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Author SHA1 Message Date
Maxim Cournoyer 633733696c
gnu: rust-av-metrics: Update to 0.7.2. Also update rust-lab to 0.11.0. 
* gnu/packages/crates-io.scm (rust-lab-0.8): Update to 0.11.0, rename to...
(rust-lab-0.11): ... this.
[cargo-development-inputs]: Update rust-approx to 0.5, rust-pretty-assertions
to 0.7 and rust-rand to 0.8.
(rust-lab-0.7): Adjust accordingly.
(rust-lab-0.4): Inherit from rust-lab-0.7 and fix source field indentation.
(rust-av-metrics-0.6): Update to 0.7.2, renaming it to...
(rust-av-metrics-0.7): ... this.
[cargo-inputs]: Update rust-lab to 0.11.
[cargo-development-inputs]: Add rust-criterion-0.3 and rust-y4m-0.7.
 2022-01-10 11:51:29 -05:00
Maxim Cournoyer 6b610674d1
gnu: rust-v-frame-0.2: Update to 0.2.5. 
* gnu/packages/crates-io.scm (rust-v-frame-0.2): Update to 0.2.5.
[skip-build?]: Remove argument.
[cargo-inputs]: Add rust-rust-hawktracer-0.7 and rust-rayon-1.
 2022-01-10 11:51:29 -05:00
Maxim Cournoyer 34fb1c4ba9
gnu: Add rust-rustc-version-0.4. 
* gnu/packages/crates-io.scm (rust-rustc-version-0.4): New variable.
(rust-rustc-version-0.3): Inherit from the above.
 2022-01-10 11:50:50 -05:00
Maxim Cournoyer 9f3ed4d57e
gnu: Add rust-concolor-control. 
* gnu/packages/crates-io.scm (rust-concolor-control): New variable.
 2022-01-10 11:49:13 -05:00
Maxim Cournoyer 330c3bee85
gnu: Add rust-concolor-query. 
* gnu/packages/crates-io.scm (rust-concolor-query): New variable.
 2022-01-10 11:49:13 -05:00
Maxim Cournoyer 8169079a5a
gnu: Add rust-cfg-expr-0.8. 
* gnu/packages/crates-io.scm (rust-cfg-expr-0.8): New variable.
 2022-01-10 11:49:12 -05:00
Maxim Cournoyer cdb2b115a8
gnu: mozjs-78: Disable rust-simd to workaround a build failure. 
* gnu/packages/gnuzilla.scm (mozjs-78)
[configure-flags]: Disable rust-simd to avoid a build failure that occurs when
Rust is newer than 1.54.0.
 2022-01-10 11:47:04 -05:00
Hartmut Goebel c3c943055d
build/python: Improve error output in sanity check. 
Instead of printing the "str()" representation of the excaption, print the
"repr()" representation. This will print the name of the exception and thus
ease understanding the actual error.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:47:03 -05:00
Maxim Cournoyer d90080db54
gnu: rust: Use rust-1.57.0. 
* gnu/packages/rust.scm (rust-1.54): Make it a private variable.  Move
definition to...
(rust-1.57): ... here.
(rust-1.55, rust-1.56): Make private.
* gnu/packages/shells.scm (nushell)[rust]: Remove argument.
 2022-01-10 11:47:03 -05:00
Maxim Cournoyer c292cf21f7
gnu: simple-scan: Add python to native inputs. 
* gnu/packages/gnome.scm (simple-scan)[native-inputs]: Add python.
 2022-01-10 11:47:03 -05:00
Maxim Cournoyer f353ed53a9
gnu: gnome-calculator: Add python to native inputs. 
* gnu/packages/gnome.scm (gnome-calculator)[native-inputs]: Add python.
 2022-01-10 11:47:03 -05:00
Maxim Cournoyer 32d38a7142
gnu: gnome-screenshot: Add python to native inputs. 
* gnu/packages/gnome.scm (gnome-screenshot)[native-inputs]: Add python.
 2022-01-10 11:47:03 -05:00
Maxim Cournoyer ff9c684ddf
gnu: file-roller: Add python to native inputs. 
* gnu/packages/gnome.scm (file-roller)[native-inputs]: Add python.
 2022-01-10 11:47:02 -05:00
Maxim Cournoyer 836daaf8f6
gnu: python-pandas: Update to 1.3.5. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.3.5.
[phases]{check}: Add a reference to the network accessing tests issue, now
reported upstream.  Reinstate the excelwriter tests.
[propagated-inputs]: Add python-xlsxwriter.
[native-inputs]: Remove python-nose.
 2022-01-10 11:47:02 -05:00
Maxim Cournoyer b92d09cda1
gnu: python-xlwt: Add comment about maintainership of the package. 
The package appears to be abandoned.

* gnu/packages/python-xyz.scm (python-xlwt): Add comment.
 2022-01-10 11:47:02 -05:00
Maxim Cournoyer 00bad443ef
gnu: python-openpyxl: Update to 3.0.9. 
* gnu/packages/python-xyz.scm (python-openpyxl): Update to 3.0.9.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer 0c83eca719
gnu: python-xlrd: Update to 2.0.1. 
* gnu/packages/python-xyz.scm (python-xlrd): Update to 2.0.1.
[source]: Use git-fetch.
[arguments]: Delete field.
[native-inputs]: Add python-pytest.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer 48baca342d
gnu: mutter: Add python to native inputs. 
* gnu/packages/gnome.scm (mutter)[native-inputs]: Add python.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer ac1f60f4fe
gnu: libgweather: Add python to native inputs. 
* gnu/packages/gnome.scm (libgweather)[native-inputs]: Add python.
 2022-01-10 11:47:01 -05:00
Maxim Cournoyer 235a083103
gnu: baobab: Add python to native inputs. 
* gnu/packages/gnome.scm (baobab)[native-inputs]: Add python.
 2022-01-10 11:47:00 -05:00
Maxim Cournoyer c1482ef315
gnu: python-pytest-timeout: Update to 2.0.2. 
* gnu/packages/check.scm (python-pytest-timeout): Update to 2.0.2.
 2022-01-10 11:47:00 -05:00
Leo Famulari 8636d02955
gnu: binutils: Fix CVE-2021-45078. 
This is for the release branch.

Should we also use a graft for the master branch? It would be even
better if we could add a binutils-next package that users could install,
in my opinion.

* gnu/packages/patches/binutils-CVE-2021-45078.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/base.scm (binutils)[source]: Use it.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:46:57 -05:00
Maxim Cournoyer db912d77a8
gnu: glib: Update to 2.70.2. 
* gnu/packages/glib.scm (glib): Update to 2.70.2.
 2022-01-10 11:44:52 -05:00
Maxim Cournoyer ec26595e30
gnu: meson: Update to 0.60.3. 
* gnu/packages/build-tools.scm (gn): Update to 0.60.3.
 2022-01-10 11:44:52 -05:00
Maxim Cournoyer abb5a92cbc
gnu: glibmm: Update to 2.70.0 and apply guix style. 
* gnu/packages/glib.scm (glibmm): Update to 2.70.0.
[native-inputs]: Use new style.
 2022-01-10 11:44:51 -05:00
Sarah Morgensen 64f7e53a5d
gnu: cpuid: Remove obsolete file permissions change. 
* gnu/packages/linux.scm (cpuid)[arguments]<#:phases>{fix-makefile}:
Remove Makefile gzip permissions patch.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:51 -05:00
Sarah Morgensen 27cc25e1a4
gnu: pre-commit: Remove obsolete phase. 
* gnu/packages/version-control.scm (pre-commit)[arguments]<#:phases>:
Remove 'make-gz-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:51 -05:00
Sarah Morgensen 95cb49b475
gnu: go-github-com-prometheus-common: Remove obsolete phase. 
* gnu/packages/syncthing.scm (go-github-com-prometheus-common)
[arguments]<#:phases>: Remove 'make-gzip-archive-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:51 -05:00
Sarah Morgensen fa7b52ff57
gnu: python-pdfminer-six: Remove obsolete phase. 
* gnu/packages/python-xyz.scm (python-pdfminer-six)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen a97d659e13
gnu: arcanist: Remove obsolete phase. 
* gnu/packages/phabricator.scm (arcanist)[arguments]<#:phases>: Remove
'make-compressed-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen b623ee2fb6
gnu: helm: Remove obsolete phase. 
* gnu/packages/music.scm (helm)[arguments]<#:phases>: Remove
'make-gz-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen 9d55296898
gnu: lmms: Remove obsolete phase. 
* gnu/packages/music.scm (lmms)[arguments]<#:phases>: Remove
'make-manpages-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen f7d4bf6205
gnu: jalv-select: Remove obsolete phase. 
* gnu/packages/music.scm (jalv-select)[arguments]<#:phases>: Remove
'make-manpages-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:50 -05:00
Sarah Morgensen 18e872b805
gnu: python-scikit-learn: Remove obsolete phase. 
* gnu/packages/machine-learning.scm (python-scikit-learn)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen b67d82972e
gnu: go-ipfs: Remove obsolete phase. 
* gnu/packages/ipfs.scm (go-ipfs)[arguments]<#:phases>: Remove
'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 1ba19f4bf1
gnu: python-plotly: Remove obsolete phase. 
* gnu/packages/graph.scm (python-plotly)[arguments]<#:phases>: Remove
'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 21566bfd49
gnu: go-github-com-gdamore-tcell: Remove obsolete phase. 
* gnu/packages/golang.scm (go-github-com-gdamore-tcell)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 8347c49e56
gnu: go-github-com-docker-distribution: Remove obsolete phase. 
* gnu/packages/golang.scm (go-github-com-docker-distribution)[arguments]
<#:phases>: Remove 'make-gzip-archive-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:49 -05:00
Sarah Morgensen 37f6126f9f
gnu: go-golang-org-x-crypto: Remove obsolete phase. 
* gnu/packages/golang.scm (go-golang-org-x-crypto)[arguments]<#:phases>:
Remove 'make-gzip-archive-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen e0940ed843
gnu: po4a: Remove obsolete phase. 
* gnu/packages/gettext.scm (po4a)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen 6dc8a61bb1
gnu: emacs: Remove obsolete phase. 
* gnu/packages/emacs.scm (emacs)[arguments]<#:phases>: Remove
'make-compressed-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen 0d04504362
gnu: cups-minimal: Remove obsolete phase. 
* gnu/packages/cups.scm (cups-minimal)[arguments]<#:phases>: Remove
'make-manpages-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen b9e703da9d
gnu: clipper: Remove obsolete phase. 
* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove
'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:48 -05:00
Sarah Morgensen 85e43978a4
gnu: python-biom-format: Remove obsolete phase. 
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]
<#:phases>: Remove 'make-files-writable phase.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:47 -05:00
Sarah Morgensen 0f71f55a60
build-system/gnu: Make gzip files writable before resetting timestamps. 
guix/build/gnu-build-system.scm (reset-gzip-timestamps): Ensure gzip
files are writable before resetting their timestamps.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer c61e742854
gnu: tbb-2020: Use ld.gold to work around segfaults in check phase. 
* gnu/packages/tbb.scm (tbb-2020)
[configure-flags]: Use -fuse-ld=gold in CFLAGS.
[native-inputs]: Add ld-gold-wrapper.
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer 5651e46983
gnu: python-igraph: Update to 0.9.8. 
* gnu/packages/graph.scm (python-igraph): Update to 0.9.8.
[origin]: Fetch from git.
[configure-flags]: Delete argument.
[phases]{build}: No longer override phase.
{check}: Preserve ordering and streamline.
{specify-libigraph-location}: New phase.
[native-inputs]: Remove pkg-config.
[home-page]: Update.
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer 3c50cb75ee
gnu: igraph: Update to 0.9.5. 
* gnu/packages/graph.scm (igraph): Update to 0.9.5.
[source]: Add snippet to fully unbundle.
[build-system]: Use cmake-build-system.
[configure-flags]: Replace all by just '-DBUILD_SHARED_LIBS=ON'.
[native-inputs]: Add pkg-config.
[inputs]{zlib}: Delete input.
{arpack-ng, plfit, suitesparse}: New inputs.
 2022-01-10 11:44:47 -05:00
Maxim Cournoyer 36681885d4
gnu: Add plfit. 
* gnu/packages/graph.scm (plfit): New variable.
 2022-01-10 11:44:46 -05:00
Maxim Cournoyer 64dac22b17
gnu: python-pysam: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0.
[source]: Add FIXME to clarify bundled libraries in use.
[phases]{check}: Streamline.
[propagated-inputs]: Use latest htslib (1.14).
[native-inputs]: Use latest samtools and bcftools (1.14).  Remove python-nose.
 2022-01-10 11:44:46 -05:00