gnu: Remove python-paste. Fails to build, no users in Guix. Note from upstream: Paste is in maintenance mode and recently moved from bitbucket to github. Patches are accepted to keep it on life support, but for the most part, please consider using other options. Fixes: guix/guix#3229 * gnu/packages/python-web.scm (python-paste): Delete variable. Change-Id: If4ee8da2a0c49f40676e32a934a6cfff81f3522d
gnu: Remove python-pastescript. It fails to build, no users in Guix. Note from upstream: Paste Script is being maintained on life support. That means that critical bugs will be fixed, and support for new versions of Python will be handled, but other than that new features are not being considered. * gnu/packages/python-web.scm (python-pastescript): Delete variable. Change-Id: I399dcebd3a4329ed80d0eb0d3a2df01266272701
gnu: Remove python-pyportmidi. This package was required only to build frescobaldi which no longer needs it, there are no other users in Guix, and it fails to build, see <https://codeberg.org/guix/guix/pulls/3191>. * gnu/packages/music.scm (python-pyportmidi): Delete variable. Fixes: guix/guix#3202 Change-Id: I2cfff4416dfa0206d8b91b2d6682a2e2dba8ee48
gnu: r-voltron: Update to 0.2.1-1.1c0810b. * gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.1-1.1c0810b. [propagated-inputs]: Add r-biocsingular. Change-Id: I3ae6971b14ceff7f6e367a3d0ca7dbaff00049ae
gnu: r-greylistchip: Fix tests. * gnu/packages/bioconductor.scm (r-greylistchip)[native-inputs]: Add r-biocstyle. Change-Id: I0804d217c7005cdbcd3b344c5cbdc22eec14ddac
gnu: r-colorout: Adjust GCC@14. * gnu/packages/cran.scm (r-colorout)[arguments]: New phase that set GCC compiler flag. Change-Id: I7616cbd7918e00faed307dcc41dd6fe9cbc02086
gnu: r-gofuncr: Fix tests. * gnu/packages/bioconductor.scm (r-gofuncr)[native-inputs]: Add r-homo-sapiens. Change-Id: I5c2759b73e98aa67136093c64d77be0a8e21e52d
gnu: r-blavaan: Adjust GCC@14. * gnu/packages/cran.scm (r-blavaan)[arguments]: Add phase that decreases GCC@14 strictness. Change-Id: Ic56b3d6ba1b92ee98b57ebfe0db4c1aa2a542b24
gnu: r-densestbayes: Adjust GCC@14. * gnu/packages/cran.scm (r-densestbayes)[arguments]: Add phase that decreases GCC@14 strictness. Change-Id: I52c45b9f693d843f25f1d61ef440e5b1cf2808d2
gnu: r-dada2: Adjust GCC@14. * gnu/packages/bioconductor.scm (r-dada2)[arguments]: Add phase that decreases GCC@14 strictness. Change-Id: Ie488f6f2ecffa38b1327ec5efb726c49c2c04319
gnu: r-dtwclust: Adjust GCC@14. * gnu/packages/cran.scm (r-dtwclust)[arguments]: Add phase that decreases GCC@14 strictness. Change-Id: I4235fb9444e67112ee0906b479445b5b1c5ef7b0
gnu: r-rffc: Adjust to R@4.5.0. * gnu/packages/cran.scm (r-rffc)[arguments]: Replace Calloc and Free by R_Calloc and R_Free. Change-Id: I5102fff078f8ca2440dae250b9d439e5440fe394 Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
gnu: r-rcppparallel: Patch TBB task.h. Patching this file lets us compile downstream packages without errors. * gnu/packages/cran.scm (r-rcppparallel)[arguments]: Add phase 'gcc-compatibility. Change-Id: I966c09887f1536dcc623d322f6b141fad069e3dd Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
gnu: r-rstan: Adjust GCC@14. * gnu/packages/bioconductor.scm (r-rstan)[arguments]: Add phase that decreases GCC@14 strictness. Change-Id: I83920c1acfd944f36625385012f0dd28bbc3decc
gnu: r-chromstar: Adjust R@4.5.0 and GCC@14. * gnu/packages/bioinformatics.scm (r-chromstar)[arguments]: Add phase that replaces C-level facilities from R@4.5.0. Change-Id: I16deb4b68beaf5665d57bd2045dc91a043c46e82
gnu: r-chipkernels: Adjust R@4.5.0 and GCC@14. * gnu/packages/bioinformatics.scm (r-chipkernels)[arguments]: Add phase that replaces C-level facilities from R@4.5.0. Change-Id: Iac58b4d871160b4cbfd8b71d771c2f2fcf174240
gnu: Remove r-assertive-reflection. Package was removed from the CRAN repository and it depends on `'is.R()` removed by R@4.5.0. * gnu/packages/cran.scm (r-assertive-reflection): Delete variable. Change-Id: I373b23e0a450c096799199d719d23dea11f5f9f3
gnu: Remove r-assertive. Package was removed from the CRAN repository and its dependency 'r-assertive-reflection' relies on the R procedure 'is.R()' which had been removed in R@4.5.0. * gnu/packages/cran.scm (r-assertive): Delete variable. Change-Id: I1a8126594162b0c0f4ef03a9177fb5b74c4754be
gnu: r-aneufinder: Adjust R@4.5.0 and GCC@14. * gnu/packages/bioconductor.scm (r-aneufinder)[arguments]: Add phases that relax GCC@14 strictness when using R@4.5.0 C-level facilities. Change-Id: If524806121e7b6f697b0cdee75cbe1aef3bb7b9a
gnu: r-paralleldist: Adjust GCC@14. * gnu/packages/cran.scm (r-paralleldist)[arguments]: Add phase that relax GCC@14 strictness. Change-Id: I7dd04d8547b35cb35fac0d1386185d37239d4a8e