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* mpi: use mpi attribute consistently as the default MPI implementationsMarkus Kowalewski2021-01-23
| | | | | | | | | | | | | | | | | | | | Use the attribute mpi to provide a system wide default MPI implementation. The default is openmpi (as before). This now allows for overriding the MPI implentation by using the overlay mechanism. Build all packages with mpich instead of the default openmpi can now be achived like this: self: super: { mpi = super.mpich; } All derivations that have been using "mpi ? null" to provide optional building with MPI have been change in the following way to allow for optional builds with MPI: { ... , mpi , useMpi ? false }
* Merge pull request #110050 from PhDyellow/master_plus_patches_3Peter Simons2021-01-20
|\ | | | | r-modules: fix gert build
| * r-modules: fix gert buildPhil Dyer2021-01-18
| | | | | | | | gert requires pkgs.libgit2 to build.
* | treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nixJonathan Ringer2021-01-19
| | | | | | | | | | | | | | | | | | | | | | | | | | continuation of #109595 pkgconfig was aliased in 2018, however, it remained in all-packages.nix due to its wide usage. This cleans up the remaining references to pkgs.pkgsconfig and moves the entry to aliases.nix. python3Packages.pkgconfig remained unchanged because it's the canonical name of the upstream package on pypi.
* | Merge pull request #93590 from lblasc/r-packagesPeter Simons2021-01-18
|\ \ | | | | | | R: remove qtbase.patch and fix few CRAN packages
| * | R: remove qtbase.patch and fix few CRAN packagesLuka Blaskovic2020-11-05
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* | | Merge pull request #109717 from teto/fix-r-wrapperPeter Simons2021-01-18
|\ \ \ | |_|/ |/| | rWrapper: use symlinkJoin instead of runCommand
| * | rWrapper: use symlinkJoin instead of runCommandMatthieu Coudron2021-01-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | While trying to build a haskell-project I got: Configuring library for inline-r-0.10.4.. cabal: The pkg-config package 'libR' version ==3.0 || >3.0 is required but it could not be found. the rWrapper was only bringing the R binary without its companion library: this fixes it.
* | | r-modules: fix clustermq and rzmq buildPhil Dyer2021-01-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | rzmq uses pkgconfig. clustermq now incorporates ZMQ libs directly, rather than using the rzmq package. clustermq now uses zeromq and pkgconfig. Both packages needed patchShebangs, due to pkgconfig.
* | | pkgs/development: stdenv.lib -> libPavol Rusnak2021-01-17
|/ / | | | | | | | | | | | | | | | | | | | | | | this takes care of the following folders in pkgs/development: * arduino * chez-modules * go-packages * guile-modules * idris-modules * perl-modules * r-modules * ruby-modules
* | Added suggested macOS fix and fixed data.table package.Tikhon Jelvis2021-01-04
| | | | | | | | `data.table` had a `postInstall` step to rename `data.table.so` to `datatable.so`, but after the package bump the file was already called `datatable.so` and `mv` command would fail.
* | r-modules: update cran and bioc packagesTikhon Jelvis2021-01-02
| | | | | | | | | | | | | | | | | | The last snapshot was 4 months ago (2020-08-19). I also found that I needed newer definitions when I was trying to fix the R arrow package. This update required a couple of manual changes: 1. Removing a few deleted packages from default.nix 2. Renaming the "assert" package to "r_assert" in generate-r-packages.R because "assert" is a keyword in Nix
* | Merge pull request #101451 from moritzschaefer/fix-r-mirror-pathSandro2020-11-27
|\ \ | | | | | | fix package path for bioc server
| * | fix package path for bioc server ↵Moritz Schaefer2020-10-23
| | | | | | | | | | | | (http://mirrors.ustc.edu.cn/bioc/3.11/bioc/src/contrib/Archive/)
* | | utillinux: rename to util-linuxGraham Christensen2020-11-24
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* | Fixes missing configure scriptMoritz Schaefer2020-10-23
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* r-modules: bioc and cran updateJustin Bedo2020-08-20
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* Merge pull request #91288 from rnhmjoj/zeromqMichele Guerini Rocco2020-07-26
|\ | | | | Remove old zeromq 3.x packages
| * rzmq: use default zeromqrnhmjoj2020-06-22
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* | rpackages.RcppParallel: Patch shebangcfhammill2020-07-13
|/ | | | Fixes hydra build error
* r-statmod: Add libiconv to buildInputsMatt Wittmann2020-05-14
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* Merge pull request #82504 from mcwitt/fix/r-mvtnormPeter Simons2020-05-11
|\ | | | | r-mvtnorm: add libiconv to buildInputs
| * r-mvtnorm: add libiconv to buildInputsMatt Wittmann2020-03-13
| | | | | | | | Fixes build failure with `ld: library not found for -liconv`
* | R: Update CRAN and bioconductor packagesAlex Branham2020-04-26
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* | treewide: use blas and lapackMatthew Bauer2020-04-17
| | | | | | | | | | | | | | | | | | | | | | | | This makes packages use lapack and blas, which can wrap different BLAS/LAPACK implementations. treewide: cleanup from blas/lapack changes A few issues in the original treewide: - can’t assume blas64 is a bool - unused commented code
* | R: Update CRAN and bioconductor packagesAlex Branham2020-04-08
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* rPackages.ggbio: patch away spelling mistakeEdward Tjörnhammar2020-02-26
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* r-modules/generic-builder: Add missing iconv library to fix build on darwin ↵tricktron2020-02-07
| | | | | (#78965) Add missing iconv dependency to fix builds of several r-modules on darwin.
* r-packages: updateMaximilian Bosch2020-01-28
| | | | | | | | | | This update was primarily done to update rPackages.V8 to 3.0 which doesn't depend on an ancient version of v8 anymore. Also dropped the `-lv8_libplatform` linker flag. It seems as this now part of `v8.so` as `v8_libplatform.so` doesn't exist anymore on recent v8 versions in nixpkgs, but the headers are still there and there aren't any "undefined reference to" errors while linking.
* R: Update CRAN and bioconductor packagesAlex Branham2020-01-23
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* rgl: fix buildLinus Heckemann2020-01-01
| | | | | | | It seems that the dev output of libGLU needs to be included explicitly for this to work. I've also moved the libraries from nativeBuildInputs to buildInputs to be more semantically correct (and maybe support cross compilation, not tested though).
* R: Update CRAN and bioconductor packagesAlex Branham2019-12-16
| | | | Closes https://github.com/NixOS/nixpkgs/pull/75010.
* Merge pull request #75021 from mnacamura/r-websocketPeter Simons2019-12-10
|\ | | | | rPackages.websocket: fix build
| * rPackages.websocket: fix buildMitsuhiro Nakamura2019-12-05
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* | treewide: Get rid of libGLU_combinedadisbladis2019-11-18
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* rPackages.glmnet: Add missing dependencyNick Partridge2019-11-01
| | | | | Fixes the error: ld: library not found for -liconv
* rPackages.ModelMetrics: fix darwin buildNick Partridge2019-10-31
| | | | | | | This fixes the error: auc_.cpp:2:10: fatal error: 'omp.h' file not found #include <omp.h>
* r-systemfonts: fix shebang of configure scriptPeter Simons2019-10-10
| | | | Closes https://github.com/NixOS/nixpkgs/pull/70813.
* r-systemfonts: fix package dependenciesDylan Simon2019-10-10
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* r-data.table: add missing zlib dependency to fix the buildPeter Simons2019-10-06
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* R: Update CRAN and bioconductor packagesAlex Branham2019-10-06
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* Merge branch 'master' into staging-nextVladimír Čunát2019-09-24
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| * Merge pull request #69333 from mnacamura/r-ucminfJörg Thalheim2019-09-24
| |\ | | | | | | r-ucminf: fix build on Darwin
| | * r-ucminf: fix build on DarwinMitsuhiro Nakamura2019-09-24
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| * | Merge pull request #69330 from mnacamura/r-rfJörg Thalheim2019-09-24
| |\ \ | | | | | | | | r-randomForest: fix build on Darwin
| | * | r-randomForest: fix build on DarwinMitsuhiro Nakamura2019-09-24
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| * | Merge pull request #69332 from mnacamura/r-minqaJörg Thalheim2019-09-24
| |\ \ | | | | | | | | r-minqa: fix build on Darwin
| | * | r-minqa: fix build on DarwinMitsuhiro Nakamura2019-09-24
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| * / r-pan: fix build on DarwinMitsuhiro Nakamura2019-09-24
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* / Re-Revert "Merge branch 'staging-next'"Vladimír Čunát2019-09-22
|/ | | | This reverts commit f8a8fc6c7c079de430fa528f688ddac781bcef16.
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