tjh.dev
1/* This file defines the composition for CRAN (R) packages. */
2
3{ R, pkgs, overrides }:
4
5let
6 inherit (pkgs) cacert fetchurl stdenv lib;
7
8 buildRPackage = pkgs.callPackage ./generic-builder.nix {
9 inherit R;
10 inherit (pkgs.darwin.apple_sdk.frameworks) Cocoa Foundation;
11 inherit (pkgs) gettext gfortran;
12 };
13
14 # Generates package templates given per-repository settings
15 #
16 # some packages, e.g. cncaGUI, require X running while installation,
17 # so that we use xvfb-run if requireX is true.
18 mkDerive = {mkHomepage, mkUrls}: args:
19 lib.makeOverridable ({
20 name, version, sha256,
21 depends ? [],
22 doCheck ? true,
23 requireX ? false,
24 broken ? false,
25 hydraPlatforms ? R.meta.hydraPlatforms
26 }: buildRPackage {
27 name = "${name}-${version}";
28 src = fetchurl {
29 inherit sha256;
30 urls = mkUrls (args // { inherit name version; });
31 };
32 inherit doCheck requireX;
33 propagatedBuildInputs = depends;
34 nativeBuildInputs = depends;
35 meta.homepage = mkHomepage (args // { inherit name; });
36 meta.platforms = R.meta.platforms;
37 meta.hydraPlatforms = hydraPlatforms;
38 meta.broken = broken;
39 });
40
41 # Templates for generating Bioconductor and CRAN packages
42 # from the name, version, sha256, and optional per-package arguments above
43 #
44 deriveBioc = mkDerive {
45 mkHomepage = {name, biocVersion}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html";
46 mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz"
47 "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ];
48 };
49 deriveBiocAnn = mkDerive {
50 mkHomepage = {name, biocVersion}: "http://www.bioconductor.org/packages/${name}.html";
51 mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ];
52 };
53 deriveBiocExp = mkDerive {
54 mkHomepage = {name, biocVersion}: "http://www.bioconductor.org/packages/${name}.html";
55 mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ];
56 };
57 deriveCran = mkDerive {
58 mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
59 mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
60 };
61
62 # Overrides package definitions with nativeBuildInputs.
63 # For example,
64 #
65 # overrideNativeBuildInputs {
66 # foo = [ pkgs.bar ]
67 # } old
68 #
69 # results in
70 #
71 # {
72 # foo = old.foo.overrideDerivation (attrs: {
73 # nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
74 # });
75 # }
76 overrideNativeBuildInputs = overrides: old:
77 lib.mapAttrs (name: value:
78 (builtins.getAttr name old).overrideDerivation (attrs: {
79 nativeBuildInputs = attrs.nativeBuildInputs ++ value;
80 })
81 ) overrides;
82
83 # Overrides package definitions with buildInputs.
84 # For example,
85 #
86 # overrideBuildInputs {
87 # foo = [ pkgs.bar ]
88 # } old
89 #
90 # results in
91 #
92 # {
93 # foo = old.foo.overrideDerivation (attrs: {
94 # buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
95 # });
96 # }
97 overrideBuildInputs = overrides: old:
98 lib.mapAttrs (name: value:
99 (builtins.getAttr name old).overrideDerivation (attrs: {
100 buildInputs = attrs.buildInputs ++ value;
101 })
102 ) overrides;
103
104 # Overrides package definitions with new R dependencies.
105 # For example,
106 #
107 # overrideRDepends {
108 # foo = [ self.bar ]
109 # } old
110 #
111 # results in
112 #
113 # {
114 # foo = old.foo.overrideDerivation (attrs: {
115 # nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
116 # propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
117 # });
118 # }
119 overrideRDepends = overrides: old:
120 lib.mapAttrs (name: value:
121 (builtins.getAttr name old).overrideDerivation (attrs: {
122 nativeBuildInputs = attrs.nativeBuildInputs ++ value;
123 propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
124 })
125 ) overrides;
126
127 # Overrides package definition requiring X running to install.
128 # For example,
129 #
130 # overrideRequireX [
131 # "foo"
132 # ] old
133 #
134 # results in
135 #
136 # {
137 # foo = old.foo.override {
138 # requireX = true;
139 # };
140 # }
141 overrideRequireX = packageNames: old:
142 let
143 nameValuePairs = map (name: {
144 inherit name;
145 value = (builtins.getAttr name old).override {
146 requireX = true;
147 };
148 }) packageNames;
149 in
150 builtins.listToAttrs nameValuePairs;
151
152 # Overrides package definition to skip check.
153 # For example,
154 #
155 # overrideSkipCheck [
156 # "foo"
157 # ] old
158 #
159 # results in
160 #
161 # {
162 # foo = old.foo.override {
163 # doCheck = false;
164 # };
165 # }
166 overrideSkipCheck = packageNames: old:
167 let
168 nameValuePairs = map (name: {
169 inherit name;
170 value = (builtins.getAttr name old).override {
171 doCheck = false;
172 };
173 }) packageNames;
174 in
175 builtins.listToAttrs nameValuePairs;
176
177 # Overrides package definition to mark it broken.
178 # For example,
179 #
180 # overrideBroken [
181 # "foo"
182 # ] old
183 #
184 # results in
185 #
186 # {
187 # foo = old.foo.override {
188 # broken = true;
189 # };
190 # }
191 overrideBroken = packageNames: old:
192 let
193 nameValuePairs = map (name: {
194 inherit name;
195 value = (builtins.getAttr name old).override {
196 broken = true;
197 };
198 }) packageNames;
199 in
200 builtins.listToAttrs nameValuePairs;
201
202 defaultOverrides = old: new:
203 let old0 = old; in
204 let
205 old1 = old0 // (overrideRequireX packagesRequireingX old0);
206 old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
207 old3 = old2 // (overrideRDepends packagesWithRDepends old2);
208 old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
209 old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
210 old6 = old5 // (overrideBroken brokenPackages old5);
211 old = old6;
212 in old // (otherOverrides old new);
213
214 # Recursive override pattern.
215 # `_self` is a collection of packages;
216 # `self` is `_self` with overridden packages;
217 # packages in `_self` may depends on overridden packages.
218 self = (defaultOverrides _self self) // overrides;
219 _self = import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
220 import ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } //
221 import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } //
222 import ./cran-packages.nix { inherit self; derive = deriveCran; };
223
224 # tweaks for the individual packages and "in self" follow
225
226 packagesWithRDepends = {
227 FactoMineR = [ self.car ];
228 pander = [ self.codetools ];
229 };
230
231 packagesWithNativeBuildInputs = {
232 abn = [ pkgs.gsl_1 ];
233 adimpro = [ pkgs.imagemagick ];
234 animation = [ pkgs.which ];
235 audio = [ pkgs.portaudio ];
236 BayesSAE = [ pkgs.gsl_1 ];
237 BayesVarSel = [ pkgs.gsl_1 ];
238 BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
239 bigGP = [ pkgs.openmpi ];
240 bio3d = [ pkgs.zlib ];
241 BiocCheck = [ pkgs.which ];
242 Biostrings = [ pkgs.zlib ];
243 bnpmr = [ pkgs.gsl_1 ];
244 cairoDevice = [ pkgs.gtk2.dev ];
245 Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
246 Cardinal = [ pkgs.which ];
247 chebpol = [ pkgs.fftw ];
248 ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
249 cit = [ pkgs.gsl_1 ];
250 curl = [ pkgs.curl.dev ];
251 data_table = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
252 devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
253 diversitree = [ pkgs.gsl_1 pkgs.fftw ];
254 EMCluster = [ pkgs.liblapack ];
255 fftw = [ pkgs.fftw.dev ];
256 fftwtools = [ pkgs.fftw.dev ];
257 Formula = [ pkgs.gmp ];
258 geoCount = [ pkgs.gsl_1 ];
259 gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
260 git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
261 GLAD = [ pkgs.gsl_1 ];
262 glpkAPI = [ pkgs.gmp pkgs.glpk ];
263 gmp = [ pkgs.gmp.dev ];
264 graphscan = [ pkgs.gsl_1 ];
265 gsl = [ pkgs.gsl_1 ];
266 h5 = [ pkgs.hdf5-cpp pkgs.which ];
267 haven = [ pkgs.libiconv ];
268 h5vc = [ pkgs.zlib.dev ];
269 HiCseg = [ pkgs.gsl_1 ];
270 imager = [ pkgs.x11 ];
271 iBMQ = [ pkgs.gsl_1 ];
272 igraph = [ pkgs.gmp pkgs.libxml2.dev ];
273 JavaGD = [ pkgs.jdk ];
274 jpeg = [ pkgs.libjpeg.dev ];
275 KFKSDS = [ pkgs.gsl_1 ];
276 kza = [ pkgs.fftw.dev ];
277 libamtrack = [ pkgs.gsl_1 ];
278 magick = [ pkgs.imagemagick.dev ];
279 mixcat = [ pkgs.gsl_1 ];
280 mvabund = [ pkgs.gsl_1 ];
281 mwaved = [ pkgs.fftw.dev ];
282 ncdf4 = [ pkgs.netcdf ];
283 nloptr = [ pkgs.nlopt ];
284 odbc = [ pkgs.unixODBC ];
285 outbreaker = [ pkgs.gsl_1 ];
286 pander = [ pkgs.pandoc pkgs.which ];
287 pbdMPI = [ pkgs.openmpi ];
288 pbdNCDF4 = [ pkgs.netcdf ];
289 pbdPROF = [ pkgs.openmpi ];
290 pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
291 pdftools = [ pkgs.poppler.dev ];
292 PKI = [ pkgs.openssl.dev ];
293 png = [ pkgs.libpng.dev ];
294 PopGenome = [ pkgs.zlib.dev ];
295 proj4 = [ pkgs.proj ];
296 protolite = [ pkgs.protobuf ];
297 qtbase = [ pkgs.qt4 ];
298 qtpaint = [ pkgs.qt4 ];
299 R2GUESS = [ pkgs.gsl_1 ];
300 R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
301 RAppArmor = [ pkgs.libapparmor ];
302 rapportools = [ pkgs.which ];
303 rapport = [ pkgs.which ];
304 readxl = [ pkgs.libiconv ];
305 rbamtools = [ pkgs.zlib.dev ];
306 rcdd = [ pkgs.gmp.dev ];
307 RcppCNPy = [ pkgs.zlib.dev ];
308 RcppGSL = [ pkgs.gsl_1 ];
309 RcppZiggurat = [ pkgs.gsl_1 ];
310 rgdal = [ pkgs.proj pkgs.gdal ];
311 rgeos = [ pkgs.geos ];
312 rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ];
313 rgl = [ pkgs.libGLU_combined pkgs.xlibsWrapper ];
314 Rglpk = [ pkgs.glpk ];
315 RGtk2 = [ pkgs.gtk2.dev ];
316 rhdf5 = [ pkgs.zlib ];
317 Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
318 Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf ];
319 RJaCGH = [ pkgs.zlib.dev ];
320 rjags = [ pkgs.jags ];
321 rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
322 Rlibeemd = [ pkgs.gsl_1 ];
323 rmatio = [ pkgs.zlib.dev ];
324 Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
325 Rmpi = [ pkgs.openmpi ];
326 RMySQL = [ pkgs.zlib pkgs.mysql.connector-c pkgs.openssl.dev ];
327 RNetCDF = [ pkgs.netcdf pkgs.udunits ];
328 RODBCext = [ pkgs.libiodbc ];
329 RODBC = [ pkgs.libiodbc ];
330 rpanel = [ pkgs.bwidget ];
331 rpg = [ pkgs.postgresql ];
332 rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
333 Rpoppler = [ pkgs.poppler ];
334 RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
335 RProtoBuf = [ pkgs.protobuf ];
336 rPython = [ pkgs.python ];
337 RSclient = [ pkgs.openssl.dev ];
338 Rserve = [ pkgs.openssl ];
339 Rssa = [ pkgs.fftw.dev ];
340 rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
341 rtiff = [ pkgs.libtiff.dev ];
342 runjags = [ pkgs.jags ];
343 RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
344 rzmq = [ pkgs.zeromq3 ];
345 SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
346 sdcTable = [ pkgs.gmp pkgs.glpk ];
347 seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
348 seqinr = [ pkgs.zlib.dev ];
349 seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
350 sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
351 showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
352 simplexreg = [ pkgs.gsl_1 ];
353 SOD = [ pkgs.opencl-headers ];
354 spate = [ pkgs.fftw.dev ];
355 ssanv = [ pkgs.proj ];
356 stsm = [ pkgs.gsl_1 ];
357 stringi = [ pkgs.icu.dev ];
358 survSNP = [ pkgs.gsl_1 ];
359 sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
360 TAQMNGR = [ pkgs.zlib.dev ];
361 tesseract = [ pkgs.tesseract pkgs.leptonica ];
362 tiff = [ pkgs.libtiff.dev ];
363 TKF = [ pkgs.gsl_1 ];
364 tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
365 topicmodels = [ pkgs.gsl_1 ];
366 udunits2 = [ pkgs.udunits pkgs.expat ];
367 V8 = [ pkgs.v8_3_14 ];
368 VBLPCM = [ pkgs.gsl_1 ];
369 VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
370 WhopGenome = [ pkgs.zlib.dev ];
371 XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
372 xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
373 XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
374 affyPLM = [ pkgs.zlib.dev ];
375 bamsignals = [ pkgs.zlib.dev ];
376 BitSeq = [ pkgs.zlib.dev ];
377 DiffBind = [ pkgs.zlib ];
378 ShortRead = [ pkgs.zlib.dev ];
379 oligo = [ pkgs.zlib.dev ];
380 gmapR = [ pkgs.zlib.dev ];
381 Rsubread = [ pkgs.zlib.dev ];
382 XVector = [ pkgs.zlib.dev ];
383 Rsamtools = [ pkgs.zlib.dev ];
384 rtracklayer = [ pkgs.zlib.dev ];
385 affyio = [ pkgs.zlib.dev ];
386 VariantAnnotation = [ pkgs.zlib.dev ];
387 snpStats = [ pkgs.zlib.dev ];
388 };
389
390 packagesWithBuildInputs = {
391 # sort -t '=' -k 2
392 svKomodo = [ pkgs.which ];
393 nat = [ pkgs.which ];
394 nat_nblast = [ pkgs.which ];
395 nat_templatebrains = [ pkgs.which ];
396 pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.binutils.bintools ];
397 RMark = [ pkgs.which ];
398 RPushbullet = [ pkgs.which ];
399 qtpaint = [ pkgs.cmake ];
400 qtbase = [ pkgs.cmake pkgs.perl ];
401 RCurl = [ pkgs.curl.dev ];
402 R2SWF = [ pkgs.pkgconfig ];
403 rggobi = [ pkgs.pkgconfig ];
404 RGtk2 = [ pkgs.pkgconfig ];
405 RProtoBuf = [ pkgs.pkgconfig ];
406 Rpoppler = [ pkgs.pkgconfig ];
407 VBmix = [ pkgs.pkgconfig ];
408 XML = [ pkgs.pkgconfig ];
409 cairoDevice = [ pkgs.pkgconfig ];
410 chebpol = [ pkgs.pkgconfig ];
411 fftw = [ pkgs.pkgconfig ];
412 geoCount = [ pkgs.pkgconfig ];
413 gdtools = [ pkgs.pkgconfig ];
414 JuniperKernel = lib.optionals stdenv.isDarwin [ pkgs.binutils.bintools ];
415 kza = [ pkgs.pkgconfig ];
416 magick = [ pkgs.pkgconfig ];
417 mwaved = [ pkgs.pkgconfig ];
418 odbc = [ pkgs.pkgconfig ];
419 openssl = [ pkgs.pkgconfig ];
420 pdftools = [ pkgs.pkgconfig ];
421 sf = [ pkgs.pkgconfig ];
422 showtext = [ pkgs.pkgconfig ];
423 spate = [ pkgs.pkgconfig ];
424 stringi = [ pkgs.pkgconfig ];
425 sys = [ pkgs.libapparmor ];
426 sysfonts = [ pkgs.pkgconfig ];
427 tesseract = [ pkgs.pkgconfig ];
428 Cairo = [ pkgs.pkgconfig ];
429 Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
430 tcltk2 = [ pkgs.tcl pkgs.tk ];
431 tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
432 rPython = [ pkgs.which ];
433 gridGraphics = [ pkgs.which ];
434 adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
435 PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
436 dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
437 mzR = [ pkgs.netcdf ];
438 };
439
440 packagesRequireingX = [
441 "accrual"
442 "ade4TkGUI"
443 "adehabitat"
444 "analogue"
445 "analogueExtra"
446 "AnalyzeFMRI"
447 "AnnotLists"
448 "AnthropMMD"
449 "aplpack"
450 "aqfig"
451 "arf3DS4"
452 "asbio"
453 "AtelieR"
454 "BAT"
455 "bayesDem"
456 "BCA"
457 "BEQI2"
458 "betapart"
459 "betaper"
460 "BiodiversityR"
461 "BioGeoBEARS"
462 "bio_infer"
463 "bipartite"
464 "biplotbootGUI"
465 "blender"
466 "cairoDevice"
467 "CCTpack"
468 "cncaGUI"
469 "cocorresp"
470 "CommunityCorrelogram"
471 "confidence"
472 "constrainedKriging"
473 "ConvergenceConcepts"
474 "cpa"
475 "DALY"
476 "dave"
477 "debug"
478 "Deducer"
479 "DeducerExtras"
480 "DeducerPlugInExample"
481 "DeducerPlugInScaling"
482 "DeducerSpatial"
483 "DeducerSurvival"
484 "DeducerText"
485 "Demerelate"
486 "detrendeR"
487 "dgmb"
488 "DivMelt"
489 "dpa"
490 "DSpat"
491 "dynamicGraph"
492 "dynBiplotGUI"
493 "EasyqpcR"
494 "EcoVirtual"
495 "ENiRG"
496 "EnQuireR"
497 "eVenn"
498 "exactLoglinTest"
499 "fat2Lpoly"
500 "fbati"
501 "FD"
502 "feature"
503 "FeedbackTS"
504 "FFD"
505 "fgui"
506 "fisheyeR"
507 "fit4NM"
508 "forams"
509 "forensim"
510 "FreeSortR"
511 "fscaret"
512 "fSRM"
513 "gcmr"
514 "GeoGenetix"
515 "geomorph"
516 "geoR"
517 "geoRglm"
518 "georob"
519 "GGEBiplotGUI"
520 "gnm"
521 "GPCSIV"
522 "GrammR"
523 "GrapheR"
524 "GroupSeq"
525 "gsubfn"
526 "GUniFrac"
527 "gWidgets2RGtk2"
528 "gWidgets2tcltk"
529 "gWidgetsRGtk2"
530 "gWidgetstcltk"
531 "HH"
532 "HiveR"
533 "HomoPolymer"
534 "ic50"
535 "iDynoR"
536 "in2extRemes"
537 "iplots"
538 "isopam"
539 "IsotopeR"
540 "JGR"
541 "KappaGUI"
542 "likeLTD"
543 "logmult"
544 "LS2Wstat"
545 "MAR1"
546 "MareyMap"
547 "memgene"
548 "MergeGUI"
549 "metacom"
550 "Meth27QC"
551 "MetSizeR"
552 "MicroStrategyR"
553 "migui"
554 "miniGUI"
555 "MissingDataGUI"
556 "mixsep"
557 "mlDNA"
558 "MplusAutomation"
559 "mpmcorrelogram"
560 "mritc"
561 "MTurkR"
562 "multgee"
563 "multibiplotGUI"
564 "nodiv"
565 "OligoSpecificitySystem"
566 "onemap"
567 "OpenRepGrid"
568 "palaeoSig"
569 "paleoMAS"
570 "pbatR"
571 "PBSadmb"
572 "PBSmodelling"
573 "PCPS"
574 "pez"
575 "phylotools"
576 "picante"
577 "PKgraph"
578 "playwith"
579 "plotSEMM"
580 "plsRbeta"
581 "plsRglm"
582 "PopGenReport"
583 "poppr"
584 "powerpkg"
585 "PredictABEL"
586 "prefmod"
587 "PrevMap"
588 "ProbForecastGOP"
589 "qtbase"
590 "qtpaint"
591 "R2STATS"
592 "r4ss"
593 "RandomFields"
594 "rareNMtests"
595 "rAverage"
596 "Rcmdr"
597 "RcmdrPlugin_BCA"
598 "RcmdrPlugin_coin"
599 "RcmdrPlugin_depthTools"
600 "RcmdrPlugin_DoE"
601 "RcmdrPlugin_doex"
602 "RcmdrPlugin_EACSPIR"
603 "RcmdrPlugin_EBM"
604 "RcmdrPlugin_EcoVirtual"
605 "RcmdrPlugin_epack"
606 "RcmdrPlugin_EZR"
607 "RcmdrPlugin_FactoMineR"
608 "RcmdrPlugin_HH"
609 "RcmdrPlugin_IPSUR"
610 "RcmdrPlugin_KMggplot2"
611 "RcmdrPlugin_lfstat"
612 "RcmdrPlugin_MA"
613 "RcmdrPlugin_mosaic"
614 "RcmdrPlugin_MPAStats"
615 "RcmdrPlugin_orloca"
616 "RcmdrPlugin_plotByGroup"
617 "RcmdrPlugin_pointG"
618 "RcmdrPlugin_qual"
619 "RcmdrPlugin_ROC"
620 "RcmdrPlugin_sampling"
621 "RcmdrPlugin_SCDA"
622 "RcmdrPlugin_SLC"
623 "RcmdrPlugin_SM"
624 "RcmdrPlugin_sos"
625 "RcmdrPlugin_steepness"
626 "RcmdrPlugin_survival"
627 "RcmdrPlugin_TeachingDemos"
628 "RcmdrPlugin_temis"
629 "RcmdrPlugin_UCA"
630 "recluster"
631 "relax"
632 "relimp"
633 "RenextGUI"
634 "reportRx"
635 "reshapeGUI"
636 "rgl"
637 "RHRV"
638 "rich"
639 "rioja"
640 "ripa"
641 "rite"
642 "RNCEP"
643 "RQDA"
644 "RSDA"
645 "rsgcc"
646 "RSurvey"
647 "RunuranGUI"
648 "sharpshootR"
649 "simba"
650 "Simile"
651 "SimpleTable"
652 "SOLOMON"
653 "soundecology"
654 "SPACECAP"
655 "spacodiR"
656 "spatsurv"
657 "sqldf"
658 "SRRS"
659 "SSDforR"
660 "statcheck"
661 "StatDA"
662 "STEPCAM"
663 "stosim"
664 "strvalidator"
665 "stylo"
666 "svDialogstcltk"
667 "svIDE"
668 "svSocket"
669 "svWidgets"
670 "SYNCSA"
671 "SyNet"
672 "tcltk2"
673 "TED"
674 "TestScorer"
675 "TIMP"
676 "titan"
677 "tkrgl"
678 "tkrplot"
679 "tmap"
680 "tspmeta"
681 "TTAinterfaceTrendAnalysis"
682 "twiddler"
683 "vcdExtra"
684 "VecStatGraphs3D"
685 "vegan"
686 "vegan3d"
687 "vegclust"
688 "VIMGUI"
689 "WMCapacity"
690 "x12GUI"
691 "xergm"
692 ];
693
694 packagesToSkipCheck = [
695 "Rmpi" # tries to run MPI processes
696 "pbdMPI" # tries to run MPI processes
697 ];
698
699 # Packages which cannot be installed due to lack of dependencies or other reasons.
700 brokenPackages = [
701 ];
702
703 otherOverrides = old: new: {
704 stringi = old.stringi.overrideDerivation (attrs: {
705 postInstall = let
706 icuName = "icudt52l";
707 icuSrc = pkgs.fetchzip {
708 url = "http://static.rexamine.com/packages/${icuName}.zip";
709 sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj";
710 stripRoot = false;
711 };
712 in ''
713 ${attrs.postInstall or ""}
714 cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs
715 '';
716 });
717
718 xml2 = old.xml2.overrideDerivation (attrs: {
719 preConfigure = ''
720 export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
721 patchShebangs configure
722 '';
723 });
724
725 Cairo = old.Cairo.overrideDerivation (attrs: {
726 NIX_LDFLAGS = "-lfontconfig";
727 });
728
729 curl = old.curl.overrideDerivation (attrs: {
730 preConfigure = "patchShebangs configure";
731 });
732
733 RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
734 patchPhase = "patchShebangs configure";
735 });
736
737 data_table = old.data_table.overrideDerivation (attrs: {
738 NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE
739 + lib.optionalString stdenv.isDarwin " -fopenmp";
740 });
741
742 rpf = old.rpf.overrideDerivation (attrs: {
743 patchPhase = "patchShebangs configure";
744 });
745
746 BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
747 patches = [ ./patches/BayesXsrc.patch ];
748 });
749
750 rJava = old.rJava.overrideDerivation (attrs: {
751 preConfigure = ''
752 export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
753 export JAVA_HOME=${pkgs.jdk}
754 '';
755 });
756
757 JavaGD = old.JavaGD.overrideDerivation (attrs: {
758 preConfigure = ''
759 export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
760 export JAVA_HOME=${pkgs.jdk}
761 '';
762 });
763
764 JuniperKernel = old.JuniperKernel.overrideDerivation (attrs: {
765 postPatch = ''
766 for file in {R,src}/*.R; do
767 sed -i 's#system("which \(otool\|install_name_tool\)"[^)]*)#"${pkgs.binutils.bintools}/bin/\1"#g' $file
768 done
769 '';
770 preConfigure = ''
771 patchShebangs configure
772 '';
773 });
774
775 Mposterior = old.Mposterior.overrideDerivation (attrs: {
776 PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
777 });
778
779 pbdZMQ = old.pbdZMQ.overrideDerivation (attrs: {
780 postPatch = lib.optionalString stdenv.isDarwin ''
781 for file in R/*.{r,r.in}; do
782 sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.binutils.bintools}/bin/\1"#g' $file
783 done
784 '';
785 });
786
787 qtbase = old.qtbase.overrideDerivation (attrs: {
788 patches = [ ./patches/qtbase.patch ];
789 });
790
791 Rmpi = old.Rmpi.overrideDerivation (attrs: {
792 configureFlags = [
793 "--with-Rmpi-type=OPENMPI"
794 ];
795 });
796
797 Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
798 configureFlags = [
799 "--with-mpfr-include=${pkgs.mpfr.dev}/include"
800 ];
801 });
802
803 RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
804 configureFlags = [
805 "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib"
806 ];
807 });
808
809 RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
810 patches = [ ./patches/RAppArmor.patch ];
811 LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
812 });
813
814 RMySQL = old.RMySQL.overrideDerivation (attrs: {
815 MYSQL_DIR="${pkgs.mysql.connector-c}";
816 preConfigure = ''
817 patchShebangs configure
818 '';
819 });
820
821 devEMF = old.devEMF.overrideDerivation (attrs: {
822 NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
823 NIX_LDFLAGS = "-lX11";
824 });
825
826 slfm = old.slfm.overrideDerivation (attrs: {
827 PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
828 });
829
830 SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
831 PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
832 });
833
834 EMCluster = old.EMCluster.overrideDerivation (attrs: {
835 patches = [ ./patches/EMCluster.patch ];
836 });
837
838 spMC = old.spMC.overrideDerivation (attrs: {
839 patches = [ ./patches/spMC.patch ];
840 });
841
842 openssl = old.openssl.overrideDerivation (attrs: {
843 PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
844 PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
845 });
846
847 Rserve = old.Rserve.overrideDerivation (attrs: {
848 patches = [ ./patches/Rserve.patch ];
849 configureFlags = [
850 "--with-server" "--with-client"
851 ];
852 });
853
854 nloptr = old.nloptr.overrideDerivation (attrs: {
855 configureFlags = [
856 "--with-nlopt-cflags=-I${pkgs.nlopt}/include"
857 "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
858 ];
859 });
860
861 V8 = old.V8.overrideDerivation (attrs: {
862 preConfigure = ''
863 export INCLUDE_DIR=${pkgs.v8_3_14}/include
864 export LIB_DIR=${pkgs.v8_3_14}/lib
865 patchShebangs configure
866 '';
867 });
868
869 acs = old.acs.overrideDerivation (attrs: {
870 preConfigure = ''
871 patchShebangs configure
872 '';
873 });
874
875 gdtools = old.gdtools.overrideDerivation (attrs: {
876 preConfigure = ''
877 patchShebangs configure
878 '';
879 NIX_LDFLAGS = "-lfontconfig -lfreetype";
880 });
881
882 magick = old.magick.overrideDerivation (attrs: {
883 preConfigure = ''
884 patchShebangs configure
885 '';
886 });
887
888 protolite = old.protolite.overrideDerivation (attrs: {
889 preConfigure = ''
890 patchShebangs configure
891 '';
892 });
893
894 rpanel = old.rpanel.overrideDerivation (attrs: {
895 preConfigure = ''
896 export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
897 '';
898 TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
899 });
900
901 OpenMx = old.OpenMx.overrideDerivation (attrs: {
902 preConfigure = ''
903 patchShebangs configure
904 '';
905 });
906
907 odbc = old.odbc.overrideDerivation (attrs: {
908 preConfigure = ''
909 patchShebangs configure
910 '';
911 });
912
913 x13binary = old.x13binary.overrideDerivation (attrs: {
914 preConfigure = ''
915 patchShebangs configure
916 '';
917 });
918
919 geojsonio = old.geojsonio.overrideDerivation (attrs: {
920 buildInputs = [ cacert ] ++ attrs.buildInputs;
921 });
922
923 rstan = old.rstan.overrideDerivation (attrs: {
924 NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
925 });
926
927 };
928in
929 self