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2021-12-04gnu: seqan-2: Use gexp for builder.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqan-2)[arguments]: Use a gexp to remove references to %build-inputs and %outputs.
2021-12-04gnu: sra-tools: Remove references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use a gexp instead of referencing %build-inputs.
2021-12-04gnu: preseq: Remove references to %outputs and %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Replace references to %outputs and %build-inputs by using a gexp.
2021-12-04gnu: preseq: Simplify snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
2021-12-04gnu: julia-forwarddiff: Disable tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-forwarddiff)[arguments]<#:tests?>: Conditionally disable tests. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-geometrybasics: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz (julia-geometrybasics)[arguments]<#:phases>: Conditionally replace the incorrect type in test suite. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-structarrays: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-structarrays)[arguments]<#:phases>: Conditionally replace the incorrect type in the test suite. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-mutablearithmetics: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-mutablearithmetics)[arguments]<#:phases>: Conditionally disable the failing test. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-woodburymatrices: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-woodburymatrices)[arguments]<#:phases>: Conditionally disable the failing test. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-intervalsets: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-intervalsets)[arguments]<#:phases>: Conditionally disable the failing test. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-reversediff: Disable tests on i686-linux.zimoun
* gnu/packages/julia-xyz (julia-reversediff)[arguments]<#:tests?>: Conditionally disable tests. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-interpolations: Disable tests in i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-interpolations)[arguments]<#:tests?>: Conditionally disable tests. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-arrayinterface: Disable tests for i686.zimoun
* gnu/packages/julia-xyz.scm (julia-arrayinterface)[arguments]<#:tests?>: Conditionally disable tests. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-mappedarrays: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-mappedarrays)[arguments]<#:phases>: Conditionally replace the incorrect type in test suite. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-blockarrays: Fix tests on i686-linux.zimoun
* 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>
2021-12-04gnu: julia-lazyarrays: Fix tests on i686-linux.zimoun
* 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>
2021-12-04gnu: julia-configurations: Fix tests on i686-linux.zimoun
* 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>
2021-12-04gnu: julia-finitedifferences: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz (julia-finitedifferences)[arguments]<#:phases>: Conditionnally disable the failing test. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-benchmarktools: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-benchmarktools)[arguments]<#:phases>: Conditionnally disable the failing tests. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: julia-datastructures: Fix tests on i686-linux.zimoun
* gnu/packages/julia-xyz.scm (julia-datastructures)[arguments]<#:phases>: Conditionnally disable the failing test. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04gnu: libunwind-julia: Fix build on i686-linux.zimoun
* 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>
2021-12-04gnu: plink-ng: Enable tests.Ricardo Wurmus
* 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.
2021-12-04gnu: plink-ng: Replace reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to %outputs by using a gexp.
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.
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