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Author SHA1 Message Date
Ludovic Courtès
cb85eb5e65 build-system/gnu: Gracefully handle dangling symlinks. 
Fixes <http://bugs.gnu.org/20081>.
Reported by Tomáš Čech <tcech@suse.cz>.

* guix/build/gnu-build-system.scm (patch-source-shebangs): Remove files
  that don't pass 'file-exists?'.
  (patch-generated-file-shebangs): Likewise.
 2015-04-23 18:52:40 +02:00
Ludovic Courtès
cd91504df2 gremlin: Add support for the expansion of $ORIGIN in RUNPATH. 
* guix/build/gremlin.scm (expand-variable, expand-origin): New
  procedures.
  (validate-needed-in-runpath): Map 'expand-origin' to the RUNPATH field
  of DYNINFO.
* tests/gremlin.scm ("expand-origin"): New test.
 2015-04-23 18:52:40 +02:00
Mark H Weaver
a635ed5ccb gnu: Add missing (gnu packages gettext) module import. 
This is a followup to 6162b95d21.

* gnu/packages/base.scm: Import (gnu packages gettext).
 2015-04-22 21:49:46 -04:00
Ludovic Courtès
d485ebba42 gnu: gcc: Do not always disable RUNPATH validation. 
* gnu/packages/gcc.scm (gcc-4.7)[arguments]: Remove explicit
  #:validate-runpath? #f.
* gnu/packages/commencement.scm (gcc-boot0)[arguments]: Remove case for
  #:validate-runpath?.
  (gcc-final)[arguments]: Add literal #:validate-runpath? #f.
* gnu/packages/cross-base.scm (cross-gcc-arguments): Remove case for
  #:validate-runpath?.
 2015-04-23 00:06:37 +02:00
Ludovic Courtès
21e583def3 gnu: gcc: Add a RUNPATH to libstdc++.so so that it finds libgcc_s.so. 
Fixes <http://bugs.gnu.org/20358>.
Reported by 宋文武 <iyzsong@gmail.com>.

* gnu/packages/gcc.scm (gcc-4.7)[arguments]: Add 'substitute*' form for
  "libstdc++-v3/src/Makefile.in".
 2015-04-23 00:06:37 +02:00
Ludovic Courtès
669b8639a2 gnu: commencement: Remove unneeded configure flag for bootstrap gettext. 
* gnu/packages/commencement.scm (gettext-boot0): Remove unneeded
  --disable-threads.
 2015-04-23 00:06:37 +02:00
Eric Bavier
cc8ddcb097 gnu: perl: Fix Module::Pluggable for symlink forests. 
* gnu/packages/patches/perl-module-pluggable-search.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/perl.scm (perl)[source]: Add patch.
 2015-04-22 14:38:14 -05:00
Mark H Weaver
d8d6d096be gnu: tzdata: Update to 2015c. 
* gnu/packages/base.scm (tzdata): Update to 2015c.
 2015-04-21 19:03:25 -04:00
Ludovic Courtès
6162b95d21 gnu: glibc: Add dependency on Gettext, to install the message catalogs. 
This fixes a bug whereby the libc.mo files were not installed, and thus
translations of libc's messages were not available.

* gnu/packages/commencement.scm (gettext-boot0): New variable.
  (glibc-final)[native-inputs]: New field.
* gnu/packages/base.scm (glibc)[native-inputs]: Add GNU-GETTEXT.
 2015-04-21 22:53:09 +02:00
Ludovic Courtès
ef593a103d gnu: libltdl: Remove unneeded patch. 
* gnu/packages/autotools.scm (libltdl)[source]: Remove 'patches'.
 2015-04-21 21:16:24 +02:00
Ludovic Courtès
4a2b74bf4c gnu: ld-wrapper: Ignore the .so argument following '-dynamic-linker'. 
Reported at <http://bugs.gnu.org/20102>.

* gnu/packages/ld-wrapper.in (library-files-linked): Rename 'path+files'
  to 'path+files+args'.  Thread the reverse list of previous arguments.
  Add case for when the previous argument is "-dynamic-linker".
 2015-04-21 21:14:28 +02:00
Ludovic Courtès
4267c637d6 gnu: ld-wrapper: Add debugging info. 
* gnu/packages/ld-wrapper.in (ld-wrapper): Add "libraries linked"
  debugging statement.
 2015-04-21 21:08:44 +02:00
Ludovic Courtès
cbbb11c8a0 gnu: Rename ld-wrapper2 to ld-wrapper. 
* gnu/packages/ld-wrapper2.in: Rename to...
* gnu/packages/ld-wrapper.in: ... this.
* gnu-system.am (MISC_DISTRO_FILES): Remove ld-wrapper2.in.
* gnu/packages/commencement.scm (fixed-ld-wrapper): Remove.
  (gcc-toolchain): Restore pre-77db91ad inputs.
 2015-04-21 21:07:11 +02:00
Ludovic Courtès
44fd6ef137 ui: Add 'symlink' replacement with better error reporting. 
* guix/ui.scm (symlink): New procedure.
 2015-04-20 22:37:20 +02:00
Ludovic Courtès
3392ce5d60 system: Make /gnu/store a read-only bind mount by default. 
* gnu/system/file-systems.scm (%immutable-store): New variable.
  (%base-file-systems): Add it.
* doc/guix.texi (File Systems): Document it.
 2015-04-20 22:21:51 +02:00
Ludovic Courtès
b86fee7848 file-systems: Use a second 'mount' call for read-only bind mounts. 
* gnu/build/file-systems.scm (MS_REMOUNT): New constant.
  (mount-file-system): Add 'flags' local variable.   When FLAGS has
  MS_BIND & MS_RDONLY, call 'mount' with MS_REMOUNT.
* gnu/services/base.scm (file-system-service) <start>: Likewise.
 2015-04-20 22:16:13 +02:00
Ludovic Courtès
38cf2ba084 gnu: Remove all #:select from (gnu packages ...) modules. 
This works around Guile bug <http://bugs.gnu.org/15540>.
Reported by Andreas Enge <andreas@enge.fr>.

* gnu/packages/engineering.scm: Don't #:select from (gnu packages ...).
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/package-management.scm: Likewise.
* gnu/packages/photo.scm: Likewise.
* gnu/packages/pulseaudio.scm: Likewise.
* gnu/packages/moe.scm: Likewise, and #:select from (guix licenses)
  instead.
 2015-04-20 15:50:59 +02:00
Ludovic Courtès
f73286345e gexp: Add printers for <gexp-input> and <gexp-output>. 
* guix/gexp.scm (write-gexp-input, write-gexp-output): New procedures.
  (<gexp-input>, <gexp-output>): Use them as printers.
 2015-04-20 15:41:41 +02:00
Ludovic Courtès
c568191a93 profiles: Create a CA certificate bundle only when it would be non-empty. 
* guix/profiles.scm (ca-certificate-bundle): Create
  $output/etc/ssl/certs if and only if CA-FILES is non-empty.
 2015-04-20 15:41:41 +02:00
Ricardo Wurmus
51c649992e gnu: Add sra-tools. 
* gnu/packages/bioinformatics.scm (sra-tools): New variable.
 2015-04-20 15:29:17 +02:00
Ricardo Wurmus
75dd242480 gnu: Add NCBI VDB. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
 2015-04-20 15:29:17 +02:00
Ricardo Wurmus
2651a5e695 gnu: Add NGS Java bindings. 
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
 2015-04-20 15:29:16 +02:00
Ricardo Wurmus
282c5087b4 gnu: Add NGS SDK. 
* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
 2015-04-20 15:28:58 +02:00
Ricardo Wurmus
85c37e29a4 gnu: Add Biopython. 
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
  variables.
 2015-04-20 15:23:23 +02:00
Eric Bavier
40b084a326 gnu: Adjust latest perl modules to new 'modify-phases' syntax. 
* gnu/packages/compression.scm (perl-compress-raw-zlib)[arguments]:
  Add missing quotes, as needed since commit f8503e2.
* gnu/packages/perl.scm (perl-ipc-run)[arguments]: Likewise.
* gnu/packages/xml.scm (perl-xml-sax)[arguments]: Likewise.
 2015-04-19 21:39:32 -05:00
宋文武
61c21ad319 gnu: Add WebKitGTK+. 
* gnu/packages/webkit.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-04-20 10:34:24 +08:00
Eric Bavier
97b05abe6d gnu: Add JSON-Any. 
* gnu/packages/perl.scm (perl-json-any): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier
47945cf353 import: cpan: Fix license string for Artistic license. 
* guix/import/cpan.scm (string->license): Remove extraneous "_0"
  suffix for Artistics licenses.
 2015-04-19 19:48:52 -05:00
Eric Bavier
ae6904dc0b gnu: nix: Propagate perl inputs. 
* gnu/packages/package-management.scm (nix)[inputs]: Move
  perl-www-curl, perl-dbi, perl-dbd-sqlite to...
  [propagated-inputs]: ...this new field
 2015-04-19 19:48:52 -05:00
Eric Bavier
8ac84f230c gnu: Add Sys-Hostname-Long. 
* gnu/packages/perl.scm (perl-sys-hostname-long): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier
10ef803e7d gnu: Add Text-Table. 
* gnu/packages/perl.scm (perl-text-table): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier
7ae9557181 gnu: Add Text-Aligner. 
* gnu/packages/perl.scm (perl-text-aligner): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier
f21671f469 gnu: Add Set-Scalar. 
* gnu/packages/perl.scm (perl-set-scalar): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier
b4dcb026d6 gnu: Add SQL-SplitStatement. 
* gnu/packages/databases.scm (perl-sql-splitstatement): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier
718c89c1a1 gnu: Add SQL-Tokenizer. 
* gnu/packages/databases.scm (perl-sql-tokenizer): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier
8ce2312875 gnu: Add Perl Readonly. 
* gnu/packages/perl.scm (perl-readonly): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
38e62c81ee gnu: Add Perl Net-Amazon-S3. 
* gnu/packages/patches/perl-net-amazon-s3-moose-warning.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/web.scm (perl-net-amazon-s3): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
3dd6bee1f2 gnu: Add XML-LibXML. 
* gnu/packages/xml.scm (perl-xml-libxml): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
18b8bbb304 gnu: Add XML-SAX; 
* gnu/packages/xml.scm (perl-xml-sax): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
1ed6d5bc86 gnu: Add XML-SAX-Base. 
* gnu/packages/xml.scm (perl-xml-sax-base): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
b715dbac7b gnu: Add XML-NamespaceSupport. 
* gnu/packages/xml.scm (perl-xml-namespacesupport): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
0955342bf7 gnu: Add Term-ProgressBar-Simple. 
* gnu/packages/perl.scm (perl-term-progressbar-simple): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
0d54bd259c gnu: Add Term-ProgressBar-Quiet. 
* gnu/packages/perl.scm (perl-term-progressbar-quiet): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
4dbac597eb gnu: Add Test-MockObject. 
* gnu/packages/perl.scm (perl-test-mockobject): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
7332618df3 gnu: Add UNIVERSAL-isa. 
* gnu/packages/perl.scm (perl-universal-isa): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
f9671ab689 gnu: Add UNIVERSAL-can. 
* gnu/packages/perl.scm (perl-universal-can): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
cc307bda85 gnu: Add Term-ProgressBar. 
* gnu/packages/perl.scm (perl-term-progressbar): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
70fe0008f7 gnu: Add TermReadKey. 
* gnu/packages/perl.scm (perl-term-readkey): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
cd718b8201 gnu: Add Class-MethodMaker. 
* gnu/packages/perl.scm (perl-class-methodmaker): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier
56da2a1abd gnu: Add IO-Interactive. 
* gnu/packages/perl.scm (perl-io-interactive): New variable.
 2015-04-19 19:48:51 -05:00