From 8450ff3ab8e315998f7e52afaf487352808c7b6a Mon Sep 17 00:00:00 2001 From: Nikolay Amiantov Date: Thu, 19 Feb 2015 23:53:36 +0300 Subject: [PATCH] rPackages: fix broken packages --- pkgs/development/r-modules/default.nix | 101 +++++++++--------- .../r-modules/patches/RMySQL.patch | 13 +++ pkgs/development/r-modules/patches/iFes.patch | 13 +++ .../r-modules/patches/openssl.patch | 30 ------ 4 files changed, 77 insertions(+), 80 deletions(-) create mode 100644 pkgs/development/r-modules/patches/RMySQL.patch create mode 100644 pkgs/development/r-modules/patches/iFes.patch delete mode 100644 pkgs/development/r-modules/patches/openssl.patch diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index a72b56d622a2..d901c8b6d639 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -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 diff --git a/pkgs/development/r-modules/patches/RMySQL.patch b/pkgs/development/r-modules/patches/RMySQL.patch new file mode 100644 index 000000000000..dc93b902cd5c --- /dev/null +++ b/pkgs/development/r-modules/patches/RMySQL.patch @@ -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 + diff --git a/pkgs/development/r-modules/patches/iFes.patch b/pkgs/development/r-modules/patches/iFes.patch new file mode 100644 index 000000000000..aca89b8d5a86 --- /dev/null +++ b/pkgs/development/r-modules/patches/iFes.patch @@ -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) + + diff --git a/pkgs/development/r-modules/patches/openssl.patch b/pkgs/development/r-modules/patches/openssl.patch deleted file mode 100644 index d89c30f61a14..000000000000 --- a/pkgs/development/r-modules/patches/openssl.patch +++ /dev/null @@ -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