Commit Graph

575 Commits

Author SHA1 Message Date
Justin Bedo
d8d5d73bac
rPackages.Rhdf5lib: enable cxx bindings 2023-03-24 09:47:44 +11:00
Justin Bedo
445df9ef48
rPackages.Rhdflib: patch linking flags 2023-03-23 15:19:58 +11:00
Justin Bedo
14db22f868
rPackages.rhdf5: fix build
use nixpkgs provided hdf5 instead of vendored library
2023-03-22 09:48:06 +11:00
Justin Bedo
442e1b87d1
rPackages.rhdf5filters: fix build
- use hdf5-blosc from nixpkgs to fix failing vendored build
- add missing build dependencies
2023-03-22 09:47:58 +11:00
Justin Bedo
ccfbc19630
rPackages.Rhdf5lib: fix build
use nixpkgs provided hdf5 and libaec to resolve failing vendored code
2023-03-22 09:47:48 +11:00
Justin Bedo
a10887cb3f
rPackages.purrr: patch configure shebang 2023-03-16 22:10:42 +11:00
Justin Bedo
0c0c6908b9
rPackages: CRAN and BioC update 2023-03-16 21:32:06 +11:00
Sandro
46e5d1e231
Merge pull request #217517 from savyajha/radian 2023-03-10 23:11:26 +01:00
Justin Bedő
4f4a054dd2
Merge pull request #219439 from nviets/sparklyr
rPackages: sparklyr environment variables
2023-03-08 03:52:05 +00:00
Nathan Viets
2f430da1c6 Replacing MRAN mirror with posit 2023-03-07 18:23:26 +01:00
nviets
7939447527
Update pkgs/development/r-modules/default.nix
Co-authored-by: Justin Bedő <cu@cua0.org>
2023-03-07 11:08:38 +01:00
nviets
62821edd2e This PR sets default SPARK_HOME and JAVA_HOME for R's sparklyr package using a patch in .onload. Preset value take precedence. SPARK_HOME points to python3Packages.pyspark rather than pkgs.spark because the former is actively maintained. 2023-03-06 12:03:04 +01:00
Savyasachee Jha
e730867dc0 python310Packages.radian: init at 0.6.4 and provide radianWrapper 2023-03-05 19:12:32 +05:30
K900
3dccc7c365 r-modules: fix eval
Not sure how this worked before. Now it at least evals.
2023-02-24 22:45:28 +03:00
Artturin
5110d8b6fb rPackages: s/overrideDerivation/overrideAttrs
and attrs.NIX_CFLAGS_COMPILE to attrs.env.NIX_CFLAGS_COMPILE

https://nixos.org/manual/nixpkgs/stable/#sec-pkg-overrideDerivation

> Do not use this function in Nixpkgs as it evaluates a Derivation before modifying it, which breaks package abstraction and removes error-checking of function arguments
2023-02-23 18:45:41 +02:00
Artturin
f9fdf2d402 treewide: move NIX_CFLAGS_COMPILE to the env attrset
with structuredAttrs lists will be bash arrays which cannot be exported
which will be a issue with some patches and some wrappers like cc-wrapper

this makes it clearer that NIX_CFLAGS_COMPILE must be a string as lists
in env cause a eval failure
2023-02-22 21:23:04 +02:00
nviets
dcd759fe65
rPackages.quarto: add quarto dependency 2023-02-17 03:25:35 +00:00
Justin Bedő
d92d0a1e54
Merge pull request #212537 from nviets/nanonext
nng: 1.5.2 -> 1.6.0-prerelease and to rPackages.nanonext dependencies
2023-02-07 02:07:00 +00:00
Nathan Viets
67e898c12e nng: 1.5.2 -> 1.6.0-prerelease and rPackages.nanonext dependency 2023-02-06 18:49:06 -06:00
Nathan Viets
3f5c9df651
rPackages: added libiconv to darwin builds and removed redundant package level calls 2023-02-07 09:39:53 +11:00
Chris Warburton
802527baa2 rPackages.classInt: add libiconv dependency to fix build on darwin
Avoids 'ld: library not found for -liconv' on x86_64-darwin
2023-01-06 12:05:12 +00:00
Justin Bedo
7ed992a3fb
rPackages: CRAN and BioC update 2022-12-15 08:51:33 +11:00
Justin Bedő
e442f93a8c
Merge pull request #204684 from trofi/rPackages.devEMF-without-xlibsWrapper
rPackages.devEMF: use xorg.* packages directly instead of xlibsWrappe…
2022-12-06 07:22:53 +00:00
Justin Bedő
43f39630df
Merge pull request #204550 from trofi/rPackages.imager-without-xlibsWrapper
rPackages.imager: use xorg.* packages directly instead of xlibsWrappe…
2022-12-06 07:16:01 +00:00
Sergei Trofimovich
b2b5c4db0b rPackages.Cairo: use xorg.* packages directly instead of xlibsWrapper indirection
Validated as no change in `out` output with `diffoscope`.
2022-12-05 21:22:13 +00:00
Sergei Trofimovich
a2fbaae04a rPackages.devEMF: use xorg.* packages directly instead of xlibsWrapper indirection
Validated as no change in `out` output with `diffoscope`.
2022-12-05 21:16:38 +00:00
Sergei Trofimovich
c5b0d1ec8e rPackages.imager: use xorg.* packages directly instead of xlibsWrapper indirection
Validated as no change in `out` output with `diffoscope`.
2022-12-04 22:36:36 +00:00
Sergei Trofimovich
2d36d576f8 rPackages.rgl: use xorg.* packages directly instead of xlibsWrapper indirection
Validated as no change in `out` output with `diffoscope`.
2022-12-04 18:44:31 +00:00
Mario Rodas
e76e9ed99c rPackages.bigmemory: fix evaluation on darwin
On Darwin pkgs.libuuid is null, hence evaluating `.dev` fails.
2022-11-24 01:46:29 -05:00
Justin Bedo
1249b08676
rPackages.RNifti: fix build 2022-11-02 10:14:57 +11:00
Justin Bedo
644b5a7ac7
rPackages.bigmemory: add missing dependency 2022-11-02 10:11:53 +11:00
Justin Bedo
3f86920ae8
rPackages: CRAN and BioC update 2022-10-31 13:46:43 +11:00
Justin Bedő
abe366dd5c
Merge pull request #196979 from Et7f3/fix-deldir
deldir: specify iconv library for darwin.
2022-10-23 23:57:56 +00:00
Et7f3
e8327603e1 rPackages.interp: specify iconv library for darwin 2022-10-21 21:21:34 +02:00
Et7f3
a88371fb6d rPackages.deldir: specify iconv library for darwin 2022-10-20 23:45:16 +02:00
Nicolas Benes
7396451d6c rPackages.mzR: unpin boost
`mzR` currently ships and builds its own copy of boost-176, see
https://github.com/sneumann/mzR/blob/master/src/README.updateboost
2022-10-20 17:41:35 +02:00
Matthieu Coudron
8e7161ed80 rPackages.rmarkdown: add pandoc as buildInput
https://github.com/rstudio/rmarkdown/blob/main/DESCRIPTION#L91 requires pandoc from system
2022-09-30 12:40:07 +02:00
Theodore Ni
e0a5a1c3a0
rPackages: reenable stackprotector on aarch64-darwin
The original error that required disabling the stack protector on
aarch64-darwin has been fixed in GCC.
2022-09-04 11:47:02 -07:00
Justin Bedo
ba3564f74b
rPackages.s2: fix openssl linking 2022-08-22 11:41:09 +10:00
Justin Bedo
d7bf754c96
rPackages: CRAN and BioC update 2022-08-18 07:11:43 +10:00
Justin Bedo
09528e6db8
rPackages: CRAN and BioC update 2022-07-02 22:36:01 +10:00
hqurve
1fc4712f15 rPackages.gifski: fix build 2022-06-18 20:37:09 -04:00
Justin Bedo
f07c969b8d
rPackages: CRAN and BioC update 2022-05-17 13:34:56 +10:00
Justin Bedo
42caad601b
rPackages.Rhdf5lib: propagate hdf5 dependency
Packages that depend on Rhdf5lib also require the dev hdf5 outputs
for correct functionality.
2022-05-15 08:49:46 +10:00
Justin Bedo
72c388eed4
rPackages.Rhdf5lib: fix build
Patch is no-longer necessary; HDF5 no-longer vendored
2022-05-06 10:54:43 +10:00
Justin Bedo
db5e7f7a92
rPackages: CRAN and BioC update 2022-04-27 09:56:24 +10:00
Justin Bedo
6675a16146
rPackages: CRAN and BioC update 2022-04-11 11:31:14 +10:00
Ben Siraphob
0d95d03c98
Merge pull request #165765 from ConnorBaker/patch-1 2022-04-04 16:56:52 -05:00
Alyssa Ross
fd78240ac8
treewide: use lib.getLib for OpenSSL libraries
At some point, I'd like to make another attempt at
71f1f4884b ("openssl: stop static binaries referencing libs"), which
was reverted in 195c7da07d.  One problem with my previous attempt is
that I moved OpenSSL's libraries to a lib output, but many dependent
packages were hardcoding the out output as the location of the
libraries.  This patch fixes every such case I could find in the tree.
It won't have any effect immediately, but will mean these packages
will automatically use an OpenSSL lib output if it is reintroduced in
future.

This patch should cause very few rebuilds, because it shouldn't make
any change at all to most packages I'm touching.  The few rebuilds
that are introduced come from when I've changed a package builder not
to use variable names like openssl.out in scripts / substitution
patterns, which would be confusing since they don't hardcode the
output any more.

I started by making the following global replacements:

    ${pkgs.openssl.out}/lib -> ${lib.getLib pkgs.openssl}/lib
    ${openssl.out}/lib -> ${lib.getLib openssl}/lib

Then I removed the ".out" suffix when part of the argument to
lib.makeLibraryPath, since that function uses lib.getLib internally.

Then I fixed up cases where openssl was part of the -L flag to the
compiler/linker, since that unambigously is referring to libraries.

Then I manually investigated and fixed the following packages:

 - pycurl
 - citrix-workspace
 - ppp
 - wraith
 - unbound
 - gambit
 - acl2

I'm reasonably confindent in my fixes for all of them.

For acl2, since the openssl library paths are manually provided above
anyway, I don't think openssl is required separately as a build input
at all.  Removing it doesn't make a difference to the output size, the
file list, or the closure.

I've tested evaluation with the OfBorg meta checks, to protect against
introducing evaluation failures.
2022-03-30 15:10:00 +00:00
Connor Baker
f50e41bfd6 rPackages: nloptr requires libiconv 2022-03-25 14:36:43 -04:00