[PATCH]: gnu: bowtie: only support x86_64-linux
Since bowtie's Makefile explicitly checks that the system it is built on is x86_64 building on MIPS and i686 should be disabled. (See bug#19708 for discussion.) This is what the attached patch does. ~~ Ricardo From 9789efe14b8cf00ebf6b39a63146483fbe220535 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus ricardo.wur...@mdc-berlin.de Date: Thu, 29 Jan 2015 10:35:52 +0100 Subject: [PATCH] gnu: bowtie: only x86_64 is supported. * gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6c337..3ea82ba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -133,6 +133,7 @@ aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.) +(supported-systems '(x86_64-linux (license license:gpl3+))) (define-public samtools -- 1.9.3
GNU Guix 0.8.1 released
We are pleased to announce the release of GNU Guix version 0.8.1, representing 804 commits by 21 people over 2.5 months. • About GNU Guix is a functional package manager for the GNU system. The Guix System Distribution is an advanced distribution of the GNU system. In addition to standard package management features, Guix supports transactional upgrades and roll-backs, unprivileged package management, per-user profiles, and garbage collection. It also offers a declarative approach to operating system configuration management. Guix uses low-level mechanisms from the Nix package manager, except that packages are defined as native Guile modules, using extensions to the Scheme language. The operating system uses the Linux-Libre kernel and the GNU dmd init system. At this stage it can be used on an i686 or x86_64 machine. It is also possible to use Guix on top of an already installed GNU/Linux system, including on mips64el and armv7. http://www.gnu.org/software/guix/ • Download Here are the compressed sources and a GPG detached signature[*]: ftp://alpha.gnu.org/gnu/guix/guix-0.8.1.tar.gz ftp://alpha.gnu.org/gnu/guix/guix-0.8.1.tar.gz.sig Here are the bootable USB installation images and their signatures[*]: ftp://alpha.gnu.org/gnu/guix/gsd-usb-install-0.8.1.i686-linux.xz ftp://alpha.gnu.org/gnu/guix/gsd-usb-install-0.8.1.i686-linux.xz.sig ftp://alpha.gnu.org/gnu/guix/gsd-usb-install-0.8.1.x86_64-linux.xz ftp://alpha.gnu.org/gnu/guix/gsd-usb-install-0.8.1.x86_64-linux.xz.sig Use a mirror for higher download bandwidth: http://www.gnu.org/order/ftp.html Here are the SHA1 checksums: 8c9466f3e7b45e0879c0ff105a97f31bd0d16570 guix-0.8.1.tar.gz 5bfc2c9f83b5f5caa37ec04624bc40993955506a gsd-usb-install-0.8.1.i686-linux.xz 5243a1abd90722d3e217226b2f6204396fe8e84f gsd-usb-install-0.8.1.x86_64-linux.xz [*] Use a .sig file to verify that the corresponding file (without the .sig suffix) is intact. First, be sure to download both the .sig file and the corresponding tarball. Then, run a command like this: gpg --verify guix-0.8.1.tar.gz.sig If that command fails because you don't have the required public key, then run this command to import it: gpg --keyserver keys.gnupg.net --recv-keys 3D9AEBB5 and rerun the 'gpg --verify' command. This release was bootstrapped with the following tools: Autoconf 2.69 Automake 1.15 Makeinfo 5.2 To install the Guix System Distribution, please see “System Installation” in the manual. • Changes since version 0.8 (excerpt from the NEWS file) ** Package management *** New ‘--share’ and ‘--expose’ options for ‘guix system vm’ See “Invoking guix system” in the manual. *** Emacs mode now automatically loads newly installed Emacs packages See “Emacs Initial Setup” in the manual. *** ‘guix-daemon’ now defaults to ‘--cores=0 --jobs=1’ In other words, at any given time, only one derivation is being built or substituted, and it can use as many cores as available. Before, there could be N derivations using N cores, which was obviously not desirable. *** Command-line tools support the ‘GUIX_BUILD_OPTIONS’ environment variable See “Invoking guix build” in the manual. *** ‘guix environment’ is faster *** New ‘--recursive’ option for ‘guix archive’ See “Invoking guix archive” in the manual. *** Missing patches required by a package definition are gracefully reported *** ‘guix lint’ supports additional checkers The new checkers are ‘gnu-description’, ‘home-page’, and ‘source’. See “Invoking guix lint” in the manual. *** New CPAN importer for ‘guix import’ See “Invoking guix import” in the manual. ** Distribution *** USB installation image has more tools Tools added since 0.8: wpa_supplicant, cryptsetup, and iw. *** Linux kernel module dependencies are automatically handled Before that, all the modules needed in the initrd would need to be explicitly listed, including their dependencies, and in topological order. *** Font packages now all have a name starting with ‘font-’ See “Fonts” in the manual. *** Shell startup files have been cleaned up /etc/profile contains only environment variable definitions, which may also be used when running a different shell. The skeletons for user’s ‘.bash_profile’ and ‘.bashrc’ files behave as documented in the Bash manual. Zsh is supported. *** The ‘root’ account gets a copy of the account skeleton files Before that, the skeleton files would only be copied to non-root accounts. *** The name service cache daemon (nscd) is configurable By default it aggressively caches host and service lookups. See “Base Services” in the manual. *** Available locale definitions are now declared in ‘operating-system’ Before, the ‘glibc’ package would contain all the existing locales, as well as the ‘locale-archive’ file, amounting to 110 MiB.
Re: [PATCH]: Add IcedTea 6
Ludovic Courtès writes: I rewrote this to instead check the generated test logs in test/ for lines starting with Error: or FAILED:. To disable tests I wrapped it in an (or #t ...) as the argument #:tests? #f does not disable a custom check phase. 'check (lambda _ ;; The make check-* targets always return zero, so we need to ;; check for errors in the associated log files to determine ;; whether any tests have failed. (use-modules (ice-9 rdelim)) (let* ((error-pattern (make-regexp ^(Error|FAILED):.*)) (checker (lambda (port) (let loop ((_ #t)) You can make it (let loop () ... (loop)). Ah, right. Fixed. One last thing: perhaps we can directly remove mips64el-linux from ‘supported-platforms’? Is it known to not build on mips64el? OK to push. I pushed without disabling any platform yet. Based on the build results I will update the package. Thanks, Ludo’. Cheers, Ricardo
Re: [PATCH]: gnu: bowtie: only support x86_64-linux
Ricardo Wurmus writes: Since bowtie's Makefile explicitly checks that the system it is built on is x86_64 building on MIPS and i686 should be disabled. (See bug#19708 for discussion.) This is what the attached patch does. Please disregard the above patch and consider the attached one instead, which also patches the Makefile (with an upstream patch for the next release) to fix the build errors on x86_64. ~~ Ricardo From cdabe548b67185e0c652ebacc90f95cfeffc5888 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus ricardo.wur...@mdc-berlin.de Date: Thu, 29 Jan 2015 10:35:52 +0100 Subject: [PATCH] gnu: bowtie: fix build errors * gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and add Makefile patch. * gnu/packages/patches/bowtie-fix-makefile.patch: New file. * gnu-system.am (MODULES): Add it. --- gnu-system.am | 1 + gnu/packages/bioinformatics.scm| 6 +++-- gnu/packages/patches/bowtie-fix-makefile.patch | 31 ++ 3 files changed, 36 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/bowtie-fix-makefile.patch diff --git a/gnu-system.am b/gnu-system.am index 6c2d66b..1211855 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -346,6 +346,7 @@ dist_patch_DATA = \ gnu/packages/patches/automake-skip-amhello-tests.patch \ gnu/packages/patches/avahi-localstatedir.patch \ gnu/packages/patches/avrdude-fix-libusb.patch \ + gnu/packages/patches/bowtie-fix-makefile.patch \ gnu/packages/patches/bigloo-gc-shebangs.patch \ gnu/packages/patches/binutils-ld-new-dtags.patch \ gnu/packages/patches/binutils-loongson-workaround.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6c337..620c809 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014 Ricardo Wurmus rek...@elephly.net +;;; Copyright © 2014, 2015 Ricardo Wurmus rek...@elephly.net ;;; ;;; This file is part of GNU Guix. ;;; @@ -95,7 +95,8 @@ BED, GFF/GTF, VCF.) ((^CPP = .*$) CPP = g++) ;; replace BUILD_HOST and BUILD_TIME for deterministic build ((-DBUILD_HOST=.*) -DBUILD_HOST=guix) - ((-DBUILD_TIME=.*) -DBUILD_TIME=0) + ((-DBUILD_TIME=.*) -DBUILD_TIME=0))) + (patches (list (search-patch bowtie-fix-makefile.patch) (build-system gnu-build-system) (inputs `((perl ,perl) (perl-clone ,perl-clone) @@ -133,6 +134,7 @@ aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.) +(supported-systems '(x86_64-linux)) (license license:gpl3+))) (define-public samtools diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch b/gnu/packages/patches/bowtie-fix-makefile.patch new file mode 100644 index 000..5ac6573 --- /dev/null +++ b/gnu/packages/patches/bowtie-fix-makefile.patch @@ -0,0 +1,31 @@ +From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001 +From: Valentin Antonescu valen...@jhu.edu +Date: Tue, 2 Dec 2014 11:19:13 -0500 +Subject: [PATCH] Make sure the Mavericks test happens only under Darwin. + +--- + Makefile | 11 +-- + 1 file changed, 5 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index d74f7c8..a4cdfa7 100644 +--- a/Makefile b/Makefile +@@ -54,12 +54,11 @@ endif + MACOS = 0 + ifneq (,$(findstring Darwin,$(shell uname))) + MACOS = 1 +-endif +- +-ifneq (,$(findstring 13,$(shell uname -r))) +- CPP = clang++ +- CC = clang +- EXTRA_FLAGS += -stdlib=libstdc++ ++ ifneq (,$(findstring 13,$(shell uname -r))) ++ CPP = clang++ ++ CC = clang ++ EXTRA_FLAGS += -stdlib=libstdc++ ++ endif + endif + + POPCNT_CAPABILITY ?= 1 -- 1.9.3
[PATCH 0/4]: Add various audio libraries
Hi Guix, this patch series adds a couple of audio libraries to gnu/packages/audio.scm. Some of them depend on the waf-build-system introduced in an earlier, separate patch set. The following packages are added: - JACK2 (with dbus support) - aubio - liblo - LV2 The latter three packages are dependencies of Ardour. ~~ Ricardo From dbc3bd203e311c75ca7f81a7f115eb2f516dd493 Mon Sep 17 00:00:00 2001 From: rekado rek...@elephly.net Date: Thu, 29 Jan 2015 10:00:56 +0100 Subject: [PATCH 1/4] gnu: Add JACK2. * gnu/packages/audio.scm (jack-2): New variable. --- gnu/packages/audio.scm | 39 ++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index b011606..a861600 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -22,9 +22,16 @@ #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system gnu) + #:use-module (guix build-system waf) #:use-module (gnu packages) #:use-module (gnu packages databases) - #:use-module (gnu packages linux)) + #:use-module (gnu packages glib) ;dbus + #:use-module (gnu packages linux) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pulseaudio) ;libsndfile, libsamplerate + #:use-module (gnu packages readline) + #:use-module (gnu packages xiph) + #:use-module (gnu packages xml)) (define-public jack-1 (package @@ -55,3 +62,33 @@ synchronous execution of all clients, and low latency operation.) ;; Most files are licensed under the GPL. However, the libjack/ tree is ;; licensed under the LGPL in order to allow for proprietary usage. (license '(license:gpl2+ license:lgpl2.1+ + +(define-public jack-2 + (package (inherit jack-1) +(name jack) +(version 1.9.10) +(source (origin + (method url-fetch) + (uri (string-append + https://github.com/jackaudio/jack2/archive/v; + version + .tar.gz)) + (sha256 + (base32 + 03b0iiyk3ng3vh5s8gaqwn565vik7910p56mlbk512bw3dhbdwc8 +(build-system waf-build-system) +(arguments + `(#:tests? #f ; no check target + #:configure-flags '(--dbus + --alsa))) +(inputs + `((alsa-lib ,alsa-lib) + (dbus ,dbus) + (expat ,expat) + (libsamplerate ,libsamplerate) + (opus ,opus) + (readline ,readline))) +(native-inputs + `((pkg-config ,pkg-config))) +;; Most files are under GPLv2+, but some headers are under LGPLv2.1+ +(license '(license:gpl2+ license:lgpl2.1+ -- 2.1.0 From ac7e1b8aa764d33d0a87e6ebb86c4e7498110f86 Mon Sep 17 00:00:00 2001 From: rekado rek...@elephly.net Date: Thu, 29 Jan 2015 10:08:53 +0100 Subject: [PATCH 2/4] gnu: Add aubio. * gnu/packages/audio.scm (aubio): New variable. --- gnu/packages/audio.scm | 41 + 1 file changed, 41 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index a861600..780ca6c 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -24,15 +24,56 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system waf) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages databases) #:use-module (gnu packages glib) ;dbus #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile, libsamplerate + #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages xiph) #:use-module (gnu packages xml)) +(define-public aubio + (package +(name aubio) +(version 0.4.1) +(source (origin + (method url-fetch) + (uri (string-append + http://aubio.org/pub/aubio-; version .tar.bz2)) + (sha256 + (base32 + 15f6nf76y7iyl2kl4ny7ky0zpxfxr8j3902afvd6ydnnkh5dzmr5 +(build-system waf-build-system) +(arguments + `(#:tests? #f ; no check target + #:configure-flags + '(--enable-fftw3f + --enable-jack + --enable-sndfile + --enable-samplerate + ;; enable compilation with avcodec once available + --disable-avcodec) + #:python ,python-2)) +(inputs + `((jack ,jack-1) + (libuuid ,util-linux) + (libsndfile ,libsndfile) + (libsamplerate ,libsamplerate) + (fftwf ,fftwf))) +(native-inputs + `((pkg-config ,pkg-config))) +(home-page http://aubio.org/;) +(synopsis A library for audio labelling) +(description + aubio is a tool designed for the extraction of annotations from audio +signals. Its features include segmenting a sound file before each of its +attacks, performing pitch detection, tapping the beat and producing midi +streams
Re: Guix != GNU GSD == True
Em Thu, 29 Jan 2015 07:30:25 -0500 Richard Stallman r...@gnu.org escreveu: I recognize that the Guix / GSD naming matter is settled, There seems to be a misunderstanding here. The distro made wit Guix is called the Guix System Distro or GuixSD. Please do NOT use the term GSD -- it would cause confusion. http://gnu.org/s/guix says: As of version 0.8.1, the Guix System Distribution (GNU GSD) can be installed on an i686 or x86_64 machine. So the very Guix web page is contributing to further the confusion. I'm not sure about its manual though. -- ,= ,-_-. =. Bruno Félix Rezende Ribeiro (oitofelix) [0x28D618AF] ((_/)o o(\_)) There is no system but GNU; `-'(. .)`-' GNU Linux-libre is one of its official kernels; \_/ All software should be free as in freedom; [GNU DISCLAIMER] I'm a GNU hacker, but my views don't necessarily match those of the GNU project. Hereby I express my own opinion, style and perception, in good faith, aiming the betterment of GNU.
Re: Guix != GNU GSD == True
[[[ To any NSA and FBI agents reading my email: please consider]]] [[[ whether defending the US Constitution against all enemies, ]]] [[[ foreign or domestic, requires you to follow Snowden's example. ]]] GNU GSD (Guix System Distribution) is a GNU-based operating system, Please recall that we are not using the term GSD to refer to the Guix-based distro. Please stop posting messages which presuppose we are using that term. -- Dr Richard Stallman President, Free Software Foundation 51 Franklin St Boston MA 02110 USA www.fsf.org www.gnu.org Skype: No way! That's nonfree (freedom-denying) software. Use Ekiga or an ordinary phone call.
Re: Guix != GNU GSD == True
[[[ To any NSA and FBI agents reading my email: please consider]]] [[[ whether defending the US Constitution against all enemies, ]]] [[[ foreign or domestic, requires you to follow Snowden's example. ]]] I recognize that the Guix / GSD naming matter is settled, There seems to be a misunderstanding here. The distro made wit Guix is called the Guix System Distro or GuixSD. Please do NOT use the term GSD -- it would cause confusion. -- Dr Richard Stallman President, Free Software Foundation 51 Franklin St Boston MA 02110 USA www.fsf.org www.gnu.org Skype: No way! That's nonfree (freedom-denying) software. Use Ekiga or an ordinary phone call.
New Esperanto PO file for 'guix' (version 0.8.1)
Hello, gentle maintainer. This is a message from the Translation Project robot. A revised PO file for textual domain 'guix' has been submitted by the Esperanto team of translators. The file is available at: http://translationproject.org/latest/guix/eo.po (We can arrange things so that in the future such files are automatically e-mailed to you when they arrive. Ask at the address below if you want this.) All other PO files for your package are available in: http://translationproject.org/latest/guix/ Please consider including all of these in your next release, whether official or a pretest. Whenever you have a new distribution with a new version number ready, containing a newer POT file, please send the URL of that distribution tarball to the address below. The tarball may be just a pretest or a snapshot, it does not even have to compile. It is just used by the translators when they need some extra translation context. The following HTML page has been updated: http://translationproject.org/domain/guix.html If any question arises, please contact the translation coordinator. Thank you for all your work, The Translation Project robot, in the name of your translation coordinator. coordina...@translationproject.org
[PATCH] gnu: Add desktop-file-utils.
* gnu/packages/gnome.scm (desktop-file-utils): New variable. --- gnu/packages/gnome.scm | 32 1 file changed, 32 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index d8b9acf..c42092d 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -313,6 +313,38 @@ Specification, the icon naming utility maps the icon names used by the GNOME and KDE desktops to the icon names proposed in the specification.) (license license:lgpl2.1+))) +(define-public desktop-file-utils + (package +(name desktop-file-utils) +(version 0.22) +(source (origin + (method url-fetch) + (uri (string-append http://www.freedesktop.org/software/; name + /releases/ name - version .tar.xz)) + (sha256 + (base32 +1ianvr2a69yjv4rpyv30w7yjsmnsb23crrka5ndqxycj4rkk4dc4 +(build-system gnu-build-system) +(native-inputs + `((pkg-config ,pkg-config))) +(inputs + `((glib ,glib))) +(home-page http://www.freedesktop.org/wiki/Software/desktop-file-utils/;) +(synopsis Utilities for working with desktop entries) +(description + This package contains a few command line utilities for working with +desktop entries: + +desktop-file-validate: validates a desktop file and prints warnings/errors + about desktop entry specification violations. + +desktop-file-install: installs a desktop file to the applications directory, + optionally munging it a bit in transit. + +update-desktop-database: updates the database containing a cache of MIME types + handled by desktop files.) +(license license:gpl2+))) + (define-public gnome-icon-theme (package (name gnome-icon-theme) -- 2.1.2
Mistakes
I made two mistakes when preparing the release: I forgot to include the ARM port in ‘NEWS’ (despite it being one of the most significant changes!), and I inadvertently pushed a dozen of Nix tags that I had locally to git.sv.gnu.org, leading to many messages to guix-commits (I removed them soon after.) Sorry for the mess! Ludo’.
Re: Guix != GNU GSD == True
El jue, 29-01-2015 a las 07:30 -0500, Richard Stallman escribió: [[[ To any NSA and FBI agents reading my email: please consider]]] [[[ whether defending the US Constitution against all enemies, ]]] [[[ foreign or domestic, requires you to follow Snowden's example. ]]] I recognize that the Guix / GSD naming matter is settled, There seems to be a misunderstanding here. The distro made wit Guix is called the Guix System Distro or GuixSD. Please do NOT use the term GSD -- it would cause confusion. Use GuixOS. System Distribution is as ambiguous as Operating System, but the latter is closer to the level of the average Jane (who is commonly familiar with the name when referring to Windows, Mac, and Android). P.S.: I'll pay my taxes later :)
Re: Guix != GNU GSD == True
GNU GSD (Guix System Distribution) is a GNU-based operating system, Please recall that we are not using the term GSD to refer to the Guix-based distro. Please stop posting messages which presuppose we are using that term. People will most probobly continue to use it, it would be better to pick a different name that will not cause _any_ confusion.
[PATCH 0/2] PHP work in progress
This patchset contains a sort-of working PHP package. Unfortunately, the build fails in a way that I have been unable to fix when the '--with-apxs2' configure flag is turned on to build the mod_php Apache httpd module. Here is the build output at the point of failure: /gnu/store/nx4zd42igyb7ghmv4mxv6ncg8wr7ypa1-bash-4.3.33/bin/bash /tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/libtool --silent --preserve-dup-deps --mode=link /tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/meta_ccld -DPHP_ATOM_INC -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/include -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/main -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3 -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/ext/date/lib -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/ext/ereg/regex -I/gnu/store/dng0rvcw4264k0r9fp7618bxsh20bi9v-libxml2-2.9.0/include/libxml2 -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/ext/sqlite3/libsqlite -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/TSRM -I/tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/Zend -D_REENTRANT -I/usr/include -g -O2 -fvisibility=hidden -pthread -DZTS -o ext/opcache/opcache.la -export-dynamic -avoid-version -prefer-pic -module -rpath /tmp/nix-build-php-5.6.3.drv-14/php-5.6.3/modules -avoid-version -module -L/gnu/store/dng0rvcw4264k0r9fp7618bxsh20bi9v-libxml2-2.9.0/lib ext/opcache/ZendAccelerator.lo ext/opcache/zend_accelerator_blacklist.lo ext/opcache/zend_accelerator_debug.lo ext/opcache/zend_accelerator_hash.lo ext/opcache/zend_accelerator_module.lo ext/opcache/zend_persist.lo ext/opcache/zend_persist_calc.lo ext/opcache/zend_shared_alloc.lo ext/opcache/zend_accelerator_util_funcs.lo ext/opcache/shared_alloc_shm.lo ext/opcache/shared_alloc_mmap.lo ext/opcache/shared_alloc_posix.lo ext/opcache/Optimizer/zend_optimizer.lo ld: ext/opcache/.libs/ZendAccelerator.o: relocation R_X86_64_32S against `.text' can not be used when making a shared object; recompile with -fPIC ext/opcache/.libs/ZendAccelerator.o: error adding symbols: Bad value collect2: error: ld returned 1 exit status The first patch contains a simple patch that could be applied right now that fixes the broken 'apxs' program in httpd. The second is the current state of php. Help wanted! Thanks! -- David Thompson Web Developer - Free Software Foundation - http://fsf.org GPG Key: 0FF1D807 Support the FSF: https://fsf.org/donate
[PATCH 1/2] gnu: httpd: Add perl input.
From 31c4cf3f61c15df66bf85197829225b1d6064f2a Mon Sep 17 00:00:00 2001 From: David Thompson dthomps...@worcester.edu Date: Thu, 29 Jan 2015 16:34:04 -0500 Subject: [PATCH 1/2] gnu: httpd: Add perl input. Perl is needed to run bin/apxs. * gnu/packages/web.scm (httpd): Add perl input. --- gnu/packages/web.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 554f2a3..dd40e0e 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -57,7 +57,8 @@ (inputs `((apr ,apr) (apr-util ,apr-util) (openssl ,openssl) - (pcre ,pcre))) + (pcre ,pcre) + (perl ,perl))) (arguments `(#:test-target test #:configure-flags (list --enable-rewrite -- 2.1.4 -- David Thompson Web Developer - Free Software Foundation - http://fsf.org GPG Key: 0FF1D807 Support the FSF: https://fsf.org/donate
[PATCH 2/2] gnu: Add php.
From 320aedada4de414e83c4c4207717d48a6ca1bbbc Mon Sep 17 00:00:00 2001
From: David Thompson dthomps...@worcester.edu
Date: Sun, 16 Nov 2014 13:48:11 -0500
Subject: [PATCH 2/2] gnu: Add php.
* gnu/packages/patches/php-fix-configure.patch: New file.
* gnu/packages/php.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
---
gnu-system.am| 1 +
gnu/packages/patches/php-fix-configure.patch | 68 +
gnu/packages/php.scm | 144 +++
3 files changed, 213 insertions(+)
create mode 100644 gnu/packages/patches/php-fix-configure.patch
create mode 100644 gnu/packages/php.scm
diff --git a/gnu-system.am b/gnu-system.am
index f09b5bd..db70fa9 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -219,6 +219,7 @@ GNU_SYSTEM_MODULES =\
gnu/packages/pem.scm\
gnu/packages/perl.scm\
gnu/packages/photo.scm \
+ gnu/packages/php.scm\
gnu/packages/pkg-config.scm \
gnu/packages/plotutils.scm \
gnu/packages/polkit.scm \
diff --git a/gnu/packages/patches/php-fix-configure.patch b/gnu/packages/patches/php-fix-configure.patch
new file mode 100644
index 000..e25057f
--- /dev/null
+++ b/gnu/packages/patches/php-fix-configure.patch
@@ -0,0 +1,68 @@
+diff -ru php-5.4.14/configure php-5.4.14-new/configure
+--- php-5.4.14/configure 2013-04-10 09:53:26.0 +0200
php-5.4.14-new/configure 2013-04-22 17:13:55.039043622 +0200
+@@ -6513,7 +6513,7 @@
+
+ case $host_alias in
+ *aix*)
+-APXS_LIBEXECDIR=`$APXS -q LIBEXECDIR`
++APXS_LIBEXECDIR=$prefix/modules
+ EXTRA_LDFLAGS=$EXTRA_LDFLAGS -Wl,-brtl -Wl,-bI:$APXS_LIBEXECDIR/httpd.exp
+ PHP_AIX_LDFLAGS=-Wl,-brtl
+ build_type=shared
+@@ -6706,7 +6706,7 @@
+ if test $? != 0; then
+ APACHE_INSTALL=$APXS -i -a -n php5 $SAPI_SHARED # Old apxs does not have -S option
+ else
+-APXS_LIBEXECDIR='$(INSTALL_ROOT)'`$APXS -q LIBEXECDIR`
++APXS_LIBEXECDIR=$prefix/modules
+ if test -z `$APXS -q SYSCONFDIR`; then
+ APACHE_INSTALL=\$(mkinstalldirs) '$APXS_LIBEXECDIR' \
+$APXS -S LIBEXECDIR='$APXS_LIBEXECDIR' \
+@@ -7909,7 +7909,7 @@
+{ (exit 1); exit 1; }; }
+ fi
+
+- APXS_LIBEXECDIR='$(INSTALL_ROOT)'`$APXS -q LIBEXECDIR`
++ APXS_LIBEXECDIR=$prefix/modules
+ if test -z `$APXS -q SYSCONFDIR`; then
+ INSTALL_IT=\$(mkinstalldirs) '$APXS_LIBEXECDIR' \
+ $APXS -S LIBEXECDIR='$APXS_LIBEXECDIR' \
+@@ -8779,7 +8779,7 @@
+{ (exit 1); exit 1; }; }
+ fi
+
+- APXS_LIBEXECDIR='$(INSTALL_ROOT)'`$APXS -q LIBEXECDIR`
++ APXS_LIBEXECDIR=$prefix/modules
+ if test -z `$APXS -q SYSCONFDIR`; then
+ INSTALL_IT=\$(mkinstalldirs) '$APXS_LIBEXECDIR' \
+ $APXS -S LIBEXECDIR='$APXS_LIBEXECDIR' \
+@@ -9634,7 +9634,7 @@
+
+ case $host_alias in
+ *aix*)
+-APXS_LIBEXECDIR=`$APXS -q LIBEXECDIR`
++APXS_LIBEXECDIR=$prefix/modules
+ EXTRA_LDFLAGS=$EXTRA_LDFLAGS -Wl,-brtl -Wl,-bI:$APXS_LIBEXECDIR/httpd.exp
+ PHP_AIX_LDFLAGS=-Wl,-brtl
+ build_type=shared
+@@ -9827,7 +9827,7 @@
+ if test $? != 0; then
+ APACHE_HOOKS_INSTALL=$APXS -i -a -n php5 $SAPI_SHARED # Old apxs does not have -S option
+ else
+-APXS_LIBEXECDIR='$(INSTALL_ROOT)'`$APXS -q LIBEXECDIR`
++APXS_LIBEXECDIR=$prefix/modules
+ if test -z `$APXS -q SYSCONFDIR`; then
+ APACHE_HOOKS_INSTALL=\$(mkinstalldirs) '$APXS_LIBEXECDIR' \
+$APXS -S LIBEXECDIR='$APXS_LIBEXECDIR' \
+@@ -59657,9 +59657,7 @@
+
+
+ if test $PHP_GETTEXT != no; then
+- for i in $PHP_GETTEXT /usr/local /usr; do
+-test -r $i/include/libintl.h GETTEXT_DIR=$i break
+- done
++ GETTEXT_DIR=$PHP_GETTEXT
+
+ if test -z $GETTEXT_DIR; then
+ { { $as_echo $as_me:$LINENO: error: Cannot locate header file libintl.h 5
diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
new file mode 100644
index 000..06dbb86
--- /dev/null
+++ b/gnu/packages/php.scm
@@ -0,0 +1,144 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2014 David Thompson da...@gnu.org
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix. If not, see http://www.gnu.org/licenses/.
+
+(define-module (gnu packages php)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix packages)
+ #:use-module (guix download)
+ #:use-module (guix utils)
+ #:use-module
[PATCH 0/5]: Add even more LV2 libraries
Hi Guix, here's another batch of LV2-related patches. They depend on some of the previous patches[1] and on the waf-build-system[2]. This patch set adds the following libraries, all of which are dependencies of Ardour (and possibly other LV2 hosts): - serd - sord - sratom - lilv - suil ~~ Ricardo [1]: http://lists.gnu.org/archive/html/guix-devel/2015-01/msg00446.html [2]: http://lists.gnu.org/archive/html/guix-devel/2015-01/msg00439.html From dc48b2ca6ec4ee1bbe8c5cba317923610ee9718e Mon Sep 17 00:00:00 2001 From: rekado rek...@elephly.net Date: Thu, 29 Jan 2015 23:08:34 +0100 Subject: [PATCH 1/5] gnu: Add serd. * gnu/packages/audio.scm (serd): New variable. --- gnu/packages/audio.scm | 25 + 1 file changed, 25 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index e513d12..e98b460 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -187,3 +187,28 @@ implementation of the Open Sound Control (OSC) protocol.) core, LV2 is a simple stable interface, accompanied by extensions which add functionality to support the needs of increasingly powerful audio software.) (license license:isc))) + +(define-public serd + (package +(name serd) +(version 0.20.0) +(source (origin + (method url-fetch) + (uri (string-append http://download.drobilla.net/serd-; + version + .tar.bz2)) + (sha256 + (base32 + 1gxbzqsm212wmn8qkdd3lbl6wbv7fwmaf9qh2nxa4yxjbr7mylb4 +(build-system waf-build-system) +(arguments `(#:tests? #f)) ; no check target +(home-page http://drobilla.net/software/serd/;) +(synopsis Library for RDF syntax supporting Turtle and NTriples) +(description + Serd is a lightweight C library for RDF syntax which supports reading +and writing Turtle and NTriples. Serd is not intended to be a swiss-army +knife of RDF syntax, but rather is suited to resource limited or performance +critical applications (e.g. converting many gigabytes of NTriples to Turtle), +or situations where a simple reader/writer with minimal dependencies is +ideal (e.g. in LV2 implementations or embedded applications).) +(license license:isc))) -- 2.1.0 From ab8639959f1485d77e5056b41b41eadbad003605 Mon Sep 17 00:00:00 2001 From: rekado rek...@elephly.net Date: Thu, 29 Jan 2015 23:09:19 +0100 Subject: [PATCH 2/5] gnu: Add sord. * gnu/packages/audio.scm (sord): New variable. --- gnu/packages/audio.scm | 24 1 file changed, 24 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index e98b460..e6cfbdd 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -212,3 +212,27 @@ critical applications (e.g. converting many gigabytes of NTriples to Turtle), or situations where a simple reader/writer with minimal dependencies is ideal (e.g. in LV2 implementations or embedded applications).) (license license:isc))) + +(define-public sord + (package +(name sord) +(version 0.12.2) +(source (origin + (method url-fetch) + (uri (string-append http://download.drobilla.net/sord-; + version + .tar.bz2)) + (sha256 + (base32 + 0rq7vafdv4vsxi6xk9zf5shr59w3kppdhqbj78185rz5gp9kh1dx +(build-system waf-build-system) +(arguments `(#:tests? #f)) ; no check target +(inputs + `((serd ,serd))) +(native-inputs + `((pkg-config ,pkg-config))) +(home-page http://drobilla.net/software/sord/;) +(synopsis C library for storing RDF data in memory) +(description + Sord is a lightweight C library for storing RDF data in memory.) +(license license:isc))) -- 2.1.0 From 2fa73ab2fbbe27dbb9c89a7e525b4b4e4e72d015 Mon Sep 17 00:00:00 2001 From: rekado rek...@elephly.net Date: Thu, 29 Jan 2015 23:10:01 +0100 Subject: [PATCH 3/5] gnu: Add sratom. * gnu/packages/audio.scm (sratom): New variable. --- gnu/packages/audio.scm | 27 +++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index e6cfbdd..744cf84 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -236,3 +236,30 @@ ideal (e.g. in LV2 implementations or embedded applications).) (description Sord is a lightweight C library for storing RDF data in memory.) (license license:isc))) + +(define-public sratom + (package +(name sratom) +(version 0.4.6) +(source (origin + (method url-fetch) + (uri (string-append http://download.drobilla.net/sratom-; + version + .tar.bz2)) + (sha256 + (base32 + 080jjiyxjnj7hf25844hd9rb01grvzz1rk8mxcdnakywmspbxfd4 +(build-system waf-build-system) +(arguments `(#:tests?
Re: Guix != GNU GSD == True
[[[ To any NSA and FBI agents reading my email: please consider]]] [[[ whether defending the US Constitution against all enemies, ]]] [[[ foreign or domestic, requires you to follow Snowden's example. ]]] People will most probobly continue to use it, it would be better to pick a different name that will not cause _any_ confusion. As long as we avoid encouraging the abbreviation GSD, it won't be a big problem. -- Dr Richard Stallman President, Free Software Foundation 51 Franklin St Boston MA 02110 USA www.fsf.org www.gnu.org Skype: No way! That's nonfree (freedom-denying) software. Use Ekiga or an ordinary phone call.
Re: guix environment
Ludovic Courtès l...@gnu.org writes: On closer inspection, I see two issues: (define (packages-transitive-inputs packages) Return a list of the transitive inputs for all PACKAGES. (define (transitive-inputs package) (filter-map (match-lambda ((_ (? package? package)) package) (_ #f)); ! (bag-transitive-inputs (package-bag package (delete-duplicates (append-map transitive-inputs packages))) Here only inputs of the form (foo PKG) are considered; things like (glib ,glib bin) are discarded. (define (for-each-search-path proc inputs derivations pure?) (let ((paths (map derivation-output-path derivations))) ; -- ! [...] Above, ‘derivation-output-path’ considers only the “out” output, ignoring others if they are needed. Here's a patch. WDYT? From 9609806fb78557d74cf5b3fb47802898ef9d1ecf Mon Sep 17 00:00:00 2001 From: David Thompson dthomps...@worcester.edu Date: Thu, 29 Jan 2015 17:53:17 -0500 Subject: [PATCH] guix: environment: Consider all package outputs. * guix/scripts/environment.scm (for-each-search-path): Iterate over all derivation output paths. (packages-transitive-inputs): Process inputs that specify an output, too. --- guix/scripts/environment.scm | 11 +-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm index ffa3a09..bb2ce53 100644 --- a/guix/scripts/environment.scm +++ b/guix/scripts/environment.scm @@ -40,7 +40,12 @@ Use the output paths of DERIVATIONS to build each search path. When PURE? is #t, the existing search path value is ignored. Otherwise, the existing search path value is appended. - (let ((paths (map derivation-output-path derivations))) + (let ((paths (append-map (lambda (drv) + (map (match-lambda + ((_ . output) +(derivation-output-path output))) + (derivation-outputs drv))) + derivations))) (for-each (match-lambda (($ search-path-specification variable directories separator) @@ -177,7 +182,9 @@ packages. Return a list of the transitive inputs for all PACKAGES. (define (transitive-inputs package) (filter-map (match-lambda - ((_ (? package? package)) package) + ((or (_ (? package? package)) + (_ (? package? package) _)) + package) (_ #f)) (bag-transitive-inputs (package-bag package -- 2.1.4 -- David Thompson Web Developer - Free Software Foundation - http://fsf.org GPG Key: 0FF1D807 Support the FSF: https://fsf.org/donate
Re: [PATCH]: Add IcedTea 6
On Thu, Jan 29, 2015 at 10:47:17AM +0100, Ricardo Wurmus wrote: I pushed without disabling any platform yet. Based on the build results I will update the package. It does not build on mips: http://hydra.gnu.org/build/224665 My guess would be that the bootstrap binaries are for i?86 platforms. Andreas
Re: [PATCH]: gnu: bowtie: only support x86_64-linux
Ricardo Wurmus ricardo.wur...@mdc-berlin.de writes: Please disregard the above patch and consider the attached one instead, which also patches the Makefile (with an upstream patch for the next release) to fix the build errors on x86_64. The ChangeLog should be this instead, of course (dist_patch_DATA instead of MODULES): * gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and add Makefile patch. * gnu/packages/patches/bowtie-fix-makefile.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Looks good to me. Okay to push! Thanks! Mark
