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2021-06-05gnu: pigx-rnaseq: Update to 0.0.13....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13. [arguments]: Remove obsolete substitutions. [inputs]: Remove fastqc and trim-galore; add hisat2 and fastp. Ricardo Wurmus
2021-06-04gnu: python-scanpy: Update to 1.7.2....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2. Roel Janssen
2021-06-04gnu: python-anndata: Update to 0.7.6....* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6. Roel Janssen
2021-06-04gnu: Use define-public in (gnu packages xiph)....* gnu/pakages/xiph.scm: Replace all manual package #:exports with define-public. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Brendan Tildesley
2021-06-04gnu: python-pydantic: Update to 1.8.2....* gnu/packages/python-xyz.scm (python-pydantic): Update to 1.8.2. [arguments]: Disable some new tests. [native-inputs]: Add PYTHON-PYTEST-MOCK. [propagated-inputs]: Add PYTHON-TYPING-EXTENSIONS. Marius Bakke
2021-06-04gnu: wfview: Update to 1.0....* gnu/packages/radio.scm (wfview): Update to 1.0. Guillaume Le Vaillant
2021-06-04gnu: smalltalk: Find glibc even when cross-compiling....glibc is named "cross-libc" instead of "libc" when cross-compiling. Smalltalk still fails to cross-compile though. * gnu/packages/smalltalk.scm (smalltalk)[arguments]{phases}<#:fix-libc>: Also search for "cross-libc" instead of only "libc" in 'inputs'. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-06-04gnu: smalltalk: Move 'zip' from 'inputs' to 'native-inputs'....The 'zip' package is not in the references of 'smalltalk'. As such, it probably should be a native input, not a regular input. This can be confirmed by trying to cross-compile the 'smalltalk' package, without this commit. The configure script will ask to install InfoZIP. * gnu/packages/smalltalk.scm (smalltalk)[inputs]{zip}: Move to ... (smalltalk)[native-inputs]{zip} ... here. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-06-04gnu: ding: Use 'inputs' in build phases instead of '%build-inputs'....In build phases, the former is preferred. * gnu/packages/dictionaries.scm (ding)[arguments]<#:phases>{install}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-06-04gnu: qemacs: Use 'native-inputs' instead of '%build-inputs'....In build phases, the former (or 'inputs', as appropriate) is preferred. * gnu/packages/text-editors.scm (qemacs)[arguments]<#:phases>{install-extra-documentation}: Use 'native-inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-06-04gnu: neovim: Use 'inputs' in phases instead of '%build-inputs'....In build phases, the former is preferred. * gnu/packages/vim.scm (neovim)[arguments]<#:phases>{set-lua-path}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-06-04gnu: smalltalk: Use 'inputs' in phases instead of '%build-inputs'....In build phases, the former is preferred. * gnu/packages/smalltalk.scm (smalltalk)[arguments]<#:phases>{fix-libc}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-06-04gnu: ci: Use 'inputs' in build phases instead of '%build-inputs'....In build phases, the former is preferred. * gnu/packages/ci.scm (cuirass)[arguments]<#:phases>{wrap-program}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-06-04gnu: Add pigx-sars-cov2-ww....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable. Ricardo Wurmus
2021-06-04gnu: sbcl-nibbles: Update to 0.14-2.dad2524....* gnu/packages/lisp-xyz.scm (sbcl-nibbles): Update to 0.14-2.dad2524. Guillaume Le Vaillant
2021-06-03gnu: remmina: Update to 1.4.18....* gnu/packages/vnc.scm (remmina)[version]: Update to 1.4.18. Raghav Gururajan
2021-06-03gnu: gajim-omemo: Update to 2.7.14....* gnu/packages/messaging.scm (gajim-omemo)[version]: Update to 2.7.14. Raghav Gururajan
2021-06-03gnu: linux-libre 4.4: Update to 4.4.271....* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.271. (linux-libre-4.4-pristine-source): Update hash. Leo Famulari
2021-06-03gnu: linux-libre 4.9: Update to 4.9.271....* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.271. (linux-libre-4.9-pristine-source): Update hash. Leo Famulari
2021-06-03gnu: linux-libre 4.14: Update to 4.14.235....* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.235. (linux-libre-4.14-pristine-source): Update hash. Leo Famulari
2021-06-03gnu: linux-libre 4.19: Update to 4.19.193....* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.193. (linux-libre-4.19-pristine-source): Update hash. Leo Famulari
2021-06-03gnu: linux-libre 5.4: Update to 5.4.124....* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.124. (linux-libre-5.4-pristine-source): Update hash. Leo Famulari
2021-06-03gnu: linux-libre 5.10: Update to 5.10.42....* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.42. (linux-libre-5.10-pristine-source): Update hash. (deblob-scripts-5.10): Update hash. Leo Famulari
2021-06-03gnu: linux-libre: Update to 5.12.9....* gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.9. (linux-libre-5.12-pristine-source): Update hash. (deblob-scripts-5.12): Update hash. Leo Famulari
2021-06-03gnu: komikku: Update to 0.29.0....* gnu/packages/gnome.scm (komikku): Update to 0.29.0. Leo Prikler
2021-06-03gnu: emacs-calibredb: Update to 2.10.0....* gnu/packages/emacs-xyz.scm (emacs-calibredb): Update to 2.10.0. Nicolas Goaziou
2021-06-03gnu: Add rfcat....* gnu/packages/radio.scm (rfcat): New variable. Guillaume Le Vaillant
2021-06-03gnu: rasdaemon: Update to 0.6.7....* gnu/packages/linux.scm (rasdaemon): Update to 0.6.7. [arguments]: Add a "--with-sysconfdefdir" configure flag. Tobias Geerinckx-Rice
2021-06-03gnu: php: Update to 7.4.20....* gnu/packages/php.scm (php): Update to 7.4.20. Tobias Geerinckx-Rice
2021-06-03gnu: fltk: Update to 1.3.6....* gnu/packages/fltk.scm (fltk): Update to 1.3.6. Tobias Geerinckx-Rice
2021-06-03gnu: amule: Use HTTPS home page....* gnu/packages/networking.scm (amule)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2021-06-03gnu: amule: Update to 2.3.3....* gnu/packages/networking.scm (amule): Update to 2.3.3. [source]: Remove patch. * gnu/packages/patches/amule-crypto-6.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2021-06-03gnu: mtools: Update to 4.0.29....* gnu/packages/mtools.scm (mtools): Update to 4.0.29. Tobias Geerinckx-Rice
2021-06-03gnu: emacs-epkg: Update to 3.3.0....* gnu/packages/emacs-xyz.scm (emacs-epkg): Update to 3.3.0. Nicolas Goaziou
2021-06-03gnu: emacs-closql: Update to 1.0.5....* gnu/packages/emacs-xyz.scm (emacs-closql): Update to 1.0.5. Nicolas Goaziou
2021-06-03gnu: emacs-ebdb: Update to 0.6.23....* gnu/packages/emacs-xyz.scm (emacs-ebdb): Update to 0.6.23. Nicolas Goaziou
2021-06-03gnu: monolith: Update to 2.5.0....* gnu/packages/web.scm (monolith): Update to 2.5.0. Nicolas Goaziou
2021-06-03gnu: rust-regex-1: Update to 1.5.4....* gnu/packages/crates-io.scm (rust-regex-1): Update to 1.5.4. Nicolas Goaziou
2021-06-03gnu: rust-aho-corasick-0.7: Update to 0.7.18....* gnu/packages/crates-io.scm (rust-aho-corasick-0.7): Update to 0.7.18. Nicolas Goaziou
2021-06-03gnu: rust-memchr-2: Update to 2.4.0....* gnu/packages/crates-io.scm (rust-memchr-2): Update to 2.4.0. Nicolas Goaziou
2021-06-03gnu: rust-regex-syntax-0.6: Update to 0.6.25....* gnu/packages/crates-io.scm (rust-regex-syntax-0.6): Update to 0.6.25. Nicolas Goaziou
2021-06-03gnu: rust-reqwest-0.11: Fix build....* gnu/packages/crates-io.scm (rust-reqwest-0.11)[arguments]: Add missing Cargo development inputs. Nicolas Goaziou
2021-06-03gnu: rust-reqwest-0.11: Update to 0.11.3....* gnu/packages/crates-io.scm (rust-reqwest-0.11): Update to 0.11.3. Nicolas Goaziou
2021-06-03gnu: rust-sha2-0.9: Update to 0.9.5....* gnu/packages/crates-io.scm (rust-sha2-0.9): Update to 0.9.5. Nicolas Goaziou
2021-06-03gnu: Add rust-cpufeatures-0.1....* gnu/packages/crates-io.scm (rust-cpufeatures-0.1): New variable. Nicolas Goaziou
2021-06-03gnu: Add rust-sha2-asm-0.6....* gnu/packages/crates-io.scm (rust-sha2-asm-0.6): New variable. (rust-sha2-asm-0.5): Inherit from above. Nicolas Goaziou
2021-06-03gnu: rust-url-2: Update to 2.2.2....* gnu/packages/crates-io.scm (rust-url-2): Update to 2.2.2. Nicolas Goaziou
2021-06-03gnu: rust-assert-cmd-1: Update to 1.0.4....* gnu/packages/crates-io.scm (rust-assert-cmd-1): Update to 1.0.4. Nicolas Goaziou
2021-06-03machine: ssh: Respect calling convention for monadic procedures....Fixes a regression introduced in 2885c3568edec35086f8feeae5b60259cbea407c. Reported by Mathieu Othacehe. * gnu/machine/ssh.scm (deploy-managed-host)[eval/error-handling]: Return two values in the standard case. Ludovic Courtès
2021-06-03gnu: Add fit-sne....* gnu/packages/bioinformatics.scm (fit-sne): New variable. Ricardo Wurmus
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