aboutsummaryrefslogtreecommitdiff
path: root/gnu.scm
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2018-12-04 16:20:59 +0100
committerRicardo Wurmus <rekado@elephly.net>2018-12-04 16:21:50 +0100
commit42c3e00c20dbc9fbdd938ddf6d5d88a92d622b77 (patch)
tree9a92d740f081a0c9804d97b7c24d32862a283b0b /gnu.scm
parent4ebfe99a3fc24d7139bd53fab6e1529f5a6d7184 (diff)
downloadguix-42c3e00c20dbc9fbdd938ddf6d5d88a92d622b77.tar.gz
guix-42c3e00c20dbc9fbdd938ddf6d5d88a92d622b77.zip
gnu: pigx-rnaseq: Update to 0.0.5.
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5. [inputs]: Replace snakemake-4 with snakemake.
Diffstat (limited to 'gnu.scm')
0 files changed, 0 insertions, 0 deletions
d modules. Adjust load path assignments. * gnu/packages/package-management.scm (guix)[propagated-inputs]: Add GUILE-GCRYPT. [arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search path. Ludovic Courtès 2018-06-01build: Check for Guile-SQLite3....* m4/guix.m4 (GUIX_CHECK_GUILE_SQLITE3): New macro. * configure.ac: Use it and define 'HAVE_GUILE_SQLITE3'. * guix/self.scm (specification->package): Add "guile-sqlite3". (compiled-guix)[guile-sqlite3]: New variable. [dependencies]: Add it. Ludovic Courtès 2018-02-26build: Require Guile >= 2.0.13....* README, configure.ac, doc/guix.texi (Requirements): Increase minimum Guile version from 2.0.9 to 2.0.13. * config-daemon.ac: Remove use of 'GUIX_CHECK_UNBUFFERED_CBIP'. * m4/guix.m4 (GUIX_CHECK_UNBUFFERED_CBIP): Remove. * guix/build/download.scm (current-http-proxy): Remove. * guix/build/syscalls.scm (%libc-errno-pointer, errno): Remove. (syscall->procedure): Use #:return-errno unconditionally. * guix/hash.scm (open-sha256-input-port)[unbuffered]: Remove outdated comment. * guix/http-client.scm (when-guile<=2.0.5-or-otherwise-broken): Remove. <top level>: Remove 'when-guile<=2.0.5-or-otherwise-broken' block. * guix/scripts/substitute.scm (fetch): Remove 'guile-version>?' conditional. * tests/hash.scm (supports-unbuffered-cbip?): Remove. <top level>: Remove 'test-skip' call. Ludovic Courtès 2018-01-06build: Detect broken 'equal?' in Guile 2.2.1....Fixes <https://bugs.gnu.org/29903>. Reported by Mathieu Lirzin <mthl@gnu.org>. * m4/guix.m4 (GUIX_ASSERT_SYNTAX_OBJECT_EQUAL): New macro. * configure.ac: Use it. Ludovic Courtès 2017-06-30build: Remove check for broken (srfi srfi-37)....This was for Guile < 2.0.9 and we've been requiring 2.0.9+ for some time already. * configure.ac: Remove 'GUIX_CHECK_SRFI_37' use and 'INSTALL_SRFI_37' conditional. * Makefile.am: Remove code in "if INSTALL_SRFI_37". (EXTRA_DIST): Remove srfi/srfi-37.scm.in. * srfi/srfi-37.scm.in: Remove. * m4/guix.m4 (GUIX_CHECK_SRFI_37): Remove. Ludovic Courtès 2017-02-20gnu: Add bootstrap-binaries for 'aarch64-linux'....These bootstrap-binaries were built against commit 8f8f250bdca917b3ce38aa0902f01b19081859a4. * gnu/packages/bootstrap/aarch64-linux/bash, gnu/packages/bootstrap/aarch64-linux/mkdir, gnu/packages/bootstrap/aarch64-linux/xz, gnu/packages/bootstrap/aarch64-linux/tar: New files. * gnu/local.mk (bootstrap_aarch64_linuxdir) (dist_bootstrap_aarch64_linux_DATA) (nodist_bootstrap_aarch64_linux_DATA): New variables. (DISTCLEANFILES): Add $(nodist_bootstrap_aarch64_linux_DATA). (gnu/packages/bootstrap/aarch64-linux/guile-2.0.14.tar.xz): New target. * build-aux/download.scm (filename->uri): Add aarch64-linux entry. * gnu/packages/bootstrap.scm (raw-build): Use guile-2.0.14.tar.xz on aarch64-linux. (glibc-dynamic-linker, %bootstrap-coreutils&co, %boostrap-binutils) (%bootstrap-glibc, %bootstrap-gcc): Add aarch64-linux cases. * m4/guix.m4 (GUIX_SYSTEM_TYPE): Add aarch64 case. (GUIX_ASSERT_SUPPORTED_SYSTEM): Add aarch64-linux to supported list. * doc/guix.texi (GNU Distribution): Add aarch64-linux to the list of supported systems. * tests/packages.scm (package-search-derivation, snippet): Add aarch64 case. Efraim Flashner 2016-11-25offload: Use Guile-SSH instead of GNU lsh....* guix/scripts/offload.scm (<build-machine>)[ssh-options]: Remove. [host-key, host-key-type]: New fields. (%lsh-command, %lshg-command, user-lsh-private-key): Remove. (user-openssh-private-key, private-key-from-file*): New procedures. (host-key->type+key, open-ssh-session): New procedures. (remote-pipe): Remove 'mode' parameter. Rewrite in terms of 'open-ssh-session' etc. Update users. (send-files)[missing-files]: Rewrite using the bidirectional channel port. Remove call to 'call-with-compressed-output-port'. (retrieve-files): Remove call to 'call-with-decompressed-port'. (machine-load): Remove exit status logic. * doc/guix.texi (Requirements): Mention Guile-SSH. (Daemon Offload Setup): Document 'host-key' and 'private-key'. Show the default value on each @item line. * m4/guix.m4 (GUIX_CHECK_GUILE_SSH): New macro. * config-daemon.ac: Use 'GUIX_CHECK_GUILE_SSH'. Set 'HAVE_DAEMON_OFFLOAD_HOOK' as a function of that. Ludovic Courtès 2016-08-10build: Correctly determine the system type for GNU/Hurd systems....* m4/guix.m4 (GUIX_SYSTEM_TYPE): Add case for gnu. Manolis Ragkousis 2016-07-20Merge branch 'master' into core-updatesLudovic Courtès 2016-07-19Add (guix zlib)....* guix/zlib.scm, tests/zlib.scm: New files. * Makefile.am (MODULES): Add guix/zlib.scm. (SCM_TESTS): Add tests/zlib.scm. * m4/guix.m4 (GUIX_LIBGCRYPT_LIBDIR): New macro. * configure.ac (LIBGCRYPT_LIBDIR): Use it. Define and substitute 'LIBZ'. * guix/config.scm.in (%libz): New variable. Ludovic Courtès 2016-06-23build: Remove unneeded conditionals for (guix build syscalls)....* m4/guix.m4: Remove 'GUIX_CHECK_LIBC_MOUNT'. * configure.ac: Remove 'BUILD_SYSCALLS_MODULE'. * Makefile.am (MODULES): Add 'guix/build/syscalls.scm'. (EXTRA_DIST): Remove conditional on BUILD_SYSCALLS_MODULE. Manolis Ragkousis 2016-03-19build: Protect against misconfiguration of localstatedir....Suggested by Jookia <166291@gmail.com>. * m4/guix.m4 (GUIX_CURRENT_LOCALSTATEDIR, GUIX_CHECK_LOCALSTATEDIR): New macros. * config-daemon.ac: Use 'GUIX_CHECK_LOCALSTATEDIR'. * Makefile.am (DISTCHECK_CONFIGURE_FLAGS): Add --localstatedir. * doc/guix.texi (Requirements): Mention --localstatedir. (The Store): Mention LOCALSTATEDIR as such. Ludovic Courtès 2016-01-13build: Use 127 as the Linux hash-bang limit....Reported by taylanbayirli@gmail.com (Taylan Ulrich Bayırlı/Kammer). * m4/guix.m4 (LINUX_HASH_BANG_LIMIT): Set to 127. Ludovic Courtès 2016-01-12build: 'make check' errors out if file name limits would be hit....* Makefile.am (SCM_TESTS, SH_TESTS, TESTS, AM_TESTS_ENVIRONMENT) (SCM_LOG_COMPILER, SH_LOG_COMPILER, AM_SCM_LOG_FLAGS) (AM_SH_LOG_FLAGS): Move within 'if CAN_RUN_TESTS'. (check-local) [!CAN_RUN_TESTS]: New target. * daemon.am (AM_TESTS_ENVIRONMENT, TESTS): Ditto. * m4/guix.m4 (GUIX_CHECK_FILE_NAME_LIMITS): Add parameter and set it. Ludovic Courtès 2016-01-12build: Warn against long hash bang lines for tests....* m4/guix.m4 (GUIX_TEST_HASH_BANG_LENGTH): New macro. (GUIX_CHECK_FILE_NAME_LIMITS): Use it. Warn against long hash bang lines in tests. Ludovic Courtès 2015-12-01build: Fix detection of ARM systems....Reported by Andreas Enge <andreas@enge.fr>. This fixes a regression introduced in 968ae903. * m4/guix.m4 (GUIX_SYSTEM_TYPE): Add extra square braquets around armv[7-9] pattern. Ludovic Courtès 2015-11-25build: Reject ARMv6 systems....Fixes <http://bugs.gnu.org/21987>. Reported by Martin Vahi <martin.vahi@softf1.com>. * m4/guix.m4 (GUIX_SYSTEM_TYPE): Restrict ARM systems to arm|armv[7-9]. Ludovic Courtès 2015-10-09build: Fix libgcrypt detection on FHS systems....Reported by Christopher Allan Webber <cwebber@dustycloud.org>. * m4/guix.m4 (GUIX_LIBGCRYPT_LIBDIR): Add "grep -e -L" to the pipeline to account for cases where the output of "libgcrypt-config --libs" lacks a -L flag. * configure.ac: When 'GUIX_LIBGCRYPT_LIBDIR' returns the empty string, set LIBGCRYPT_LIBDIR to "no". * config-daemon.ac: Add missing space. Ludovic Courtès 2015-10-06build: Automatically determine libgcrypt's file name....* m4/guix.m4 (GUIX_LIBGCRYPT_LIBDIR): New macro. * configure.ac: Use it when no --with-libgcrypt-* option was passed. * README: Do not recommend --with-libgcrypt-prefix. Co-authored-by: 宋文武 <iyzsong@gmail.com> Ludovic Courtès 2015-08-27build: Do not build (guix build syscalls) if 'mount' is missing from libc....This disables compilation of this module on GNU/Hurd. Reported by Manolis Ragkousis <manolis837@gmail.com>. * m4/guix.m4 (GUIX_CHECK_LIBC_MOUNT): New variable. * configure.ac: Use it. Define 'BUILD_SYSCALLS_MODULE' conditional. * Makefile.am (MODULES, EXTRA_DIST): Make 'guix/build/syscalls.scm' conditional on BUILD_SYSCALLS_MODULE. Ludovic Courtès 2015-05-19build: Make sure $CXX supports C++11....* m4/guix.m4 (GUIX_CHECK_CXX11, GUIX_ASSERT_CXX11): New macros. * config-daemon.ac: Use 'AC_LANG([C++])' and 'GUIX_ASSERT_CXX11'.C * doc/guix.texi (Requirements): Mention C++11 support. Ludovic Courtès 2015-02-24build: Reject or warn against file name length limit overruns....* m4/guix.m4 (GUIX_TEST_ROOT_DIRECTORY, LINUX_HASH_BANG_LIMIT, SOCKET_FILE_NAME_LIMIT, GUIX_SOCKET_FILE_NAME_LENGTH, GUIX_TEST_SOCKET_FILE_NAME_LENGTH, GUIX_HASH_BANG_LENGTH, GUIX_CHECK_FILE_NAME_LIMITS): New macros. * configure.ac: Use 'GUIX_CHECK_FILE_NAME_LIMITS'. * config-daemon.ac: Use 'GUIX_TEST_ROOT_DIRECTORY'. * test-env.in: Check socket name length and emit warning if it exceeds 107. Ludovic Courtès