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-rw-r--r--gnu-system.am4
-rw-r--r--gnu/packages/acl.scm4
-rw-r--r--gnu/packages/admin.scm13
-rw-r--r--gnu/packages/base.scm23
-rw-r--r--gnu/packages/bdw-gc.scm11
-rw-r--r--gnu/packages/commencement.scm12
-rw-r--r--gnu/packages/file.scm8
-rw-r--r--gnu/packages/gawk.scm9
-rw-r--r--gnu/packages/gnutls.scm8
-rw-r--r--gnu/packages/guile.scm6
-rw-r--r--gnu/packages/image.scm12
-rw-r--r--gnu/packages/libffi.scm7
-rw-r--r--gnu/packages/mc.scm11
-rw-r--r--gnu/packages/mcrypt.scm7
-rw-r--r--gnu/packages/patches/coreutils-dummy-man.patch10
-rw-r--r--gnu/packages/patches/coreutils-skip-nohup.patch28
-rw-r--r--gnu/packages/patches/file-CVE-2014-3587.patch16
-rw-r--r--gnu/packages/patches/glibc-CVE-2014-5119.patch212
-rw-r--r--gnu/packages/patches/libffi-mips-n32-fix.patch21
-rw-r--r--gnu/packages/pretty-print.scm112
-rw-r--r--guix/build/gnu-build-system.scm30
-rw-r--r--guix/build/utils.scm5
22 files changed, 361 insertions, 208 deletions
diff --git a/gnu-system.am b/gnu-system.am
index 9328d13083..510a217b98 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -302,7 +302,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/clucene-pkgconfig.patch			\
   gnu/packages/patches/cmake-fix-tests.patch			\
   gnu/packages/patches/coreutils-dummy-man.patch		\
-  gnu/packages/patches/coreutils-skip-nohup.patch		\
   gnu/packages/patches/cpio-gets-undeclared.patch		\
   gnu/packages/patches/cssc-gets-undeclared.patch               \
   gnu/packages/patches/cssc-missing-include.patch               \
@@ -312,6 +311,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/doxygen-test.patch			\
   gnu/packages/patches/doxygen-tmake.patch			\
   gnu/packages/patches/emacs-configure-sh.patch			\
+  gnu/packages/patches/file-CVE-2014-3587.patch			\
   gnu/packages/patches/findutils-absolute-paths.patch		\
   gnu/packages/patches/flashrom-use-libftdi1.patch		\
   gnu/packages/patches/flex-bison-tests.patch			\
@@ -323,6 +323,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/glib-tests-prlimit.patch			\
   gnu/packages/patches/glib-tests-timer.patch			\
   gnu/packages/patches/glibc-bootstrap-system.patch		\
+  gnu/packages/patches/glibc-CVE-2014-5119.patch		\
   gnu/packages/patches/glibc-ldd-x86_64.patch			\
   gnu/packages/patches/gnunet-fix-scheduler.patch		\
   gnu/packages/patches/gnunet-fix-tests.patch    		\
@@ -343,7 +344,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/kmod-module-directory.patch		\
   gnu/packages/patches/libbonobo-activation-test-race.patch	\
   gnu/packages/patches/libevent-dns-tests.patch			\
-  gnu/packages/patches/libffi-mips-n32-fix.patch		\
   gnu/packages/patches/liboop-mips64-deplibs-fix.patch		\
   gnu/packages/patches/libmad-mips-newgcc.patch			\
   gnu/packages/patches/libtheora-config-guess.patch		\
diff --git a/gnu/packages/acl.scm b/gnu/packages/acl.scm
index 37c0b71dc9..ef15022566 100644
--- a/gnu/packages/acl.scm
+++ b/gnu/packages/acl.scm
@@ -28,7 +28,7 @@
 (define-public acl
   (package
     (name "acl")
-    (version "2.2.51")
+    (version "2.2.52")
     (source
      (origin
       (method url-fetch)
@@ -36,7 +36,7 @@
                           version ".src.tar.gz"))
       (sha256
        (base32
-        "09aj30m49ivycl3irram8c3givc0crivjm3ymw0nhfaxrwhlb186"))))
+        "08qd9s3wfhv0ajswsylnfwr5h0d7j9d4rgip855nrh400nxp940p"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index c2599746d8..4d60c17989 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -648,18 +648,7 @@ system administrator.")
                       "")
                      (("^install: (.*)install-sudoers(.*)" _ before after)
                       ;; Don't try to create /etc/sudoers.
-                      (string-append "install: " before after "\n")))
-
-                   ;; XXX FIXME sudo 1.8.10p3 was bootstrapped with a
-                   ;; prerelease libtool, which fails on MIPS in the absence
-                   ;; of /usr/bin/file.  As a temporary workaround, we patch
-                   ;; the configure script to hardcode use of the little
-                   ;; endian N32 ABI on MIPS.
-                   ,@(if (equal? "mips64el-linux" (or (%current-target-system)
-                                                      (%current-system)))
-                         '((substitute* "configure"
-                             (("\\$emul") "elf32ltsmipn32")))
-                         '()))
+                      (string-append "install: " before after "\n"))))
                  %standard-phases)
 
        ;; XXX: The 'testsudoers' test series expects user 'root' to exist, but
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 49a2c83dd5..cbe115f8a8 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -25,6 +25,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages acl)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages ed)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages perl)
@@ -122,14 +123,14 @@ implementation offers several extensions over the standard utility.")
 (define-public tar
   (package
    (name "tar")
-   (version "1.27.1")
+   (version "1.28")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/tar/tar-"
-                                version ".tar.bz2"))
+                                version ".tar.xz"))
             (sha256
              (base32
-              "1iip0fk0wqhxb0jcwphz43r4fxkx1y7mznnhmlvr618jhp7b63wv"))))
+              "1wi2zwm4c9r3h3b8y4w0nm0qq897kn8kyj9k22ba0iqvxj48vvk4"))))
    (build-system gnu-build-system)
    (synopsis "Managing tar archives")
    (description
@@ -154,12 +155,9 @@ standard utility.")
              (base32
               "1sqckf560pzwgniy00vcpdv2c9c11s4cmhlm14yqgg8avd3bl94i"))))
    (build-system gnu-build-system)
-   (native-inputs '())                      ; FIXME: needs `ed' for the tests
-   (arguments
-    '(#:tests? #f)
+   (native-inputs `(("ed", ed)))
     ;; TODO: When cross-compiling, add this:
     ;;  '(#:configure-flags '("ac_cv_func_strnlen_working=yes"))
-    )
    (synopsis "Apply differences to originals, with optional backups")
    (description
     "Patch is a program that applies changes to files based on differences
@@ -225,17 +223,15 @@ used to apply commands with arbitrarily long arguments.")
 (define-public coreutils
   (package
    (name "coreutils")
-   (version "8.22")
+   (version "8.23")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/coreutils/coreutils-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "04hjzzv434fb8ak3hh3dyhdvg3hqjjwvjmjxqzk1gh2jh6cr8gjv"))
-            (patches (list (search-patch "coreutils-dummy-man.patch")
-                           ;; TODO: remove this patch for >= 8.23
-                           (search-patch "coreutils-skip-nohup.patch")))))
+              "0bdq6yggyl7nkc2pbl6pxhhyx15nyqhz3ds6rfn448n6rxdwlhzc"))
+            (patches (list (search-patch "coreutils-dummy-man.patch")))))
    (build-system gnu-build-system)
    (inputs `(("acl"  ,acl)                        ; TODO: add SELinux
              ("gmp"  ,gmp)))
@@ -377,7 +373,8 @@ library for working with executable and object formats is also included.")
                 (("use_ldconfig=yes")
                  "use_ldconfig=no")))
             (modules '((guix build utils)))
-            (patches (list (search-patch "glibc-ldd-x86_64.patch")))))
+            (patches (list (search-patch "glibc-CVE-2014-5119.patch")
+                           (search-patch "glibc-ldd-x86_64.patch")))))
    (build-system gnu-build-system)
 
    ;; Glibc's <limits.h> refers to <linux/limit.h>, for instance, so glibc
diff --git a/gnu/packages/bdw-gc.scm b/gnu/packages/bdw-gc.scm
index ebb02b1d74..66158912d7 100644
--- a/gnu/packages/bdw-gc.scm
+++ b/gnu/packages/bdw-gc.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -64,15 +65,15 @@ C or C++ programs, though that is not its primary goal.")
 (define-public libatomic-ops
   (package
     (name "libatomic-ops")
-    (version "7.4.0")
+    (version "7.4.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://www.hboehm.info/gc/gc_source/libatomic_ops-"
+                    "http://www.ivmaisoft.com/_bin/atomic_ops/libatomic_ops-"
                     version ".tar.gz"))
               (sha256
                (base32
-                "0njv3n63zw6v45k68z6dz14g2hpk5p230ncwmdfkglsljb1cqx98"))))
+                "1pdm0h1y7bgkczr8byg20r6bq15m5072cqm5pny4f9crc9gn3yh4"))))
     (build-system gnu-build-system)
     (outputs '("out" "debug"))
     (synopsis "Accessing hardware atomic memory update operations")
@@ -88,14 +89,14 @@ lock-free code, experiment with thread programming paradigms, etc.")
 
 (define-public libgc
   (package (inherit libgc-7.2)
-    (version "7.4.0")
+    (version "7.4.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.hboehm.info/gc/gc_source/gc-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "10z2nph62ilab063wygg2lv0jxlsbcf2az9w1lx01jzqj5lzry31"))))
+                "18mg28rr6kwr5clc65k4l4hkyy4kd16amx831sjf8q2lqkbhlck3"))))
 
     ;; New dependencies.
     (native-inputs `(("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index a1d2fcaaed..79c22a5974 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -26,6 +26,8 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages ed)
+  #:use-module (gnu packages file)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages multiprecision)
@@ -106,11 +108,20 @@
                                  (current-source-location)
                                  #:guile %bootstrap-guile)))
 
+(define file-boot0
+  (package-with-bootstrap-guile
+   (package-with-explicit-inputs file
+                                 `(("make" ,gnu-make-boot0)
+                                   ,@%bootstrap-inputs)
+                                 (current-source-location)
+                                 #:guile %bootstrap-guile)))
+
 
 (define %boot0-inputs
   `(("make" ,gnu-make-boot0)
     ("diffutils" ,diffutils-boot0)
     ("findutils" ,findutils-boot0)
+    ("file" ,file-boot0)
     ,@%bootstrap-inputs))
 
 (define* (nix-system->gnu-triplet
@@ -663,6 +674,7 @@ store.")
                ("gzip" ,gzip)
                ("bzip2" ,bzip2)
                ("xz" ,xz)
+               ("file" ,file)
                ("diffutils" ,diffutils)
                ("patch" ,patch)
                ("sed" ,sed)
diff --git a/gnu/packages/file.scm b/gnu/packages/file.scm
index f53c22f4cd..601b158128 100644
--- a/gnu/packages/file.scm
+++ b/gnu/packages/file.scm
@@ -27,17 +27,15 @@
 (define-public file
   (package
    (name "file")
-   (version "5.18")
+   (version "5.19")
    (source (origin
             (method url-fetch)
             (uri (string-append "ftp://ftp.astron.com/pub/file/file-"
                    version ".tar.gz"))
             (sha256 (base32
-                     "01xz106biz6x4h5ilymg5v3367djvgnfp4lm87132cjqdmqgn6b5"))))
+                     "0z1sgrcfy6d285kj5izy1yypf371bjl3247plh9ppk0svaxv714l"))
+            (patches (list (search-patch "file-CVE-2014-3587.patch")))))
    (build-system gnu-build-system)
-   (native-inputs
-    ;; This package depends upon a native install of itself.
-     (if (%current-target-system) `(("file" ,file)) '() ))
    (synopsis "file, a file type guesser")
    (description
     "The file command is a file type guesser, a command-line tool that tells
diff --git a/gnu/packages/gawk.scm b/gnu/packages/gawk.scm
index 6185409fb7..84b5bd17a7 100644
--- a/gnu/packages/gawk.scm
+++ b/gnu/packages/gawk.scm
@@ -57,15 +57,12 @@
                                (string-append "### " match))))
                           '())
 
-                    ;; XXX FIXME gawk 4.1.1 was bootstrapped with a prerelease
-                    ;; libtool, which fails on MIPS in the absence of
-                    ;; /usr/bin/file.  As a temporary workaround, we patch
-                    ;; the configure script to hardcode use of the little
-                    ;; endian N32 ABI on MIPS.
+                    ;; XXX FIXME prerelease libtool fails on MIPS in the
+                    ;; absence of /usr/bin/file.
                     ,@(if (equal? "mips64el-linux" (or (%current-target-system)
                                                        (%current-system)))
                           '((substitute* "extension/configure"
-                              (("\\$emul") "elf32ltsmipn32")))
+                              (("/usr/bin/file") (which "file"))))
                           '())))
                 %standard-phases)))
    (inputs `(("libsigsegv" ,libsigsegv)
diff --git a/gnu/packages/gnutls.scm b/gnu/packages/gnutls.scm
index 917dfdd228..89fc86d6ad 100644
--- a/gnu/packages/gnutls.scm
+++ b/gnu/packages/gnutls.scm
@@ -63,7 +63,7 @@ specifications.")
 (define-public gnutls
   (package
     (name "gnutls")
-    (version "3.2.15")
+    (version "3.2.16")
     (source (origin
              (method url-fetch)
              (uri
@@ -75,12 +75,8 @@ specifications.")
                              "/gnutls-" version ".tar.xz"))
              (sha256
               (base32
-               "1fbpr9r1r2y803s3avwjpy1higqsz85dyb302kvmh0i29frwgg9h"))))
+               "1bmwhg8y3mz5w2klclf5dz9502477kaj8r8db7k45fwb9ah3c63q"))))
     (build-system gnu-build-system)
-    (arguments
-     ;; Work around build issue reported at
-     ;; <https://lists.gnu.org/archive/html/guix-devel/2014-03/msg00027.html>.
-     '(#:make-flags '("CPPFLAGS=-DENABLE_RSA_EXPORT")))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (inputs
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index cb14f0e6c7..1169158113 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -122,11 +122,7 @@ without requiring the source code to be rewritten.")
    (native-inputs `(("pkgconfig" ,pkg-config)))
    (inputs `(("libffi" ,libffi)
              ("readline" ,readline)
-
-             ;; TODO: On next core-updates, make Bash input unconditional.
-             ,@(if (%current-target-system)
-                   `(("bash" ,bash))
-                   '())))
+             ("bash" ,bash)))
 
    (propagated-inputs
     `( ;; These ones aren't normally needed here, but since `libguile-2.0.la'
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 014266cbb0..06f62715c4 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -19,7 +19,6 @@
 (define-module (gnu packages image)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages file)
   #:use-module ((guix licenses) #:renamer (symbol-prefix-proc 'license:))
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -97,20 +96,11 @@ image files in PBMPLUS PPM/PGM, GIF, BMP, and Targa file formats.")
    (inputs `(("zlib" ,zlib)
              ("libjpeg-8" ,libjpeg-8)))
              ;; currently does not compile with libjpeg version 9
-   (native-inputs `(("file" ,file)))
    (arguments
     `(#:configure-flags
       (list (string-append "--with-jpeg-include-dir="
                            (assoc-ref %build-inputs "libjpeg-8")
-                           "/include"))
-      #:phases
-      (alist-cons-before
-       'configure 'patch-configure
-       (lambda _
-         (substitute* "configure"
-           (("`/usr/bin/file")
-            (string-append "`" (which "file")))))
-      %standard-phases)))
+                           "/include"))))
    (synopsis "Libtiff, a library for handling TIFF files")
    (description
     "Libtiff provides support for the Tag Image File Format (TIFF), a format
diff --git a/gnu/packages/libffi.scm b/gnu/packages/libffi.scm
index c5e265087e..33e10d6fc2 100644
--- a/gnu/packages/libffi.scm
+++ b/gnu/packages/libffi.scm
@@ -29,11 +29,11 @@
          ;; available in $includedir where some users expect them.
          '(lambda* (#:key outputs #:allow-other-keys)
             (define out (assoc-ref outputs "out"))
-            (symlink (string-append out "/lib/libffi-3.0.13/include")
+            (symlink (string-append out "/lib/libffi-3.1/include")
                      (string-append out "/include")))))
    (package
     (name "libffi")
-    (version "3.0.13")
+    (version "3.1")
     (source (origin
              (method url-fetch)
              (uri
@@ -41,8 +41,7 @@
                              name "-" version ".tar.gz"))
              (sha256
               (base32
-               "077ibkf84bvcd6rw1m6jb107br63i2pp301rkmsbgg6300adxp8x"))
-             (patches (list (search-patch "libffi-mips-n32-fix.patch")))))
+               "1sznmrhcswwbyqla9y2ximlkzbxks59wjfs3lh7qf8ayranyxzlp"))))
     (build-system gnu-build-system)
     (arguments `(#:phases (alist-cons-after 'install 'post-install
                                             ,post-install-phase
diff --git a/gnu/packages/mc.scm b/gnu/packages/mc.scm
index aba14d59ac..6e3747c943 100644
--- a/gnu/packages/mc.scm
+++ b/gnu/packages/mc.scm
@@ -28,7 +28,6 @@
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages check)
-  #:use-module (gnu packages file)
   #:use-module (gnu packages perl))
 
 (define-public mc
@@ -46,7 +45,6 @@
       (patches (list (search-patch "mc-fix-ncurses-build.patch")))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)
-                     ("file" ,file)
                      ("perl" ,perl)))
     (inputs `(("aspell" ,aspell)
               ("ncurses" ,ncurses)
@@ -55,14 +53,7 @@
               ("check" ,check)))
     (arguments
      `(#:configure-flags
-       '("--with-screen=ncurses" "--enable-aspell")
-       #:phases
-       (alist-cons-before
-        'configure 'patch-configure
-        (lambda _
-          (substitute* "configure"
-            (("/usr/bin/file") (which "file"))))
-        %standard-phases)))
+       '("--with-screen=ncurses" "--enable-aspell")))
     (home-page "http://www.midnight-commander.org")
     (synopsis "Graphical file manager")
     (description
diff --git a/gnu/packages/mcrypt.scm b/gnu/packages/mcrypt.scm
index eac8c72c5e..12a4827224 100644
--- a/gnu/packages/mcrypt.scm
+++ b/gnu/packages/mcrypt.scm
@@ -23,8 +23,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages file))
+  #:use-module (gnu packages perl))
 
 (define-public mcrypt
   (package
@@ -68,7 +67,6 @@ them.")
        (base32
         "0gipgb939vy9m66d3k8il98rvvwczyaw2ixr8yn6icds9c3nrsz4"))))
     (build-system gnu-build-system)
-    (native-inputs `(("file" ,file)))
     (home-page "http://mcrypt.sourceforge.net/")
     (synopsis "Encryption algorithm library")
     (description
@@ -95,8 +93,7 @@ XTEA, 3WAY, TWOFISH, BLOWFISH, ARCFOUR, WAKE and more.")
       (patches (list (search-patch "mhash-keygen-test-segfault.patch")))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("file" ,file)
-       ("perl" ,perl)))                 ;for tests
+     `(("perl" ,perl)))                 ;for tests
     (home-page "http://mhash.sourceforge.net/")
     (synopsis "Thread-safe hash library")
     (description
diff --git a/gnu/packages/patches/coreutils-dummy-man.patch b/gnu/packages/patches/coreutils-dummy-man.patch
index f6a6a31002..a43cfc47c3 100644
--- a/gnu/packages/patches/coreutils-dummy-man.patch
+++ b/gnu/packages/patches/coreutils-dummy-man.patch
@@ -7,15 +7,15 @@ would appear when compiling:
 
   dummy-man: too many non-option arguments
 
---- coreutils-8.22/Makefile.in	2013-12-13 16:20:00.000000000 +0100
-+++ coreutils-8.22/Makefile.in	2014-02-28 10:53:27.000000000 +0100
-@@ -9977,8 +9977,8 @@ man/yes.1:       src/yes
+--- coreutils-8.23/Makefile.in	2014-07-18 18:22:24.000000000 -0400
++++ coreutils-8.23/Makefile.in	2014-08-03 20:21:10.849158313 -0400
+@@ -14076,8 +14076,8 @@
  	  && $(run_help2man)						\
  		     --source='$(PACKAGE_STRING)'			\
  		     --include=$(srcdir)/man/$$name.x			\
--		     --output=$$t/$$name.1 $$t/$$name			\
+-		     --output=$$t/$$name.1 $$t/$$argv			\
  		     --info-page='coreutils \(aq'$$name' invocation\(aq' \
-+		     --output=$$t/$$name.1 $$t/$$name			\
++		     --output=$$t/$$name.1 $$t/$$argv			\
  	  && sed \
  	       -e 's|$*\.td/||g' \
  	       -e '/For complete documentation/d' \
diff --git a/gnu/packages/patches/coreutils-skip-nohup.patch b/gnu/packages/patches/coreutils-skip-nohup.patch
deleted file mode 100644
index f5283a6b21..0000000000
--- a/gnu/packages/patches/coreutils-skip-nohup.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-commit 5dce6bdfafc930dfd17d5d16aea7d1add3472066
-Author: Pádraig Brady <P@draigBrady.com>
-Date:   Wed Mar 5 15:14:07 2014 +0000
-
-    tests: fix false failure in nohup.sh in non tty builds
-    
-    * tests/misc/nohup.sh: When running tests without a controlling tty,
-    an exec failure is triggered in a subshell, which causes POSIX
-    shells to immediately exit the subshell.  This was brought
-    to notice by the newly conforming bash 4.3.
-    Fixes http:/bugs.gnu.org/16940
-
-diff --git a/tests/misc/nohup.sh b/tests/misc/nohup.sh
-index 6d2b515..2328b43 100755
---- a/tests/misc/nohup.sh
-+++ b/tests/misc/nohup.sh
-@@ -63,6 +63,11 @@ rm -f nohup.out err
- # to stderr must be fatal.  Requires stdout to be terminal.
- if test -w /dev/full && test -c /dev/full; then
- (
-+  # POSIX shells immediately exit the subshell on exec error.
-+  # So check we can write to /dev/tty before the exec, which
-+  # isn't possible if we've no controlling tty for example.
-+  test -c /dev/tty && >/dev/tty || exit 0
-+
-   exec >/dev/tty
-   test -t 1 || exit 0
-   nohup echo hi 2> /dev/full
diff --git a/gnu/packages/patches/file-CVE-2014-3587.patch b/gnu/packages/patches/file-CVE-2014-3587.patch
new file mode 100644
index 0000000000..cf88bf5f3e
--- /dev/null
+++ b/gnu/packages/patches/file-CVE-2014-3587.patch
@@ -0,0 +1,16 @@
+Fixes CVE-2014-3587.  Copied from upstream commit
+0641e56be1af003aa02c7c6b0184466540637233.
+
+--- file-5.19/src/cdf.c.orig	2014-06-09 09:04:37.000000000 -0400
++++ file-5.19/src/cdf.c	2014-08-26 11:55:23.887118898 -0400
+@@ -824,6 +824,10 @@
+ 		q = (const uint8_t *)(const void *)
+ 		    ((const char *)(const void *)p + ofs
+ 		    - 2 * sizeof(uint32_t));
++		if (q < p) {
++			DPRINTF(("Wrapped around %p < %p\n", q, p));
++			goto out;
++		}
+ 		if (q > e) {
+ 			DPRINTF(("Ran of the end %p > %p\n", q, e));
+ 			goto out;
diff --git a/gnu/packages/patches/glibc-CVE-2014-5119.patch b/gnu/packages/patches/glibc-CVE-2014-5119.patch
new file mode 100644
index 0000000000..de063a2da5
--- /dev/null
+++ b/gnu/packages/patches/glibc-CVE-2014-5119.patch
@@ -0,0 +1,212 @@
+Remove support for loadable gconv transliteration modules.
+The support for transliteration modules has been non-functional for
+over a decade, and the removal is prompted by security defects.  The
+normal gconv conversion modules are still supported.  Transliteration
+with //TRANSLIT is still possible, and the //IGNORE specifier
+continues to be  supported. (CVE-2014-5119)
+
+Based on upstream commits a1a6a401ab0a3c9f15fb7eaebbdcee24192254e8
+and f9df71e895d3552d557e783fdb9d133328195645
+by Florian Weimer <fweimer@redhat.com>.
+
+--- glibc-2.19/ChangeLog.orig	2014-02-07 04:04:38.000000000 -0500
++++ glibc-2.19/ChangeLog	2014-08-26 14:35:12.368861387 -0400
+@@ -1,3 +1,10 @@
++2014-08-26  Florian Weimer  <fweimer@redhat.com>
++
++	[BZ #17187]
++	* iconv/gconv_trans.c (struct known_trans, search_tree, lock,
++	trans_compare, open_translit, __gconv_translit_find):
++	Remove module loading code.
++
+ 2014-02-06  Carlos O'Donell  <carlos@redhat.com>
+ 
+ 	[BZ #16529]
+--- glibc-2.19/iconv/gconv_trans.c.orig	2014-02-07 04:04:38.000000000 -0500
++++ glibc-2.19/iconv/gconv_trans.c	2014-08-26 14:37:26.269525364 -0400
+@@ -238,181 +238,12 @@
+   return __GCONV_ILLEGAL_INPUT;
+ }
+ 
+-
+-/* Structure to represent results of found (or not) transliteration
+-   modules.  */
+-struct known_trans
+-{
+-  /* This structure must remain the first member.  */
+-  struct trans_struct info;
+-
+-  char *fname;
+-  void *handle;
+-  int open_count;
+-};
+-
+-
+-/* Tree with results of previous calls to __gconv_translit_find.  */
+-static void *search_tree;
+-
+-/* We modify global data.   */
+-__libc_lock_define_initialized (static, lock);
+-
+-
+-/* Compare two transliteration entries.  */
+-static int
+-trans_compare (const void *p1, const void *p2)
+-{
+-  const struct known_trans *s1 = (const struct known_trans *) p1;
+-  const struct known_trans *s2 = (const struct known_trans *) p2;
+-
+-  return strcmp (s1->info.name, s2->info.name);
+-}
+-
+-
+-/* Open (maybe reopen) the module named in the struct.  Get the function
+-   and data structure pointers we need.  */
+-static int
+-open_translit (struct known_trans *trans)
+-{
+-  __gconv_trans_query_fct queryfct;
+-
+-  trans->handle = __libc_dlopen (trans->fname);
+-  if (trans->handle == NULL)
+-    /* Not available.  */
+-    return 1;
+-
+-  /* Find the required symbol.  */
+-  queryfct = __libc_dlsym (trans->handle, "gconv_trans_context");
+-  if (queryfct == NULL)
+-    {
+-      /* We cannot live with that.  */
+-    close_and_out:
+-      __libc_dlclose (trans->handle);
+-      trans->handle = NULL;
+-      return 1;
+-    }
+-
+-  /* Get the context.  */
+-  if (queryfct (trans->info.name, &trans->info.csnames, &trans->info.ncsnames)
+-      != 0)
+-    goto close_and_out;
+-
+-  /* Of course we also have to have the actual function.  */
+-  trans->info.trans_fct = __libc_dlsym (trans->handle, "gconv_trans");
+-  if (trans->info.trans_fct == NULL)
+-    goto close_and_out;
+-
+-  /* Now the optional functions.  */
+-  trans->info.trans_init_fct =
+-    __libc_dlsym (trans->handle, "gconv_trans_init");
+-  trans->info.trans_context_fct =
+-    __libc_dlsym (trans->handle, "gconv_trans_context");
+-  trans->info.trans_end_fct =
+-    __libc_dlsym (trans->handle, "gconv_trans_end");
+-
+-  trans->open_count = 1;
+-
+-  return 0;
+-}
+-
+-
+ int
+ internal_function
+ __gconv_translit_find (struct trans_struct *trans)
+ {
+-  struct known_trans **found;
+-  const struct path_elem *runp;
+-  int res = 1;
+-
+-  /* We have to have a name.  */
+-  assert (trans->name != NULL);
+-
+-  /* Acquire the lock.  */
+-  __libc_lock_lock (lock);
+-
+-  /* See whether we know this module already.  */
+-  found = __tfind (trans, &search_tree, trans_compare);
+-  if (found != NULL)
+-    {
+-      /* Is this module available?  */
+-      if ((*found)->handle != NULL)
+-	{
+-	  /* Maybe we have to reopen the file.  */
+-	  if ((*found)->handle != (void *) -1)
+-	    /* The object is not unloaded.  */
+-	    res = 0;
+-	  else if (open_translit (*found) == 0)
+-	    {
+-	      /* Copy the data.  */
+-	      *trans = (*found)->info;
+-	      (*found)->open_count++;
+-	      res = 0;
+-	    }
+-	}
+-    }
+-  else
+-    {
+-      size_t name_len = strlen (trans->name) + 1;
+-      int need_so = 0;
+-      struct known_trans *newp;
+-
+-      /* We have to continue looking for the module.  */
+-      if (__gconv_path_elem == NULL)
+-	__gconv_get_path ();
+-
+-      /* See whether we have to append .so.  */
+-      if (name_len <= 4 || memcmp (&trans->name[name_len - 4], ".so", 3) != 0)
+-	need_so = 1;
+-
+-      /* Create a new entry.  */
+-      newp = (struct known_trans *) malloc (sizeof (struct known_trans)
+-					    + (__gconv_max_path_elem_len
+-					       + name_len + 3)
+-					    + name_len);
+-      if (newp != NULL)
+-	{
+-	  char *cp;
+-
+-	  /* Clear the struct.  */
+-	  memset (newp, '\0', sizeof (struct known_trans));
+-
+-	  /* Store a copy of the module name.  */
+-	  newp->info.name = cp = (char *) (newp + 1);
+-	  cp = __mempcpy (cp, trans->name, name_len);
+-
+-	  newp->fname = cp;
+-
+-	  /* Search in all the directories.  */
+-	  for (runp = __gconv_path_elem; runp->name != NULL; ++runp)
+-	    {
+-	      cp = __mempcpy (__stpcpy ((char *) newp->fname, runp->name),
+-			      trans->name, name_len);
+-	      if (need_so)
+-		memcpy (cp, ".so", sizeof (".so"));
+-
+-	      if (open_translit (newp) == 0)
+-		{
+-		  /* We found a module.  */
+-		  res = 0;
+-		  break;
+-		}
+-	    }
+-
+-	  if (res)
+-	    newp->fname = NULL;
+-
+-	  /* In any case we'll add the entry to our search tree.  */
+-	  if (__tsearch (newp, &search_tree, trans_compare) == NULL)
+-	    {
+-	      /* Yickes, this should not happen.  Unload the object.  */
+-	      res = 1;
+-	      /* XXX unload here.  */
+-	    }
+-	}
+-    }
+-
+-  __libc_lock_unlock (lock);
+-
+-  return res;
++  /* Transliteration module loading has been removed because it never
++     worked as intended and suffered from a security vulnerability.
++     Consequently, this function always fails.  */
++  return 1;
+ }
diff --git a/gnu/packages/patches/libffi-mips-n32-fix.patch b/gnu/packages/patches/libffi-mips-n32-fix.patch
deleted file mode 100644
index 87ec48f883..0000000000
--- a/gnu/packages/patches/libffi-mips-n32-fix.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Fix handling of uint32_t arguments on the MIPS N32 ABI.
-
-Patch by Mark H Weaver <mhw@netris.org>.
-
---- libffi/src/mips/ffi.c.orig	2013-03-16 07:19:39.000000000 -0400
-+++ libffi/src/mips/ffi.c	2013-10-22 01:11:03.111985247 -0400
-@@ -170,7 +170,14 @@
- 		break;
- 		  
- 	      case FFI_TYPE_UINT32:
-+#ifdef FFI_MIPS_N32
-+		/* The N32 ABI requires that 32-bit integers
-+		   be sign-extended to 64-bits, regardless of
-+		   whether they are signed or unsigned. */
-+		*(ffi_arg *)argp = *(SINT32 *)(* p_argv);
-+#else
- 		*(ffi_arg *)argp = *(UINT32 *)(* p_argv);
-+#endif
- 		break;
- 
- 	      /* This can only happen with 64bit slots.  */
diff --git a/gnu/packages/pretty-print.scm b/gnu/packages/pretty-print.scm
index 8c51b54f18..07837eb1ac 100644
--- a/gnu/packages/pretty-print.scm
+++ b/gnu/packages/pretty-print.scm
@@ -30,8 +30,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gperf)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages file))
+  #:use-module (gnu packages perl))
 
 (define-public a2ps
   (package
@@ -53,45 +52,39 @@
        ("imagemagick" ,imagemagick)))
     (native-inputs
      `(("gperf" ,gperf)
-       ("perl" ,perl)
-       ("file" ,file)))
+       ("perl" ,perl)))
     (arguments
      '(#:phases (alist-cons-before
-                 'configure 'patch-configure
+                 'build 'patch-scripts
                  (lambda _
-                   (substitute* "configure"
-                     (("/usr/bin/file") (which "file"))))
+                   (substitute*
+                       '("afm/make_fonts_map.sh"
+                         "tests/defs"
+                         "tests/backup.tst"
+                         "tests/styles.tst")
+                     (("/bin/rm") (which "rm"))))
                  (alist-cons-before
-                  'build 'patch-scripts
-                  (lambda _
-                    (substitute*
-                        '("afm/make_fonts_map.sh"
-                          "tests/defs"
-                          "tests/backup.tst"
-                          "tests/styles.tst")
-                      (("/bin/rm") (which "rm"))))
-                  (alist-cons-before
-                   'check 'patch-test-files
-                   ;; Alternatively, we could unpatch the shebangs in tstfiles
-                   (lambda* (#:key inputs #:allow-other-keys)
-                     (let ((perl (assoc-ref inputs "perl")))
-                       (substitute* '("tests/ps-ref/includeres.ps"
-                                      "tests/gps-ref/includeres.ps")
-                         (("/usr/local/bin/perl")
-                          (string-append perl "/bin/perl"))))
-                     ;; Some of the reference postscript contain a 'version 3'
-                     ;; string that in inconsistent with the source text in the
-                     ;; tstfiles directory.  Erroneous search-and-replace?
-                     (substitute* '("tests/ps-ref/InsertBlock.ps"
-                                    "tests/gps-ref/InsertBlock.ps"
-                                    "tests/ps-ref/bookie.ps"
-                                    "tests/gps-ref/bookie.ps")
-                       (("version 3") "version 2"))
-                     (substitute* '("tests/ps-ref/psmandup.ps"
-                                    "tests/gps-ref/psmandup.ps")
-                       (("#! */bin/sh") (string-append
-                                         "#!" (which "sh")))))
-                   %standard-phases)))))
+                  'check 'patch-test-files
+                  ;; Alternatively, we could unpatch the shebangs in tstfiles
+                  (lambda* (#:key inputs #:allow-other-keys)
+                    (let ((perl (assoc-ref inputs "perl")))
+                      (substitute* '("tests/ps-ref/includeres.ps"
+                                     "tests/gps-ref/includeres.ps")
+                        (("/usr/local/bin/perl")
+                         (string-append perl "/bin/perl"))))
+                    ;; Some of the reference postscript contain a 'version 3'
+                    ;; string that in inconsistent with the source text in the
+                    ;; tstfiles directory.  Erroneous search-and-replace?
+                    (substitute* '("tests/ps-ref/InsertBlock.ps"
+                                   "tests/gps-ref/InsertBlock.ps"
+                                   "tests/ps-ref/bookie.ps"
+                                   "tests/gps-ref/bookie.ps")
+                      (("version 3") "version 2"))
+                    (substitute* '("tests/ps-ref/psmandup.ps"
+                                   "tests/gps-ref/psmandup.ps")
+                      (("#! */bin/sh") (string-append
+                                        "#!" (which "sh")))))
+                  %standard-phases))))
     (home-page "http://www.gnu.org/software/a2ps")
     (synopsis "Any file to PostScript, including pretty-printing")
     (description
@@ -115,16 +108,9 @@ special cases, such as pretty-printing \"--help\" output.")
        (base32
         "13rkc0fga10xyf56yy9dnq95zndnfadkhxflnp24skszj21y8jqh"))))
     (build-system gnu-build-system)
-    (native-inputs `(("file" ,file)))
     (arguments
      ;; Must define DIFF_CMD for tests to pass
-     '(#:configure-flags '("CPPFLAGS=-DDIFF_CMD=\\\"diff\\\"")
-       #:phases (alist-cons-before
-                 'configure 'patch-configure
-                 (lambda _
-                   (substitute* "configure"
-                     (("/usr/bin/file") (which "file"))))
-                 %standard-phases)))
+     '(#:configure-flags '("CPPFLAGS=-DDIFF_CMD=\\\"diff\\\"")))
     (home-page "http://www.gnu.org/software/trueprint")
     (synopsis "Pretty-print C sources and other plain text to PostScript")
     (description
@@ -178,34 +164,28 @@ different programming languages.")
      `(("boost" ,boost)))
     (native-inputs
      `(("bison" ,bison)
-       ("flex" ,flex)
-       ("file" ,file)))
+       ("flex" ,flex)))
     (arguments
      `(#:configure-flags
        (list (string-append "--with-boost="
                             (assoc-ref %build-inputs "boost")))
        #:parallel-tests? #f             ;There appear to be race conditions
        #:phases (alist-cons-before
-                 'configure 'patch-configure
+                 'check 'patch-test-files
                  (lambda _
-                   (substitute* "configure"
-                     (("/usr/bin/file") (which "file"))))
-                 (alist-cons-before
-                  'check 'patch-test-files
-                  (lambda _
-                    ;; Unpatch shebangs in test input so that source-highlight
-                    ;; is still able to infer input language
-                    (substitute* '("tests/test.sh"
-                                   "tests/test2.sh"
-                                   "tests/test.tcl")
-                      (((string-append "#! *" (which "sh"))) "#!/bin/sh"))
-                    ;; Initial patching unrecoverably removes whitespace, so
-                    ;; remove it also in the comparison output.
-                    (substitute* '("tests/test.sh.html"
-                                   "tests/test2.sh.html"
-                                   "tests/test.tcl.html")
-                      (("#! */bin/sh") "#!/bin/sh")))
-                  %standard-phases))))
+                   ;; Unpatch shebangs in test input so that source-highlight
+                   ;; is still able to infer input language
+                   (substitute* '("tests/test.sh"
+                                  "tests/test2.sh"
+                                  "tests/test.tcl")
+                     (((string-append "#! *" (which "sh"))) "#!/bin/sh"))
+                   ;; Initial patching unrecoverably removes whitespace, so
+                   ;; remove it also in the comparison output.
+                   (substitute* '("tests/test.sh.html"
+                                  "tests/test2.sh.html"
+                                  "tests/test.tcl.html")
+                     (("#! */bin/sh") "#!/bin/sh")))
+                 %standard-phases)))
     (home-page "http://www.gnu.org/software/src-highlite")
     (synopsis "Produce a document with syntax highlighting from a source file")
     (description
diff --git a/guix/build/gnu-build-system.scm b/guix/build/gnu-build-system.scm
index 8636931ed9..17fa7afd8d 100644
--- a/guix/build/gnu-build-system.scm
+++ b/guix/build/gnu-build-system.scm
@@ -106,6 +106,35 @@ working directory."
       (and (zero? (system* "tar" "xvf" source))
            (chdir (first-subdirectory ".")))))
 
+;; See <http://bugs.gnu.org/17840>.
+(define* (patch-usr-bin-file #:key native-inputs inputs
+                             (patch-/usr/bin/file? #t)
+                             #:allow-other-keys)
+  "Patch occurrences of /usr/bin/file in configure, if present."
+  (when patch-/usr/bin/file?
+    (let ((file "configure")
+          (file-command (or (and=> (assoc-ref (or native-inputs inputs) "file")
+                                   (cut string-append <> "/bin/file"))
+                            (which "file"))))
+      (cond ((not (file-exists? file))
+             (format (current-error-port)
+                     "patch-usr-bin-file: warning: `~a' not found~%"
+                     file))
+            ((not file-command)
+             (format (current-error-port)
+                     "patch-usr-bin-file: warning: `file' not found in PATH~%"))
+            (else
+             (let ((st (stat file)))
+               (substitute* file
+                 (("/usr/bin/file")
+                  (begin
+                    (format (current-error-port)
+                            "patch-usr-bin-file: ~a: changing `~a' to `~a'~%"
+                            file "/usr/bin/file" file-command)
+                    file-command)))
+               (set-file-time file st))))))
+  #t)
+
 (define* (patch-source-shebangs #:key source #:allow-other-keys)
   "Patch shebangs in all source files; this includes non-executable
 files such as `.in' templates.  Most scripts honor $SHELL and
@@ -353,6 +382,7 @@ makefiles."
   (let-syntax ((phases (syntax-rules ()
                          ((_ p ...) `((p . ,p) ...)))))
     (phases set-paths unpack
+            patch-usr-bin-file
             patch-source-shebangs configure patch-generated-file-shebangs
             build check install
             patch-shebangs strip)))
diff --git a/guix/build/utils.scm b/guix/build/utils.scm
index 2f3dc9cad0..d169053c7b 100644
--- a/guix/build/utils.scm
+++ b/guix/build/utils.scm
@@ -582,14 +582,15 @@ When KEEP-MTIME? is true, the atime/mtime of FILE are kept unchanged."
 
   (let ((st (stat file)))
    (substitute* file
-     (("^ *SHELL[[:blank:]]*=[[:blank:]]*([[:graph:]]*/)([[:graph:]]+)[[:blank:]]*" _ dir shell)
+     (("^ *SHELL[[:blank:]]*=[[:blank:]]*([[:graph:]]*/)([[:graph:]]+)(.*)$"
+       _ dir shell args)
       (let* ((old (string-append dir shell))
              (new (or (find-shell shell) old)))
         (unless (string=? new old)
           (format (current-error-port)
                   "patch-makefile-SHELL: ~a: changing `SHELL' from `~a' to `~a'~%"
                   file old new))
-        (string-append "SHELL = " new "\n"))))
+        (string-append "SHELL = " new args))))
 
    (when keep-mtime?
      (set-file-time file st))))
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-01-22 20:47:58 +0000