diff options
| -rw-r--r-- | doc/guix.texi | 14 | ||||
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/audio.scm | 20 | ||||
| -rw-r--r-- | gnu/packages/bioconductor.scm | 173 | ||||
| -rw-r--r-- | gnu/packages/bootloaders.scm | 58 | ||||
| -rw-r--r-- | gnu/packages/databases.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/emacs-xyz.scm | 60 | ||||
| -rw-r--r-- | gnu/packages/firmware.scm | 65 | ||||
| -rw-r--r-- | gnu/packages/geo.scm | 65 | ||||
| -rw-r--r-- | gnu/packages/java.scm | 42 | ||||
| -rw-r--r-- | gnu/packages/linux.scm | 16 | ||||
| -rw-r--r-- | gnu/packages/music.scm | 40 | ||||
| -rw-r--r-- | gnu/packages/pascal.scm | 58 | ||||
| -rw-r--r-- | gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch | 100 | ||||
| -rw-r--r-- | gnu/packages/virtualization.scm | 69 | ||||
| -rw-r--r-- | gnu/services/base.scm | 4 | ||||
| -rw-r--r-- | gnu/services/mail.scm | 120 | ||||
| -rw-r--r-- | guix/read-print.scm | 2 | ||||
| -rw-r--r-- | tests/cpio.scm | 12 | ||||
| -rw-r--r-- | tests/guix-package.sh | 4 |
20 files changed, 560 insertions, 367 deletions
diff --git a/doc/guix.texi b/doc/guix.texi index c031c8d880..fd03da8c97 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -25729,6 +25729,11 @@ Data type representing the configuration of opensmtpd. @item @code{package} (default: @var{opensmtpd}) Package object of the OpenSMTPD SMTP server. +@item @code{shepherd-requirement} (default: @code{'()}) +This option can be used to provide a list of symbols naming Shepherd services +that this service will depend on, such as @code{'networking} +if you want to configure OpenSMTPD to listen on non-loopback interfaces. + @item @code{config-file} (default: @code{%default-opensmtpd-config-file}) File-like object of the OpenSMTPD configuration file to use. By default it listens on the loopback network interface, and allows for mail from @@ -39719,11 +39724,10 @@ The service type for an @emph{extensible} service looks like this: (compose concatenate) ;concatenate the list of rules (extend (lambda (config rules) - (match config - (($ <udev-configuration> udev initial-rules) - (udev-configuration - (udev udev) ;the udev package to use - (rules (append initial-rules rules))))))))) + (udev-configuration + (inherit config) + (rules (append (udev-configuration-rules config) + rules))))))) @end lisp This is the service type for the diff --git a/gnu/local.mk b/gnu/local.mk index 56634e090c..faad95d902 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1381,6 +1381,7 @@ dist_patch_DATA = \ %D%/packages/patches/julia-tracker-16-compat.patch \ %D%/packages/patches/libffi-3.3-powerpc-fixes.patch \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ + %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch \ %D%/packages/patches/libobjc2-unbundle-robin-map.patch \ %D%/packages/patches/librime-fix-build-with-gcc10.patch \ %D%/packages/patches/libvirt-add-install-prefix.patch \ diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index b1d3007b8c..b1a16ef3d3 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -853,26 +853,16 @@ engineers, musicians, soundtrack editors and composers.") (define-public audacity (package (name "audacity") - (version "3.2.1") + (version "3.2.2") (source (origin - ;; If built from the release tag, Audacity will describe itself - ;; as an "Alpha test version" and suggest to users that they use - ;; the "latest stable released version". - ;; XXX: For 3.2.1 we rebelliously use a git tag anyway because the only - ;; "processed" download is a .zip containing a .tar.gz which does not - ;; fare well with the patch and snippet machinery: - ;; https://github.com/audacity/audacity/issues/3811 - ;; TODO: Find a way to control the "alpha" status even when using git - ;; so we're not reliant on preprocessed source code. (method git-fetch) (uri (git-reference (url "https://github.com/audacity/audacity") (commit (string-append "Audacity-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "00mal30jxbcacs1ka4yb5s8xq81zm7mv3y8l5hvg77abkyvfvdzf")) + (base32 "1akp9marc4y2g9mwwgfnl43q0gbb2dv7vhsnybh8wdn8ql30hfdw")) (patches (search-patches "audacity-ffmpeg-fallback.patch")) (modules '((guix build utils))) (snippet @@ -940,7 +930,11 @@ engineers, musicians, soundtrack editors and composers.") ;; TODO: enable this flag once we've packaged all dependencies ;; "-Daudacity_obey_system_dependencies=on" ;; disable crash reports, updates, ..., anything that phones home - "-Daudacity_has_networking=off") + "-Daudacity_has_networking=off" + ;; When building from Git — even from a release tag — this is undefined, + ;; and Audacity assumes that is is an ‘alpha’ version and includes debug + ;; symbols and extra code. Force level 2, ‘release’. + "-DAUDACITY_BUILD_LEVEL=2") #:imported-modules ((guix build glib-or-gtk-build-system) ,@%cmake-build-system-modules) #:modules diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29768dc7c2..53c7d048c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2334,13 +2334,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6")))) + "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -3292,13 +3292,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.0.2") + (version "3.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx")))) + "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -3335,13 +3335,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8")))) + "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -3600,13 +3600,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg")))) + "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs @@ -3914,13 +3914,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l")))) + "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -3936,6 +3936,7 @@ negative control samples.") r-mass r-matrixstats r-methylkit + r-minfi r-nnls r-quadprog r-rsq @@ -4996,13 +4997,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.3") + (version "1.32.4") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0z2g3p6ip4g865na9bmqaa7w2s52769pmjr3hpiv6x8bhifh3nm5")))) + "1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -5363,26 +5364,26 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.38.1") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk")))) + "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel - r-genefilter r-geneplotter r-genomicranges r-ggplot2 r-iranges r-locfit + r-matrixstats r-rcpp r-rcpparmadillo r-s4vectors @@ -5595,13 +5596,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.40.0") + (version "3.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg")))) + "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -5720,14 +5721,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.80.0") + (version "1.80.2") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7")))) + "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5810,13 +5811,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.3") + (version "1.34.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv")))) + "1nskqmlar85zg96c1fbacl7dqg6r0gl814rc7yh482y4wgmwyg0r")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -5870,13 +5871,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.50.2") + (version "1.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz")))) + "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -5948,13 +5949,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.50.1") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966")))) + "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -6111,13 +6112,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.72.1") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192")))) + "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -6180,13 +6181,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1")))) + (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) @@ -7313,13 +7314,13 @@ comprehensive scDblFinder method.") (define-public r-scmap (package (name "r-scmap") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm")))) + (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -7860,13 +7861,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng")))) + "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -8233,14 +8234,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.62.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2")))) + "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -8378,14 +8379,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.8.1") + (version "3.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj")))) + "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -9096,13 +9097,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "12jbqigg4k2ngrk2anbrrxrwkp57bbzdz492lg8lc6w1gygp5yip")))) + "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -9623,14 +9624,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.72.0") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld")))) + "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -9781,14 +9782,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.26.0") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi")))) + "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3")))) (build-system r-build-system) (arguments (list @@ -10670,14 +10671,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.22.0") + (version "2.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0")))) + "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -11018,14 +11019,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag")))) + "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -11140,14 +11141,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.18.1") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr")))) + "0nzcr23m58z3h0n0frxf26z14j7ilcl4fjy7rqm7f2i1wyld70zl")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -11218,13 +11219,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a")))) + "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -11987,14 +11988,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh")))) + "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -12003,6 +12004,7 @@ investigation using RNA-seq data.") r-delayedarray r-delayedmatrixstats r-gseabase + r-matrix r-mixtools r-r-utils r-shiny @@ -12823,14 +12825,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.34.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2")))) + "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -13263,14 +13265,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.12.0") + (version "2.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n")))) + "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -13496,14 +13498,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.26.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w")))) + "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -13719,38 +13721,30 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m")))) + "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-bh + r-biobase r-biocgenerics - r-clue + r-cpp11 r-data-table r-flowclust r-flowcore - r-flowstats r-flowviz r-flowworkspace r-graph - r-gtools - r-ks - r-lattice - r-mass r-ncdfflow - r-plyr - r-r-utils r-rbgl - r-rcolorbrewer - r-rcpp - r-rrcov)) + r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") @@ -13950,14 +13944,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.17.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk")))) + "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -15620,13 +15614,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23")))) + "1xplkzm29v6aysfhb6kf2nnmvc37jmcvv6vsgbx8z8qccn96jk02")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -15638,6 +15632,7 @@ functionality.") r-rcurl r-xml r-runit)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -16206,14 +16201,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.60.0") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda")))) + "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -16227,13 +16222,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.36.0") + (version "0.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs")))) + "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -16717,13 +16712,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp")))) + (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -16824,14 +16819,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.1") + (version "1.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2")))) + "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -16904,14 +16899,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih")))) + "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -17506,13 +17501,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.58.0") + (version "1.58.3") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq")))) + (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 3c96453e5c..b968ecd441 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016, 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> -;;; Copyright © 2016, 2017, 2018, 2021 Marius Bakke <marius@gnu.org> +;;; Copyright © 2016-2018, 2021-2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2016, 2017 Danny Milosavljevic <dannym@scratchpost.org> ;;; Copyright © 2016, 2017 David Craven <david@craven.ch> ;;; Copyright © 2017, 2018, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> @@ -1532,3 +1532,59 @@ existing PXE ROM on your network card, or you can chainload into iPXE to obtain the features of iPXE without the hassle of reflashing.") (license license:gpl2+)))) +(define-public ipxe-qemu + (package/inherit ipxe + (name "ipxe-qemu") + (native-inputs + (modify-inputs (package-native-inputs ipxe) + (prepend edk2-tools))) + (arguments + (let ((roms + ;; Alist of ROM -> (VID . DID) entries. This list and below + ;; build steps are taken from QEMUs roms/Makefile. + '(("e1000" . ("8086" . "100e")) + ("e1000e" . ("8086" . "10d3")) + ("eepro100" . ("8086" . "1209")) + ("ne2k_pci" . ("1050" . "0940")) + ("pcnet" . ("1022" . "2000")) + ("rtl8139" . ("10ec" . "8139")) + ("virtio" . ("1af4" . "1000")) + ("vmxnet3" . ("15ad" . "07b0"))))) + (substitute-keyword-arguments (package-arguments ipxe) + ((#:modules modules) + `((ice-9 match) ,@modules)) + ((#:make-flags flags) + #~(append (delete "everything" #$flags) + '("CONFIG=qemu") + (map (match-lambda + ((_ . (vid . did)) + (string-append "bin/" vid did ".rom"))) + '#$roms) + (map (match-lambda + ((_ . (vid . did)) + (string-append "bin-efi/" + vid did ".efidrv"))) + '#$roms))) + ((#:phases phases) + #~(modify-phases #$phases + (replace 'install + (lambda _ + (let ((firmware (string-append #$output "/share/firmware"))) + (mkdir-p firmware) + (for-each + (match-lambda + ((name . (vid . did)) + (let ((rom (string-append "bin/" vid did ".rom"))) + (copy-file rom + (string-append firmware + "/pxe-" name ".rom")) + (invoke "EfiRom" + "-b" rom + "-l" "0x02" + "-f" (string-append "0x" vid) + "-i" (string-append "0x" did) + "-ec" (string-append "bin-efi/" + vid did ".efidrv") + "-o" (string-append firmware + "/efi-" name ".rom"))))) + '#$roms))))))))))) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 387755b8ec..83515ad17e 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1621,14 +1621,14 @@ types are supported, as is encryption.") (define-public emacs-rec-mode (package (name "emacs-rec-mode") - (version "1.9.0") + (version "1.9.1") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "rec-mode-" version ".tar")) (sha256 (base32 - "1w1q6kh567fd8xismq9i6wr1y893lypd30l452yvydi1qjiq1n6x")) + "0f60bw07l6kk1kkjjxsk30p6rxj9mpngaxqy8piyabnijfgjzd3s")) (snippet #~(begin (delete-file "rec-mode.info"))))) (build-system emacs-build-system) (arguments diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f97775ce95..6e1d05dceb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1283,6 +1283,38 @@ leveraging built-in functionality.") (license (list license:gpl3+ license:fdl1.3+)))) ; GFDLv1.3+ for the manual +(define-public emacs-fzf + (let ((commit "21912ebc7e1084aa88c9d8b7715e782a3978ed23") + (revision "0")) + (package + (name "emacs-fzf") + (version (git-version "0.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bling/fzf.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gdqjh8996hb06bnnyhi94k69mjfrzyfgq00a9s4wwagv28sqmkj")))) + (build-system emacs-build-system) + (arguments + (list + #:tests? #f ;no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-fzf-executable + (lambda* (#:key inputs #:allow-other-keys) + (emacs-substitute-variables "fzf.el" + ("fzf/executable" (search-input-file inputs "/bin/fzf")))))))) + (inputs (list fzf)) + (home-page "https://github.com/bling/fzf.el") + (synopsis "Emacs front-end for Fzf finder") + (description "This package provides an Emacs front-end for Fzf general +purpose finder.") + (license license:gpl3+)))) + (define-public emacs-minions (package (name "emacs-minions") @@ -3581,7 +3613,7 @@ Its features are: (define-public emacs-citeproc-el (package (name "emacs-citeproc-el") - (version "0.9.1") + (version "0.9.2") (source (origin (method git-fetch) @@ -3590,7 +3622,7 @@ Its features are: (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0rkwqn9pcimfcyq19wlrcij0kcjyhbwisla7vwbhjj8ang0bq9rm")))) + (base32 "0p9gch5iijia5pm9rzlv50xcad2g9mis9mc90nvh31in9xjcccpz")))) (build-system emacs-build-system) (arguments `(#:emacs ,emacs)) ;need libxml support @@ -10196,7 +10228,7 @@ replaced with the directory you choose.") (define-public emacs-consult-notmuch (package (name "emacs-consult-notmuch") - (version "0.8") + (version "0.8.1") (source (origin (method git-fetch) @@ -10205,7 +10237,7 @@ replaced with the directory you choose.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "18r47cj89qli534irah3lwwzsnik5bcf61clnrkhafqv9y51m67z")))) + (base32 "0gcd69i99prnskh1na7clydqgh1y9rbzkdc6dy9zmin9hfdrw1yd")))) (build-system emacs-build-system) (propagated-inputs (list emacs-consult emacs-notmuch)) @@ -14436,7 +14468,7 @@ programming and reproducible research.") (define-public emacs-org-contrib (package (name "emacs-org-contrib") - (version "0.4") + (version "0.4.1") (source (origin (method git-fetch) @@ -14445,7 +14477,7 @@ programming and reproducible research.") (commit (string-append "release_" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "06b1rpywj596nnnap6pj6fnmcq8fcc4i30zv7qsvs3ryxciw01fb")))) + (base32 "0f3zjy3ybkqmvvlx04251add0vcz248qibxy5akal96l8bdhjajx")))) (build-system emacs-build-system) (arguments `(#:phases @@ -16491,14 +16523,14 @@ the center of the screen and not at the bottom.") (define-public emacs-posframe (package (name "emacs-posframe") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "posframe-" version ".tar")) (sha256 - (base32 "0j5nchfpbrf9fsr82lnvhnq6vi33gv3glsbqn18knnby8m7sxzci")))) + (base32 "05qkwb3ys05chn0maz7q19kp539m7p5acb8di4rni4vjjlkpx2bj")))) (build-system emacs-build-system) ;; emacs-minimal does not include the function font-info. (arguments @@ -20413,7 +20445,7 @@ according to a parsing expression grammar.") (define-public emacs-eldev (package (name "emacs-eldev") - (version "1.3") + (version "1.3.1") (source (origin (method git-fetch) @@ -20422,7 +20454,7 @@ according to a parsing expression grammar.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "112jv9rz6brglffwsablnhafhhnfnq89k9vh8xzbbi6i4xz2l1ak")))) + (base32 "14rrh5ycwd3r5k3df8aif4jii645m5jgplxky3hrjgr8vxd951h8")))) (build-system emacs-build-system) (arguments (list @@ -27087,7 +27119,7 @@ Debug server.") (define-public emacs-bfuture (package (name "emacs-bfuture") - (version "1.0.1") + (version "1.0.2") (source (origin (method git-fetch) @@ -27096,7 +27128,7 @@ Debug server.") (commit (string-append "v" version)))) (sha256 (base32 - "1m4v4xbsvg26z7nvg2c8q7x1nvv7v4ajm56l0nbkwcbdbrgahpva")) + "1qflkyr7fafw84mksxs25mka133y8ak8nsga3al29014pshbvzxn")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (arguments @@ -34649,7 +34681,7 @@ across sessions.") (define-public emacs-vertico-posframe (package (name "emacs-vertico-posframe") - (version "0.5.9") + (version "0.6.0") (source (origin (method url-fetch) (uri (string-append @@ -34657,7 +34689,7 @@ across sessions.") ".tar")) (sha256 (base32 - "1d1b8lfhr8zxa0dwsiqb1wzawx90l6lrr26jl17gpj85iyj3imq6")))) + "1cwi26jz9dn8la6zxxai2pfkcpz8lwf4cd8hr44lak6x0ca9bwr3")))) (build-system emacs-build-system) (propagated-inputs (list emacs-posframe emacs-vertico)) (home-page "https://github.com/tumashu/vertico-posframe") diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 8c8949a5da..2e2b48162f 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -522,6 +522,7 @@ executing in M-mode.") (description "SeaBIOS is an implementation of a 16bit x86 BIOS. SeaBIOS can run in an emulator or it can run natively on X86 hardware with the use of coreboot.") + (supported-systems '("i686-linux" "x86_64-linux")) ;; Dual licensed. (license (list license:gpl3+ license:lgpl3+ ;; src/fw/acpi-dsdt.dsl is lgpl2 @@ -530,6 +531,70 @@ coreboot.") ;; cpl with a linking exception. license:cpl1.0)))) +(define-public edk2-tools + (package + (name "edk2-tools") + (version "202211") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tianocore/edk2") + (commit (string-append "edk2-stable" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1264542mm0mffjcmw5sw34h94n405swz5z56rw1ragp3j62144iy")))) + (build-system gnu-build-system) + (arguments + (list #:make-flags + #~(list (string-append "BUILD_CC=" #$(cc-for-target))) + #:test-target "Tests" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'change-directory + (lambda _ + (chdir "BaseTools"))) + (add-after 'change-directory 'disable-some-tools + (lambda _ + ;; Disable building brotli and xz, since we package them + ;; separately, and it would require fetching submodules. + (substitute* "Source/C/GNUmakefile" + (("^[[:blank:]]+BrotliCompress[[:blank:]]+\\\\") + "\\") + (("^[[:blank:]]+LzmaCompress[[:blank:]]+\\\\") + "\\")))) + (replace 'build + (lambda* (#:key (make-flags #~'()) #:allow-other-keys) + ;; The default build target also runs tests. + (apply invoke "make" "-C" "Source/C" make-flags))) + (delete 'configure) + (replace 'install + (lambda _ + (mkdir #$output) + (copy-recursively "Source/C/bin" + (string-append #$output "/bin"))))))) + (native-inputs + (list python-wrapper)) + (inputs + (list `(,util-linux "lib"))) ;for libuuid + (home-page + "https://github.com/tianocore/tianocore.github.io/wiki/EDK-II-Tools-List") + (synopsis "EFI development tools") + (description + "This package contains tools for processing UEFI firmware content. +Executables included are: + +@itemize +@item @code{EfiRom}: Build Option ROM images. +@item @code{GenFfs}: Generate FFS files. +@item @code{GenFv}: Generate a PI firmware volume image. +@item @code{GenFw}: Get image data from PE32 files. +@item @code{GenSec}: Generate EFI_SECTION type files. +@item @code{VfrCompile}: Parse preprocessed UEFI and Framework VFR files. +@item @code{VolInfo}: Display the contents of a firmware volume. +@end itemize") + (license license:bsd-2))) + (define-public ovmf (let ((commit "13a50a6fe1dcfa6600c38456ee24e0f9ecf51b5f") (revision "1")) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index cefe973f4a..2185af7a98 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -293,7 +293,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.") (define-public geos (package (name "geos") - (version "3.11.0") + (version "3.11.1") (source (origin (method url-fetch) (uri (string-append "http://download.osgeo.org/geos/geos-" @@ -301,7 +301,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.") ".tar.bz2")) (sha256 (base32 - "12l59pxawyizmc4wn20dvjn7aifqwkim4ysmc78h91mayjmqravr")))) + "1qhbirv1rbznv99ha0pa0zybvcsn0dsz2xfc65vr8bgrm77v63kd")))) (build-system cmake-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -409,6 +409,7 @@ and driving.") (method url-fetch) (uri (string-append "http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-" version ".tar.gz")) + (patches (search-patches "libgeotiff-fix-tests-with-proj-9.1.1.patch")) (sha256 (base32 "1mjmgv48x51ppax5dnb6lq7z600czxll53bx6jbzqwd4m93i7aq5")) (modules '((guix build utils))) @@ -599,7 +600,7 @@ fully fledged Spatial SQL capabilities.") (define-public proj (package (name "proj") - (version "9.1.0") + (version "9.1.1") (source (origin (method url-fetch) @@ -607,7 +608,7 @@ fully fledged Spatial SQL capabilities.") version ".tar.gz")) (sha256 (base32 - "0593vd9sac0c98j1f4rammd90d4xnhygbr6d49i8il6ajjdj7cl1")))) + "0fbd1vj4cj19kwh03vdn0a4hr0xaacvi876yyyw5xfsj1q0x8g00")))) (build-system cmake-build-system) (native-inputs (list googletest pkg-config)) (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc @@ -701,14 +702,14 @@ projections.") (define-public python-pyproj (package (name "python-pyproj") - (version "3.3.1") + (version "3.4.0") (source (origin (method url-fetch) (uri (pypi-uri "pyproj" version)) (sha256 (base32 - "1gjg63irs44djyqbp9gg7s02d0y5i9cd1a83phyzp5fcj56y3n5k")))) + "0czbfl5dd7jckbwvinfwiwdb99sxj796gfn3a9zqbsdc4xcl8257")))) (build-system python-build-system) (arguments `(#:phases @@ -1045,7 +1046,7 @@ development.") (define-public gdal (package (name "gdal") - (version "3.5.1") + (version "3.6.1") (source (origin (method url-fetch) (uri (string-append @@ -1053,7 +1054,7 @@ development.") version ".tar.gz")) (sha256 (base32 - "1l93q7xf6qx9ck5axfkf3ygmvclxkvrjd8x00ckn7j0d0750ci3w")) + "1qckwnygszxkkq40bf87s3m1sab6jj9jyakdvskh0qf7dq8zjarf")) (modules '((guix build utils))) (snippet `(begin @@ -1083,19 +1084,27 @@ development.") json-c libgeotiff libjpeg-turbo + libjxl libpng libtiff libwebp + lz4 netcdf openssl + openjpeg pcre2 postgresql ; libpq proj qhull sqlite - zlib)) + swig + zlib + zstd)) (native-inputs - (list pkg-config)) + (list pkg-config + python)) + (propagated-inputs + (list python-numpy)) (home-page "https://gdal.org/") (synopsis "Raster and vector geospatial data format library") (description "GDAL is a translator library for raster and vector geospatial @@ -1124,25 +1133,6 @@ utilities for data translation and processing.") ;; frmts/mrf/libLERC license:asl2.0)))) -(define-public python-gdal - (package (inherit gdal) - (name "python-gdal") - (build-system python-build-system) - (arguments - '(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (add-before 'build 'chdir - (lambda _ - (chdir "swig/python") - #t))))) - (native-inputs '()) - (propagated-inputs - (list python-numpy)) - (inputs - (list gdal)) - (synopsis "GDAL (Geospatial Data Abstraction Library) python bindings"))) - (define-public python-pyshp (package (name "python-pyshp") @@ -1177,13 +1167,13 @@ utilities for data translation and processing.") (package (name "python-cartopy") ;; This is a post-release fix that adds build_ext to setup.py. - (version "0.20.3") + (version "0.21.0") (source (origin (method url-fetch) (uri (pypi-uri "Cartopy" version)) (sha256 - (base32 "01lhnkhw22jp6hnrs5qvgkq4fqcni2sx7ydiyv8w8xxx5wpglq0d")))) + (base32 "0hnfs75dcnz12ximah5xn9566r8zz189lxikmj4lrs9jl4l3l7ff")))) (build-system python-build-system) (arguments `(#:phases @@ -1206,13 +1196,12 @@ utilities for data translation and processing.") python-scipy python-shapely)) (inputs - (list geos - ;; cartopy's setup.py looks for the proj executable. - ;; Not sure if it actually makes use of it since it - ;; probably uses proj only through pyproj. - proj)) + (list geos)) (native-inputs - (list python-cython python-flufl-lock python-pytest)) + (list python-cython + python-flufl-lock + python-pytest + python-pytest-mpl)) (home-page "https://scitools.org.uk/cartopy/docs/latest/") (synopsis "Cartographic library for visualisation") (description @@ -2551,6 +2540,7 @@ growing set of geoscientific methods.") "ProcessingQgisAlgorithmsTestPt2" "ProcessingQgisAlgorithmsTestPt3" "ProcessingQgisAlgorithmsTestPt4" + "ProcessingGdalAlgorithmsRasterTest" "ProcessingGdalAlgorithmsVectorTest" "ProcessingGrass7AlgorithmsImageryTest" "ProcessingGrass7AlgorithmsRasterTestPt1" @@ -2668,7 +2658,6 @@ growing set of geoscientific methods.") python-chardet python-dateutil python-future - python-gdal python-jinja2 python-numpy python-owslib diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index f80406cab9..fc7ea120a8 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1761,18 +1761,18 @@ new Date();")) (define-public openjdk11 (package (name "openjdk") - (version "11.0.15") + (version "11.0.17") (source (origin (method url-fetch) (uri (string-append "https://openjdk-sources.osci.io/openjdk11/openjdk-" version "-ga.tar.xz")) - (file-name (string-append name "-" version ".tar.bz2")) + (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "0di91nnms2iq1svgq72r5y17am17r4vh2lq43k0bkcwpc84d6nd8")) + "1prvqy0ysz0999wrhsrbz6vrknpqfihl9l74l16ph93g89dqi5ia")) (modules '((guix build utils))) (snippet - '(for-each delete-file (find-files "." ".*.(bin|exe|jar)$"))))) + '(for-each delete-file (find-files "." "\\.(bin|exe|jar)$"))))) (build-system gnu-build-system) (outputs '("out" "jdk" "doc")) (arguments @@ -1851,8 +1851,7 @@ new Date();")) (format (current-error-port) "warning: failed to substitute: ~a~%" file)))) - (find-files "." - "\\.c$|\\.h$"))))) + (find-files "." "\\.c$|\\.h$"))))) (add-before 'build 'write-source-revision-file (lambda _ (with-output-to-file ".src-rev" @@ -1879,7 +1878,7 @@ new Date();")) ,@make-flags)))) (replace 'install (lambda _ - (let ((images (car (find-files "build" ".*-server-release" + (let ((images (car (find-files "build" "-server-release" #:directories? #t)))) (copy-recursively (string-append images "/images/jdk") #$output:jdk) @@ -1913,7 +1912,7 @@ new Date();")) (invoke "unzip" archive)) (delete-file archive) (with-directory-excursion dir - (let ((char-data-files (find-files "." "CharacterData.*"))) + (let ((char-data-files (find-files "." "CharacterData"))) (for-each (lambda (file) (substitute* file (((string-append "This file was generated " @@ -1924,7 +1923,7 @@ new Date();")) "file")))) char-data-files))) (with-directory-excursion dir - (let ((files (find-files "." ".*" #:directories? #t))) + (let ((files (find-files "." #:directories? #t))) (apply invoke "zip" "-0" "-X" archive files)))))) (add-after 'strip-character-data-timestamps 'remove-extraneous-files (lambda* (#:key outputs #:allow-other-keys) @@ -1949,7 +1948,7 @@ new Date();")) (invoke "unzip" archive)) (delete-file archive) (for-each (compose repack-archive canonicalize-path) - (find-files dir "(ct.sym|\\.jar)$")) + (find-files dir "(ct\\.sym|\\.jar)$")) (let ((reset-file-timestamp (lambda (file) (let ((s (lstat file))) @@ -1959,7 +1958,7 @@ new Date();")) (for-each reset-file-timestamp (find-files dir #:directories? #t))) (with-directory-excursion dir - (let ((files (find-files "." ".*" #:directories? #t))) + (let ((files (find-files "." #:directories? #t))) (apply invoke "zip" "-0" "-X" archive files))))))) (for-each repack-archive (find-files #$output:doc "\\.zip$")) @@ -2019,6 +2018,7 @@ new Date();")) libxtst)) (native-inputs (list autoconf + bash ; not bash-minimal, needs ulimit openjdk10 `(,openjdk10 "jdk") gnu-make-4.2 @@ -2100,8 +2100,8 @@ blacklisted.certs.pem" "#! java BlacklistedCertsConverter SHA-256\n")))))))))) (define-public openjdk13 - (make-openjdk openjdk12 "13.0.7" - "0wrrr0d7lz1v8qqm752mn4gz5l2vpl2kmx4ac3ysvk4mljc924hp")) + (make-openjdk openjdk12 "13.0.13" + "0pxf4dlig61k0pg7amg4mi919hzam7nzwckry01avgq1wj8ambji")) (define-public openjdk14 (make-openjdk @@ -2119,8 +2119,8 @@ blacklisted.certs.pem" (define-public openjdk15 (make-openjdk - openjdk14 "15.0.3" - "168cr08nywp0q3vyj8njkhsmmnyd8rz9r58hk4xhzdzc6bdfkl1i" + openjdk14 "15.0.9" + "1k3x06fv89l84ysjsyw8s89q8blghq85m6xjzv373x6297ln8n7a" (source (origin (inherit (package-source base)) (modules '()) @@ -2137,13 +2137,13 @@ blacklisted.certs.pem" (append `(,openjdk14 "jdk")))))) (define-public openjdk16 - (make-openjdk openjdk15 "16.0.1" - "1ggddsbsar4dj2fycfqqqagqil7prhb30afvq6933rz7pa9apm2f")) + (make-openjdk openjdk15 "16.0.2" + "0587px2qbz07g3xi4a3ya6m630p72dvkxcn0bj1813pxnwvcgigz")) (define-public openjdk17 (make-openjdk - openjdk16 "17.0.3" - "0slmd6ww947gxpp4yr2wmr5z975bg86qh7zqfp2radf2q77ql65b" + openjdk16 "17.0.5" + "1asnysg6kxdkrmb88y6qihdr12ljsyxv0mg6hlcs7cwxgsdlqkfs" (arguments (substitute-keyword-arguments (package-arguments openjdk16) ((#:phases phases) @@ -2155,8 +2155,8 @@ blacklisted.certs.pem" (("^#!.*") "#! java BlockedCertsConverter SHA-256\n")))))))))) (define-public openjdk18 - (make-openjdk openjdk17 "18" - "1bv6bdhkmwvn10l0xy8yi9xibds640hs5zsvx0jp7wrxa3qw4qy8")) + (make-openjdk openjdk17 "18.0.2" + "1yimfdkwpinhg5cf1mcrzk9xvjwnray3cx762kypb9jcwbranjwx")) ;;; Convenience alias to point to the latest version of OpenJDK. (define-public openjdk openjdk18) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 41fb24f82a..4cb97d1b82 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -480,7 +480,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.0-version "6.0.13") +(define-public linux-libre-6.0-version "6.0.14") (define-public linux-libre-6.0-gnu-revision "gnu") (define deblob-scripts-6.0 (linux-libre-deblob-scripts @@ -490,7 +490,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "16g2bin3xay30zfss1vlb7pwcss5giaxaksp4v1gk05wn51wjrqr"))) (define-public linux-libre-6.0-pristine-source (let ((version linux-libre-6.0-version) - (hash (base32 "191dlxcmbx8vy6z2k04jq2kr6hwnaknsnsyycvqnjmvmdf6i3lq8"))) + (hash (base32 "0862g1djm2hlcw44ks08494pbsd44syb7k0z8dqjbynggxz8zway"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.0))) @@ -498,7 +498,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; <https://www.kernel.org/category/releases.html> -(define-public linux-libre-5.15-version "5.15.83") +(define-public linux-libre-5.15-version "5.15.84") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -508,12 +508,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1m73pgx8v047xb2gck2g7j7khniis8c9akn9vhzgsdfglrf8p6fj"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "1wvzfhzqq9dps508wmp2gblfz93ipppnjzqm0n8pi1acq11hhna0"))) + (hash (base32 "05w29fh1k40iwsm7h67i86lv6jw075micav5b5dy7hjrn06c739i"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.159") +(define-public linux-libre-5.10-version "5.10.160") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -523,12 +523,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0a96g4pjdgwvxn2wpz6rfc8nwdlkw138r9pp66kvfrrn08i313ii"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "19yfi5vknxnw0cb8274q3pb5zjs6ny04n16m8xjdfdmznrbvza8v"))) + (hash (base32 "02w4mapfhds26ahqy5ijm5a6mlh9a5f4q3488l898qz8r9m0gm9h"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.227") +(define-public linux-libre-5.4-version "5.4.228") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts @@ -538,7 +538,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1bgblfkcnrabnr9hpdl07qgps57h6bq4v5pjrxs798vq43db66va"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "14q5gy48j78vwnqivrgpdhj778n2jq5l7yiw5na1rwqmfh1wbvsy"))) + (hash (base32 "0935dq7zbpf0fkppl3q96a2gh1zrmq01h1nivzgmdhjlmhn3n9c0"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index bde01cb312..5be767a138 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4730,7 +4730,7 @@ standalone JACK client and an LV2 plugin is also available.") (define-public sfizz (package (name "sfizz") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/sfztools/sfizz" @@ -4738,34 +4738,38 @@ standalone JACK client and an LV2 plugin is also available.") "/sfizz-" version ".tar.gz")) (sha256 (base32 - "1pk67xvyqkvhjz2q5hbj5v0mnfvdvvl8vl5bsh6ymwiq3glkd41l")) + "1wsr3dpn7a7whqn480m02kp6n4raamnfi3imhf2q8k58md1yn9jw")) (modules '((guix build utils))) (snippet - ;; TODO: pugixml is bundled, but can only be removed in - ;; versions after 1.0.0. '(for-each delete-file-recursively '("external/abseil-cpp" "external/simde" "plugins/editor/external/vstgui4" - "plugins/vst"))))) + "plugins/vst" + "src/external/pugixml"))))) (build-system cmake-build-system) (arguments - `(#:configure-flags - (list "-DSFIZZ_LV2_UI=OFF" - "-DSFIZZ_VST=OFF" - "-DSFIZZ_VST2=OFF" - "-DSFIZZ_TESTS=ON" - "-DSFIZZ_USE_SYSTEM_ABSEIL=ON"))) + (list + #:configure-flags + #~(list "-DSFIZZ_LV2_UI=OFF" + "-DSFIZZ_VST=OFF" + "-DSFIZZ_VST2=OFF" + "-DSFIZZ_TESTS=ON" + "-DSFIZZ_USE_SYSTEM_ABSEIL=ON" + "-DSFIZZ_USE_SYSTEM_PUGIXML=ON" + ;; XXX: Guix SIMDe version 0.7.2 is not enough. + ;; "-DSFIZZ_USE_SYSTEM_SIMDE=ON" + ))) (native-inputs (list pkg-config)) (inputs - `(("abseil-cpp" ,abseil-cpp) - ("glib" ,glib) - ("jack" ,jack-2) - ("lv2" ,lv2) - ("libsamplerate" ,libsamplerate) - ("pugixml" ,pugixml) - ("simde" ,simde))) + (list abseil-cpp + glib + jack-2 + lv2 + libsamplerate + pugixml + simde)) (home-page "https://sfz.tools/sfizz/") (synopsis "SFZ parser and synth library") (description "Sfizz provides an SFZ parser and synth C++ library. It diff --git a/gnu/packages/pascal.scm b/gnu/packages/pascal.scm index 8c193830fd..f563f077dc 100644 --- a/gnu/packages/pascal.scm +++ b/gnu/packages/pascal.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2017 Kei Kebreau <address@hidden> ;;; Copyright © 2020 Eric Bavier <bavier@posteo.net> ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2022 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,6 +24,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (gnu packages) @@ -229,43 +231,39 @@ many useful extensions to the Pascal programming language.") (define-public p2c (package (name "p2c") - (version "2.01") + (version "2.02") (source (origin (method url-fetch) - (uri (string-append "https://alum.mit.edu/www/toms/p2c/p2c-" - version ".tar.gz")) + (uri (string-append "http://users.fred.net/tds/lab/p2c/p2c-" + version ".zip")) (sha256 (base32 - "03x72lv6jrvikbrpz4kfq1xp61l2jw5ki6capib71lxs65zndajn")))) + "17q6s0vbz298pks80bxf4r6gm8kwbrml1q3vfs6g6yj75sqj58xs")))) (build-system gnu-build-system) (arguments - `(#:make-flags - (let ((out (assoc-ref %outputs "out"))) - (list (string-append "CC=" ,(cc-for-target)) - (string-append "HOMEDIR=" out "/lib/p2c") - (string-append "INCDIR=" out "/include/p2c") - (string-append "BINDIR=" out "/bin") - (string-append "LIBDIR=" out "/lib") - (string-append "MANDIR=" out "/share/man/man1") - "MANFILE=p2c.man.inst")) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'mkdir - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir-p (string-append out "/share/man")) - (mkdir-p (string-append out "/lib")) - (mkdir-p (string-append out "/bin")) - (mkdir-p (string-append out "/include"))) - #t)) - (add-before 'build 'chdir - (lambda* (#:key make-flags #:allow-other-keys) - (chdir "src") - #t))))) + (list + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "HOMEDIR=" #$output "/lib/p2c") + (string-append "INCDIR=" #$output "/include/p2c") + (string-append "BINDIR=" #$output "/bin") + (string-append "LIBDIR=" #$output "/lib") + (string-append "MANDIR=" #$output "/share/man/man1") + "MANFILE=p2c.man.inst") + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'mkdir + (lambda _ + (mkdir-p (string-append #$output "/share/man")) + (mkdir-p (string-append #$output "/lib")) + (mkdir-p (string-append #$output "/bin")) + (mkdir-p (string-append #$output "/include")))) + (add-before 'build 'chdir + (lambda _ (chdir "src")))))) (native-inputs - (list perl which)) + (list perl unzip which)) (synopsis "p2c converts Pascal programs to C programs") (description "This package provides @command{p2c}, a program to convert Pascal source code to C source code, and @command{p2cc}, a compiler for diff --git a/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch new file mode 100644 index 0000000000..b4bf292c1e --- /dev/null +++ b/gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch @@ -0,0 +1,100 @@ +From: Even Rouault <even.rouault@spatialys.com> +Date: Sat, 26 Nov 2022 13:23:12 +0100 +Subject: Fix test failures with PROJ 9.1.1 + +https://github.com/OSGeo/libgeotiff/pull/82 +--- + bin/listgeo.c | 7 ++++++- + test/testlistgeo | 4 ++-- + test/testlistgeo_out.dist | 14 -------------- + 3 files changed, 8 insertions(+), 17 deletions(-) + +diff --git a/bin/listgeo.c b/bin/listgeo.c +index 06c45f70..acad54c6 100644 +--- a/bin/listgeo.c ++++ b/bin/listgeo.c +@@ -29,6 +29,7 @@ void Usage() + " -tfw: Generate a .tfw (ESRI TIFF World) file for the target file.\n" + " -proj4: Report PROJ.4 equivalent projection definition.\n" + " -no_norm: Don't report 'normalized' parameter values.\n" ++ " -no_corners: Don't report corner coordinates.\n" + " filename: Name of the GeoTIFF file to report on.\n" ); + + exit( 1 ); +@@ -42,6 +43,7 @@ int main(int argc, char *argv[]) + int i, norm_print_flag = 1, proj4_print_flag = 0; + int tfw_flag = 0, inv_flag = 0, dec_flag = 0; + int st_test_flag = 0; ++ int corners = 1; + + /* + * Handle command line options. +@@ -50,6 +52,8 @@ int main(int argc, char *argv[]) + { + if( strcmp(argv[i],"-no_norm") == 0 ) + norm_print_flag = 0; ++ else if( strcmp(argv[i],"-no_corners") == 0 ) ++ corners = 0; + else if( strcmp(argv[i],"-tfw") == 0 ) + tfw_flag = 1; + else if( strcmp(argv[i],"-proj4") == 0 ) +@@ -130,7 +134,8 @@ int main(int argc, char *argv[]) + + TIFFGetField( tif, TIFFTAG_IMAGEWIDTH, &xsize ); + TIFFGetField( tif, TIFFTAG_IMAGELENGTH, &ysize ); +- GTIFPrintCorners( gtif, &defn, stdout, xsize, ysize, inv_flag, dec_flag ); ++ if( corners ) ++ GTIFPrintCorners( gtif, &defn, stdout, xsize, ysize, inv_flag, dec_flag ); + } + + } +diff --git a/test/testlistgeo b/test/testlistgeo +index 596301b4..9a41e74f 100755 +--- a/test/testlistgeo ++++ b/test/testlistgeo +@@ -59,11 +59,11 @@ $EXE ${DATA_DIR}/ProjLinearUnitsGeoKey_9036.tif >>${OUT} + echo "" >>${OUT} + + echo "Testing listgeo ProjectedCSTypeGeoKey_28191_cassini_soldner.tif" >> ${OUT} +-$EXE ${DATA_DIR}/ProjectedCSTypeGeoKey_28191_cassini_soldner.tif >>${OUT} ++$EXE -no_corners ${DATA_DIR}/ProjectedCSTypeGeoKey_28191_cassini_soldner.tif >>${OUT} + echo "" >>${OUT} + + echo "Testing listgeo cassini_soldner.tif" >> ${OUT} +-$EXE ${DATA_DIR}/cassini_soldner.tif >>${OUT} ++$EXE -no_corners ${DATA_DIR}/cassini_soldner.tif >>${OUT} + echo "" >>${OUT} + + echo "Testing listgeo ProjectedCSTypeGeoKey_27200_new_zealand_mapping_grid.tif" >> ${OUT} +diff --git a/test/testlistgeo_out.dist b/test/testlistgeo_out.dist +index 742f0fce..20221cec 100644 +--- a/test/testlistgeo_out.dist ++++ b/test/testlistgeo_out.dist +@@ -299,13 +299,6 @@ Ellipsoid: 7010/Clarke 1880 (Benoit) (6378300.79,6356566.43) + Prime Meridian: 8901/Greenwich (0.000000/ 0d 0' 0.00"E) + Projection Linear Units: 9001/metre (1.000000m) + +-Corner Coordinates: +-Upper Left ( 440720.000, 3751320.000) ( 40d47'28.08"E, 64d13'29.57"N) +-Lower Left ( 440720.000, 3751260.000) ( 40d47'27.69"E, 64d13'27.64"N) +-Upper Right ( 440780.000, 3751320.000) ( 40d47'32.51"E, 64d13'29.40"N) +-Lower Right ( 440780.000, 3751260.000) ( 40d47'32.12"E, 64d13'27.47"N) +-Center ( 440750.000, 3751290.000) ( 40d47'30.10"E, 64d13'28.52"N) +- + Testing listgeo cassini_soldner.tif + Geotiff_Information: + Version: 1 +@@ -348,13 +341,6 @@ Projection Method: CT_CassiniSoldner + ProjFalseNorthingGeoKey: 126867.909000 m + Projection Linear Units: 9001/metre (1.000000m) + +-Corner Coordinates: +-Upper Left ( 440720.000, 3751320.000) ( 40d47'28.08"E, 64d13'29.57"N) +-Lower Left ( 440720.000, 3751260.000) ( 40d47'27.69"E, 64d13'27.64"N) +-Upper Right ( 440780.000, 3751320.000) ( 40d47'32.51"E, 64d13'29.40"N) +-Lower Right ( 440780.000, 3751260.000) ( 40d47'32.12"E, 64d13'27.47"N) +-Center ( 440750.000, 3751290.000) ( 40d47'30.10"E, 64d13'28.52"N) +- + Testing listgeo ProjectedCSTypeGeoKey_27200_new_zealand_mapping_grid.tif + Geotiff_Information: + Version: 1 diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index d0f5fd5af4..6890f13233 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -175,13 +175,10 @@ (modules '((guix build utils))) (snippet '(begin - ;; TODO: Scrub all firmwares from this directory! - (with-directory-excursion "pc-bios" - ;; Delete firmwares provided by SeaBIOS. - (for-each delete-file (find-files "." "^(bios|vgabios).*\\.bin$"))) ;; Delete bundled code that we provide externally. + ;; TODO: Unbundle SeaBIOS! (for-each delete-file-recursively - '("dtc" "meson" "roms/seabios")))))) + '("dtc" "meson")))))) (outputs '("out" "static" "doc")) ;5.3 MiB of HTML docs (build-system gnu-build-system) (arguments @@ -192,20 +189,15 @@ (not (string=? "i686-linux" (%current-system)))) #:configure-flags #~(let ((gcc (search-input-file %build-inputs "/bin/gcc")) - (meson (search-input-file %build-inputs "bin/meson")) - (seabios (search-input-file %build-inputs - "share/firmware/bios.bin")) (out #$output)) (list (string-append "--cc=" gcc) ;; Some architectures insist on using HOST_CC. (string-append "--host-cc=" gcc) - (string-append "--meson=" meson) (string-append "--prefix=" out) - "--sysconfdir=/etc" + (string-append "--meson=" (search-input-file %build-inputs + "bin/meson")) "--enable-fdt=system" - (string-append "--firmwarepath=" out "/share/qemu:" - (dirname seabios)) (string-append "--smbd=" out "/libexec/samba-wrapper") "--disable-debug-info" ;for space considerations ;; The binaries need to be linked against -lrt. @@ -219,33 +211,6 @@ ,@%gnu-build-system-modules) #:phases #~(modify-phases %standard-phases - ;; Since we removed the bundled firmwares above, many tests - ;; can't work. Re-add them here. - (add-after 'unpack 'replace-firmwares - (lambda* (#:key inputs #:allow-other-keys) - (let* ((seabios (dirname (search-input-file - inputs "share/firmware/bios.bin"))) - (seabios-firmwares (find-files seabios "\\.bin$")) - (allowed-differences - ;; Ignore minor differences (addresses etc) in the firmware - ;; data tables compared to what the test suite expects. - '("tests/data/acpi/pc/SSDT.dimmpxm" - "tests/data/acpi/pc/DSDT.dimmpxm" - "tests/data/acpi/pc/ERST.acpierst" - "tests/data/acpi/q35/ERST.acpierst" - "tests/data/acpi/q35/DSDT.cxl")) - (allowed-differences-whitelist - (open-file "tests/qtest/bios-tables-test-allowed-diff.h" - "a"))) - (with-directory-excursion "pc-bios" - (for-each (lambda (file) - (symlink file (basename file))) - seabios-firmwares)) - (for-each (lambda (file) - (format allowed-differences-whitelist - "\"~a\",~%" file)) - allowed-differences) - (close-port allowed-differences-whitelist)))) (add-after 'unpack 'extend-test-time-outs (lambda _ ;; These tests can time out on heavily-loaded and/or slow storage. @@ -312,22 +277,17 @@ (mkdir-p "b/qemu") (chdir "b/qemu") (apply invoke "../../configure" configure-flags))) - ;; Configure, build and install QEMU user-emulation static binaries. (add-after 'configure 'configure-user-static (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((static (assoc-ref outputs "static")) (gcc (search-input-file inputs "/bin/gcc")) - (seabios (search-input-file inputs "/share/firmware/bios.bin")) ;; This is the common set of configure flags; it is ;; duplicated here to isolate this phase from manipulations ;; to the #:configure-flags build argument, as done in ;; derived packages such as qemu-minimal. (configure-flags (list (string-append "--cc=" gcc) (string-append "--host-cc=" gcc) - (string-append "--firmwarepath=" - #$output "/share/qemu:" - (dirname seabios)) "--sysconfdir=/etc" "--disable-debug-info"))) (mkdir-p "../user-static") @@ -353,15 +313,6 @@ (scandir "." (cut string-suffix? "-linux-user" <>)))))))) - - (add-after 'install 'delete-firmwares - (lambda _ - ;; Delete firmares that are accessible on --firmwarepath. - ;; For some reason tests fail if we simply remove them from - ;; pc-bios/meson.build, hence this roundabout way. - (with-directory-excursion (string-append #$output "/share/qemu") - (for-each delete-file - (find-files "." "^(vga)?bios(-[a-z0-9-]+)?\\.bin$"))))) ;; Create a wrapper for Samba. This allows QEMU to use Samba without ;; pulling it in as an input. Note that you need to explicitly install ;; Samba in your Guix profile for Samba support. @@ -406,7 +357,6 @@ exec smbd $@"))) pixman pulseaudio sdl2 - seabios spice usbredir util-linux @@ -417,16 +367,13 @@ exec smbd $@"))) zlib `(,zstd "lib"))) (native-inputs - ;; Note: acpica is here only to pretty-print firmware differences with IASL - ;; (see the replace-firmwares phase above). - (list acpica - bison - flex - gettext-minimal + (list gettext-minimal `(,glib "bin") ;gtester, etc. + perl + flex + bison meson-0.63 ninja - perl pkg-config python-wrapper python-sphinx diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 52b94e060b..6993e1f174 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -2494,11 +2494,11 @@ notably to select, copy, and paste text. The default options use the #$kmscon-command ;; The installer needs to be able to display glyphs from - ;; various scripts, so give it access to freefont. + ;; various scripts, so give it access to unifont. ;; TODO: Make this configurable. #:environment-variables (list (string-append "XDG_DATA_DIRS=" - #$font-gnu-freefont "/share")))) + #$font-gnu-unifont "/share")))) (stop #~(make-kill-destructor))))) (description "Start the @command{kmscon} virtual terminal emulator for the Linux @dfn{kernel mode setting} (KMS)."))) diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm index 2dc235a585..6f588679b1 100644 --- a/gnu/services/mail.scm +++ b/gnu/services/mail.scm @@ -1651,6 +1651,8 @@ by @code{dovecot-configuration}. @var{config} may also be created by opensmtpd-configuration? (package opensmtpd-configuration-package (default opensmtpd)) + (shepherd-requirement opensmtpd-configuration-shepherd-requirement + (default '())) ; list of symbols (config-file opensmtpd-configuration-config-file (default %default-opensmtpd-config-file)) (setgid-commands? opensmtpd-setgid-commands? (default #t))) @@ -1666,18 +1668,18 @@ action outbound relay match from local for any action outbound ")) -(define opensmtpd-shepherd-service - (match-lambda - (($ <opensmtpd-configuration> package config-file) - (list (shepherd-service - (provision '(smtpd)) - (requirement '(loopback)) - (documentation "Run the OpenSMTPD daemon.") - (start (let ((smtpd (file-append package "/sbin/smtpd"))) - #~(make-forkexec-constructor - (list #$smtpd "-f" #$config-file) - #:pid-file "/var/run/smtpd.pid"))) - (stop #~(make-kill-destructor))))))) +(define (opensmtpd-shepherd-service config) + (match-record config <opensmtpd-configuration> + (package config-file shepherd-requirement) + (list (shepherd-service + (provision '(smtpd)) + (requirement `(loopback ,@shepherd-requirement)) + (documentation "Run the OpenSMTPD daemon.") + (start (let ((smtpd (file-append package "/sbin/smtpd"))) + #~(make-forkexec-constructor + (list #$smtpd "-f" #$config-file) + #:pid-file "/var/run/smtpd.pid"))) + (stop #~(make-kill-destructor)))))) (define %opensmtpd-accounts (list (user-group @@ -1698,58 +1700,56 @@ match from local for any action outbound (home-directory "/var/empty") (shell (file-append shadow "/sbin/nologin"))))) -(define opensmtpd-activation - (match-lambda - (($ <opensmtpd-configuration> package config-file) - (let ((smtpd (file-append package "/sbin/smtpd"))) - #~(begin - (use-modules (guix build utils)) - ;; Create mbox and spool directories. - (mkdir-p "/var/mail") - (mkdir-p "/var/spool/smtpd") - (chmod "/var/spool/smtpd" #o711) - (mkdir-p "/var/spool/mail") - (chmod "/var/spool/mail" #o711)))))) +(define (opensmtpd-activation config) + (match-record config <opensmtpd-configuration> (package config-file) + (let ((smtpd (file-append package "/sbin/smtpd"))) + #~(begin + (use-modules (guix build utils)) + ;; Create mbox and spool directories. + (mkdir-p "/var/mail") + (mkdir-p "/var/spool/smtpd") + (chmod "/var/spool/smtpd" #o711) + (mkdir-p "/var/spool/mail") + (chmod "/var/spool/mail" #o711))))) (define %opensmtpd-pam-services (list (unix-pam-service "smtpd"))) -(define opensmtpd-set-gids - (match-lambda - (($ <opensmtpd-configuration> package config-file set-gids?) - (if set-gids? - (list - (setuid-program - (program (file-append package "/sbin/smtpctl")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/sendmail")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/send-mail")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/makemap")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/mailq")) - (setuid? #false) - (setgid? #true) - (group "smtpq")) - (setuid-program - (program (file-append package "/sbin/newaliases")) - (setuid? #false) - (setgid? #true) - (group "smtpq"))) - '())))) +(define (opensmtpd-set-gids config) + (match-record config <opensmtpd-configuration> (package config-file setgid-commands?) + (if setgid-commands? + (list + (setuid-program + (program (file-append package "/sbin/smtpctl")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/sendmail")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/send-mail")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/makemap")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/mailq")) + (setuid? #false) + (setgid? #true) + (group "smtpq")) + (setuid-program + (program (file-append package "/sbin/newaliases")) + (setuid? #false) + (setgid? #true) + (group "smtpq"))) + '()))) (define opensmtpd-service-type (service-type diff --git a/guix/read-print.scm b/guix/read-print.scm index a6aaa149e4..8a720ef2ef 100644 --- a/guix/read-print.scm +++ b/guix/read-print.scm @@ -288,11 +288,13 @@ expressions and blanks that were read." ('define-gexp-compiler 2) ('define-record-type 2) ('define-record-type* 4) + ('define-configuration 2) ('let 2) ('let* 2) ('letrec 2) ('letrec* 2) ('match 2) + ('match-record 3) ('when 2) ('unless 2) ('package 1) diff --git a/tests/cpio.scm b/tests/cpio.scm index 516de0655b..832101d1bb 100644 --- a/tests/cpio.scm +++ b/tests/cpio.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2015, 2022 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -31,12 +31,18 @@ (define %cpio-program (which "cpio")) +(define %test-file + (search-path %load-path "guix.scm")) + (test-begin "cpio") +;; The cpio format expects 'ino' to fit in 32 bits. If we have a bigger inode +;; number, skip this test. +(test-skip + (if (>= (stat:ino (lstat %test-file)) (expt 2 32)) 1 0)) (test-assert "file->cpio-header + write-cpio-header + read-cpio-header" - (let* ((file (search-path %load-path "guix.scm")) - (header (file->cpio-header file))) + (let* ((header (file->cpio-header %test-file))) (call-with-values (lambda () (open-bytevector-output-port)) diff --git a/tests/guix-package.sh b/tests/guix-package.sh index dedba2fd74..cc416ec6a1 100644 --- a/tests/guix-package.sh +++ b/tests/guix-package.sh @@ -149,11 +149,11 @@ cat > "$module_dir/foo.scm"<<EOF #:use-module (gnu packages base)) (define-public deprecated - (deprecated-package "fileutils" coreutils)) + (deprecated-package "fileutils-is-the-old-name" coreutils)) EOF guix build -L "$module_dir" -e '(@ (foo) deprecated)' -n -test "`guix package -L "$module_dir" -s ^fileutils$ | grep ^name:`" = "" +test "`guix package -L "$module_dir" -s ^fileutils-is-the-old-name$ | grep ^name:`" = "" rm -rf "$module_dir" |