Mitsuhiro Nakamura
3001a1f3ff
r-pan: fix build on Darwin
2019-09-24 07:59:04 +09:00
Mitsuhiro Nakamura
8df7139996
r-randomForest: fix build on Darwin
2019-09-24 07:23:25 +09:00
Vladimír Čunát
22a216849b
Re-Revert "Merge branch 'staging-next'"
...
This reverts commit f8a8fc6c7c
.
2019-09-22 09:38:09 +02:00
Vladimír Čunát
f8a8fc6c7c
Revert "Merge branch 'staging-next'"
...
This reverts commit 41af38f372
, reversing
changes made to f0fec244ca
.
Let's delay this. We have some serious regressions.
2019-09-21 20:05:09 +02:00
Izorkin
329a88efa7
treewide: replace mysql.connector-c to libmysqlclient
2019-09-09 15:55:34 +03:00
volth
7b8fb5c06c
treewide: remove redundant quotes
2019-09-08 23:38:31 +00:00
cfhammill
8e5aae5a19
Fix broken builds for rgdal and sf R packages
...
Builds were failing to include PROJ, depending on proj.dev
appears to fix it.
2019-09-02 16:23:24 +03:00
Peter Simons
8ac6b77eff
Merge pull request #66204 from jabranham/r-pkgs
...
R: Update CRAN and bioconductor packages
2019-08-07 10:24:37 +02:00
Alex Branham
eab786451f
R: Update CRAN and bioconductor packages
2019-08-06 08:49:39 -05:00
Dominic Steinitz
4788c7eb28
Ensure sundialr builds on macos.
2019-08-06 13:45:44 +01:00
Frederik Rietdijk
7cf5909fad
Merge staging-next into staging
2019-07-09 15:44:08 +02:00
Thomas Tuegel
51d78034a1
wrapQtAppsHook: Remove ad hoc Qt wrappers
2019-07-05 10:42:08 -05:00
Alex Branham
46bca1d643
R: Update CRAN and bioconductor packages
2019-07-02 15:48:06 -05:00
Alex Branham
00b202e34a
rPackages.git2r: Use system libgit2
...
Otherwise git2r builds a bundled libgit2
2019-06-14 10:05:07 -05:00
c0bw3b
9cb260d091
[treewide] delete unused patches
2019-05-04 19:52:24 +02:00
Alex Branham
0a80d3dc82
R: update CRAN and Bioconductor package sets
...
Closes https://github.com/NixOS/nixpkgs/pull/59186 .
2019-04-11 20:37:18 +02:00
Peter Simons
3c9ff308e7
Merge pull request #58467 from mnacamura/r-sys
...
r-sys: remove obsolete dependency
2019-03-28 12:42:19 +01:00
Mitsuhiro Nakamura
157921f2e7
rPackages: fix missing dependency to libiconv
2019-03-28 12:11:47 +09:00
Mitsuhiro Nakamura
d07c3139ed
r-sys: remove obsolete dependency
2019-03-28 11:20:04 +09:00
Alex Branham
8dcba2b842
R: update CRAN and Bioconductor package sets
...
Closes https://github.com/NixOS/nixpkgs/pull/57423 .
2019-03-14 19:50:37 +01:00
Markus Ankenbrand
7fcfbcdbc9
rPackages.phytools: fix installation
2019-03-06 11:39:48 +01:00
Alex Branham
ec03ed450c
update R package set
...
Closes https://github.com/NixOS/nixpkgs/pull/55462 .
2019-02-10 11:16:19 +01:00
Alex Branham
48541ab6b9
R: update CRAN and BIOC package sets
...
Closes https://github.com/NixOS/nixpkgs/pull/53414 .
2019-01-08 09:34:37 +01:00
Alex Branham
6f7459b40b
R: update CRAN package set
2018-12-12 11:17:25 -06:00
Edmund Wu
a898f88d57
rstudioWrapper: include desktop file
2018-12-07 16:44:01 -05:00
Joachim F
f0dbbdf970
Merge pull request #51581 from joachifm/rWrapper-local-runCommand
...
Implement R wrappers as local-only runCommand
2018-12-07 09:17:44 +00:00
Christian Kauhaus
3b445042ac
rPackages.littler: fix build ( #51282 )
...
littler gives a wrapped called `r` (or `lr` for non-case-preserving
systems like Darwin) which works as shebang or pipe target.
The build was completely broken before (missing deps).
Symlink executables and manpage into standard locations so that this
packages also works in `environment.systemPackages`.
2018-12-06 17:22:31 +01:00
Joachim Fasting
21d83e5b11
rstudioWrapper: use runCommand, local build only
...
This seems more appropriate for a wrapper generator.
2018-12-05 20:59:41 +01:00
Joachim Fasting
d2b467a2de
rWrapper: use runCommand, local build only
...
This seems more appropriate for a wrapper generator.
2018-12-05 20:59:35 +01:00
Timo Kaufmann
63b39af496
pythonPackages.rpy2: various fixes ( #51084 )
...
- make sure libreadline is found at runtime
- make sure python libraries are found at runtime
- add libraries necessary to pass the testsuite and standard libraries
2018-11-27 18:24:37 +01:00
Massimo Redaelli
5afe1e7c70
rstudio: fix qt plugins not found
2018-11-23 23:10:29 +01:00
Averell Dalton
25e68e3048
r-ps: patchShebangs in ./configure to fix build
2018-11-02 23:02:04 +01:00
Peter Simons
c9e1380626
r-nloptr: fix build by adding pkgconfig
2018-11-02 17:50:18 +01:00
Peter Simons
9b63cc6313
r-rlang: patch shebang in configure script to fix the build
2018-11-02 17:50:18 +01:00
Tom McLaughlin
cac5c9401e
R: update CRAN and BIOC package sets
...
Closes https://github.com/NixOS/nixpkgs/pull/49430 .
2018-11-02 17:50:18 +01:00
Rob Vermaas
3f719b0fad
Fix build for rPackages.units
...
(cherry picked from commit 1eb1fec3ae
)
2018-10-08 12:53:43 +02:00
ivanbrennan
989f24befc
git2r: add SSH support
...
When building the devtools R module, which depends on git2r, it reports
that libssh2 cannot be found, and falls back to building without SSH
support. Adding libssh2.dev to git2r's native build inputs fixes this.
2018-09-11 16:39:20 -04:00
Ryan Mulligan
73ae8e53e2
rPackages.RPostgres: fix configure paths and includes
...
closes #46208
2018-09-09 14:37:28 -07:00
Mitsuhiro Nakamura
5e42a081a3
r-jqr: fix build ( #45333 )
2018-08-20 00:08:28 +02:00
volth
e6d3c65442
r-packages: fix regression
2018-08-04 06:19:08 +00:00
Mitsuhiro Nakamura
0a541aa38c
rPackages.buildRPackage: fix error if requireX is missing
2018-08-03 01:08:35 +09:00
Mitsuhiro Nakamura
559997179d
rPackages: export buildRPackage
2018-08-03 01:08:07 +09:00
volth
52f53c69ce
pkgs/*: remove unreferenced function arguments
2018-07-21 02:48:04 +00:00
Markus Ankenbrand
775fd4bfba
rPackages.haven: fix installation
2018-07-12 11:07:27 +02:00
Mitsuhiro Nakamura
c072024409
rPackages.reprex: fix build
2018-07-11 23:16:49 +09:00
Markus Ankenbrand
89f44c1314
rPackages.rhdf5: fix installation
...
Fix #43285
2018-07-10 16:38:11 +02:00
Peter Simons
03476783a5
R: fix evaluation errors
2018-07-07 12:10:46 +02:00
Peter Simons
49c649d573
R: update CRAN package set to snapshot 2018-07-06
2018-07-07 12:10:46 +02:00
Peter Simons
d984656a2a
R: update package set
...
The CRAN snapshot is at "2018-07-03". Bioc is now at 3.8.
2018-07-07 12:10:46 +02:00
Markus Ankenbrand
9eeea0b9ef
rPackages.rhdf5: fix installation
...
Fix #42878
2018-07-02 18:51:18 +02:00
Daiderd Jordan
654960c1cd
Merge pull request #42290 from mnacamura/r-igraph-darwin
...
rPackages.igraph: fix Darwin build
2018-06-20 19:52:36 +02:00
Mitsuhiro Nakamura
f972a30f16
rPackages.igraph: fix Darwin build
2018-06-20 11:08:29 +09:00
Mitsuhiro Nakamura
dada18527a
rPackages.RcppEigen: fix Darwin build
2018-06-20 10:59:18 +09:00
Josef Kemetmüller
aeda45821d
rPackages.mgcv: fix darwin build
...
This fixes the error:
ld: library not found for -liconv
2018-06-07 00:00:42 +02:00
Josef Kemetmüller
0275562a12
rPackages.Matrix: fix darwin build
...
This fixes the error:
ld: library not found for -liconv
2018-06-07 00:00:07 +02:00
Josef Kemetmüller
d8ad2ad916
rPackages.nlme: fix darwin build
...
This fixes the error:
ld: library not found for -liconv
2018-06-06 23:59:09 +02:00
Josef Kemetmüller
e023f117f8
rPackages.KernSmooth: fix darwin build
...
This fixes the error:
ld: library not found for -liconv
2018-06-06 23:58:46 +02:00
Josef Kemetmüller
5d092b3052
rPackages.cluster: fix darwin build
...
This fixes the error:
ld: library not found for -liconv
2018-06-06 23:57:08 +02:00
Mitsuhiro Nakamura
89a5e6db55
rPackages.JuniperKernel: fix non-Darwin build
2018-05-15 17:50:11 +09:00
Mitsuhiro Nakamura
d35604d910
rPackages: fix binutils path on Darwin
2018-05-12 20:51:43 +09:00
Peter Simons
94295e3cee
R: update CRAN and BIOC package sets
2018-04-24 09:19:38 +02:00
Shea Levy
05e375d710
Merge remote-tracking branch 'origin/master' into staging
2018-03-28 09:36:47 -04:00
Graham Christensen
92d53362d4
Move all nixpkgs doc files in to the doc directory
...
This makes a makefile-driven developer workflow nicer.
2018-03-25 19:52:00 -04:00
Matthew Bauer
9109a90479
treewide: remove some more gettext references
2018-03-22 16:50:14 -05:00
Peter Simons
9c207cd922
R: fix evaluation errors
2018-03-15 21:14:29 +01:00
Peter Simons
52dce0fb38
R: update the CRAN and BIOC package sets
2018-03-15 19:39:55 +01:00
Averell Dalton
028e67abce
rPackages.mongolite: fix build
2018-03-10 04:01:49 +01:00
Vladimír Čunát
565bd805e6
Merge branch 'master'
2018-03-05 14:53:27 +01:00
Peter Simons
a06b81b8ad
Merge pull request #35651 from mnacamura/r-xml2-darwin
...
rPackages.xml2: fix darwin build
2018-02-26 20:16:16 +01:00
Mitsuhiro Nakamura
4b1627d313
rPackages.xml2: fix darwin build
2018-02-26 10:47:57 +09:00
Mitsuhiro Nakamura
671e3f5c4d
rPackages.JuniperKernel: fix darwin build
2018-02-26 10:00:00 +09:00
Alexander V. Nikolaev
0acec7e984
treewide: transition mesa to libGLU_combined
2018-02-24 17:06:49 +02:00
Justin Bedo
8d03d9b9af
rPackages: add bioconductor archive url
2018-02-21 09:58:17 +11:00
Justin Bedo
cfc07bcf0e
bioconductor: 3.4 -> 3.6
2018-02-21 09:58:17 +11:00
Mitsuhiro Nakamura
c4658ac0a4
rPackages.pbdZMQ: fix package loading on Darwin
2018-02-10 00:54:28 +09:00
Mitsuhiro Nakamura
2533720976
rPackages.data_table: OpenMP support on Darwin
2018-01-19 19:30:55 +09:00
Daiderd Jordan
5a02143c20
Merge pull request #33010 from LnL7/cacert-hook
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cacert: add hook that sets SSL_CERT_FILE
2018-01-07 09:55:15 +01:00
Robin Gloster
ee1c85aee9
mariadb: lib -> connector-c
2017-12-29 02:18:35 +01:00
Daiderd Jordan
091c2b9f04
cacert: cleanup exporting SSL_CERT_FILE
2017-12-27 21:36:32 +01:00
Peter Simons
65b15c40f1
R: update package set
2017-12-01 13:48:26 +01:00
Peter Simons
458331408e
r-openssl: fix build
2017-11-30 18:45:47 +01:00
John Ericson
405412dfd9
Merge pull request #31775 from obsidiansystems/stdenv-both-propagated-files
...
stdenv setup: Always use both propagated files
2017-11-22 15:23:37 -05:00
John Ericson
da19c34d0f
stdenv setup: Always use both propagated files
...
This continues #23374 , which always kept around both attributes, by
always including both propagated files: `propgated-native-build-inputs`
and `propagated-build-inputs`. `nativePkgs` and `crossPkgs` are still
defined as before, however, so this change should only barely
observable.
This is an incremental step to fully keeping the dependencies separate
in all cases.
2017-11-21 10:44:44 -05:00
Matthew Justin Bauer
24e38f3075
r-modules: fix eval
...
Fixes #31508
2017-11-12 21:49:41 -06:00
Maciej Kazulak
42b70ae5ed
nixpkgs manual: add rstudio shell.nix example
...
Provide an example of a self-contained shell.nix for rstudio with
additional packages.
2017-11-04 12:26:08 +01:00
Hamish Mackenzie
8870d1a67d
r-modules: Fix a number of popular R packages
...
The R V8 package still depends on V8 3.14 so this is also included.
2017-10-21 11:29:21 +01:00
Peter Simons
11131d5fc1
R: update package set
2017-09-29 15:21:09 +02:00
Peter Simons
aa9bebf261
R: update package set
2017-08-31 21:59:06 +02:00
Mitsuhiro Nakamura
c5fe03ace2
r-pbdZMQ: fix Darwin install
2017-07-14 14:32:51 +09:00
Peter Simons
b1ebe7a72c
r-modules: update package set
2017-07-02 09:51:42 +02:00
Chris Hodapp
29969a5ec7
rstudio: Fix recompilation issue with custom package set
...
This attempts to fix the issue described at
https://github.com/NixOS/nixpkgs/pull/22219#issuecomment-291801133 .
Any change to the custom packages passed to RStudio causes this to
completely rebuild RStudio, which is completely unnecessary and also a
bit of a hindrance as it's a fairly slow build.
This rolls back most of that old PR, and instead implements something
more like rWrapper. Existing configurations with the old useRPackages
will break.
2017-05-01 09:46:40 -04:00
Peter Simons
85a9e6dcdf
R: update list of broken packages (and some cosmetic)
2017-04-24 15:39:54 +02:00
Peter Simons
430cbcfd2b
R: update CRAN and BIOC package sets
2017-04-24 15:39:08 +02:00
Chris Hodapp
80beb55cfc
imager (r-modules): add pkgs.x11 to fix build, unmark imager/ForestTools as broken
2017-04-20 14:18:01 -04:00
Peter Simons
add394d8f1
r-modules: update CRAN package set
2017-03-07 14:56:46 +01:00
Peter Simons
f4595fa555
r-modules: drop broken irkernel package set
...
We can no longer update that package set since, apparently, it has moved
to a different packaging scheme.
2017-03-07 14:56:46 +01:00
Peter Simons
3dc4e12ff0
r-modules: remove weird version assertion
2017-03-07 14:56:46 +01:00
Nikolay Amiantov
477b507a4f
rPackages: remove old cuda-related patches
...
gputools doesn't build but because of unrelated linking issues.
2017-02-28 17:31:07 +03:00
Nikolay Amiantov
6f3e071755
rPackages: try to unbreak reverse dependencies of cudatoolkit
2017-02-28 17:22:06 +03:00
Domen Kožar
ffe935ee86
Merge pull request #23104 from dtzWill/fix/generate-shell
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R/generate-shell: Use R from current tree, fix missing wget dep.
2017-02-27 14:06:17 +01:00
Domen Kožar
a7dc912460
Merge pull request #23069 from lukego/R-packages-readme
...
r-modules/README.md: mention generate-shell.nix
2017-02-27 14:04:35 +01:00
Domen Kožar
4ccb553b70
Merge pull request #22817 from jbedo/r
...
R: 3.2.4 -> 3.3.2
2017-02-27 14:02:13 +01:00
Domen Kožar
7ed28a0b78
R: fix bio3d build
2017-02-27 13:51:55 +01:00
Justin Bedo
4c2d75f58c
R: unmark edgeR and limma as broken
2017-02-24 15:52:10 +11:00
Justin Bedo
4bb8727284
R: 3.2.4 -> 3.3.2
2017-02-24 15:22:12 +11:00
Will Dietz
2f303bc10e
R/generate-shell: Use R from current tree, fix missing wget dep.
...
Without this change, the 'R' version used might be the wrong
one which changes the package lists used.
Fixes #19530 .
2017-02-23 07:46:20 -06:00
Luke Gorrie
a000ec038e
r-modules/README.md: mention generate-shell.nix
2017-02-22 04:48:50 +00:00
Eelco Dolstra
9d6a55aefd
~/.nixpkgs -> ~/.config/nixpkgs
...
The former is still respected as a fallback for config.nix for
backwards compatibility (but not for overlays because they're a new
feature).
2017-02-01 16:07:55 +01:00
Chris Hodapp
7638578342
RStudio: Optionally allow packages from custom R environment
...
https://nixos.org/nixpkgs/manual/#r-packages contains a method for
setting up an R environment with a specific set of libraries, and it
creates an R wrapper which points R to those libraries.
The package RStudio relies on the standard R package, which then
cannot access any of the libraries specified in a custom R
environment. While one may easily use pkgs.rstudio.override to change
rstudio's R dependency to the custom R environment, this accomplishes
nothing because while RStudio runs the correct R wrapper it clears out
the environment variable R_LIBS_SITE - and so it is still unable to
use any of those packages.
In order to work around this problem, these changes allow the user to
optionally modify rstudio's wrapper to set environment variable
R_PROFILE_USER to an R script which sets R's .libPaths(..) to point to
the same libraries; that script is generated from R_LIBS_SITE in the R
wrapper.
By default, this change has no effect. If R is overridden to
something else, and if useRPackages is changed from its default of
false, then the change described above is made; for instance:
{
packageOverrides = pkgs: let self = pkgs.pkgs; in
rec {
rEnv = pkgs.rWrapper.override {
packages = with self.rPackages; [
dplyr ggplot2 e1071 rpart reshape
];
};
rstudioEnv = pkgs.rstudio.override { R = rEnv; useRPackages = true; };
};
}
2017-01-27 18:54:50 -05:00
mimadrid
8954412fcc
r-modules: fix snpStats package
2017-01-06 21:07:25 +01:00
mimadrid
b5a0925663
r-modules: fix VariantAnnotation package
2017-01-06 21:07:25 +01:00
mimadrid
6540b6507d
r-modules: fix rtracklayer package
2017-01-06 21:07:25 +01:00
mimadrid
baf65d5000
r-modules: fix Rsubread package
2017-01-06 21:07:25 +01:00
mimadrid
9ebab25442
r-modules: fix gmapR package
2017-01-06 21:07:25 +01:00
mimadrid
286e86f3a5
r-modules: fix oligo package
2017-01-06 21:07:25 +01:00
mimadrid
afd1a4c933
r-modules: fix affyio package
2017-01-06 21:07:25 +01:00
mimadrid
4c0c3c7493
r-modules: fix BitSeq package
2017-01-06 21:07:24 +01:00
mimadrid
272b447ea7
r-modules: fix bamsignals package
2017-01-06 21:07:24 +01:00
mimadrid
c5e4754ca7
r-modules: fix affyPLM package
2017-01-06 21:07:24 +01:00
mimadrid
1d7fd8f3c4
r-modules: fix xml2 package
2017-01-06 21:07:24 +01:00
mimadrid
5b813c2ab0
r-modules: fix XBRL package
2017-01-06 21:07:24 +01:00
mimadrid
512be9e14a
r-modules: fix WhopGenome package
2017-01-06 21:07:24 +01:00
mimadrid
f9d84f8b65
r-modules: fix tkrplot package
2017-01-06 21:07:24 +01:00
mimadrid
0b3e62bb12
r-modules: fix tiff package
2017-01-06 21:07:23 +01:00
mimadrid
9420fa23c6
r-modules: fix TAQMNGR package
2017-01-06 21:07:23 +01:00
mimadrid
2303e63116
r-modules: fix spate package
2017-01-06 21:07:23 +01:00
mimadrid
fcbed4b654
r-modules: fix showtext package
2017-01-06 21:07:23 +01:00
mimadrid
8a6b58d51d
r-modules: fix seqminer package
2017-01-06 21:07:23 +01:00
mimadrid
e1a5eeef06
r-modules: fix seqinr package
2017-01-06 21:07:22 +01:00
mimadrid
1ef67b9e78
r-modules: fix RVowpalWabbit package
2017-01-06 21:05:54 +01:00
mimadrid
ae2723a144
r-modules: fix rtiff package
2017-01-06 21:05:54 +01:00
mimadrid
d7ac90dd0c
r-modules: fix rtfbs package
2017-01-06 21:05:53 +01:00
mimadrid
fd175e4084
r-modules: fix Rssa package
2017-01-06 21:05:52 +01:00
mimadrid
bd2aaada6e
r-modules: fix RSclient package
2017-01-06 21:05:52 +01:00
mimadrid
53235dbe14
r-modules: fix rphast package
2017-01-06 21:05:52 +01:00
mimadrid
780fb79e32
r-modules: fix Rmpfr package
2017-01-06 21:05:51 +01:00
mimadrid
a58db75ccb
r-modules: fix rmatio package
2017-01-06 21:05:51 +01:00
mimadrid
674a2077dd
r-modules: fix rJava package
2017-01-06 21:05:51 +01:00
mimadrid
13a582688f
r-modules: fix RJaCGH package
2017-01-06 21:05:51 +01:00
mimadrid
9922867fa8
r-modules: fix Rhtslib package
2017-01-06 21:05:50 +01:00
mimadrid
bb60f939ae
r-modules: fix Rhpc package
2017-01-06 21:05:50 +01:00
mimadrid
e1bc505da9
r-modules: fix rggobi package
2017-01-06 21:05:50 +01:00
mimadrid
9f2b5e0425
r-modules: fix RGtk2 package
2017-01-06 21:05:50 +01:00
mimadrid
3342f8bd59
r-modules: fix RcppOctave package
2017-01-06 21:05:50 +01:00
mimadrid
ba86a39645
r-modules: fix RcppCNPy package
2017-01-06 21:05:49 +01:00
mimadrid
dd159d06b6
r-modules: fix rcdd package
2017-01-06 21:05:49 +01:00
mimadrid
8b229baf33
r-modules: fix rbamtools package
2017-01-06 21:05:49 +01:00
mimadrid
558f67e85f
r-modules: fix R2SWF package
2017-01-06 21:05:48 +01:00
mimadrid
277efe9896
r-modules: fix sysfonts package
2017-01-06 21:05:48 +01:00
mimadrid
062c9037d1
r-modules: fix PopGenome package
2017-01-06 21:05:48 +01:00
mimadrid
c5ef08cc65
r-modules: fix PKI package
2017-01-06 21:05:48 +01:00
mimadrid
1e9071948f
r-modules: fix mwaved package
2017-01-06 21:05:48 +01:00
mimadrid
4e7de52c26
r-module: fix kza package
2017-01-06 21:05:47 +01:00
mimadrid
debb12ce1a
r-module: fix jpeg package
2017-01-06 21:05:47 +01:00
mimadrid
e3a2c97c7b
r-modules: fix gmp package
2017-01-06 21:05:47 +01:00
mimadrid
72eb6a8644
r-modules: fix fftwtools package
2017-01-06 21:05:47 +01:00
mimadrid
427c4d954a
r-modules: fix fftw package
2017-01-06 21:05:47 +01:00
mimadrid
b88b8ea05b
r-modules: fix devEMF package
2017-01-06 21:05:47 +01:00
mimadrid
6c6aab3e5b
r-modules: fix cairoDevice package
2017-01-06 21:05:47 +01:00
mimadrid
f717538866
r-modules: fix git2r package
2017-01-06 21:05:47 +01:00
mimadrid
88fcfafafe
r-modules: fix BayesXsrc package
2017-01-06 21:05:46 +01:00
mimadrid
6f9124e118
r-modules: fix Cairo package
2017-01-06 21:05:46 +01:00
mimadrid
321d5a01b6
r-modules: fix seewave package
2017-01-06 16:31:30 +01:00
Mike Sperber
6c226b1e7a
rPackages.DescTools: unbreak build outside of Linux. ( #20787 )
...
DescTools does not require X during build, so remove it from that list.
2016-12-13 16:25:44 +01:00
Andreas Herrmann
98fce78cb3
r-modules: Fix png
package
...
The package requires the `dev` output of `libpng`.
2016-12-12 10:53:10 +01:00
Langston Barrett
2b300c9bef
r-modules: add more environment documentation
...
Use nix-shell with a `default.nix` rather than using
config.nix
2016-10-13 22:18:16 +00:00
Andreas Herrmann
cf3a2e99ad
r-modules: edgeR is broken due to broken url
2016-09-27 17:47:16 +02:00
Andreas Herrmann
54915ecf0d
r-modules: Fix h5 and rhdf5
...
and some packages that depend on them.
2016-09-27 17:46:06 +02:00
Peter Simons
23c122d277
r-openssl: fix build some more
2016-09-10 12:28:13 +02:00
Peter Simons
1196540a1d
r-openssl: fix build
2016-09-09 15:13:07 +02:00
Peter Simons
fe0256cd01
r-curl: fix build
2016-09-09 15:12:54 +02:00
Peter Simons
b2113f7893
r-XML: fix build
2016-09-09 14:36:49 +02:00
Thomas Tuegel
787875c287
r-stringi: fix build by including icu.dev output
2016-09-07 17:19:20 -05:00
Tuomas Tynkkynen
2258b21e4b
treewide: Add lots of platforms to packages with no meta
...
Build-tested on x86_64 Linux and on Darwin.
2016-08-02 21:17:44 +03:00
Michael Stone
c1d24efd6a
darwin: R: provide gettext and gfortran as buildInputs on Darwin.
...
As discussed in #10623 , many R modules fail to build on Darwin without the
libraries and compilers provided by these packages.
For more detail, please see comment:
https://github.com/NixOS/nixpkgs/pull/10623#issuecomment-172375342
2016-07-22 13:31:40 -04:00
Ben Darwin
a896233396
jags: 3.4.0 -> 4.1.0 ( #16804 )
...
* jags: 3.4.0 -> 4.1.0
* unbreak rjags and dependent packages
2016-07-18 13:11:18 +02:00
Tuomas Tynkkynen
2a73de6e6c
treewide: Make explicit that 'dev' output of openssl is used
2016-05-19 10:02:23 +02:00
Tuomas Tynkkynen
3f8b08f506
treewide: Make explicit that 'dev' output of mpfr is used
2016-05-19 10:00:49 +02:00
Tuomas Tynkkynen
b465dc202f
boost: Kill unnecessary 'lib' output
...
This was split in somewhere pre-2014 without the current infra which
automates parts of this, in particular the output propagation.
2016-04-28 00:41:28 +03:00
Peter Simons
a6978ded09
Merge pull request #14144 from jefdaj/r-bioc-data-packages
...
r-modules: update CRAN, add Bioconductor data packages
2016-04-15 14:46:19 +02:00
Jeffrey David Johnson
2291885f9e
mark bioc packages broken; should match hydra now
2016-04-14 14:34:11 -07:00
Jeffrey David Johnson
f88843f545
mark bioc packages broken; should match hydra now
2016-04-14 09:54:46 -07:00
Jeffrey David Johnson
2f6581df00
r-modules: mark mzR broken
2016-04-12 14:16:43 -07:00
Jeffrey David Johnson
2ceec79ad5
work on fixing up bioconductor packages
2016-03-31 16:16:34 -07:00
Jeffrey David Johnson
3c0fb5ede1
work on fixing up bioconductor packages
2016-03-31 11:36:39 -07:00
Jeffrey David Johnson
c9934bbcb8
work on fixing up bioconductor packages
2016-03-31 11:17:21 -07:00
Jeffrey David Johnson
518fd135ed
work on fixing up bioconductor packages
2016-03-27 23:14:24 -07:00
Jeffrey David Johnson
e98a231af8
work on fixing up bioconductor packages
2016-03-26 11:26:29 -07:00
Jeffrey David Johnson
05fc143451
work on fixing up bioconductor packages
2016-03-25 09:15:02 -07:00
Jeffrey David Johnson
1911d4925e
work on fixing up bioconductor package
2016-03-25 00:30:20 -07:00
Jeffrey David Johnson
4cd2202918
work on fixing up bioconductor packages
2016-03-24 14:51:21 -07:00
Jeffrey David Johnson
66bcbfb93d
r-modules: update CRAN, add Bioconductor data pkgs
2016-03-22 22:50:54 -07:00
Vladimír Čunát
09af15654f
Merge master into closure-size
...
The kde-5 stuff still didn't merge well.
I hand-fixed what I saw, but there may be more problems.
2016-03-08 09:58:19 +01:00
Michel Kuhlmann
312494180d
nixpkgs manual: add basic R documentation, fixes #13362
...
also fixes #13243
2016-02-22 10:16:06 +01:00
Vladimír Čunát
ae74c356d9
Merge recent 'staging' into closure-size
...
Let's get rid of those merge conflicts.
2016-02-03 16:57:19 +01:00
Tuomas Tynkkynen
555292017e
treewide: Mass replace 'xorg.libXft}/lib' to refer the 'out' output
2016-01-24 10:03:37 +02:00
Tobias Geerinckx-Rice
32d40f0f98
Remove no longer (or never) referenced patches
...
55 files changed, 6041 deletions. Tested with `nix-build -A tarball`.
2016-01-24 02:02:21 +01:00
Vladimír Čunát
716aac2519
Merge branch 'staging' into closure-size
2016-01-19 09:55:31 +01:00
Asko Soukka
a225a650bf
R: fix Darwin build
...
Merged manually from https://github.com/NixOS/nixpkgs/pull/10623 .
2016-01-06 22:20:40 +01:00
Michel Kuhlmann
26f80d7a6f
r-modules: update list of broken packages
...
Closes https://github.com/NixOS/nixpkgs/pull/12181 .
2016-01-06 21:50:36 +01:00
Michel Kuhlmann
4c3d76d3c8
r-modules: regenerate CRAN packages
2016-01-04 09:19:24 +01:00
Vladimír Čunát
f9f6f41bff
Merge branch 'master' into closure-size
...
TODO: there was more significant refactoring of qtbase and plasma 5.5
on master, and I'm deferring pointing to correct outputs to later.
2015-12-31 09:53:02 +01:00
Peter Simons
3a8112f7da
r-modules: prefer gsl 1.x since 2.x is unsupported by r-gsl-1.9.x
2015-12-29 21:22:59 +01:00
Luca Bruno
a412927924
Merge remote-tracking branch 'origin/master' into closure-size
2015-11-25 21:37:30 +01:00
Peter Simons
de02462a36
r-modules: update list of broken packages
2015-11-25 11:39:28 +01:00
Nikolay Amiantov
bd4297dc4d
r-modules: regenerate CRAN, BIOC and IRKernel
2015-11-25 11:39:28 +01:00
Nikolay Amiantov
287f99bada
r-modules: use HTTPS, allow passing args from generated set, use MRAN
2015-11-25 11:39:28 +01:00
Peter Simons
fa5de61315
r-tikzDevice: update to new texlive
2015-11-24 17:30:28 +01:00
Vladimír Čunát
333d69a5f0
Merge staging into closure-size
...
The most complex problems were from dealing with switches reverted in
the meantime (gcc5, gmp6, ncurses6).
It's likely that darwin is (still) broken nontrivially.
2015-11-20 14:32:58 +01:00
Peter Simons
d7e6a46770
r-modules: update list of broken builds to avoid Hydra errors
2015-11-18 15:23:46 +01:00
Michel Kuhlmann
cab1f3de5e
R: regenerate CRAN packages
2015-11-17 14:34:27 +01:00
Asko Soukka
d8e3a981c5
r-modules: init IRkernel packages
2015-10-30 03:48:23 +02:00
Vladimír Čunát
99e4371526
curl: split into multiple outputs
...
Also use pkgconfig to be safer and fix (some) referrers.
2015-10-13 20:18:48 +02:00
Michel Kuhlmann
ec8f31d26c
R: fix some modules with configure-shebang-error
...
- xml2: fix configure script
- rversion, devtools: mark as unbroken
dependency R-curl was fixed in 513e31185b
2015-10-12 10:02:48 +02:00
Peter Simons
7c516259e7
r-modules: update list of broken packages
2015-10-05 14:15:41 +02:00
Vladimír Čunát
38313d5d87
libxml2,libxslt: split into multiple outputs
...
Fixed all references, hopefully.
libxml2Python is slightly hacky now, but it seems to work.
2015-10-05 13:44:16 +02:00
Karn Kallio
94629aa57d
R: regenerate CRAN and BIOC packages
2015-10-04 20:06:49 +02:00
Nikolay Amiantov
513e31185b
R-curl: fix configure script
2015-10-04 20:06:49 +02:00
Vladimír Čunát
88c9f8b574
xlibs: replace occurrences by xorg
...
This seems to have been confusing people, using both xlibs and xorg, etc.
- Avoided renaming local (and different) xlibs binding in gcc*.
- Fixed cases where both xorg and xlibs were used.
Hopefully everything still works as before.
2015-09-15 12:54:34 +02:00
Vladimír Čunát
21e3ff658a
x11: replace its usage by xlibsWrapper directly
...
Scilab note: the parameters already had pointed to nonexistent dirs
before this set of refactoring. But that config wasn't even used by
default.
2015-09-15 12:08:24 +02:00
Bjørn Forsman
22321f2e58
cudatoolkit: don't move $out/include to $out/usr_include
...
This effectively reverts 86c283824f
("If cuda headers are presented to nix [...]") and all the following
workarounds that was added due to that commit.
As far as I can tell[1] this hack isn't needed anymore. And moving
includes to $out/usr_include causes pain for cudatoolkit users, so
better get rid of it.
In patches that did more than the $out/usr_include workaround, I only
changed the line back to $out/include instead of re-generating the
patches and fully removing the changed line.
[1]: I build tested blender and caffe, and temporarily added
recurseIntoAttrs to rPackages and haskellPackages so that nox-review
could get proper coverage. However, many of the packages do not build
even before this patch. I also built CUDA samples with cudatoolkit7
that ran fine.
2015-09-10 10:35:40 +02:00
Peter Simons
5d1bcf2f4e
R: fix Hydra build & evaluation errors
2015-08-06 20:13:50 +02:00
Peter Simons
36fc26c0fc
R: regenerate CRAN and BIOC packages
2015-08-06 20:13:50 +02:00
Peter Simons
7a0fa8f898
r-modules: fix evaluation errors
2015-08-06 20:13:49 +02:00
Michel Kuhlmann
18cff91fb7
R: regenerate CRAN and BIOC packages
...
Closes https://github.com/NixOS/nixpkgs/pull/9037 .
2015-08-06 20:13:49 +02:00
Peter Simons
73ad191afb
r-modules: fix Hydra evaluation errors
2015-08-06 20:13:49 +02:00
Nikolay Amiantov
e3461ce259
rPackages.stringi: add ICU data tables
2015-07-28 12:33:29 +03:00
Peter Simons
b59685de83
r-stringi: fix build
2015-07-12 02:38:42 +02:00
Michel Kuhlmann
bb2b683e63
R: regenerate CRAN and BIOC packages
2015-07-09 14:52:17 +02:00
Peter Simons
bb42c215e2
R: improve support for CRAN and Bioconductor package sets
...
- Update the instructions for re-generating each of the package set files.
- Provide test-evaluation.nix expression to verify that the package sets evaluates.
- Update list of known broken packages.
2015-06-17 23:19:56 +02:00
Jeffrey David Johnson
93a742fd28
R: add support for Bioconductor packages
2015-06-17 23:19:56 +02:00
Peter Simons
362e60a5dc
r-modules: fix rapportools
2015-06-16 12:48:50 +02:00
Peter Simons
21c18c4f0a
r-modules: fix rapport
2015-06-16 12:48:50 +02:00
Peter Simons
ccd6988b3d
r-modules: fix xml2
2015-06-16 12:48:50 +02:00
Peter Simons
8ac6350ce7
r-modules: fix pander
2015-06-16 12:48:50 +02:00
Peter Simons
9fc5317055
r-modules: fix curl
2015-06-16 12:48:50 +02:00
Peter Simons
d4c810cccd
r-modules: disable broken packages to avoid Hydra evaluation errors
2015-06-16 12:48:49 +02:00
Peter Simons
b667cb6163
Merge pull request #8298 from abbradar/r-updates
...
R updates
2015-06-15 20:31:57 +02:00
Nikolay Amiantov
29779ae642
R: regenerate CRAN packages
2015-06-12 03:44:39 +03:00
Nikolay Amiantov
9bb5e7edbd
generate-cran-packages: make executable
2015-06-12 03:44:38 +03:00
Thomas Tuegel
8245caedf1
rPackages.SamplerCompare: build with openblas
2015-06-09 11:47:40 -05:00
Thomas Tuegel
58754130cc
rPackages.slfm: build with openblas
2015-06-09 11:47:26 -05:00
Thomas Tuegel
77aa1c990e
rPackages.Mposterior: build with openblas
2015-06-09 11:47:12 -05:00
Thomas Tuegel
b120a737fd
rPackages.BayesLogit: build with openblas
2015-06-09 11:43:00 -05:00
Peter Simons
949746f9f5
r-modules: disable broken builds
2015-05-15 13:48:38 +02:00
Peter Simons
278df52729
r-xml2: fix build
2015-05-15 13:47:27 +02:00
Peter Simons
aaa9f837a9
r-modules: fix Hydra evaluation errors
2015-05-13 11:31:39 +02:00
Michel Kuhlmann
aabee7eb46
r-modules: regenerate 2015-05-11T14:48:00+0100
2015-05-12 07:47:41 +02:00
Peter Simons
e313cd711e
r-modules: disable broken builds on Hydra
2015-04-20 17:38:46 +02:00
Peter Simons
0b088ce581
r-modules: revert "disable builds that depend on broken gdal library"
...
This reverts commit 9e9b5e6e69
. gdal has
been fixed in 1645795c53
.
2015-04-19 17:52:50 +02:00