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rPackages: tree bump and package fixes
This commit is contained in:
Justin Bedő 2024-04-05 13:22:50 +11:00 committed by GitHub
commit 375e28ef0a
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GPG Key ID: B5690EEEBB952194
6 changed files with 3470 additions and 2927 deletions

4
pkgs/development/r-modules/bioc-annotation-packages.nix generated
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@ -7,7 +7,7 @@
let derive2 = derive { biocVersion = "3.18"; };
in with self; {
AHCytoBands = derive2 { name="AHCytoBands"; version="0.99.1"; sha256="0svxxhj3mh5gqik45ikcxnlhnma8n1c0rv8pycj2034cb9ms1dbv"; depends=[]; };
AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.1.10"; sha256="0mqginwp70rwsmqwdl64awj4jr78n17rbaxmik86sk4n98fgd4xf"; depends=[AnnotationHubData ensembldb]; };
AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.1.11"; sha256="1mh8aji48a6fad6bd1333qmc3dw7b5hf4v7xw0zhmfbnld64gz0s"; depends=[AnnotationHubData ensembldb]; };
AHLRBaseDbs = derive2 { name="AHLRBaseDbs"; version="1.7.0"; sha256="1nbgqv1c3nyhlniqvqdc5cf8kyys323z1ia5jw54hxwi1jdyclfg"; depends=[AnnotationHub]; };
AHMeSHDbs = derive2 { name="AHMeSHDbs"; version="1.7.0"; sha256="0hxik2xzvbgv6a936mvax5kyv65drr36r9rf7rlv124jinlbxw82"; depends=[AnnotationHub]; };
AHPathbankDbs = derive2 { name="AHPathbankDbs"; version="0.99.5"; sha256="10wcrglm521xcrfbzc39dkbjvg1pkz0zq70vgnh68akiwmdirp89"; depends=[AnnotationHub]; };
@ -348,7 +348,7 @@ in with self; {
excluderanges = derive2 { name="excluderanges"; version="0.99.8"; sha256="19pdwlhqlz420yss371bsqhkx8c7wxr0sv4wsycnc0mlplwq4bsf"; depends=[GenomicRanges]; };
fitCons_UCSC_hg19 = derive2 { name="fitCons.UCSC.hg19"; version="3.7.1"; sha256="19isa4x8js0pdb4k8a11bw3bzmzv6jc4jphzrvav7piqkvrgykzx"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; };
fly_db0 = derive2 { name="fly.db0"; version="3.18.0"; sha256="1pksr9jwdd5izf2yc7fb935pic84nvlxa458h0da9lryglc0w5rg"; depends=[AnnotationDbi]; };
geneplast_data = derive2 { name="geneplast.data"; version="0.99.8"; sha256="1dd7jbgr1binab11npc4qk6caa4n3hzcfdjbsi56f0xic73f8w1b"; depends=[ape BiocFileCache dplyr geneplast igraph purrr readr tibble treeio]; };
geneplast_data = derive2 { name="geneplast.data"; version="0.99.9"; sha256="1i31kx4kckfg965s9l3pilvmg847av3rpa05aql43259ccyng4hi"; depends=[ape BiocFileCache dplyr geneplast igraph purrr readr tibble tidyr treeio]; };
geneplast_data_string_v91 = derive2 { name="geneplast.data.string.v91"; version="0.99.6"; sha256="0mc26d0sgmpmfmqsqinqv5k6vhg0hlc8hsjkcnvf369yav224nq1"; depends=[]; };
genomewidesnp5Crlmm = derive2 { name="genomewidesnp5Crlmm"; version="1.0.6"; sha256="06dmwnjy3gb53y6nr02dmp22qzfl5d63wppazrabcqbzwimhnvp8"; depends=[]; };
genomewidesnp6Crlmm = derive2 { name="genomewidesnp6Crlmm"; version="1.0.7"; sha256="16qcxa32fmbdcv5dck0grsnqyfcqql7wpxa1l6andv9hrvabv2jx"; depends=[]; };

16
pkgs/development/r-modules/bioc-experiment-packages.nix generated
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@ -43,10 +43,10 @@ in with self; {
ConnectivityMap = derive2 { name="ConnectivityMap"; version="1.38.0"; sha256="0ixvmkyps62f10c0s4z0jas2106hnvijknai6abial6i3plffnsc"; depends=[]; };
CopyNeutralIMA = derive2 { name="CopyNeutralIMA"; version="1.20.0"; sha256="11l994nhi813qs1vmrqjgclw11k5hrsmcrlj5x5wqmqmnjjw1dsy"; depends=[ExperimentHub Rdpack]; };
CopyhelpeR = derive2 { name="CopyhelpeR"; version="1.34.0"; sha256="1zfsxi65lln93fb87l6fgp7vxldb4fvnf95h91dl424xyq6qjp1h"; depends=[]; };
DAPARdata = derive2 { name="DAPARdata"; version="1.32.0"; sha256="1bf8sv9fpp9mpyb5r83a6r2b92d5nc0gwiys2avd0nlmzjddj4jw"; depends=[MSnbase]; };
DAPARdata = derive2 { name="DAPARdata"; version="1.32.1"; sha256="1iwiq5z1jnsrdp3pnhxlb2rvcfg91xp7xp2k0ry7r0gr9hjnnhr7"; depends=[MSnbase]; };
DExMAdata = derive2 { name="DExMAdata"; version="1.10.0"; sha256="1a2hrvbkhpwmjha0iwd17xv60d1cdl7iswc942bcac80mn6sw305"; depends=[Biobase]; };
DLBCL = derive2 { name="DLBCL"; version="1.42.1"; sha256="0an4g45977knk2qsvwjjm66l7rrb26pbk8sbb1zjvmrqym1qviqj"; depends=[Biobase graph]; };
DMRcatedata = derive2 { name="DMRcatedata"; version="2.20.0"; sha256="07gkhal6rhj9b4yasmb3dfix38cd99p2bf79agl8vbrmzd0mjvhc"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; };
DLBCL = derive2 { name="DLBCL"; version="1.42.2"; sha256="06x4jbyz0m9pzwxjl326rl5zahq5km5rryncbq99cz6mml2asn21"; depends=[Biobase graph]; };
DMRcatedata = derive2 { name="DMRcatedata"; version="2.20.3"; sha256="0fhk71j60s693vh333277ra0vgjys15h6r593v2j1y970650pq0a"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; };
DNAZooData = derive2 { name="DNAZooData"; version="1.2.0"; sha256="0d5466b830s82laamig1rw0p0n6i4npb11iyziv1sfvs4y8pbhl8"; depends=[BiocFileCache HiCExperiment rjson S4Vectors]; };
DeSousa2013 = derive2 { name="DeSousa2013"; version="1.38.0"; sha256="1xjygkr8rc1m9sv5bwph3wdf9hhcfdw8zji547nw0ayrg5d49689"; depends=[affy AnnotationDbi Biobase cluster ConsensusClusterPlus frma frmaTools gplots hgu133plus2_db hgu133plus2frmavecs pamr rgl ROCR siggenes survival sva]; };
DmelSGI = derive2 { name="DmelSGI"; version="1.34.0"; sha256="1qsvw7jrn070yfrgrkw9wsdb05g8ai5hmcqmyr78qs5qny0cz919"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; };
@ -83,7 +83,7 @@ in with self; {
HCAData = derive2 { name="HCAData"; version="1.18.0"; sha256="1rd1qra8g7dn9pg2mhh2j40p7p6ny838n4w6mx5ryw4xky95lf41"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
HCATonsilData = derive2 { name="HCATonsilData"; version="1.0.0"; sha256="1h5hrfslhyiqc855bb23rz9hahnpcy47h2lz1k0dj8glrjldq0jp"; depends=[base64enc ExperimentHub HDF5Array htmltools rmarkdown S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
HD2013SGI = derive2 { name="HD2013SGI"; version="1.42.0"; sha256="1xxc85al19qxj17rj1k4q0xp3wgkxr007akmq3an7mqrah0y8hm8"; depends=[EBImage geneplotter gplots limma LSD RColorBrewer splots vcd]; };
HDCytoData = derive2 { name="HDCytoData"; version="1.22.0"; sha256="1xqwkwxaaj5yylx9pzvka8pj9gxg1z4g23d2sralcvqzcz7q13zn"; depends=[ExperimentHub flowCore SummarizedExperiment]; };
HDCytoData = derive2 { name="HDCytoData"; version="1.22.1"; sha256="1048xgypsw257ihy0ysfxy5443dzhzp2rkjjvpivvrhw4dzl25ir"; depends=[ExperimentHub flowCore SummarizedExperiment]; };
HEEBOdata = derive2 { name="HEEBOdata"; version="1.40.0"; sha256="1xijrm32p191qydz1gkm8321b8ycb9h6y6m1qvc8shlhbbzw705h"; depends=[]; };
HIVcDNAvantWout03 = derive2 { name="HIVcDNAvantWout03"; version="1.42.0"; sha256="0kyblhc6fdc5c45qyqcr2qnmp1zrwdrc0j91fml04pw5yxrf6dw0"; depends=[]; };
HMP16SData = derive2 { name="HMP16SData"; version="1.22.0"; sha256="1ns7yyw0w8rrkw87awrrzxmb44gkkb1cn6j3cbzj8fbrd9whl30d"; depends=[AnnotationHub assertthat dplyr ExperimentHub kableExtra knitr magrittr readr S4Vectors stringr SummarizedExperiment tibble]; };
@ -192,7 +192,7 @@ in with self; {
SNAData = derive2 { name="SNAData"; version="1.48.0"; sha256="0qd48ggg1wjy5h47hzl9iqzy13gsxxn4f7fq4b0ra35vhckmcvyf"; depends=[graph]; };
SNAGEEdata = derive2 { name="SNAGEEdata"; version="1.38.0"; sha256="17wbf4xsljkryzjpk57kvjbiln0ig8d717j953wy0inz7vzdkpkn"; depends=[]; };
SNPhoodData = derive2 { name="SNPhoodData"; version="1.32.0"; sha256="0p8361lmlfz496ivw9qaqkg7b3hr4gb9g9r73fxp6amy2xncb00g"; depends=[]; };
STexampleData = derive2 { name="STexampleData"; version="1.10.0"; sha256="1rhq1743aa9bw54d2c74yclwd56a5vq5jppfzxz7mmv3cf5x3ar9"; depends=[ExperimentHub SpatialExperiment]; };
STexampleData = derive2 { name="STexampleData"; version="1.10.1"; sha256="1fr29mnczvglpkwh4vdy6klahv014ikmxwx055x4grkxvygbqm23"; depends=[ExperimentHub SpatialExperiment]; };
SVM2CRMdata = derive2 { name="SVM2CRMdata"; version="1.34.0"; sha256="1k7cjakxcqq86xvx0d0799hb94hi7w05amd9yncd0nf4dcy6zm0f"; depends=[]; };
SimBenchData = derive2 { name="SimBenchData"; version="1.10.0"; sha256="1g5wff2hx3sra48wcvwh3hs9lpfavq2pqflcm9wfcch9y10m8iqd"; depends=[ExperimentHub S4Vectors]; };
Single_mTEC_Transcriptomes = derive2 { name="Single.mTEC.Transcriptomes"; version="1.30.0"; sha256="1w3f71mfq74sjlsasi87gvqs2mhny41zm22zswz9km5msi8r2wva"; depends=[]; };
@ -224,7 +224,7 @@ in with self; {
VectraPolarisData = derive2 { name="VectraPolarisData"; version="1.6.0"; sha256="0zr94qgyj365sy7cyzjsm9zbxyv6zbd8lwfr1nqz0p6f6hb9b8qw"; depends=[ExperimentHub SpatialExperiment]; };
WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.34.0"; sha256="1p8z4p1s5l4hlp78ifiy3gan1n8iljaafbqv88vxwbjh2x9gfnjl"; depends=[]; };
WGSmapp = derive2 { name="WGSmapp"; version="1.14.0"; sha256="0yv323mkv681f20dzjh1xaz19xbn4j777xxlmq27rvmk3j1vfah9"; depends=[GenomicRanges]; };
WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.4.0"; sha256="1r6an1lxjsrdi4y0prfyy9jjjazicy9bwykinf5dvkac2h3zhs81"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.4.1"; sha256="00ws47shsfnwi6c3ah56bm6dvicfhfr50jadll613fddv7cxkfsw"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.40.0"; sha256="1qzbsmqn9y1483108pzh8zkiw1q1xzghincrcmz8cl2a4q10hyxf"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; };
adductData = derive2 { name="adductData"; version="1.18.0"; sha256="16c79wy55p4ryglxph80dibfm1ni8c5yfk6fnmq064ihw4zwcld5"; depends=[AnnotationHub ExperimentHub]; };
affycompData = derive2 { name="affycompData"; version="1.40.0"; sha256="183wgbc4j7f9d4rwr9smndnmw1i390abak23wp6p02zk340qmvq4"; depends=[affycomp Biobase]; };
@ -274,13 +274,13 @@ in with self; {
curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.10.0"; sha256="0fgvpxc1878lm8l0bib12zzwrgsap0vw4zn77qpz1mljnz43shcb"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.40.1"; sha256="18163l0g3g042m2qgz143smxia3lp8v7rddkqmkg4hzns7baxfaa"; depends=[Biobase BiocGenerics]; };
curatedTBData = derive2 { name="curatedTBData"; version="1.8.0"; sha256="116ck61pw6diili326x0x8p7f8d5w624n4w3pd212vhq8555yrqs"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment rlang]; };
curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.24.0"; sha256="0kfdzc5arzsrdaps7b3r718yawpv1x7wms5jp90j8cxpn0hz07az"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.24.1"; sha256="0hr66p8l54nzfsizcxxd2njy44xnia607wvfhrgv46f3f8s95z02"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
davidTiling = derive2 { name="davidTiling"; version="1.42.0"; sha256="1xfkyncwi9zrynk6dqsmacmkxx2qvj1axda3wn55b1vbw2wimpyf"; depends=[Biobase GO_db tilingArray]; };
depmap = derive2 { name="depmap"; version="1.16.0"; sha256="1vb3f5ar2jlkjyhp7rv4imlylinm6fi94ki277jgdaxn12v78qxj"; depends=[AnnotationHub dplyr ExperimentHub]; };
derfinderData = derive2 { name="derfinderData"; version="2.20.0"; sha256="1h8rl8mnxk2lsl8xa8mihvbd77yw32fpxdbhhn4rv1v8i5j35r7l"; depends=[]; };
diffloopdata = derive2 { name="diffloopdata"; version="1.30.0"; sha256="1f0gnwpjxkby7kd2bphnz4lv7gx9k297yqz0b954m7adp1sh6aqa"; depends=[]; };
diggitdata = derive2 { name="diggitdata"; version="1.34.0"; sha256="01r356zdy4pi8z90pbww8q7dfmq09zf148d5sq3w22z1ypsy6zm1"; depends=[Biobase viper]; };
dorothea = derive2 { name="dorothea"; version="1.14.0"; sha256="1vinixcpl4hjjfw48qfngsvw1yr82yscdxrsgagdm8gm7b72qjgh"; depends=[bcellViper decoupleR dplyr magrittr]; };
dorothea = derive2 { name="dorothea"; version="1.14.1"; sha256="0bjmnqly57y69axnz5q2rqz7j7dnz1xzbhbzcalv99kybjiyqyb5"; depends=[bcellViper decoupleR dplyr magrittr]; };
dressCheck = derive2 { name="dressCheck"; version="0.40.0"; sha256="1mb6cmyf61rb7jdwczhzcvadgqijij53w03d87xq7zqsc7jxi9z3"; depends=[Biobase]; };
dyebiasexamples = derive2 { name="dyebiasexamples"; version="1.42.0"; sha256="06sp4fxsph3w84g960s65sy1vc032p2xj3sf0v94nh78f6myg0mj"; depends=[GEOquery marray]; };
easierData = derive2 { name="easierData"; version="1.8.0"; sha256="138x8i1zd4cvlawg9pa5ia1kmmdaxm0g9lkivzxl077s9vlpjp8d"; depends=[AnnotationHub ExperimentHub SummarizedExperiment]; };

382
pkgs/development/r-modules/bioc-packages.nix generated
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5906
pkgs/development/r-modules/cran-packages.nix generated
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79
pkgs/development/r-modules/default.nix
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@ -304,8 +304,10 @@ let
};
packagesWithRDepends = {
spectralGraphTopology = [ self.CVXR ];
FactoMineR = [ self.car ];
pander = [ self.codetools ];
rmsb = [ self.rstantools ];
};
packagesWithNativeBuildInputs = {
@ -359,11 +361,11 @@ let
HiCseg = [ pkgs.gsl ];
imager = [ pkgs.xorg.libX11.dev ];
iBMQ = [ pkgs.gsl ];
igraph = with pkgs; [ gmp libxml2.dev ];
JavaGD = [ pkgs.jdk ];
jpeg = [ pkgs.libjpeg.dev ];
jqr = [ pkgs.jq.dev ];
KFKSDS = [ pkgs.gsl ];
KSgeneral = with pkgs; [ pkg-config ];
kza = [ pkgs.fftw.dev ];
leidenAlg = [ pkgs.gmp.dev ];
Libra = [ pkgs.gsl ];
@ -404,6 +406,7 @@ let
RcppZiggurat = [ pkgs.gsl ];
reprex = [ pkgs.which ];
rgdal = with pkgs; [ proj.dev gdal ];
gdalcubes = [ pkgs.pkg-config ];
rgeos = [ pkgs.geos ];
Rglpk = [ pkgs.glpk ];
RGtk2 = [ pkgs.gtk2.dev ];
@ -443,6 +446,7 @@ let
seqminer = with pkgs; [ zlib.dev bzip2 ];
sf = with pkgs; [ gdal proj geos libtiff curl ];
strawr = with pkgs; [ curl.dev ];
string2path = [ pkgs.cargo ];
terra = with pkgs; [ gdal proj geos ];
apcf = with pkgs; [ geos ];
SemiCompRisks = [ pkgs.gsl ];
@ -464,6 +468,7 @@ let
topicmodels = [ pkgs.gsl ];
udunits2 = with pkgs; [ udunits expat ];
units = [ pkgs.udunits ];
unigd = [ pkgs.pkg-config ];
vdiffr = [ pkgs.libpng.dev ];
V8 = [ pkgs.v8 ];
XBRL = with pkgs; [ zlib libxml2.dev ];
@ -471,21 +476,18 @@ let
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ];
affyPLM = [ pkgs.zlib.dev ];
bamsignals = [ pkgs.zlib.dev ];
BitSeq = [ pkgs.zlib.dev ];
DiffBind = [ pkgs.zlib ];
DiffBind = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
ShortRead = [ pkgs.zlib.dev ];
oligo = [ pkgs.zlib.dev ];
gmapR = [ pkgs.zlib.dev ];
Rsubread = [ pkgs.zlib.dev ];
XVector = [ pkgs.zlib.dev ];
Rsamtools = with pkgs; [ zlib.dev curl.dev ];
Rsamtools = with pkgs; [ zlib.dev curl.dev bzip2 xz ];
rtracklayer = [ pkgs.zlib.dev ];
affyio = [ pkgs.zlib.dev ];
VariantAnnotation = with pkgs; [ zlib.dev curl.dev ];
snpStats = [ pkgs.zlib.dev ];
vcfppR = [ pkgs.curl.dev pkgs.bzip2 pkgs.zlib.dev pkgs.xz];
hdf5r = [ pkgs.hdf5.dev ];
httpgd = with pkgs; [ cairo.dev ];
SymTS = [ pkgs.gsl ];
VBLPCM = [ pkgs.gsl ];
@ -516,6 +518,7 @@ let
RationalMatrix = [ pkgs.pkg-config pkgs.gmp.dev];
RcppCWB = [ pkgs.pkg-config pkgs.pcre2 ];
redux = [ pkgs.pkg-config ];
rswipl = with pkgs; [ cmake pkg-config ];
rrd = [ pkgs.pkg-config ];
Rbwa = [ pkgs.zlib.dev ];
trackViewer = [ pkgs.zlib.dev ];
@ -562,9 +565,13 @@ let
fftw = [ pkgs.pkg-config ];
gdtools = [ pkgs.pkg-config ];
archive = [ pkgs.libarchive];
gdalcubes = with pkgs; [ proj.dev gdal sqlite.dev netcdf ];
SuperGauss = [ pkgs.pkg-config pkgs.fftw.dev];
cartogramR = [ pkgs.fftw.dev ];
jqr = [ pkgs.jq.lib ];
kza = [ pkgs.pkg-config ];
igraph = with pkgs; [ gmp libxml2.dev glpk ];
image_textlinedetector = with pkgs; [ pkg-config opencv ];
lwgeom = with pkgs; [ pkg-config proj.dev sqlite.dev ];
magick = [ pkgs.pkg-config ];
mwaved = [ pkgs.pkg-config ];
@ -583,11 +590,13 @@ let
CLVTools = [ pkgs.gsl ];
excursions = [ pkgs.gsl ];
JMcmprsk = [ pkgs.gsl ];
KSgeneral = [ pkgs.fftw.dev ];
mashr = [ pkgs.gsl ];
hadron = [ pkgs.gsl ];
AMOUNTAIN = [ pkgs.gsl ];
Rsymphony = with pkgs; [ pkg-config doxygen graphviz subversion ];
tcltk2 = with pkgs; [ tcl tk ];
rswipl = with pkgs; [ ncurses.dev libxcrypt zlib.dev ];
tikzDevice = with pkgs; [ which texliveMedium ];
gridGraphics = [ pkgs.which ];
adimpro = with pkgs; [ which xorg.xdpyinfo ];
@ -603,9 +612,10 @@ let
bio3d = with pkgs; [ zlib.dev ];
arrangements = with pkgs; [ gmp.dev ];
spp = with pkgs; [ zlib.dev ];
bamsignals = with pkgs; [ zlib.dev xz.dev bzip2 ];
Rbowtie = with pkgs; [ zlib.dev ];
gaston = with pkgs; [ zlib.dev ];
csaw = with pkgs; [ zlib.dev curl ];
csaw = with pkgs; [ zlib.dev xz.dev bzip2.dev curl ];
DirichletMultinomial = with pkgs; [ gsl ];
DiffBind = with pkgs; [ zlib.dev ];
CNEr = with pkgs; [ zlib ];
@ -613,8 +623,9 @@ let
rmumps = with pkgs; [ zlib.dev ];
HiCDCPlus = [ pkgs.zlib.dev ];
PopGenome = [ pkgs.zlib.dev ];
QuasR = [ pkgs.zlib.dev ];
QuasR = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
Rbowtie2 = [ pkgs.zlib.dev ];
maftools = with pkgs; [ zlib.dev bzip2 xz.dev ];
Rmmquant = [ pkgs.zlib.dev ];
SICtools = with pkgs; [ zlib.dev ncurses.dev ];
Signac = [ pkgs.zlib.dev ];
@ -623,11 +634,12 @@ let
zlib = [ pkgs.zlib.dev ];
divest = [ pkgs.zlib.dev ];
hipread = [ pkgs.zlib.dev ];
jackalope = with pkgs; [ zlib.dev xz.dev ];
jackalope = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
largeList = [ pkgs.zlib.dev ];
mappoly = [ pkgs.zlib.dev ];
VariantAnnotation = with pkgs; [ zlib.dev curl.dev bzip2.dev xz.dev ];
matchingMarkets = [ pkgs.zlib.dev ];
methylKit = [ pkgs.zlib.dev ];
methylKit = with pkgs; [ zlib.dev bzip2.dev xz.dev ];
ndjson = [ pkgs.zlib.dev ];
podkat = [ pkgs.zlib.dev ];
qrqc = [ pkgs.zlib.dev ];
@ -640,6 +652,7 @@ let
seqbias = [ pkgs.zlib.dev ];
sparkwarc = [ pkgs.zlib.dev ];
RoBMA = [ pkgs.jags ];
pexm = [ pkgs.jags ];
rGEDI = with pkgs; [ libgeotiff.dev libaec zlib.dev hdf5.dev ];
rawrr = [ pkgs.mono ];
HDF5Array = [ pkgs.zlib.dev ];
@ -674,6 +687,7 @@ let
RcppAlgos = [ pkgs.gmp.dev ];
RcppBigIntAlgos = [ pkgs.gmp.dev ];
spaMM = [ pkgs.gsl ];
unigd = with pkgs; [ cairo.dev libpng.dev ];
HilbertVisGUI = [ pkgs.gtkmm2.dev ];
textshaping = with pkgs; [ harfbuzz.dev freetype.dev fribidi libpng ];
DropletUtils = [ pkgs.zlib.dev ];
@ -882,12 +896,14 @@ let
"aroma_affymetrix"
"aroma_cn"
"aroma_core"
"connections"
"csodata"
"DiceView"
"MSnID"
"OmnipathR"
"precommit"
"PSCBS"
"iemisc"
"repmis"
"R_cache"
"R_filesets"
@ -1054,6 +1070,29 @@ let
patchPhase = "patchShebangs configure";
});
exifr = old.exifr.overrideAttrs (attrs: {
postPatch = ''
for f in .onLoad .onAttach ; do
substituteInPlace R/load_hook.R \
--replace-fail \
"$f <- function(libname, pkgname) {" \
"$f <- function(libname, pkgname) {
options(
exifr.perlpath = \"${lib.getBin pkgs.perl}/bin/perl\",
exifr.exiftoolcommand = \"${lib.getBin pkgs.exiftool}/bin/exiftool\"
)"
done
'';
});
NGCHM = old.NGCHM.overrideAttrs (attrs: {
postPatch = ''
substituteInPlace "inst/base.config/conf.d/01-server-protocol-scl.R" \
--replace-fail \
"/bin/hostname" "${lib.getBin pkgs.hostname}/bin/hostname"
'';
});
ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: {
env = (attrs.env or { }) // {
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.isDarwin " -fopenmp";
@ -1151,6 +1190,10 @@ let
NIX_LDFLAGS = "-lX11";
});
hdf5r = old.hdf5r.overrideAttrs (attrs: {
buildInputs = attrs.buildInputs ++ [ new.Rhdf5lib.hdf5 ];
});
slfm = old.slfm.overrideAttrs (attrs: {
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
});
@ -1183,6 +1226,10 @@ let
];
});
universalmotif = old.universalmotif.overrideAttrs (attrs: {
patches = [ ./patches/universalmotif.patch];
});
V8 = old.V8.overrideAttrs (attrs: {
postPatch = ''
substituteInPlace configure \
@ -1417,6 +1464,10 @@ let
flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
RcppCGAL = old.RcppCGAL.overrideAttrs (_: {
postPatch = "patchShebangs configure";
});
httr2 = old.httr2.overrideAttrs (attrs: {
preConfigure = "patchShebangs configure";
});
@ -1433,7 +1484,7 @@ let
});
Rhdf5lib = let
hdf5 = pkgs.hdf5_1_10.overrideAttrs (attrs: {configureFlags = attrs.configureFlags ++ ["--enable-cxx"];});
hdf5 = pkgs.hdf5_1_10.overrideAttrs (attrs: {configureFlags = attrs.configureFlags ++ [ "--enable-cxx" ];});
in old.Rhdf5lib.overrideAttrs (attrs: {
propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ hdf5.dev pkgs.libaec ];
patches = [ ./patches/Rhdf5lib.patch ];
@ -1497,6 +1548,12 @@ let
patchShebangs src/library/ps/configure
'';
});
pkgdepends = old.pkgdepends.overrideAttrs (attrs: {
postPatch = ''
patchShebangs configure
'';
});
};
in
self

10
pkgs/development/r-modules/patches/universalmotif.patch Normal file
View File

@ -0,0 +1,10 @@
diff --git a/src/Makevars b/src/Makevars
index 6e08950..e66fbbd 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1,5 +1 @@
CXX_STD=CXX11
-PKG_LIBS=`"$(R_HOME)/bin/Rscript" -e "RcppThread::LdFlags()"`
-strippedLib: $(SHLIB)
- if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
-.phony: strippedLib