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2021-12-04gnu: plink: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace reference to %build-inputs.
2021-12-04gnu: plink: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from build phase.
2021-12-04gnu: rsem: Update to 1.3.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3. [arguments]: Build with gnu++11 standard; patch sources for compatibility.
2021-12-04gnu: rsem: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from build phases.
2021-12-04gnu: rsem: Remove references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
2021-12-04gnu: rsem: Remove trailing #T from snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
2021-12-04gnu: prodigal: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-04gnu: prank: Bind INPUTS in 'install phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install phase to remove references to %build-inputs.
2021-12-04gnu: prank: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from build phases.
2021-12-04gnu: mash: Replace references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
2021-12-04gnu: mash: Move htslib and capnproto to regular inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and capnproto from here... [inputs]: ...to here.
2021-12-04gnu: mash: Simplify snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
2021-12-04gnu: mafft: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from build phase.
2021-12-04gnu: mafft: Replace references to %build-inputs and %outputs.Ricardo Wurmus
* 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.
2021-12-04gnu: jellyfish: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
2021-12-04gnu: fastp: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
2021-12-04gnu: java-picard: Replace reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
2021-12-04gnu: java-htsjdk: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
2021-12-04gnu: fxtract: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
2021-12-04gnu: delly: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to %outputs with a gexp.
2021-12-03gnu: libbigwig: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to %outputs with a gexp.
2021-12-03gnu: cd-hit: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to %outputs with gexp.
2021-12-03gnu: bowtie1: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-03gnu: bowtie: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to %outputs with a gexp.
2021-12-03gnu: bless: Remove reference to %build-inputs.Ricardo Wurmus
* 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.
2021-12-03gnu: bless: Remove trailing #T from snippet and build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all trailing #Ts.
2021-12-03gnu: bedtools: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of referencing %outputs.
2021-12-03gnu: qtltools: Replace references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of referencing %build-inputs.
2021-12-03gnu: bamutils: Update to 1.0.14.Ricardo Wurmus
* 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.
2021-12-03gnu: bamutils: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03gnu: bamm: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of %build-inputs.
2021-12-03gnu: python2-openpyxl: Explicitly build with Python 2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-openpyxl)[arguments]: Add value for #:python field.
2021-12-03gnu: python-plastid: Update to 0.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
2021-12-02gnu: glade: Remove dependency on GJS on non-x86_64.Ludovic Courtès
* gnu/packages/gnome.scm (glade3)[arguments]: Add optional 'skip-gjs-test' phase. [native-inputs]: Provide GJS only when 'target-x86-64?'.
2021-12-02gnu: Remove librsvg@2.50 from the Xfce dependency graph.Ludovic Courtès
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.
2021-12-02gnu: librsvg: Add 'librsvg-for-system' procedure.Ludovic Courtès
* gnu/packages/gnome.scm (librsvg-for-system): New procedure.
2021-12-02gnu: librsvg: Reintroduce version 2.40.Ludovic Courtès
* gnu/packages/gnome.scm (librsvg-2.40): New variable.
2021-12-02gnu: prinseq: Fix use of SEARCH-INPUT-FILE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument to SEARCH-INPUT-FILE.
2021-12-02gnu: gnome-shell: Do not wrap in LD_LIBRARY_PATH.Ricardo Wurmus
Fixes <https://bugs.gnu.org/37123>. * gnu/packages/gnome.scm (gnome-shell)[arguments]: Remove LD_LIBRARY_PATH from wrapper.
2021-12-02gnu: python2-matplotlib: Disable sanity-check.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Delete 'sanity-check phase.
2021-12-02gnu: python2-matplotlib: Remove trailing #T.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Remove trailing #T from build phase.
2021-12-02Revert "gnu: Change source file-name suffix in rust packages."Efraim Flashner
This reverts commit 07a80e30a10e2a6ed4760f12711f8a91391398e4. This commit affects rust crates that are inputs to librsvg, which causes many packages to be rebuilt.
2021-12-02gnu: tor: Limit test suite adjustments to affected architectures.Efraim Flashner
This is a follow-up to 68d090002a1a5623494006fca3e2c2c97d3ff676. * gnu/packages/tor.scm (tor)[arguments]: Only add custom 'adjust-test-suite phase on aarch64, powerpc32.
2021-12-02gnu: python2-numpy: Delete file that depends on deleted test.Ricardo Wurmus
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.
2021-12-02gnu: Change source file-name suffix in rust packages.Z572
* 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>
2021-12-02gnu: python2-numpy: Do not inherit native-inputs.Ricardo Wurmus
* 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.
2021-12-01gnu: petsc-{complex,openmpi,complex-openmpi}: Use gexps.Ludovic Courtès
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.
2021-12-01gnu: scalapack: Update to 2.1.0.Ludovic Courtès
* 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.
2021-12-01installer: parted: Use the swap-space record.Mathieu Othacehe
* gnu/installer/parted.scm (user-partitions->configuration): Use the swap-space record.
2021-12-01tests: install: Use the swap-space record.Mathieu Othacehe
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.
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