zimoun [Wed, 1 Dec 2021 15:53:53 +0000 (16:53 +0100)]
gnu: julia-blockarrays: Fix tests on i686-linux.
* gnu/packages/julia-xyz.scm (julia-blockarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
zimoun [Wed, 1 Dec 2021 15:53:52 +0000 (16:53 +0100)]
gnu: julia-lazyarrays: Fix tests on i686-linux.
* gnu/packages/julia-xyz.scm (julia-lazyarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
zimoun [Wed, 1 Dec 2021 15:53:51 +0000 (16:53 +0100)]
gnu: julia-configurations: Fix tests on i686-linux.
* gnu/packages/julia-xyz.scm (julia-configurations)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
zimoun [Wed, 1 Dec 2021 15:53:50 +0000 (16:53 +0100)]
gnu: julia-finitedifferences: Fix tests on i686-linux.
* gnu/packages/julia-xyz (julia-finitedifferences)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
zimoun [Wed, 1 Dec 2021 15:53:49 +0000 (16:53 +0100)]
gnu: julia-benchmarktools: Fix tests on i686-linux.
* gnu/packages/julia-xyz.scm (julia-benchmarktools)[arguments]<#:phases>:
Conditionnally disable the failing tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
zimoun [Wed, 1 Dec 2021 15:53:48 +0000 (16:53 +0100)]
gnu: julia-datastructures: Fix tests on i686-linux.
* gnu/packages/julia-xyz.scm (julia-datastructures)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
zimoun [Wed, 1 Dec 2021 15:53:47 +0000 (16:53 +0100)]
gnu: libunwind-julia: Fix build on i686-linux.
* gnu/packages/julia.scm (libunwind)[origin]<patches>: Add patch.
* gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch: New file.
* gnu/local/mk (dist_patch_DATA): Register it.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
Ricardo Wurmus [Sat, 4 Dec 2021 15:00:08 +0000 (16:00 +0100)]
gnu: plink-ng: Enable tests.
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
Ricardo Wurmus [Sat, 4 Dec 2021 14:35:28 +0000 (15:35 +0100)]
gnu: plink-ng: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
Ricardo Wurmus [Sat, 4 Dec 2021 14:31:31 +0000 (15:31 +0100)]
gnu: plink: Remove reference to %build-inputs.
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
Ricardo Wurmus [Sat, 4 Dec 2021 14:31:08 +0000 (15:31 +0100)]
gnu: plink: Remove trailing #T.
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
Ricardo Wurmus [Sat, 4 Dec 2021 14:27:39 +0000 (15:27 +0100)]
gnu: rsem: Update to 1.3.3.
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
Ricardo Wurmus [Sat, 4 Dec 2021 14:26:48 +0000 (15:26 +0100)]
gnu: rsem: Remove trailing #T.
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
Ricardo Wurmus [Sat, 4 Dec 2021 14:26:01 +0000 (15:26 +0100)]
gnu: rsem: Remove references to %build-inputs.
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
Ricardo Wurmus [Sat, 4 Dec 2021 14:25:26 +0000 (15:25 +0100)]
gnu: rsem: Remove trailing #T from snippet.
* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
Ricardo Wurmus [Sat, 4 Dec 2021 14:13:11 +0000 (15:13 +0100)]
gnu: prodigal: Remove reference to %outputs.
* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
Ricardo Wurmus [Sat, 4 Dec 2021 14:11:28 +0000 (15:11 +0100)]
gnu: prank: Bind INPUTS in 'install phase.
* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
Ricardo Wurmus [Sat, 4 Dec 2021 14:11:04 +0000 (15:11 +0100)]
gnu: prank: Remove trailing #T.
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
Ricardo Wurmus [Fri, 3 Dec 2021 23:32:01 +0000 (00:32 +0100)]
gnu: mash: Replace references to %build-inputs.
* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 23:31:20 +0000 (00:31 +0100)]
gnu: mash: Move htslib and capnproto to regular inputs.
* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
Ricardo Wurmus [Fri, 3 Dec 2021 23:30:44 +0000 (00:30 +0100)]
gnu: mash: Simplify snippet.
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
Ricardo Wurmus [Fri, 3 Dec 2021 23:22:27 +0000 (00:22 +0100)]
gnu: mafft: Remove trailing #T.
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
Ricardo Wurmus [Fri, 3 Dec 2021 23:21:27 +0000 (00:21 +0100)]
gnu: mafft: Replace references to %build-inputs and %outputs.
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
Ricardo Wurmus [Fri, 3 Dec 2021 23:19:08 +0000 (00:19 +0100)]
gnu: jellyfish: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 23:16:10 +0000 (00:16 +0100)]
gnu: fastp: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 23:06:43 +0000 (00:06 +0100)]
gnu: java-picard: Replace reference to %build-inputs.
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 23:03:54 +0000 (00:03 +0100)]
gnu: java-htsjdk: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 23:02:20 +0000 (00:02 +0100)]
gnu: fxtract: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 23:00:26 +0000 (00:00 +0100)]
gnu: delly: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 22:57:24 +0000 (23:57 +0100)]
gnu: libbigwig: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 22:56:11 +0000 (23:56 +0100)]
gnu: cd-hit: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 22:54:10 +0000 (23:54 +0100)]
gnu: bowtie1: Replace reference to %outputs.
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 22:52:43 +0000 (23:52 +0100)]
gnu: bowtie: Remove reference to %outputs.
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
Ricardo Wurmus [Fri, 3 Dec 2021 22:51:16 +0000 (23:51 +0100)]
gnu: bless: Remove reference to %build-inputs.
* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp. Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
Ricardo Wurmus [Fri, 3 Dec 2021 22:48:46 +0000 (23:48 +0100)]
gnu: bless: Remove trailing #T from snippet and build phases.
* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
Ricardo Wurmus [Fri, 3 Dec 2021 22:36:18 +0000 (23:36 +0100)]
gnu: bedtools: Remove reference to %outputs.
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
Ricardo Wurmus [Fri, 3 Dec 2021 22:26:48 +0000 (23:26 +0100)]
gnu: qtltools: Replace references to %build-inputs.
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
Ricardo Wurmus [Fri, 3 Dec 2021 12:53:54 +0000 (13:53 +0100)]
gnu: bamutils: Update to 1.0.14.
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
Ricardo Wurmus [Thu, 2 Dec 2021 21:49:14 +0000 (22:49 +0100)]
gnu: bamutils: Remove reference to %outputs.
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
Ricardo Wurmus [Thu, 2 Dec 2021 21:36:37 +0000 (22:36 +0100)]
gnu: bamm: Remove reference to %build-inputs.
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
Ricardo Wurmus [Thu, 2 Dec 2021 19:32:55 +0000 (20:32 +0100)]
gnu: python2-openpyxl: Explicitly build with Python 2.
* gnu/packages/python-xyz.scm (python2-openpyxl)[arguments]: Add value
for #:python field.
Ricardo Wurmus [Thu, 2 Dec 2021 19:28:51 +0000 (20:28 +0100)]
gnu: python-plastid: Update to 0.5.1.
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
Ludovic Courtès [Thu, 2 Dec 2021 12:42:31 +0000 (13:42 +0100)]
gnu: glade: Remove dependency on GJS on non-x86_64.
* gnu/packages/gnome.scm (glade3)[arguments]: Add optional
'skip-gjs-test' phase.
[native-inputs]: Provide GJS only when 'target-x86-64?'.
Ludovic Courtès [Thu, 2 Dec 2021 12:16:13 +0000 (13:16 +0100)]
gnu: Remove librsvg@2.50 from the Xfce dependency graph.
This allows us to build Xfce on non-x86_64 platforms.
* gnu/packages/gstreamer.scm (gst-plugins-good)[inputs]: Use
'librsvg-for-system' instead of 'librsvg'.
* gnu/packages/gtk.scm (guile-rsvg)[inputs]: Likewise.
* gnu/packages/xfce.scm (xfce4-xkb-plugin)[inputs]: Likewise.
Ludovic Courtès [Thu, 2 Dec 2021 12:15:31 +0000 (13:15 +0100)]
gnu: librsvg: Add 'librsvg-for-system' procedure.
* gnu/packages/gnome.scm (librsvg-for-system): New procedure.
Ludovic Courtès [Thu, 2 Dec 2021 10:18:02 +0000 (11:18 +0100)]
gnu: librsvg: Reintroduce version 2.40.
* gnu/packages/gnome.scm (librsvg-2.40): New variable.
Ricardo Wurmus [Thu, 2 Dec 2021 10:26:55 +0000 (11:26 +0100)]
gnu: prinseq: Fix use of SEARCH-INPUT-FILE.
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument
to SEARCH-INPUT-FILE.
Ricardo Wurmus [Thu, 2 Dec 2021 09:52:45 +0000 (10:52 +0100)]
gnu: gnome-shell: Do not wrap in LD_LIBRARY_PATH.
Fixes <https://bugs.gnu.org/37123>.
* gnu/packages/gnome.scm (gnome-shell)[arguments]: Remove LD_LIBRARY_PATH from
wrapper.
Ricardo Wurmus [Thu, 2 Dec 2021 09:30:40 +0000 (10:30 +0100)]
gnu: python2-matplotlib: Disable sanity-check.
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Delete
'sanity-check phase.
Ricardo Wurmus [Thu, 2 Dec 2021 09:29:59 +0000 (10:29 +0100)]
gnu: python2-matplotlib: Remove trailing #T.
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Remove
trailing #T from build phase.
Efraim Flashner [Thu, 2 Dec 2021 09:08:42 +0000 (11:08 +0200)]
Revert "gnu: Change source file-name suffix in rust packages."
This reverts commit
07a80e30a10e2a6ed4760f12711f8a91391398e4.
This commit affects rust crates that are inputs to librsvg, which causes
many packages to be rebuilt.
Efraim Flashner [Thu, 2 Dec 2021 08:37:54 +0000 (10:37 +0200)]
gnu: tor: Limit test suite adjustments to affected architectures.
This is a follow-up to
68d090002a1a5623494006fca3e2c2c97d3ff676.
* gnu/packages/tor.scm (tor)[arguments]: Only add custom
'adjust-test-suite phase on aarch64, powerpc32.
Ricardo Wurmus [Thu, 2 Dec 2021 08:44:27 +0000 (09:44 +0100)]
gnu: python2-numpy: Delete file that depends on deleted test.
This is a follow-up to commit
ec4892c742ff4e2f00d0fc2595843890ef16afa3.
* gnu/packages/python-xyz.scm (python2-numpy)[arguments]: Also delete a second
test file that depends on the previously deleted test file.
Z572 [Wed, 1 Dec 2021 12:41:07 +0000 (20:41 +0800)]
gnu: Change source file-name suffix in rust packages.
* gnu/packages/rust-apps.scm (rust-cbindgen)[source]: Change source
file-name suffix from '.crate' to '.tar.gz'.
* gnu/packages/crates-graphics.scm (rust-ansi-term-0.12): Likewise.
(rust-ansi-term-0.11): Likewise.
(rust-rgb-0.8): Likewise.
* gnu/packages/crates-io.scm (rust-adler32-1): Likewise.
(rust-antidote-1): Likewise.
(rust-atty-0.2): Likewise.
(rust-autocfg-0.1): Likewise.
(rust-backtrace-sys-0.1): Likewise.
(rust-base-x-0.2): Likewise.
(rust-bencher-0.1): Likewise.
(rust-bitflags-1): Likewise.
(rust-blas-sys-0.7): Likewise.
(rust-cargon-0.0): Likewise.
(rust-cblas-sys-0.1): Likewise.
(rust-cc-1): Likewise.
(rust-cfg-if-0.1): Likewise.
(rust-clang-sys-0.26): Likewise.
(rust-clap-2): Likewise.
(rust-clicolors-control-1): Likewise.
(rust-cloudabi-0.1): Likewise.
(rust-cloudabi-0.0): Likewise.
(rust-cmake-0.1): Likewise.
(rust-compiler-builtins-0.1): Likewise.
(rust-constant-time-eq-0.1): Likewise.
(rust-core-foundation-sys-0.6): Likewise.
(rust-data-encoding-2): Likewise.
(rust-defmac-0.2): Likewise.
(rust-defmac-0.1): Likewise.
(rust-dirs-1): Likewise.
(rust-discard-1): Likewise.
(rust-doc-comment-0.3): Likewise.
(rust-dtoa-0.4): Likewise.
(rust-dtoa-0.2): Likewise.
(rust-fallible-iterator-0.2): Likewise.
(rust-filetime-0.2): Likewise.
(rust-findshlibs-0.5): Likewise.
(rust-fixedbitset-0.2): Likewise.
(rust-fixedbitset-0.1): Likewise.
(rust-fnv-1): Likewise.
(rust-foreign-types-shared-0.2): Likewise.
(rust-fs-extra-1): Likewise.
(rust-fuchsia-cprng-0.1): Likewise.
(rust-fuchsia-zircon-0.3): Likewise.
(rust-fuchsia-zircon-sys-0.3): Likewise.
(rust-futures-0.1): Likewise.
(rust-futures-core-preview-0.3): Likewise.
(rust-futures-cpupool-0.1): Likewise.
(rust-futures-io-preview-0.3): Likewise.
(rust-futures-sink-preview-0.3): Likewise.
(rust-getopts-0.2): Likewise.
(rust-glob-0.3): Likewise.
(rust-glob-0.2): Likewise.
(rust-heapsize-0.4): Likewise.
(rust-heapsize-0.3): Likewise.
(rust-heapsize-plugin-0.1): Likewise.
(rust-heck-0.3): Likewise.
(rust-hex-0.3): Likewise.
(rust-hex-0.2): Likewise.
(rust-hostname-0.1): Likewise.
(rust-iovec-0.1): Likewise.
(rust-itoa-0.4): Likewise.
(rust-itoa-0.1): Likewise.
(rust-json-0.11): Likewise.
(rust-kernel32-sys-0.2): Likewise.
(rust-language-tags-0.2): Likewise.
(rust-lazy-static-1): Likewise.
(rust-libloading-0.5): Likewise.
(rust-lock-api-0.1): Likewise.
(rust-log-0.4): Likewise.
(rust-maplit-1): Likewise.
(rust-matches-0.1): Likewise.
(rust-matrixmultiply-0.2): Likewise.
(rust-matrixmultiply-0.1): Likewise.
(rust-md5-0.7): Likewise.
(rust-md5-0.6): Likewise.
(rust-memmap-0.7): Likewise.
(rust-memmap-0.6): Likewise.
(rust-mime-0.3): Likewise.
(rust-miniz-oxide-0.3): Likewise.
(rust-miniz-sys-0.1): Likewise.
(rust-miow-0.3): Likewise.
(rust-miow-0.2): Likewise.
(rust-modifier-0.1): Likewise.
(rust-net2-0.2): Likewise.
(rust-nodrop-0.1): Likewise.
(rust-nodrop-union-0.1): Likewise.
(rust-num-traits-0.1): Likewise.
(rust-numtoa-0.1): Likewise.
(rust-openssl-probe-0.1): Likewise.
(rust-owning-ref-0.4): Likewise.
(rust-parity-wasm-0.40): Likewise.
(rust-peeking-take-while-0.1): Likewise.
(rust-percent-encoding-2): Likewise.
(rust-percent-encoding-1): Likewise.
(rust-permutohedron-0.2): Likewise.
(rust-pico-sys-0.0): Likewise.
(rust-pkg-config-0.3): Likewise.
(rust-plain-0.2): Likewise.
(rust-plugin-0.2): Likewise.
(rust-pocket-resources-0.3): Likewise.
(rust-ppv-lite86-0.2): Likewise.
(rust-proc-macro2-1): Likewise.
(rust-quick-error-2): Likewise.
(rust-quick-error-1): Likewise.
(rust-quote-1): Likewise.
(rust-rand-0.7): Likewise.
(rust-rand-0.6): Likewise.
(rust-rand-0.3): Likewise.
(rust-rand-chacha-0.1): Likewise.
(rust-rand-core-0.4): Likewise.
(rust-rand-core-0.3): Likewise.
(rust-rand-hc-0.2): Likewise.
(rust-rand-hc-0.1): Likewise.
(rust-rand-isaac-0.1): Likewise.
(rust-rand-jitter-0.1): Likewise.
(rust-rand-os-0.1): Likewise.
(rust-rand-pcg-0.3): Likewise.
(rust-rand-pcg-0.2): Likewise.
(rust-rand-pcg-0.1): Likewise.
(rust-rand-xorshift-0.1): Likewise.
(rust-rawpointer-0.2): Likewise.
(rust-rawpointer-0.1): Likewise.
(rust-rdrand-0.4): Likewise.
(rust-redox-syscall-0.1): Likewise.
(rust-redox-termios-0.1): Likewise.
(rust-resolv-conf-0.6): Likewise.
(rust-rustc-demangle-0.1): Likewise.
(rust-rustc-serialize-0.3): Likewise.
(rust-rustc-std-workspace-core-1): Likewise.
(rust-ryu-1): Likewise.
(rust-safemem-0.3): Likewise.
(rust-same-file-1): Likewise.
(rust-schannel-0.1): Likewise.
(rust-scoped-threadpool-0.1): Likewise.
(rust-scoped-tls-1): Likewise.
(rust-scoped-tls-0.1): Likewise.
(rust-scopeguard-1): Likewise.
(rust-scopeguard-0.3): Likewise.
(rust-security-framework-sys-0.3): Likewise.
(rust-semver-parser-0.9): Likewise.
(rust-semver-parser-0.7): Likewise.
(rust-serde-derive-1): Likewise.
(rust-shlex-1): Likewise.
(rust-shlex-0.1): Likewise.
(rust-slab-0.4): Likewise.
(rust-socket2-0.3): Likewise.
(rust-sourcefile-0.1): Likewise.
(rust-spin-0.5): Likewise.
(rust-stacker-0.1): Likewise.
(rust-static-assertions-1): Likewise.
(rust-static-assertions-0.3): Likewise.
(rust-stdweb-internal-runtime-0.1): Likewise.
(rust-stdweb-internal-test-macro-0.1): Likewise.
(rust-streaming-stats-0.2): Likewise.
(rust-strsim-0.9): Likewise.
(rust-strsim-0.8): Likewise.
(rust-synstructure-test-traits-0.1): Likewise.
(rust-tar-0.4): Likewise.
(rust-tempdir-0.3): Likewise.
(rust-tempfile-3): Likewise.
(rust-term-0.4): Likewise.
(rust-term-0.2): Likewise.
(rust-termcolor-1): Likewise.
(rust-termion-1): Likewise.
(rust-termios-0.3): Likewise.
(rust-thread-id-3): Likewise.
(rust-thread-local-1): Likewise.
(rust-thread-local-0.3): Likewise.
(rust-threadpool-1): Likewise.
(rust-time-0.1): Likewise.
(rust-tokio-mock-task-0.1): Likewise.
(rust-toml-0.5): Likewise.
(rust-tracing-core-0.1): Likewise.
(rust-traitobject-0.1): Likewise.
(rust-try-from-0.3): Likewise.
(rust-try-lock-0.2): Likewise.
(rust-typeable-0.1): Likewise.
(rust-typemap-0.3): Likewise.
(rust-typenum-1): Likewise.
(rust-ucd-trie-0.1): Likewise.
(rust-ucd-util-0.1): Likewise.
(rust-unicode-xid-0.2): Likewise.
(rust-unicode-xid-0.1): Likewise.
(rust-unreachable-1): Likewise.
(rust-unsafe-any-0.4): Likewise.
(rust-untrusted-0.7): Likewise.
(rust-vcpkg-0.2): Likewise.
(rust-vec-map-0.8): Likewise.
(rust-version-check-0.9): Likewise.
(rust-version-check-0.1): Likewise.
(rust-void-1): Likewise.
(rust-wasi-0.5): Likewise.
(rust-wasm-bindgen-shared-0.2): Likewise.
(rust-wasm-bindgen-test-macro-0.2): Likewise.
(rust-widestring-0.4): Likewise.
(rust-winapi-0.3): Likewise.
(rust-winapi-0.2): Likewise.
(rust-winapi-build-0.1): Likewise.
(rust-winapi-util-0.1): Likewise.
(rust-wincolor-1): Likewise.
(rust-winutil-0.1): Likewise.
(rust-ws2-32-sys-0.2): Likewise.
(rust-xattr-0.2): Likewise.
(rust-xdg-2): Likewise.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
Ricardo Wurmus [Wed, 1 Dec 2021 23:59:16 +0000 (00:59 +0100)]
gnu: python2-numpy: Do not inherit native-inputs.
* gnu/packages/python-xyz.scm (python2-numpy)[native-inputs]: Do not inherit
from Python 3 variant; use only python2-cython, python2-pytest, and gfortran.
[arguments]: Add phase 'delete-failing-test.
Ludovic Courtès [Wed, 1 Dec 2021 22:11:50 +0000 (23:11 +0100)]
gnu: petsc-{complex,openmpi,complex-openmpi}: Use gexps.
This is a followup to
07ac13a26a0d7c8319afb42c55fc2116ec44668f, which
omitted to switch to gexps in packages that inherit from 'petsc'.
Reported by Mathieu Othacehe <othacehe@gnu.org>.
* gnu/packages/maths.scm (petsc-complex)[arguments]: Use gexps.
(petsc-openmpi)[arguments]: Likewise.
(petsc-complex-openmpi)[arguments]: Likewise.
Ludovic Courtès [Wed, 1 Dec 2021 21:49:33 +0000 (22:49 +0100)]
gnu: scalapack: Update to 2.1.0.
* gnu/packages/maths.scm (scalapack): Update to 2.1.0.
[source]: Remove "scalapack-blacs-mpi-deprecations.patch" and add
"scalapack-gcc-10-compilation.patch".
[arguments]: Add 'skip-faulty-test' phase.
* gnu/packages/patches/scalapack-blacs-mpi-deprecations.patch: Remove.
* gnu/packages/patches/scalapack-gcc-10-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
Mathieu Othacehe [Wed, 1 Dec 2021 19:59:06 +0000 (20:59 +0100)]
installer: parted: Use the swap-space record.
* gnu/installer/parted.scm (user-partitions->configuration): Use the
swap-space record.
Mathieu Othacehe [Wed, 1 Dec 2021 18:20:24 +0000 (19:20 +0100)]
tests: install: Use the swap-space record.
This fixes the following error:
In gnu/services/base.scm:
2228:56 4 (_ #<<uuid> type: dce bv: #vu8(17 17 17 17 34 34 51 51 …>)
In gnu/build/file-systems.scm:
239:13 3 (swap-space->flags-bit-mask #<<uuid> type: dce bv: #vu8…>)
In ice-9/boot-9.scm:
1685:16 2 (raise-exception _ #:continuable? _)
1685:16 1 (raise-exception _ #:continuable? _)
1685:16 0 (raise-exception _ #:continuable? _)
ice-9/boot-9.scm:1685:16: In procedure raise-exception:
In procedure swap-space-priority: Wrong type argument: #<<uuid> type: dce bv: #vu8(17 17 17 17 34 34 51 51 68 68 18 52 86 120 154 188)>
* gnu/tests/install.scm (installation-target-os-for-gui-tests): Use the
swap-space record.
Efraim Flashner [Wed, 1 Dec 2021 08:49:29 +0000 (10:49 +0200)]
gnu: tor: Fix build issue on some architectures.
* gnu/packages/tor.scm (tor)[arguments]: Add phase to remove sandbox
during one of the tests.
Vivien Kraus [Mon, 29 Nov 2021 23:05:18 +0000 (00:05 +0100)]
gnu: gnome-builder: Use libsoup 2.
* gnu/packages/gnome.scm (gnome-builder) [phase 'patch-meson]: Don’t search
for webkit2gtk-4.1.
[inputs]: Replace devhelp with devhelp-with-libsoup2 and
webkit with webkit-with-libsoup2.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Vivien Kraus [Mon, 29 Nov 2021 23:03:07 +0000 (00:03 +0100)]
gnu: devhelp: Add a libsoup 2 variant.
* gnu/packages/gnome.scm (devhelp-with-libsoup2): New variable.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Mathieu Othacehe [Wed, 1 Dec 2021 08:23:51 +0000 (09:23 +0100)]
gnu: Remove duplicated patch.
* gnu/local.mk (dist_patch_DATA): Remove duplicated line.
Mathieu Othacehe [Mon, 29 Nov 2021 14:40:11 +0000 (15:40 +0100)]
gnu: freecad: Fix build.
* gnu/packages/patches/freecad-boost-serialization.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/engineering.scm (freecad) [source]: Use it.
[arguments]{#:configure-flags}: Turn it into a GEXP and adapt it.
Mathieu Othacehe [Mon, 29 Nov 2021 14:37:45 +0000 (15:37 +0100)]
gnu: Remove vtk-8.
* gnu/packages/image-processing.scm (vtk-8): Remove it.
Mathieu Othacehe [Mon, 29 Nov 2021 14:38:59 +0000 (15:38 +0100)]
gnu: freecad: Switch to vtk-9.
Switch to vtk-9 with the relevant patch to be able to get rid of vtk-8.
* gnu/packages/patches/freecad-vtk9.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/engineering.scm (freecad)[source]: Use it.
zimoun [Tue, 30 Nov 2021 11:14:27 +0000 (12:14 +0100)]
gnu: ghc: Fix build on i686-linux.
* gnu/packages/haskell.scm (ghc-8.10)[arguments]<#:phases>: Disable
failing test.
Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
Mathieu Othacehe [Mon, 29 Nov 2021 13:58:39 +0000 (14:58 +0100)]
gnu: agg: Fix build.
* gnu/packages/patches/agg-2.5-gcc8.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/graphics.scm (agg)[source]: Use it.
Vinicius Monego [Mon, 29 Nov 2021 00:04:21 +0000 (00:04 +0000)]
gnu: darktable: Build with OpenEXR 3.
* gnu/packages/photo.scm (darktable)[arguments]<#:phases>: Rename
'set-LDFLAGS-and-CPATH to 'set-LDFLAGS. Don't set CPATH.
[inputs]: Remove ilmbase. Add imath. Replace openexr-2 with openexr.
Signed-off-by: Leo Famulari <leo@famulari.name>
Vinicius Monego [Mon, 29 Nov 2021 00:04:20 +0000 (00:04 +0000)]
gnu: darktable: Build with libsoup 2.
* gnu/packages/photo.scm (darktable)[inputs]: Change libsoup to
libsoup-minimal-2.
Signed-off-by: Leo Famulari <leo@famulari.name>
Ludovic Courtès [Sun, 28 Nov 2021 23:00:38 +0000 (00:00 +0100)]
gnu: slepc: Update to 3.16.1.
* gnu/packages/maths.scm (slepc): Update to 3.16.1.
[native-inputs]: Use PYTHON instead of PYTHON-2. Add WHICH.
[properties]: New field.
Ludovic Courtès [Sun, 28 Nov 2021 22:54:31 +0000 (23:54 +0100)]
gnu: petsc: Update to 3.16.1.
* gnu/packages/maths.scm (petsc): Update to 3.16.1.
[native-inputs]: Use PYTHON instead of PYTHON-2. Add WHICH.
[arguments]: Rewrite using gexps. Pass '--with-openblas-dir'. In
'configure' phase, modify "config/example_template.py".
Ludovic Courtès [Sun, 28 Nov 2021 22:04:51 +0000 (23:04 +0100)]
gnu: python2-requests: Remove dependency on python-charset-normalizer.
The python-charset-normalizer package is Python 3 only.
* gnu/packages/python-web.scm (python-requests)[properties]: New field.
(python2-requests): Rewrite to remove 'python-charset-normalizer' from
'propagated-inputs'.
Ludovic Courtès [Sun, 28 Nov 2021 21:57:10 +0000 (22:57 +0100)]
gnu: python-notify2: Propagate python-dbus.
* gnu/packages/python-xyz.scm (python-notify2)[native-inputs]: Rename to...
[propagated-inputs]: ... this.
Ludovic Courtès [Sun, 28 Nov 2021 21:55:22 +0000 (22:55 +0100)]
gnu: python-dbus: Register 'python2-dbus' as the Python 2 variant.
This allows things like 'python2-notify2' to actually use the Python 2
variant of 'python-dbus'.
* gnu/packages/python-xyz.scm (python-dbus)[properties]: New field.
(python2-dbus)[inputs]: Remove unnecessary 'alist-delete' argument.
Ricardo Wurmus [Sun, 28 Nov 2021 22:30:46 +0000 (23:30 +0100)]
gnu: krfb: Use latest pipewire.
* gnu/packages/kde-systemtools.scm (krfb)[inputs]: Replace pipewire with
pipewire-0.3.
Ricardo Wurmus [Sun, 28 Nov 2021 21:31:46 +0000 (22:31 +0100)]
gnu: pipewire-0.3: Add optional inputs.
* gnu/packages/linux.scm (pipewire-0.3)[inputs]: Add avahi and ldacbt.
Ricardo Wurmus [Sun, 28 Nov 2021 21:31:09 +0000 (22:31 +0100)]
gnu: pipewire-0.3: Update to 0.3.40.
* gnu/packages/linux.scm (pipewire-0.3): Update to 0.3.40.
[arguments]: Disable session managers to avoid missing input.
Ludovic Courtès [Sat, 27 Nov 2021 21:27:09 +0000 (22:27 +0100)]
gnu: rust: Add 'supported-systems' field.
* gnu/packages/rust.scm (rust-1.39)[supported-systems]: New field.
(rust-1.40)[supported-systems]: Remove.
Ludovic Courtès [Sat, 27 Nov 2021 21:29:00 +0000 (22:29 +0100)]
services: polkit: Choose between polkit-mozjs and polkit-duktape.
* gnu/services/dbus.scm (%default-polkit): New variable.
(<polkit-configuration>)[polkit]: Default to it.
Ludovic Courtès [Sat, 27 Nov 2021 21:25:35 +0000 (22:25 +0100)]
gnu: polkit: Rename default variable to 'polkit-mozjs'.
* gnu/packages/polkit.scm (polkit*): Rename to...
(polkit-mozjs): ... this. Adjust users.
Ludovic Courtès [Sat, 27 Nov 2021 21:10:38 +0000 (22:10 +0100)]
gexp: 'file-append' correctly handles bases without an expander.
This fixes this use case:
(file-append (let-system ...) ...)
* guix/gexp.scm (file-append-compiler): When BASE lacks an expander,
delegate to LOWERED.
* tests/gexp.scm ("let-system in file-append"): New test.
Ludovic Courtès [Sat, 27 Nov 2021 17:38:33 +0000 (18:38 +0100)]
services: Document the 'delete' clause of 'modify-services'.
* doc/guix.texi (Service Reference): Mention the 'delete' clause of
'modify-services'.
* gnu/services.scm (modify-services): Likewise in docstring.
Leo Famulari [Sat, 27 Nov 2021 21:14:11 +0000 (16:14 -0500)]
gnu: blanket: Update to 0.5.0.
* gnu/packages/task-management.scm (blanket): Update to 0.5.0.
Pierre Langlois [Sat, 27 Nov 2021 01:18:06 +0000 (01:18 +0000)]
gnu: glibc-for-bootstrap: Build with GCC 7.
Fixes <https://issues.guix.gnu.org/52066>.
* gnu/packages/make-bootstrap.scm (glibc-for-bootstrap)[native-inputs]:
Add gcc-7.
Vinicius Monego [Sat, 27 Nov 2021 13:21:53 +0000 (13:21 +0000)]
gnu: marble-qt: Add optional dependencies.
* gnu/packages/kde.scm (marble-qt)[arguments]<#:configure-flags>: Remove
"-DCMAKE_BUILD_TYPE=Release" and "-DWITH_KF5=FALSE". Add
"-DBUILD_MARBLE_TOOLS=YES" and "-DBUILD_TOUCH=YES".
[native-inputs]: Add extra-cmake-modules.
[inputs]: Sort alphabetically. Add gpsd, kcoreaddons, kcrash, kdoctools,
ki18n, kio, knewstuff, kparts, krunner, kwallet, perl, phonon, protobuf,
qtserialport, qtsvg, shapelib, shared-mime-info, zlib. Remove qtwebkit.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Vinicius Monego [Sat, 27 Nov 2021 13:21:52 +0000 (13:21 +0000)]
gnu: marble-qt: Update to 21.08.3.
* gnu/packages/kde.scm (marble-qt): Update to 21.08.3.
[build-system]: Use qt-build-system.
[arguments]<#:configure-flags>: Pass "-DBUILD_MARBLE_TESTS=FALSE".
[license]: Change to lgpl2.1+.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Vinicius Monego [Sat, 27 Nov 2021 13:21:51 +0000 (13:21 +0000)]
gnu: marble-qt: Move to (gnu packages kde).
* gnu/packages/geo.scm (marble-qt): Move to (gnu packages kde).
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Mathieu Othacehe [Sat, 27 Nov 2021 12:43:02 +0000 (13:43 +0100)]
gnu: libosinfo: Use osinfo-db-next.
* gnu/packages/virtualization.scm (libosinfo)[inputs]: Use osinfo-db-next
instead of osinfo-db.
Mathieu Othacehe [Sat, 27 Nov 2021 12:42:56 +0000 (13:42 +0100)]
gnu: Add osinfo-db-next.
* gnu/packages/virtualization.scm (osinfo-db-next): New variable.
Mathieu Othacehe [Sat, 27 Nov 2021 12:42:12 +0000 (13:42 +0100)]
gnu: gnome-boxes: Add Guix logo support.
* gnu/packages/patches/gnome-boxes-add-guix-logo.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnome.scm (gnome-boxes): Use it.
Ludovic Courtès [Sat, 27 Nov 2021 10:46:46 +0000 (11:46 +0100)]
gnu: krunner: Remove reference to '%build-inputs'.
* gnu/packages/kde-frameworks.scm (krunner)[arguments]: Replace reference
to '%build-inputs' by 'inputs' keyword argument.
Ludovic Courtès [Sat, 27 Nov 2021 10:46:19 +0000 (11:46 +0100)]
gnu: akonadi: Remove references to '%outputs' and '%build-inputs'.
* gnu/packages/kde-pim.scm (akonadi)[arguments]: Remove references to
'%outputs' and '%build-inputs'.
Ludovic Courtès [Sat, 27 Nov 2021 10:35:30 +0000 (11:35 +0100)]
gnu: libksysguard: Remove reference to '%outputs'.
* gnu/packages/kde-plasma.scm (libksysguard)[arguments]: Remove
reference to '%outputs' and use gexps.
Ludovic Courtès [Sat, 27 Nov 2021 10:31:12 +0000 (11:31 +0100)]
gnu: bluez-qt: Remove reference to '%output'.
* gnu/packages/kde-frameworks.scm (bluez-qt)[arguments]: Replace
reference to '%output' by a gexp.
Ludovic Courtès [Sat, 27 Nov 2021 10:25:21 +0000 (11:25 +0100)]
gnu: k3b: Remove references to '%outputs' and '%build-inputs'.
* gnu/packages/kde-multimedia.scm (k3b)[arguments]: Remove references to
'%build-inputs' and '%outputs'.
Ludovic Courtès [Sat, 27 Nov 2021 10:24:33 +0000 (11:24 +0100)]
gnu: kmplayer: Remove reference to '%build-inputs'.
* gnu/packages/kde-multimedia.scm (kmplayer)[arguments]: Use
'this-package-input' instead of '%build-inputs'.
Ludovic Courtès [Sat, 27 Nov 2021 00:20:45 +0000 (01:20 +0100)]
gnu: kamoso: Remove reference to '%build-inputs'.
* gnu/packages/kde-multimedia.scm (kamoso)[arguments]: Rewrite using
a gexp.
Guillaume Le Vaillant [Sat, 27 Nov 2021 09:47:34 +0000 (10:47 +0100)]
gnu: surf: Build with libsoup2.
* gnu/packages/suckless.scm (surf)[inputs]: Replace webkitgtk with
webkitgtk-with-libsoup2.
Jack Hill [Sat, 27 Nov 2021 07:16:44 +0000 (02:16 -0500)]
gnu: luakit: Build with libsoup2.
* gnu/packages/web-browsers.scm [luakit](inputs): Replace webkitgtk with
webkitgtk-with-libsoup2.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
HCoop / jackhill / guix / guix.git / log