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rPackages: fix broken packages

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This commit is contained in:
Nikolay Amiantov 2015-02-19 23:53:36 +03:00
parent 3e6531c174
commit 8450ff3ab8
4 changed files with 77 additions and 80 deletions
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101
pkgs/development/r-modules/default.nix
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@ -199,11 +199,14 @@ let
packagesWithRDepends = {
# sort -t '=' -k 2
FactoMineR = [ self.car ];
};
packagesWithNativeBuildInputs = {
# sort -t '=' -k 2
graphscan = [ pkgs.gsl ];
RAppArmor = [ pkgs.apparmor ];
BNSP = [ pkgs.gsl ];
SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
curl = [ pkgs.curl pkgs.openldap ];
Rssa = [ pkgs.fftw ];
@ -219,11 +222,12 @@ let
RCA = [ pkgs.gmp ];
gmp = [ pkgs.gmp ];
rcdd = [ pkgs.gmp ];
Rlibeemd = [ pkgs.gsl ];
igraph = [ pkgs.gmp ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
sdcTable = [ pkgs.gmp pkgs.glpk ];
Rmpfr = [ pkgs.gmp pkgs.mpfr ];
BNSP = [ pkgs.gsl ];
Formula = [ pkgs.gmp ];
BayesSAE = [ pkgs.gsl ];
BayesVarSel = [ pkgs.gsl ];
HiCseg = [ pkgs.gsl ];
@ -244,10 +248,13 @@ let
topicmodels = [ pkgs.gsl ];
RcppGSL = [ pkgs.gsl ];
bnpmr = [ pkgs.gsl ];
V8 = [ pkgs.v8 ];
geoCount = [ pkgs.gsl ];
devEMF = [ pkgs.xlibs.libXft ];
gsl = [ pkgs.gsl ];
mvabund = [ pkgs.gsl ];
diversitree = [ pkgs.gsl pkgs.fftw ];
TKF = [ pkgs.gsl ];
VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
RGtk2 = [ pkgs.gtk2 ];
cairoDevice = [ pkgs.gtk2 ];
@ -260,6 +267,8 @@ let
jpeg = [ pkgs.libjpeg ];
EMCluster = [ pkgs.liblapack ];
png = [ pkgs.libpng ];
pbdMPI = [ pkgs.openmpi ];
bigGP = [ pkgs.openmpi ];
rtiff = [ pkgs.libtiff ];
tiff = [ pkgs.libtiff ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
@ -294,7 +303,7 @@ let
BayesXsrc = [ pkgs.readline pkgs.ncurses ];
udunits2 = [ pkgs.udunits pkgs.expat ];
tkrplot = [ pkgs.xlibs.libX11 ];
rzmq = [ pkgs.zeromq2 ];
rzmq = [ pkgs.zeromq3 ];
PopGenome = [ pkgs.zlib ];
RJaCGH = [ pkgs.zlib ];
RcppCNPy = [ pkgs.zlib ];
@ -302,8 +311,9 @@ let
rmatio = [ pkgs.zlib ];
RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
seqminer = [ pkgs.zlib pkgs.bzip2 ];
rphast = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
rtfbs = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
seqinr = [ pkgs.zlib ];
rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
@ -317,6 +327,12 @@ let
packagesWithBuildInputs = {
# sort -t '=' -k 2
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_nblast = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
RMark = [ pkgs.which ];
RPushbullet = [ pkgs.which ];
qtpaint = [ pkgs.cmake ];
qtbase = [ pkgs.cmake pkgs.perl ];
gmatrix = [ pkgs.cudatoolkit ];
@ -341,10 +357,12 @@ let
Cairo = [ pkgs.pkgconfig ];
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
qtutils = [ pkgs.qt4 ];
ecoretriever = [ pkgs.which ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.texLive ];
tikzDevice = [ pkgs.which pkgs.texLive ];
rPython = [ pkgs.which ];
CARramps = [ pkgs.which pkgs.cudatoolkit ];
gridGraphics = [ pkgs.which ];
gputools = [ pkgs.which pkgs.cudatoolkit ];
rpud = [ pkgs.which pkgs.cudatoolkit ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
@ -374,6 +392,8 @@ let
"DeducerPlugInScaling"
"DeducerSpatial"
"DeducerSurvival"
"HomoPolymer"
"MetSizeR"
"DeducerText"
"Demerelate"
"DescTools"
@ -623,6 +643,7 @@ let
"gmatrix" # requires CUDA runtime
"npRmpi" # tries to run MPI processes
"sprint" # tries to run MPI processes
"pbdMPI" # tries to run MPI processes
];
# Packages which cannot be installed due to lack of dependencies or other reasons.
@ -631,38 +652,12 @@ let
"retistruct" # depends on broken RImageJROI
"CARrampsOcl" # depends on OpenCL
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
"alm" # jsonlite.so: undefined symbol: XXX
"archivist" # jsonlite.so: undefined symbol: XXX
"bold" # jsonlite.so: undefined symbol: XXX
"enigma" # jsonlite.so: undefined symbol: XXX
"exCon" # jsonlite.so: undefined symbol: XXX
"gender" # jsonlite.so: undefined symbol: XXX
"jSonarR" # jsonlite.so: undefined symbol: XXX
"leafletR" # jsonlite.so: undefined symbol: XXX
"opencpu" # jsonlite.so: undefined symbol: XXX
"pdfetch" # jsonlite.so: undefined symbol: XXX
"polidata" # jsonlite.so: undefined symbol: XXX
"pollstR" # jsonlite.so: undefined symbol: XXX
"rbison" # jsonlite.so: undefined symbol: XXX
"RGA" # jsonlite.so: undefined symbol: XXX
"rHealthDataGov" # jsonlite.so: undefined symbol: XXX
"rinat" # jsonlite.so: undefined symbol: XXX
"rjstat" # jsonlite.so: undefined symbol: XXX
"rmongodb" # jsonlite.so: undefined symbol: XXX
"rnoaa" # jsonlite.so: undefined symbol: XXX
"RSiteCatalyst" # jsonlite.so: undefined symbol: XXX
"rsunlight" # jsonlite.so: undefined symbol: XXX
"rWBclimate" # jsonlite.so: undefined symbol: XXX
"SGP" # jsonlite.so: undefined symbol: XXX
"slackr" # jsonlite.so: undefined symbol: XXX
"SocialMediaMineR" # jsonlite.so: undefined symbol: XXX
"webutils" # jsonlite.so: undefined symbol: XXX
"WikipediR" # jsonlite.so: undefined symbol: XXX
"demi" # requires affy, affxparser, and oligo
"KANT" # requires affy, and Biobase
"pathClass" # requires affy, and Biobase
"msarc" # requires AnnotationDbi
"ACNE" # requires aroma_affymetrix
"Statomica" # requires Biobase, multtest
"aroma_affymetrix" # requires aroma_core
"calmate" # requires aroma_core
"NSA" # requires aroma_core
@ -689,7 +684,11 @@ let
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
"FunctionalNetworks" # requires breastCancerVDX, and Biobase
"rJPSGCS" # requires chopsticks
"OpenCL" # requires CL/opencl.h
"OpenCL" # FIXME: requires CL/opencl.h
"Rsymphony" # FIXME: requires SYMPHONY
"V8" # compilation error
"js" # requires broken V8
"minimist" # requires broken V8
"clpAPI" # requires clp
"pcaL1" # requires clp
"bmrm" # requires clpAPI
@ -701,8 +700,8 @@ let
"ParDNAcopy" # requires DNAcopy
"PSCBS" # requires DNAcopy
"dcGOR" # requires dnet
"bcool" # requires doMPI
"gitter" # requires EBImage
"speaq" # requires MassSpecWavelet
"Rcell" # requires EBImage
"RockFab" # requires EBImage
"babel" # requires edgeR
@ -712,6 +711,7 @@ let
"QuasiSeq" # requires edgeR
"SimSeq" # requires edgeR
"BcDiag" # requires fabia
"BACA" # requires RDAVIDWebService
"superbiclust" # requires fabia
"curvHDR" # requires flowCore
"RbioRXN" # requires fmcsR, and KEGGREST
@ -745,9 +745,9 @@ let
"gridDebug" # requires gridGraphviz
"RAM" # requires Heatplus
"RcppRedis" # requires Hiredis
"HTSDiff" # requires HTSCluster
"interval" # requires Icens
"FAMT" # requires impute
"fdrDiscreteNull" # requires edgeR
"moduleColor" # requires impute
"PMA" # requires impute
"samr" # requires impute
@ -771,6 +771,7 @@ let
"plmDE" # requires limma
"SQDA" # requires limma
"PerfMeas" # requires limma, graph, and RBGL
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
"rLindo" # requires LINDO API
"magma" # requires MAGMA
"HiPLARM" # requires MAGMA or PLASMA
@ -779,7 +780,6 @@ let
"bigGP" # requires MPI running. HELP WANTED!
"doMPI" # requires MPI running. HELP WANTED!
"metaMix" # requires MPI running. HELP WANTED!
"pbdMPI" # requires MPI running. HELP WANTED!
"pmclust" # requires MPI running. HELP WANTED!
"MSeasyTkGUI" # requires MSeasyTkGUI
"hddplot" # requires multtest
@ -899,6 +899,9 @@ let
"taxize" # requres bold
"cudaBayesreg" # requres Rmath
"rsprng" # requres sprng
"rDEA" # no such file or directory
"jomo" # linking errors
"mixture" # mixture.so: undefined symbol: dtrmm_
"evobiR" # requres taxiz
"bdvis" # requres taxize
"RNeXML" # requres taxize
@ -909,7 +912,6 @@ let
"rainfreq" # SDMTools.so: undefined symbol: X
"MigClim" # SDMTools.So: Undefined Symbol: X
"PatternClass" # SDMTools.So: Undefined Symbol: X
"qtbase" # the smokegen binary cannot find libQtCore.so.4 etc. at runtime
"jvmr" # tries to download files during its build
"h2o" # tries to download some h2o.jar during its build
];
@ -919,6 +921,11 @@ let
preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include/curl";
});
iFes = old.iFes.overrideDerivation (attrs: {
patches = [ ./patches/iFes.patch ];
CUDA_HOME = "${pkgs.cudatoolkit}";
});
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
patchPhase = "patchShebangs configure";
});
@ -983,9 +990,12 @@ let
});
RMySQL = old.RMySQL.overrideDerivation (attrs: {
configureFlags = [
"--with-mysql-dir=${pkgs.mysql}"
];
patches = [ ./patches/RMySQL.patch ];
MYSQL_DIR="${pkgs.mysql}";
});
devEMF = old.devEMF.overrideDerivation (attrs: {
NIX_CFLAGS_LINK = "-L${pkgs.xlibs.libXft}/lib -lXft";
});
slfm = old.slfm.overrideDerivation (attrs: {
@ -1046,8 +1056,7 @@ let
});
openssl = old.openssl.overrideDerivation (attrs: {
patches = [ ./patches/openssl.patch ];
OPENSSL_HOME = "${pkgs.openssl}";
OPENSSL_INCLUDES = "${pkgs.openssl}/include";
});
Rserve = old.Rserve.overrideDerivation (attrs: {
@ -1064,14 +1073,6 @@ let
];
});
# Depends on broken ecespa package.
selectspm = old.selectspm.override { hydraPlatforms = stdenv.lib.platforms.none; };
# Depends on broken qtbase package.
qtutils = old.qtutils.override { hydraPlatforms = stdenv.lib.platforms.none; };
qtpaint = old.qtpaint.override { hydraPlatforms = stdenv.lib.platforms.none; };
bamboo = old.bamboo.override { hydraPlatforms = stdenv.lib.platforms.none; };
};
in
self

13
pkgs/development/r-modules/patches/RMySQL.patch Normal file
View File

@ -0,0 +1,13 @@
diff -ru3 RMySQL_orig/configure RMySQL/configure
--- RMySQL_orig/configure 2015-02-19 22:49:15.812455730 +0300
+++ RMySQL/configure 2015-02-19 22:49:42.066407256 +0300
@@ -1,7 +1,7 @@
# If $MYSQL_DIR is specified, use that
if [ "$MYSQL_DIR" ]; then
- echo "PKG_CPPFLAGS= -I$MYSQL_DIR/include" > src/Makevars
- echo "PKG_LIBS= -L$MYSQL_DIR/lib -lmysqlclient -lz" >> src/Makevars
+ echo "PKG_CPPFLAGS= -I$MYSQL_DIR/include/mysql" > src/Makevars
+ echo "PKG_LIBS= -L$MYSQL_DIR/lib/mysql -lmysqlclient -lz" >> src/Makevars
exit 0
fi

13
pkgs/development/r-modules/patches/iFes.patch Normal file
View File

@ -0,0 +1,13 @@
diff -u3 -r iFes_orig/src/config.mk iFes/src/config.mk
--- iFes_orig/src/config.mk 2014-12-09 14:19:58.000000000 +0300
+++ iFes/src/config.mk 2015-02-19 22:47:24.426804174 +0300
@@ -12,7 +12,7 @@
endif
# set CUDA_INC to CUDA header dir on your system
-CUDA_INC := $(CUDA_HOME)/include
+CUDA_INC := $(CUDA_HOME)/usr_include
ARCH := $(shell uname -m)

30
pkgs/development/r-modules/patches/openssl.patch
View File

@ -1,30 +0,0 @@
diff -ru -x '*~' openssl_orig/configure openssl/configure
--- openssl_orig/configure 2014-11-08 02:32:33.000000000 +0900
+++ openssl/configure 2014-11-29 20:57:19.919495325 +0900
@@ -4,14 +4,15 @@
# if present, hence this script is not really required. On CRAN, we use
# the $OPENSSL_INCLUDES variable; elsewhere we assume to the standard
# linux location: /usr/include/openssl.
-if [ -z "$OPENSSL_INCLUDES" ]; then
- OPENSSL_INCLUDES="/usr/include"
-else
- echo "PKG_CPPFLAGS= -I$OPENSSL_INCLUDES" >> src/Makevars
-fi
+# if [ -z "$OPENSSL_INCLUDES" ]; then
+# OPENSSL_INCLUDES="/usr/include"
+# else
+# echo "PKG_CPPFLAGS= -I$OPENSSL_INCLUDES" >> src/Makevars
+# fi
-# Verify that openssl RNG is present
-if [ ! -e $OPENSSL_INCLUDES/openssl/rand.h ]; then
- echo "File $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
- exit 1
-fi
+# # Verify that openssl RNG is present
+# if [ ! -e $OPENSSL_INCLUDES/openssl/rand.h ]; then
+# echo "File $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
+# exit 1
+# fi
+echo "PKG_LIBS= -L"${OPENSSL_HOME}/lib" -lssl -lcrypto" > src/Makevars
\ No newline at end of file