce17..d94a6d5 100644 MODULES_MLPACK=$(PROJECT_NAME).mlpack MODULES_MLPACK_PP=$(PROJECT_NAME)_pp.mlpack @@ -80,11 +81,11 @@ veryclean: clean - rm -f $(PATH_OCAMLDOC)/*.html $(PATH_OCAMLDOC)/*.css - + rm -f $(PATH_OCAMLDOC)/*.html $(PATH_OCAMLDOC)/*.css + install: FORCE - cp $(PATH_BUILD)/src/report/report.byte $(PATH_OCAML_PREFIX)/bin/bisect-report; \ + cp $(PATH_BUILD)/src/report/report.byte $(PREFIX)/bin/bisect-report; \ - if [ "$(PPX)" = "TRUE" ]; then \ + if [ "$(PPX)" = "TRUE" ]; then \ - cp $(PATH_BUILD)/src/syntax/bisect_ppx.byte $(PATH_OCAML_PREFIX)/bin; \ + cp $(PATH_BUILD)/src/syntax/bisect_ppx.byte $(PREFIX)/bin; \ - fi; \ -- (test -x $(PATH_OCAML_PREFIX)/bin/ocamlopt && cp $(PATH_BUILD)/src/report/report.native $(PATH_OCAML_PREFIX)/bin/bisect-report.opt || true); \ -+ (test -x $(PATH_OCAML_PREFIX)/bin/ocamlopt && cp $(PATH_BUILD)/src/report/report.native $(PREFIX)/bin/bisect-report.opt || true); \ - if [ -x "$(PATH_OCAMLFIND)" ]; then \ - $(PATH_OCAMLFIND) query $(PROJECT_NAME) && $(PATH_OCAMLFIND) remove $(PROJECT_NAME) || true; \ - $(PATH_OCAMLFIND) install $(PROJECT_NAME) META -optional \ + fi; \ +- (which ocamlopt && cp $(PATH_BUILD)/src/report/report.native $(PATH_OCAML_PREFIX)/bin/bisect-report.opt || true); \ ++ (which ocamlopt && cp $(PATH_BUILD)/src/report/report.native $(PREFIX)/bin/bisect-report.opt || true); \ + if [ -x "$(PATH_OCAMLFIND)" ]; then \ + $(PATH_OCAMLFIND) query $(PROJECT_NAME) && $(PATH_OCAMLFIND) remove $(PROJECT_NAME) || true; \ + $(PATH_OCAMLFIND) install $(PROJECT_NAME) META -optional \ diff --git a/configure b/configure -index bb7ebf4..61a3095 100755 +index bb7ebf4..43ef46b 100755 --- a/configure +++ b/configure @@ -21,7 +21,9 @@ @@ -79,47 +91,193 @@ index bb7ebf4..61a3095 100755 ppx='TRUE';; *) - echo "usage: $0 [-ocaml-prefix <path>] [-ocamlfind <path>] [-no-native-dynlink] [-devel]"; -+ echo "usage: $0 [-prefix <path>] [-ocaml-prefix <path>] [-ocamlfind <path>] [-no-native-dynlink] [-devel]"; ++ echo "usage: $0 [-prefix <path>] [-ocaml-prefix <path>] [-camlp4-prefix <path>] [-ocamlfind <path>] [-no-native-dynlink] [-devel]"; exit 1;; esac shift @@ -57,6 +63,9 @@ if [ "$no_camlp4" = "TRUE" -a "$ppx" = "FALSE" ]; then exit 1 fi - + +# prefix default value +test -z $prefix && prefix=$ocaml_prefix + # make options make_quiet=`make -f - <<EOF default: gnumake -@@ -67,11 +76,13 @@ EOF` +@@ -66,7 +75,9 @@ EOF` + # file creation echo "# timestamp: `date`" > Makefile.config ++echo "PREFIX=$prefix" >> Makefile.config echo "PATH_OCAML_PREFIX=$ocaml_prefix" >> Makefile.config +echo "PATH_CAMLP4_PREFIX=$camlp4_prefix" >> Makefile.config echo "PATH_OCAMLFIND=$ocamlfind" >> Makefile.config echo "NATIVE_DYNLINK=$native_dynlink" >> Makefile.config echo "WARNINGS=$devel" >> Makefile.config - echo "NO_CAMLP4=$no_camlp4" >> Makefile.config - echo "PPX=$ppx" >> Makefile.config - echo "MAKE_QUIET=$make_quiet" >> Makefile.config -+echo "PREFIX=$prefix" >> Makefile.config - echo "" >> Makefile.config - echo 'Makefile.config successfully created' -diff --git a/myocamlbuild.ml b/myocamlbuild.ml -index 8aa25fd..09a7d48 100644 ---- a/myocamlbuild.ml -+++ b/myocamlbuild.ml -@@ -70,7 +70,7 @@ let () = - | After_rules -> - let camlp4of = - try -- let path_bin = Filename.concat (Sys.getenv "PATH_OCAML_PREFIX") "bin" in -+ let path_bin = Filename.concat (Sys.getenv "PATH_CAMLP4_PREFIX") "bin" in - Filename.concat path_bin "camlp4of" - with _ -> "camlp4of" in - flag ["ocaml"; "compile"; "pp_camlp4of"] (S[A"-pp"; A camlp4of]); --- -2.7.4 +diff --git a/tests/Makefile b/tests/Makefile +index 1aba27f..9642323 100644 +--- a/tests/Makefile ++++ b/tests/Makefile +@@ -41,7 +41,7 @@ one: FORCE + else \ + echo "Running tests for '$(NAME)'..." | tee -a _log; \ + (cd $(NAME) && \ +- $(MAKE) PATH_OCAML_BIN=$(PATH_OCAML_PREFIX)/bin \ ++ $(MAKE) PATH_OCAML_BIN=$(PATH_OCAML_PREFIX)/bin PATH_CAMLP4_PREFIX=$(PATH_CAMLP4_PREFIX) \ + COMPILER=ocamlc EXECUTABLE=bytecode RUN=./ LIB_EXT=cma EXE_SUFFIX='' \ + REPORT=../../_build/src/report/report.byte && \ + cd ..) || echo '*** error' >> _log; \ +diff --git a/tests/camlp4-comments/Makefile b/tests/camlp4-comments/Makefile +index 33fca72..a918118 100644 +--- a/tests/camlp4-comments/Makefile ++++ b/tests/camlp4-comments/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cmp + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -o $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -o $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cmp +diff --git a/tests/camlp4-exclude-file/Makefile b/tests/camlp4-exclude-file/Makefile +index ab13983..e2520fa 100644 +--- a/tests/camlp4-exclude-file/Makefile ++++ b/tests/camlp4-exclude-file/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cmp + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -exclude-file exclusions -o $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -exclude-file exclusions -o $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cmp +diff --git a/tests/camlp4-exclude/Makefile b/tests/camlp4-exclude/Makefile +index 18aada4..d71a7bc 100644 +--- a/tests/camlp4-exclude/Makefile ++++ b/tests/camlp4-exclude/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cmp + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -exclude 'f.*' -o $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -exclude 'f.*' -o $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cmp +diff --git a/tests/camlp4-instrument-fast/Makefile b/tests/camlp4-instrument-fast/Makefile +index f60767f..8506e38 100644 +--- a/tests/camlp4-instrument-fast/Makefile ++++ b/tests/camlp4-instrument-fast/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cmp + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo -mode fast $$file -o $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo -mode fast $$file -o $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cmp +diff --git a/tests/camlp4-instrument/Makefile b/tests/camlp4-instrument/Makefile +index 33fca72..a918118 100644 +--- a/tests/camlp4-instrument/Makefile ++++ b/tests/camlp4-instrument/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cmp + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -o $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/camlp4o$(EXE_SUFFIX) str.cma ../../_build/bisect_pp.cmo $$file -o $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cmp +diff --git a/tests/combine-expr/Makefile b/tests/combine-expr/Makefile +index 46ae9eb..e8e2af2 100644 +--- a/tests/combine-expr/Makefile ++++ b/tests/combine-expr/Makefile +@@ -1,4 +1,4 @@ +-COMPILE_FLAGS=-I ../../_build -pp '$(PATH_OCAML_BIN)/camlp4o str.cma -I ../../_build bisect_pp.cmo' bisect.$(LIB_EXT) $(FLAGS) ++COMPILE_FLAGS=-I ../../_build -pp '$(PATH_CAMLP4_PREFIX)/bin/camlp4o str.cma -I ../../_build bisect_pp.cmo' bisect.$(LIB_EXT) $(FLAGS) + + default: clean compile run report + +diff --git a/tests/ppx-comments/Makefile b/tests/ppx-comments/Makefile +index f8c645a..667526f 100644 +--- a/tests/ppx-comments/Makefile ++++ b/tests/ppx-comments/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cm* + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte' -dsource $$file 2> $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte' -dsource $$file 2> $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cm* +diff --git a/tests/ppx-exclude-file/Makefile b/tests/ppx-exclude-file/Makefile +index a575a77..0dd1a20 100644 +--- a/tests/ppx-exclude-file/Makefile ++++ b/tests/ppx-exclude-file/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cm* + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte -exclude-file exclusions' -dsource $$file 2> $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte -exclude-file exclusions' -dsource $$file 2> $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cm* +diff --git a/tests/ppx-exclude/Makefile b/tests/ppx-exclude/Makefile +index a517af4..f502a42 100644 +--- a/tests/ppx-exclude/Makefile ++++ b/tests/ppx-exclude/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cm* + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/ocamlc -c -I ../../_build -ppx "../../_build/src/syntax/bisect_ppx.byte -exclude 'f.*'" -dsource $$file 2> $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/ocamlc -c -I ../../_build -ppx "../../_build/src/syntax/bisect_ppx.byte -exclude 'f.*'" -dsource $$file 2> $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cm* +diff --git a/tests/ppx-instrument-fast/Makefile b/tests/ppx-instrument-fast/Makefile +index da78bb6..1195988 100644 +--- a/tests/ppx-instrument-fast/Makefile ++++ b/tests/ppx-instrument-fast/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cm* + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte -mode fast' -dsource $$file 2> $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte -mode fast' -dsource $$file 2> $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cm* +diff --git a/tests/ppx-instrument/Makefile b/tests/ppx-instrument/Makefile +index f8c645a..667526f 100644 +--- a/tests/ppx-instrument/Makefile ++++ b/tests/ppx-instrument/Makefile +@@ -2,7 +2,7 @@ default: + @rm -fr *.result *.cm* + @for file in *.ml; do \ + echo " testing '$$file' ..."; \ +- $(PATH_OCAML_BIN)/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte' -dsource $$file 2> $$file.result; \ ++ $(PATH_CAMLP4_PREFIX)/bin/ocamlc -c -I ../../_build -ppx '../../_build/src/syntax/bisect_ppx.byte' -dsource $$file 2> $$file.result; \ + diff -q $$file.reference $$file.result || exit 1; \ + done + @rm -fr *.result *.cm* +diff --git a/tests/report/Makefile b/tests/report/Makefile +index a7ffe44..a968bf9 100644 +--- a/tests/report/Makefile ++++ b/tests/report/Makefile +@@ -1,4 +1,4 @@ +-COMPILE_FLAGS=-I ../../_build -pp '$(PATH_OCAML_BIN)/camlp4o str.cma -I ../../_build bisect_pp.cmo' bisect.$(LIB_EXT) $(FLAGS) ++COMPILE_FLAGS=-I ../../_build -pp '$(PATH_CAMLP4_PREFIX)/bin/camlp4o str.cma -I ../../_build bisect_pp.cmo' bisect.$(LIB_EXT) $(FLAGS) + XMLLINT=$(shell which xmllint) + + default: clean compile run report +-- +2.18.0 diff --git a/gnu/packages/patches/tomsfastmath-constness.patch b/gnu/packages/patches/tomsfastmath-constness.patch new file mode 100644 index 0000000000..7c6ab5bbec --- /dev/null +++ b/gnu/packages/patches/tomsfastmath-constness.patch @@ -0,0 +1,76 @@ +From dac089515901d6bf315cd15a6e744b8d2c02c1cb Mon Sep 17 00:00:00 2001 +From: Sebastian Andrzej Siewior <sebastian@breakpoint.cc> +Date: Sat, 31 Oct 2015 22:48:07 +0100 +Subject: [PATCH] tfm: make a few functions static + +clamav expects them to be static and it does not seem bad to do so. + +Signed-off-by: Sebastian Andrzej Siewior <sebastian@breakpoint.cc> +--- + src/bin/fp_read_radix.c | 2 +- + src/bin/fp_read_signed_bin.c | 2 +- + src/bin/fp_read_unsigned_bin.c | 2 +- + src/headers/tfm.h | 6 +++--- + 4 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/src/bin/fp_read_radix.c b/src/bin/fp_read_radix.c +index 0b5e826..431afa0 100644 +--- a/src/bin/fp_read_radix.c ++++ b/src/bin/fp_read_radix.c +@@ -9,7 +9,7 @@ + */ + #include <tfm_private.h> + +-int fp_read_radix(fp_int *a, char *str, int radix) ++int fp_read_radix(fp_int *a, const char *str, int radix) + { + int y, neg; + char ch; +diff --git a/src/bin/fp_read_signed_bin.c b/src/bin/fp_read_signed_bin.c +index e2b8003..6467d19 100644 +--- a/src/bin/fp_read_signed_bin.c ++++ b/src/bin/fp_read_signed_bin.c +@@ -9,7 +9,7 @@ + */ + #include <tfm_private.h> + +-void fp_read_signed_bin(fp_int *a, unsigned char *b, int c) ++void fp_read_signed_bin(fp_int *a, const unsigned char *b, int c) + { + /* read magnitude */ + fp_read_unsigned_bin (a, b + 1, c - 1); +diff --git a/src/bin/fp_read_unsigned_bin.c b/src/bin/fp_read_unsigned_bin.c +index 3ee64c0..2ee89cb 100644 +--- a/src/bin/fp_read_unsigned_bin.c ++++ b/src/bin/fp_read_unsigned_bin.c +@@ -9,7 +9,7 @@ + */ + #include <tfm_private.h> + +-void fp_read_unsigned_bin(fp_int *a, unsigned char *b, int c) ++void fp_read_unsigned_bin(fp_int *a, const unsigned char *b, int c) + { + /* zero the int */ + fp_zero (a); +diff --git a/src/headers/tfm.h b/src/headers/tfm.h +index af87b56..f406388 100644 +--- a/src/headers/tfm.h ++++ b/src/headers/tfm.h +@@ -467,14 +467,14 @@ int fp_prime_random_ex(fp_int *a, int t, int size, int flags, tfm_prime_callback + int fp_count_bits(fp_int *a); + + int fp_unsigned_bin_size(fp_int *a); +-void fp_read_unsigned_bin(fp_int *a, unsigned char *b, int c); ++void fp_read_unsigned_bin(fp_int *a, const unsigned char *b, int c); + void fp_to_unsigned_bin(fp_int *a, unsigned char *b); + + int fp_signed_bin_size(fp_int *a); +-void fp_read_signed_bin(fp_int *a, unsigned char *b, int c); ++void fp_read_signed_bin(fp_int *a, const unsigned char *b, int c); + void fp_to_signed_bin(fp_int *a, unsigned char *b); + +-int fp_read_radix(fp_int *a, char *str, int radix); ++int fp_read_radix(fp_int *a, const char *str, int radix); + + int fp_radix_size(fp_int *a, int radix, int *size); + int fp_toradix(fp_int *a, char *str, int radix); diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c2f73e3f5c..ba7ebcbdbe 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2381,48 +2381,22 @@ logic-free templating system Mustache.") (define-public python-joblib (package (name "python-joblib") - (version "0.10.3") + (version "0.13.0") (source (origin (method url-fetch) (uri (pypi-uri "joblib" version)) (sha256 (base32 - "0787k919zlfmgymprz5bzv0v1df5bbirlf3awrghmjgvkrd9dci9")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Remove pre-compiled .pyc files from source. - (for-each delete-file-recursively - (find-files "." "__pycache__" #:directories? #t)) - (for-each delete-file (find-files "." "\\.pyc$")) - #t)))) + "0612nazad8dxmn3xghfrmjax6456l4xy6hn9cngs7vydi14ds7v5")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'check 'disable-failing-tests - (lambda _ - ;; This numpydoc tests fails for unknown reasons - (delete-file "doc/sphinxext/numpydoc/tests/test_docscrape.py") - ;; This numpydoc test depends on matplotlib, which is not a - ;; required input. - (delete-file "doc/sphinxext/numpydoc/tests/test_plot_directive.py") - ;; These tests fail to execute sys.executable - (substitute* "joblib/test/test_parallel.py" - (("import nose" line) - (string-append "from nose.plugins.skip import SkipTest\n" line)) - (("def test_nested_parallel_warnings" line) - (string-append "@SkipTest\n" line)) - (("def test_parallel_with_interactively_defined_functions" line) - (string-append "@SkipTest\n" line))) - #t))))) - ;; Provide nose to enable tests command + (replace 'check + (lambda _ (invoke "pytest" "-v" "joblib")))))) (native-inputs - `(("python-nose" ,python-nose) - ("python-sphinx" ,python-sphinx) - ("python-docutils" ,python-docutils) - ("python-numpydoc" ,python-numpydoc))) - (home-page "http://pythonhosted.org/joblib/") + `(("python-pytest" ,python-pytest))) + (home-page "https://joblib.readthedocs.io/") (synopsis "Using Python functions as pipeline jobs") (description "Joblib is a set of tools to provide lightweight pipelining in Python. @@ -9875,7 +9849,7 @@ and/or Xon/Xoff. The port is accessed in RAW mode.") (define-public python-kivy (package (name "python-kivy") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) @@ -9883,7 +9857,7 @@ and/or Xon/Xoff. The port is accessed in RAW mode.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1394zh6kvf7k5d8vlzxcsfcailr3q59xwg9b1n7qaf25bvyq1h98")))) + "1zzxjdp78hfjjiklzr82l4zwibwcq4j6kgicspqs6iyyfn5yisbw")))) (build-system python-build-system) (arguments `(#:tests? #f ; Tests require many optional packages @@ -10126,26 +10100,41 @@ Python to manipulate OpenDocument 1.2 files.") (define-public python-natsort (package (name "python-natsort") - (version "5.0.2") + (version "5.4.1") (source (origin (method url-fetch) (uri (pypi-uri "natsort" version)) (sha256 (base32 - "0bh6j0l8iapjnsgg3bs6q075cnzjl6zw1vlgqyv3qrygm2cxypkn")))) + "0i732amg6yzkx4g4c9j09jmqq39q377x9cl2nbkm5hax2c2v0wxf")))) (build-system python-build-system) (arguments - `(#:phases + `(#:modules ((guix build utils) + (guix build python-build-system) + (srfi srfi-1) + (srfi srfi-26) + (ice-9 ftw)) + #:phases (modify-phases %standard-phases (add-before 'check 'set-cachedir ;; Tests require write access to $HOME by default - (lambda _ (setenv "PYTHON_EGG_CACHE" "/tmp") #t))))) + (lambda _ (setenv "PYTHON_EGG_CACHE" "/tmp") #t)) + (replace 'check + (lambda _ + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append + cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" + (getenv "PYTHONPATH"))) + (invoke "pytest" "-v"))))))) (native-inputs `(("python-hypothesis" ,python-hypothesis) - ("python-pytest-cache" ,python-pytest-cache) ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-flakes" ,python-pytest-flakes) - ("python-pytest-pep8" ,python-pytest-pep8))) + ("python-pytest-mock" ,python-pytest-mock) + ("python-pytest" ,python-pytest))) (propagated-inputs ; TODO: Add python-fastnumbers. `(("python-pyicu" ,python-pyicu))) (home-page "https://github.com/SethMMorton/natsort") @@ -10167,8 +10156,6 @@ functionality in the command line.") (package (inherit base) (native-inputs `(("python2-pathlib" ,python2-pathlib) - ("python2-mock" ,python2-mock) - ("python2-enum34" ,python2-enum34) ,@(package-native-inputs base)))))) (define-public python-glances diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index a5b661e34d..6144e236a7 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com> +;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -18,10 +18,13 @@ (define-module (gnu packages simulation) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) + #:use-module (gnu packages check) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages flex) #:use-module (gnu packages gettext) @@ -35,6 +38,8 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) @@ -42,7 +47,9 @@ #:use-module (gnu packages xorg) #:use-module (guix download) #:use-module (guix build utils) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) @@ -221,3 +228,484 @@ with gas/liquid interfaces. Large problems may be split into smaller, connected problems for efficient solution on parallel systems.") (license license:gpl3+) (home-page "https://openfoam.org"))) + +(define-public python-fenics-dijitso + (package + (name "python-fenics-dijitso") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-dijitso" version)) + (sha256 + (base32 + "1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9")))) + (build-system python-build-system) + (inputs + `(("openmpi" ,openmpi) + ("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest-cov" ,python-pytest-cov))) + (propagated-inputs + `(("python-mpi4py" ,python-mpi4py))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (replace 'check + (lambda _ + (setenv "HOME" "/tmp") + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + (invoke "./runtests.sh")) + #t))))) + (home-page "https://bitbucket.org/fenics-project/dijitso/") + (synopsis "Distributed just-in-time building of shared libraries") + (description + "Dijitso provides a core component of the @code{FEniCS} framework, +namely the just-in-time compilation of C++ code that is generated from +Python modules. It is called from within a C++ library, using ctypes +to import the dynamic shared library directly. + +As long as the compiled code can provide a simple factory function to +a class implementing a predefined C++ interface, there is no limit to +the complexity of that interface. Parallel support depends on the +@code{mpi4py} interface.") + (license license:lgpl3+))) + +(define-public python-fenics-ufl + (package + (name "python-fenics-ufl") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-ufl" version)) + (sha256 + (base32 + "1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla")))) + (build-system python-build-system) + (inputs + `(("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + (invoke "py.test")) + #t))))) + (home-page "https://bitbucket.org/fenics-project/ufl/") + (synopsis "Unified language for form-compilers") + (description "The Unified Form Language (UFL) is a domain specific +language for declaration of finite element discretizations of +variational forms. More precisely, it defines a flexible interface +for choosing finite element spaces and defining expressions for weak +forms in a notation close to mathematical notation. + +UFL is part of the FEniCS Project.") + (license license:lgpl3+))) + +(define-public python-fenics-fiat + (package + (name "python-fenics-fiat") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-fiat" version)) + (sha256 + (base32 + "0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-sympy" ,python-sympy))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + (invoke "py.test" "unit/")) + #t))))) + (home-page "https://bitbucket.org/fenics-project/fiat/") + (synopsis "Tabulation of finite element function spaces") + (description + "The FInite element Automatic Tabulator (FIAT) supports +generation of arbitrary order instances of the Lagrange elements on +lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same +element shapes. Further, H(div) and H(curl) conforming finite element +spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini +and Nedelec are supported on triangles and tetrahedra. Upcoming +versions will also support Hermite and nonconforming elements. + +FIAT is part of the FEniCS Project.") + (license license:lgpl3+))) + +(define-public python-fenics-ffc + (package + (name "python-fenics-ffc") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-ffc" version)) + (sha256 + (base32 + "1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-fenics-dijitso" ,python-fenics-dijitso) + ("python-fenics-fiat" ,python-fenics-fiat) + ("python-fenics-ufl" ,python-fenics-ufl))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "HOME" (getcwd)) + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + ;; FIXME: the tests in subdirectory + ;; 'unit/ufc/finite_element' require the ffc_factory + ;; extension module. This module, located in the 'libs' + ;; subdirectory, needs to be built and made accessible + ;; prior to running the tests. + (invoke "py.test" "unit/" "--ignore=unit/ufc/") + (with-directory-excursion "uflacs" + (invoke "py.test" "unit/"))) + #t))))) + (home-page "https://bitbucket.org/fenics-project/ffc/") + (synopsis "Compiler for finite element variational forms") + (description "The FEniCS Form Compiler (FFC) is a compiler for +finite element variational forms. From a high-level description of +the form, it generates efficient low-level C++ code that can be used +to assemble the corresponding discrete operator (tensor). In +particular, a bilinear form may be assembled into a matrix and a +linear form may be assembled into a vector. FFC may be used either +from the command line (by invoking the @code{ffc} command) or as a +Python module (@code{import ffc}). + +FFC is part of the FEniCS Project.") + ;; There are two files released with a public domain licence; + ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'. + (license (list license:public-domain license:lgpl3+)))) + +(define-public fenics-dolfin + (package + (name "fenics-dolfin") + (version "2018.1.0.post1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://bitbucket.org/fenics-project/dolfin/get/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Make sure we don't use the bundled test framework. + (delete-file-recursively "test/unit/cpp/catch") + (substitute* "test/unit/cpp/main.cpp" + ;; Use standard search paths for 'catch' header file. + (("#include.*") + "#include <catch.hpp>\n")) + (substitute* "test/unit/cpp/CMakeLists.txt" + ;; Add extra include directories required by the unit tests. + (("(^target_link_libraries.*)" line) + (string-append line "\n" + "target_include_directories(" + "unittests PRIVATE " + "${DOLFIN_SOURCE_DIR} " + "${DOLFIN_SOURCE_DIR}/dolfin " + "${DOLFIN_BINARY_DIR})\n")) + (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back) + (string-append front + "$ENV{CATCH_DIR}" + "/include" back "\n"))) + (substitute* "demo/CMakeLists.txt" + ;; Add extra include directories required by the demo tests. + (("(^#find_package.*)" line) + (string-append line "\n" + "include_directories(" + "${DOLFIN_SOURCE_DIR} " + "${DOLFIN_SOURCE_DIR}/dolfin " + "${DOLFIN_BINARY_DIR})\n"))) + #t)))) + (build-system cmake-build-system) + (inputs + `(("blas" ,openblas) + ("boost" ,boost) + ("eigen" ,eigen) + ("hdf5" ,hdf5-parallel-openmpi) + ("lapack" ,lapack) + ("libxml2" ,libxml2) + ("openmpi" ,openmpi) + ("python" ,python-3) + ("scotch" ,pt-scotch32) + ("suitesparse" ,suitesparse) + ("sundials" ,sundials-openmpi) + ("zlib" ,zlib))) + (native-inputs + `(("catch" ,catch-framework2) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("ffc" ,python-fenics-ffc) + ("petsc" ,petsc-openmpi) + ("slepc" ,slepc-openmpi))) + (arguments + `(#:configure-flags + `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF" + "-DDOLFIN_ENABLE_HDF5:BOOL=ON" + "-DDOLFIN_ENABLE_MPI:BOOL=ON" + "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF" + "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON" + "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON" + "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF") + #:phases + (modify-phases %standard-phases + (add-after 'patch-usr-bin-file 'mpi-setup + ,%openmpi-setup) + (add-after 'patch-source-shebangs 'set-paths + (lambda _ + ;; Define paths to store locations. + (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas")) + (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch")) + (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack")) + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) + (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch")) + (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials")) + (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse")) + #t)) + (add-before 'check 'pre-check + (lambda _ + ;; The Dolfin repository uses git-lfs, whereby web links are + ;; substituted for large files. Guix does not currently support + ;; git-lfs, so only the links are downloaded. The tests that + ;; require the absent meshes cannot run and are skipped. + ;; + ;; Two other serial tests fail and are skipped. + ;; i) demo_stokes-iterative_serial, + ;; The MPI_Comm_rank() function was called before MPI_INIT was + ;; invoked + ;; ii) demo_multimesh-stokes_serial: + ;; Warning: Found no facets matching domain for boundary + ;; condition. + ;; + ;; One mpi test fails and is skipped. + ;; i) demo_stokes-iterative_mpi: + ;; The MPI_Comm_rank() function was called before MPI_INIT was + ;; invoked + (call-with-output-file "CTestCustom.cmake" + (lambda (port) + (display + (string-append + "set(CTEST_CUSTOM_TESTS_IGNORE " + "demo_bcs_serial " + "demo_bcs_mpi " + "demo_eigenvalue_serial " + "demo_eigenvalue_mpi " + "demo_navier-stokes_serial " + "demo_navier-stokes_mpi " + "demo_stokes-taylor-hood_serial " + "demo_stokes-taylor-hood_mpi " + "demo_subdomains_serial " + "demo_advection-diffusion_serial " + "demo_advection-diffusion_mpi " + "demo_auto-adaptive-navier-stokes_serial " + "demo_contact-vi-snes_serial " + "demo_contact-vi-snes_mpi " + "demo_contact-vi-tao_serial " + "demo_contact-vi-tao_mpi " + "demo_curl-curl_serial " + "demo_curl-curl_mpi " + "demo_dg-advection-diffusion_serial " + "demo_dg-advection-diffusion_mpi " + "demo_elasticity_serial " + "demo_elasticity_mpi " + "demo_elastodynamics_serial " + "demo_elastodynamics_mpi " + "demo_lift-drag_serial " + "demo_lift-drag_mpi " + "demo_mesh-quality_serial " + "demo_mesh-quality_mpi " + "demo_multimesh-stokes_serial " + "demo_stokes-iterative_serial " + "demo_stokes-iterative_mpi " + ")\n") port))) + #t)) + (replace 'check + (lambda _ + (and (invoke "make" "unittests") + (invoke "make" "demos") + (invoke "ctest" "-R" "unittests") + (invoke "ctest" "-R" "demo" "-R" "serial") + (invoke "ctest" "-R" "demo" "-R" "mpi"))))))) + (home-page "https://bitbucket.org/fenics-project/dolfin/") + (synopsis "Problem solving environment for differential equations") + (description + "DOLFIN is a computational framework for finding numerical +solutions to problems described by differential equations. Numerical +models in DOLFIN are constructed using general families of finite +elements. Data structures are provided for discretizing the governing +system on a computational mesh. A compact syntax, similar to +mathematical notation, is made available for defining function spaces +and expressing variational forms. Interfaces to specialized matrix +solvers are provided for solving the resultant linear systems. + +@code{fenics-dolfin} is part of the FEniCS project. It is the C++ +user interface to the FEniCS core components and external libraries.") + ;; The source code for the DOLFIN C++ library is licensed under the + ;; GNU Lesser General Public License, version 3 or later, with the + ;; following exceptions: + ;; + ;; public-domain: dolfin/geometry/predicates.cpp + ;; dolfin/geometry/predicates.h + ;; + ;; zlib: dolfin/io/base64.cpp + ;; dolfin/io/base64.h + ;; + ;; expat: dolfin/io/pugiconfig.hpp + ;; dolfin/io/pugixml.cpp + ;; dolfin/io/pugixml.hpp + (license (list license:public-domain + license:zlib + license:expat + license:lgpl3+)))) + +(define-public fenics + (package (inherit fenics-dolfin) + (name "fenics") + (build-system python-build-system) + (inputs + `(("pybind11" ,pybind11) + ("python-matplotlib" ,python-matplotlib) + ,@(alist-delete "python" (package-inputs fenics-dolfin)))) + (native-inputs + `(("cmake" ,cmake) + ("ply" ,python-ply) + ("pytest" ,python-pytest) + ("python-decorator" ,python-decorator) + ("python-pkgconfig" ,python-pkgconfig) + ,@(package-native-inputs fenics-dolfin))) + (propagated-inputs + `(("dolfin" ,fenics-dolfin) + ("petsc4py" ,python-petsc4py) + ("slepc4py" ,python-slepc4py))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'set-paths + (lambda _ + ;; Define paths to store locations. + (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11")) + ;; Move to python sub-directory. + (chdir "python") + #t)) + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'pre-check + (lambda _ + ;; Exclude tests that require meshes supplied by git-lfs. + (substitute* "demo/test.py" + (("(.*stem !.*)" line) + (string-append + line "\n" + "excludeList = [\n" + "'multimesh-quadrature', \n" + "'multimesh-marking', \n" + "'mixed-poisson-sphere', \n" + "'mesh-quality', \n" + "'lift-drag', \n" + "'elastodynamics', \n" + "'dg-advection-diffusion', \n" + "'contact-vi-tao', \n" + "'contact-vi-snes', \n" + "'collision-detection', \n" + "'buckling-tao', \n" + "'auto-adaptive-navier-stokes', \n" + "'advection-diffusion', \n" + "'subdomains', \n" + "'stokes-taylor-hood', \n" + "'stokes-mini', \n" + "'navier-stokes', \n" + "'eigenvalue']\n" + "demos = [" + "d for d in demos if d[0].stem not in " + "excludeList]\n"))) + (setenv "HOME" (getcwd)) + (setenv "PYTHONPATH" + (string-append + (getcwd) "/build/lib.linux-x86_64-" + ,(version-major+minor (package-version python)) ":" + (getenv "PYTHONPATH"))) + ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP. + (setenv "OPENBLAS_NUM_THREADS" "1") + #t)) + (replace 'check + (lambda _ + (with-directory-excursion "test" + ;; Note: The test test_snes_set_from_options() in the file + ;; unit/nls/test_PETScSNES_solver.py fails and is ignored. + (and (invoke "py.test" "unit" "--ignore" + "unit/nls/test_PETScSNES_solver.py") + (invoke "mpirun" "-np" "3" "python" "-B" "-m" + "pytest" "unit" "--ignore" + "unit/nls/test_PETScSNES_solver.py"))) + (with-directory-excursion "demo" + ;; Check demos. + (invoke "python" "generate-demo-files.py") + (and (invoke "python" "-m" "pytest" "-v" "test.py") + (invoke "python" "-m" "pytest" "-v" "test.py" + "--mpiexec=mpiexec" "--num-proc=3"))) + #t)) + (add-after 'install 'install-demo-files + (lambda* (#:key outputs #:allow-other-keys) + (let* ((demos (string-append + (assoc-ref outputs "out") + "/share/python-dolfin/demo"))) + (mkdir-p demos) + (with-directory-excursion "demo" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append demos "/" dir))) + (unless (equal? "." dir) + (mkdir-p tgt-dir) + (install-file file tgt-dir)))) + (find-files "." ".*\\.(py|gz|xdmf)$")))) + #t))))) + (home-page "https://fenicsproject.org/") + (synopsis "High-level environment for solving differential equations") + (description + "@code{fenics} is a computing platform for solving general classes of +problems that involve differential equations. @code{fenics} facilitates +access to efficient methods for dealing with ordinary differential +equations (ODEs) and partial differential equations (PDEs). Systems of +equations such as these are commonly encountered in areas of engineering, +mathematics and the physical sciences. It is particularly well-suited to +problems that can be solved using the Finite Element Method (FEM). + +@code{fenics} is the top level of the set of packages that are developed +within the FEniCS project. It provides the python user interface to the +FEniCS core components and external libraries.") + (license license:lgpl3+))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 57fb99ef28..66f57ac879 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2300,14 +2300,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.0.2") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1djfpnphkcxx8idk5rjfzg8r8dnqsgc0shh2pw8lns5hap2wc5rc")))) + "0ldxgcr33lawwr8wp14kdk2678gpkvqkzv6g333bhck1hn6qspzv")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) @@ -4706,14 +4706,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.1") + (version "5.4.2") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "1vcl4nl8by2vj2k9k84imy5m850khkgd8q02a8ica1h8vz9ijgn4")))) + "09152swfpa3fzhmrq5cwb5kxgvrxvigv1m4v6rhcibrdhfd1x8x4")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 04d28044dd..e0ad6248a5 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -2279,3 +2279,55 @@ used to keep a folder in sync between computers.") ;; The web app is released under the AGPLv3+. (license (list license:gpl3+ license:agpl3+)))) + +(define-public git-when-merged + ;; Use an unreleased version to get a PY3 compatibility fix. + (let ((commit "ab6af7865a0ba55ba364a6c507e0be6f84f31c6d")) + (package + (name "git-when-merged") + (version (string-append "1.2.0-" (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mhagger/git-when-merged/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0iyk2psf97bc9h43m89p3xjmm79fsx99i7px29g4lcnmdy5kmz0p")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (install-file "bin/git-when-merged" + (string-append (assoc-ref outputs "out") + "/bin")) + #t)) + (add-before 'install 'patch-git + (lambda* (#:key inputs #:allow-other-keys) + (let ((git (string-append (assoc-ref inputs "git") + "/bin/git"))) + (substitute* "bin/git-when-merged" + (("'git'") (string-append "'" git "'"))) + #t))) + (add-after 'install 'wrap-script + (lambda* (#:key outputs #:allow-other-keys) + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/git-when-merged") + `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))) + #t))))) + (inputs + `(("git" ,git) + ("python" ,python-wrapper))) + (home-page "https://github.com/mhagger/git-when-merged") + (synopsis "Determine when a commit was merged into a Git branch") + (description "This Git extension defines a subcommand, +@code{when-merged}, whose core operation is to find the merge that brought a +given commit into the specified ref(s). It has various options that control +how information about the merge is displayed.") + (license license:gpl2+)))) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index db1654afac..c8437bdf4e 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -5645,14 +5645,14 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 (base32 - "1cbg09l7w2zbgxb4qjm9p873p0lzrihlzsk5xxi3cpxdckn6zsrm")))) + "0dlcjrw96x72grg6j915070x8x98l7629pn86gf148iknflm7gd5")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs |