gnu: boost: Use modify-phases. * gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
build: '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.
build: 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.
doc: Show bootstrapping at the package level. * doc/images/bootstrap-packages.dot: New file. * doc.am (DOT_FILES): Add it. * doc/guix.texi (Bootstrapping): Show 'guix graph' commands. Includes 'images/bootstrap-packages' and comment it.
gnu: sudo: Add fix for CVE-2015-5602. * gnu/packages/patches/sudo-CVE-2015-5602.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/admin.scm (sudo)[source]: Add patch.
gnu: global: Use modify-phases syntax. * gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
gnu: global: Update to 6.5.2. * gnu/packages/code.scm (global): Update to 6.5.2.
gnu: icedtea-6: Fix directory name in "unpack" phase. * gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-".
gnu: linux-libre: Update to 4.4. * gnu/packages/linux.scm (linux-libre): Update to 4.4. * gnu/packages/linux-libre-i686.conf, gnu/packages/linux-libre-x86_64.conf: Update from <https://jxself.org/git/kernel-configs.git>.
gnu: Add fxtract. * gnu/packages/bioinformatics.scm (fxtract): New variable.
gnu: youtube-dl: Update to 2016.01.09. * gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
gnu: gp2c: Update to 0.0.9pl5. * gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
gnu: texlive: Use modify-phases syntax. * gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax.
gnu: man-pages: Update to 4.04. * gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location.
build: Fix out-of-tree building of documentation. * doc.am (.dot.png, .dot.pdf, .dot.eps): Put the generated files into $(srcdir).
gnu: bedtools: Update to 2.25.0. * gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
gnu: bedtools: Use modify-phases. * gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
gnu: r: Update to 3.2.3. * gnu/packages/statistics.scm (r): Update to 3.2.3.
gnu: icecat: Update to 38.5.2-gnu1. * gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
gnu: ruby-2.1: Update to 2.1.8. * gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.