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* gnu: Add n2p2.Pierre-Antoine Bouttier2022-05-05
| | | | | | * gnu/packages/maths.scm (n2p2): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
* gnu: icedove: Update to 91.9.0 [fixes CVE-2022-1520].Jonathan Brielmaier2022-05-05
| | | | * gnu/packages/gnuzilla.scm (icedove): Update to 91.9.0.
* gnu: python-pari-jupyter: Update to 1.4.1.Andreas Enge2022-05-05
| | | | | * gnu/packages/python-xyz.scm (python-pari-jupyter): Update to 1.4.1. [home-page]: Update after maintainer change.
* gnu: cm: Update to 0.4.0.Andreas Enge2022-05-05
| | | | * gnu/packages/algebra.scm (cm): Update to 0.4.0.
* gnu: ungoogled-chromium: Update to 101.0.4951.54-1.Marius Bakke2022-05-03
| | | | | * gnu/packages/chromium.scm (%chromium-version): Set to 101.0.4951.54. (%ungoogled-origin, ungoogled-chromium): Update hashes.
* gnu: icecat: Update to 91.9.0-guix0-preview1 [security fixes].Mark H Weaver2022-05-03
| | | | | | | | Includes fixes for CVE-2022-29909, CVE-2022-29911, CVE-2022-29912, CVE-2022-29914, CVE-2022-29916, and CVE-2022-29917. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes.
* gnu: dealii: Update to 9.3.3.Paul A. Patience2022-05-03
| | | | | | | | | | * gnu/packages/maths.scm (dealii): Update to 9.3.3. * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: Delete file. * gnu/packages/patches/dealii-fix-sundials.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: dealii: Add SUNDIALS dependency.Paul A. Patience2022-05-03
| | | | | | | | * gnu/packages/maths.scm (dealii)[propagated-inputs]: Add sundials-5. Reformat list to clarify comment. (dealii-openmpi)[propagated-inputs]: Add sundials-openmpi-5. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: dealii-openmpi: Remove input labels.Paul A. Patience2022-05-03
| | | | | | | * gnu/packages/maths.scm (dealii-openmpi)[inputs]: Remove labels. [propagated-inputs]: Same. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: dealii: Remove trailing booleans.Paul A. Patience2022-05-03
| | | | | | | | | * gnu/packages/maths.scm (dealii)[snippet]: Remove trailing boolean (and therefore the 'begin'). [native-inputs, inputs]: Reindent. [arguments]<#:phases>: Remove trailing boolean. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: sundials: Add 5.8.0.Paul A. Patience2022-05-03
| | | | | | | * gnu/packages/maths.scm (sundials-5, sundials-openmpi-5): New variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: sundials: Update to 6.2.0.Paul A. Patience2022-05-03
| | | | | | * gnu/packages/maths.scm (sundials): Update to 6.2.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: sundials-openmpi: Add HYPRE dependency.Paul A. Patience2022-05-03
| | | | | | | | | * gnu/packages/maths.scm (sundials-openmpi)[propagated-inputs]: Add hypre-openmpi. [arguments]<#:configure-flags>: Add -DENABLE_HYPRE, -DHYPRE_INCLUDE_DIR and -DHYPRE_LIBRARY_DIR. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: sundials: Fix various issues.Paul A. Patience2022-05-03
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This commit fixes various issues. First, some of SUNDIALS's CMake variables were renamed at some point between 5.2.0 and 5.7.0, in particular KLU_ENABLE, which was changed to ENABLE_KLU. Since sundials-julia is essentially SUNDIALS 5.2.0, its configure flags need to be different from those of the sundials package. Second, commit 61bcd648ca215e3d8e75b3a3f49bfb94d66f7c79, which updated SUNDIALS to 6.1.1, accidentally completely disabled PETSc support for sundials-openmpi (PETSc is supported only with MPI) by removing the relevant configure flags. Third, SUNDIALS's default index size is 64 bits, but PETSc's is 32 bits, and they need to be the same; this issue is discussed in the next three paragraphs. The default index size in SUNDIALS 3.1.1 (which was the sundials package's version previous to the aforementioned commit) was also 64 bits (though it was configured through the SUNDIALS_INDEX_TYPE CMake variable, which could take the values INT64_T or INT32_T), but SUNDIALS's configure script didn't warn of any incompatibility with PETSc's 32-bit indices. I don't know if this was an accidental omission from the configure script or if SUNDIALS's index size didn't have to correspond to PETSc's at the time. Keeping 64-bit indices in SUNDIALS would require adding a package for PETSc with 64-bit indices (using the --with-64-bit-indices configure flag), possibly named petsc64-openmpi (to follow the style of the SCOTCH packages, i.e., scotch, scotch32, etc., though there the unadorned package name represents the 64-bit version, unlike the unadorned petsc), which would in turn require a package for METIS with 64-bit indices (using IDXTYPEWIDTH=64). However, SUNDIALS is an optional dependency of deal.II, both of which have PETSc as an optional dependency, and deal.II's index size (which defaults to 32 bits) must match PETSc's. In other words, the current deal.II package can build with SUNDIALS only if SUNDIALS has 32-bit indices. Furthermore, users needing 64-bit indices in SUNDIALS probably also need them in PETSc and other libraries. If and when 64-bit indices are deemed necessary, we can add all the package variations at once (for SUNDIALS, PETSc, METIS, deal.II and any others). * gnu/packages/maths.scm (sundials)[source]: Reuse version in URL. [native-inputs]: Capitalize and punctuate comment. [inputs]: Remove petsc, now unnecessary gfortran, and obsolete comment. Move TODO item to sundials-openmpi. [arguments]<#:configure-flags>: Add -DSUNDIALS_INDEX_SIZE=32 to match PETSc's 32-bit indices. Remove obsolete -DEXAMPLES_ENABLE_F77, -DEXAMPLES_ENABLE_F90 and -DFCMIX_ENABLE. Mention new but currently unusable -DBUILD_FORTRAN_MODULE_INTERFACE and -DEXAMPLES_ENABLE_F2003. Rename KLU_ENABLE to ENABLE_KLU. (sundials-openmpi): Use package/inherit. [inputs]: Move openmpi and petsc-openmpi from here... [propagated-inputs]: ...to here. Clarify comment. [arguments]<#:configure-flags>: Add -DENABLE_PETSC and -DPETSC_DIR, the equivalents of which were accidentally removed in commit 61bcd648ca215e3d8e75b3a3f49bfb94d66f7c79. <#:phases>: Replace a tab with spaces. [synopsis]: Replace OpenMPI with MPI to conform to other package synopses. (sundials-julia)[inputs]: Add gfortran. [arguments]<#:configure-flags>: Set only, and manually, -DCMAKE_C_FLAGS, -DSUNDIALS_INDEX_SIZE, -DKLU_ENABLE, -DKLU_INCLUDE_DIR, -DKLU_LIBRARY_DIR and -DLAPACK_ENABLE instead of inheriting from the sundials package, because some of SUNDIALS's CMake variables have changed name. [synopsis]: Capitalize “LAPACK”. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: petsc-openmpi: Fix header inclusions.Paul A. Patience2022-05-03
| | | | | | | * gnu/packages/maths.scm (petsc-openmpi)[arguments]: Add 'patch-header-inclusions' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: pipefs: Correctly handle lack of extensions.Ludovic Courtès2022-05-03
| | | | | | | | | | | | | | Previously, in the absence of extensions of 'pipefs-service-type', we'd get a wrong-type-arg exception while folding services: In gnu/services/nfs.scm: 134:37 1 (_ #<<pipefs-configuration> mount-point: "/var/lib/nfs…> …) In ice-9/boot-9.scm: 1685:16 0 (raise-exception _ #:continuable? _) In procedure car: Wrong type argument in position 1 (expecting pair): () * gnu/services/nfs.scm (pipefs-service-type)[extend]: Gracefully handle the case where VALUES is the empty list, as done in 'gss-service-type'.
* gnu: Mutt: Update to 2.2.4.Leo Famulari2022-05-02
| | | | * gnu/packages/mail.scm (mutt): Update to 2.2.4.
* gnu: linux-libre 4.19: Update to 4.19.241.Leo Famulari2022-05-02
| | | | | * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.241. (linux-libre-4.19-pristine-source): Update hash.
* gnu: linux-libre 5.15: Update to 5.15.37.Leo Famulari2022-05-02
| | | | | * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.37. (linux-libre-5.15-pristine-source): Update hash.
* gnu: mes: Update to 0.24.Jan (janneke) Nieuwenhuizen2022-05-02
| | | | | * gnu/packages/mes.scm (mes-next)[source]: Update to 0.24. [native-inputs]: Add m2-planet.
* gnu: m2-planet: Update to 1.9.0.Jan (janneke) Nieuwenhuizen2022-05-02
| | | | * gnu/packages/mes.scm (m2-planet): Update to 1.9.0.
* gnu: mescc-tools: Update to 1.4.0.Jan (janneke) Nieuwenhuizen2022-05-02
| | | | * gnu/packages/mes.scm (mescc-tools): Update to 1.4.0.
* gnu: Add xschem.Konstantinos Agiannis2022-05-02
| | | | | | * gnu/packages/engineering.scm (xschem): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: Make sure Shepherd destructors match constructors.Ludovic Courtès2022-05-02
| | | | | | | | | | | | | This is a followup to b06ecc57515d4e3c8b2228e8142654e9a26ba6e1, 211fe3f66e6dfdaa64974931c458ab1d92afc182, and fd57ce267c4083fe98242caa31075d2bd62903bf. * gnu/services/base.scm (guix-publish-shepherd-service): Change 'stop' method to use 'make-systemd-destructor' when 'make-systemd-constructor' is used. * gnu/services/dict.scm (dicod-shepherd-service): Change 'stop' method to use 'make-inetd-destructor' when 'make-inetd-constructor' is used. * gnu/services/messaging.scm (bitlbee-shepherd-service): Likewise.
* gnu: python-hic2cool: Fix build.Ricardo Wurmus2022-05-02
| | | | | * gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix incompatibility with h5py 3; disable two tests.
* gnu: Add r-agimicrorna.Mădălin Ionel Patrașcu2022-05-02
| | | | | | * gnu/packages/bioconductor.scm (r-agimicrorna): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-adductomicsr.Mădălin Ionel Patrașcu2022-05-02
| | | | | | * gnu/packages/bioconductor.scm (r-adductomicsr): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-orgmassspecr.Mădălin Ionel Patrașcu2022-05-02
| | | | * gnu/packages/cran.scm (r-orgmassspecr): New variable.
* gnu: Add r-adductdata.Mădălin Ionel Patrașcu2022-05-02
| | | | * gnu/packages/bioconductor.scm (r-adductdata): New variable.
* gnu: Add python-scrapy.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-web.scm (python-scrapy): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-itemloaders.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-xyz.scm (python-itemloaders): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-parsel.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-web.scm (python-parsel): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-protego.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-web.scm (python-protego): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-itemadapter.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-xyz.scm (python-itemadapter): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-queuelib.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-xyz.scm (python-queuelib): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-pydispatcher.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-xyz.scm (python-pydispatcher): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-sybil.Felix Gruber2022-05-02
| | | | | | * gnu/packages/python-check.scm (python-sybil): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: bear: Update to 3.0.19.Greg Hogan2022-05-02
| | | | | | * gnu/packages/build-tools.scm (bear): Update to 3.0.19. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: spdlog: Update to 1.10.0.Greg Hogan2022-05-02
| | | | | | * gnu/packages/logging.scm (spdlog): Update to 1.10.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: fmt: Update to 8.1.1.Greg Hogan2022-05-02
| | | | | | * gnu/packages/pretty-print.scm (fmt): Update to 8.1.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: apl: Use G-expressions.Paul A. Patience2022-05-02
| | | | | | * gnu/packages/apl.scm (apl)[arguments]: Use G-expressions. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: apl: Remove input labels.Paul A. Patience2022-05-02
| | | | | | * gnu/packages/apl.scm (apl)[inputs]: Remove labels and sort. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: apl: Update to 1.8-r1550.Paul A. Patience2022-05-02
| | | | | | | | | | | This commit fixes a failing build caused by -Werror (the configure script no longer sets the -Werror compilation flag). * gnu/packages/apl.scm (apl): Update to 1.8-r1550. [arguments]: Add 'fix-configure' phase. [license]: Prefix with 'license:'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add emacs-git-email.Niklas Eklund2022-05-02
| | | | | | * gnu/packages/emacs-xyz.scm (emacs-git-email): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: ugrep: Update to 3.7.9.kiasoc52022-05-02
| | | | | | * gnu/packages/search.scm (ugrep): Update to 3.7.9. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: aws-sdk-cpp: Remove openssl input.Greg Hogan2022-05-02
| | | | | | | * gnu/packages/cpp.scm (aws-sdk-cpp): [inputs]: Remove openssl. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: s2n: Link to aws-lc as libcrypto dependency.Greg Hogan2022-05-02
| | | | | | | | | * gnu/packages/tls.scm (s2n): [arguments]: Fix for openssl as replacement input for aws-lc. [propagated-inputs]: Add aws-lc and remove openssl. [supported-systems]: Only support x86_64-linux. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: aws-lc: Fix checksum and enable tests.Greg Hogan2022-05-02
| | | | | | | | * gnu/packages/tls.scm (aws-lc): [source]: Fix checksum. [arguments]: Enable tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: aws-crt-cpp: Fix comment formatting.Greg Hogan2022-05-02
| | | | | | * gnu/packages/cpp.scm (aws-crt-cpp): Fix comment formatting. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: aws-c-mqtt: Fix comment formatting.Greg Hogan2022-05-02
| | | | | | * gnu/packages/c.scm (aws-c-mqtt): Fix comment formatting. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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