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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
}
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r-modules: fix gert build
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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.
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R: remove qtbase.patch and fix few CRAN packages
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gert requires pkgs.libgit2 to build.
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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.
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`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.
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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
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fix package path for bioc server
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(http://mirrors.ustc.edu.cn/bioc/3.11/bioc/src/contrib/Archive/)
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Remove old zeromq 3.x packages
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Fixes hydra build error
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r-mvtnorm: add libiconv to buildInputs
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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
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Fixes build failure with `ld: library not found for -liconv`
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(#78965)
Add missing iconv dependency to fix builds of several r-modules on darwin.
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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.
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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).
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rPackages.websocket: fix build
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Fixes the error:
ld: library not found for -liconv
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This fixes the error:
auc_.cpp:2:10: fatal error: 'omp.h' file not found
#include <omp.h>
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Closes https://github.com/NixOS/nixpkgs/pull/70813.
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r-ucminf: fix build on Darwin
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r-randomForest: fix build on Darwin
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r-minqa: fix build on Darwin
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This reverts commit f8a8fc6c7c079de430fa528f688ddac781bcef16.
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This reverts commit 41af38f3728bd64b80721c44ed1fb019978cbc1b, reversing
changes made to f0fec244ca380b9d3e617ee7b419c59758c8b0f1.
Let's delay this. We have some serious regressions.
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Builds were failing to include PROJ, depending on proj.dev
appears to fix it.
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