cran-packages: updated sources

pkgs/development/r-modules/broken-packages.nix

@@ -3,9 +3,9 @@
   # sort -t '#' -k 2
 
   "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
-  "Actigraphy" # SDMTools.so: undefined symbol: X
   "MigClim" # SDMTools.So: Undefined Symbol: X
   "PatternClass" # SDMTools.So: Undefined Symbol: X
+  "Actigraphy" # SDMTools.so: undefined symbol: X
   "lefse" # SDMTools.so: undefined symbol: X
   "raincpc" # SDMTools.so: undefined symbol: X
   "rainfreq" # SDMTools.so: undefined symbol: X
@@ -39,7 +39,7 @@
   "slackr" # jsonlite.so: undefined symbol: XXX
   "webutils" # jsonlite.so: undefined symbol: XXX
   "msarc" # requires AnnotationDbi
-  "ppiPre" # requires AnnotationDbi
+  "MetaLandSim" # requires Biobase
   "RobLox" # requires Biobase
   "RobLoxBioC" # requires Biobase
   "compendiumdb" # requires Biobase
@@ -49,13 +49,17 @@
   "GExMap" # requires Biobase and multtest
   "IsoGene" # requires Biobase, and affy
   "mGSZ" # requires Biobase, and limma
+  "netweavers" # requires BiocGenerics, Biobase, and limma
   "NCmisc" # requires BiocInstaller
+  "EMDomics" # requires BiocParallel
   "RADami" # requires Biostrings
+  "ionflows" # requires Biostrings
   "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
   "SimRAD" # requires Biostrings, and ShortRead
   "SeqFeatR" # requires Biostrings, qvalue, and widgetTools
   "OpenCL" # requires CL/opencl.h
   "cplexAPI" # requires CPLEX
+  "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
   "CHAT" # requires DNAcopy
   "PSCBS" # requires DNAcopy
   "ParDNAcopy" # requires DNAcopy
@@ -63,6 +67,7 @@
   "RockFab" # requires EBImage
   "gitter" # requires EBImage
   "rggobi" # requires GGobi
+  "PANDA" # requires GO.db
   "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
   "PubMedWordcloud" # requires GOsummaries
   "ExomeDepth" # requires GenomicRanges, and Rsamtools
@@ -102,6 +107,7 @@
   "dagbag" # requires Rlapack
   "ltsk" # requires Rlapack and Rblas
   "REBayes" # requires Rmosek
+  "cqrReg" # requires Rmosek
   "LinRegInteractive" # requires Rpanel
   "RVideoPoker" # requires Rpanel
   "ArrayBin" # requires SAGx
@@ -141,9 +147,9 @@
   "superbiclust" # requires fabia
   "curvHDR" # requires flowCore
   "RbioRXN" # requires fmcsR, and KEGGREST
+  "D2C" # requires gRbase
   "LogisticDx" # requires gRbase
   "gRain" # requires gRbase
-  "gRbase" # requires gRbase
   "gRc" # requires gRbase
   "gRim" # requires gRbase
   "topologyGSA" # requires gRbase
@@ -155,6 +161,7 @@
   "eulerian" # requires graph
   "gRapHD" # requires graph
   "msSurv" # requires graph
+  "QuACN" # requires graph, RBGL
   "RnavGraph" # requires graph, and RBGL
   "iRefR" # requires graph, and RBGL
   "pcalg" # requires graph, and RBGL
@@ -164,7 +171,6 @@
   "gridGraphviz" # requires graph, and Rgraphviz
   "ddepn" # requires graph, and genefilter
   "gridDebug" # requires gridGraphviz
-  "DRI" # requires impute
   "FAMT" # requires impute
   "PMA" # requires impute
   "WGCNA" # requires impute
@@ -203,6 +209,7 @@
   "pbdDMAT" # requires pbdMPI
   "pbdSLAP" # requires pbdMPI
   "LOST" # requires pcaMethods
+  "agridat" # requires pcaMethods
   "multiDimBio" # requires pcaMethods
   "crmn" # requires pcaMethods, and Biobase
   "imputeLCMD" # requires pcaMethods, and impute
@@ -272,12 +279,13 @@
   "dnet" # requires supraHex, graph, Rgraphviz, and Biobase
   "plsRcox" # requires survcomp
   "rsig" # requires survcomp
+  "leapp" # requires sva
   "ttScreening" # requires sva, and limma
   "cudaBayesreg" # requres Rmath
   "taxize" # requres bold
   "rsprng" # requres sprng
+  "evobiR" # requres taxiz
   "RNeXML" # requres taxize
   "TR8" # requres taxize
   "bdvis" # requres taxize
-  "evobiR" # requres taxiz
 ]

pkgs/development/r-modules/default-overrides.nix

@@ -125,10 +125,6 @@ stdenv: pkgs: old: new: {
     patches = [ ./patches/BayesBridge.patch ];
   });
 
-  dbarts = old.dbarts.overrideDerivation (attrs: {
-    patches = [ ./patches/dbarts.patch ];
-  });
-
   openssl = old.openssl.overrideDerivation (attrs: {
     patches = [ ./patches/openssl.patch ];
     OPENSSL_HOME = "${pkgs.openssl}";

pkgs/development/r-modules/packages-requireing-x.nix

@@ -3,11 +3,14 @@
   "AnnotLists"
   "AnthropMMD"
   "AtelieR"
+  "BAT"
   "BCA"
   "BEQI2"
   "BHMSMAfMRI"
+  "BioGeoBEARS"
   "BiodiversityR"
   "CCTpack"
+  "CommunityCorrelogram"
   "ConvergenceConcepts"
   "DALY"
   "DSpat"
@@ -18,38 +21,49 @@
   "DeducerSpatial"
   "DeducerSurvival"
   "DeducerText"
+  "Demerelate"
   "DescTools"
   "DivMelt"
   "ENiRG"
   "EcoVirtual"
   "EnQuireR"
+  "FAiR"
+  "FD"
   "FFD"
   "FeedbackTS"
+  "FreeSortR"
   "GGEBiplotGUI"
   "GPCSIV"
+  "GUniFrac"
   "Geneland"
   "GeoGenetix"
   "GeoXp"
+  "GrammR"
   "GrapheR"
   "GroupSeq"
   "HH"
   "HiveR"
+  "IsotopeR"
   "JGR"
   "KappaGUI"
   "LS2Wstat"
   "MAR1"
   "MTurkR"
+  "MVPARTwrap"
   "MareyMap"
   "MergeGUI"
   "Meth27QC"
+  "MicroStrategyR"
   "MissingDataGUI"
   "MplusAutomation"
   "OligoSpecificitySystem"
   "OpenRepGrid"
   "PBSadmb"
   "PBSmodelling"
+  "PCPS"
   "PKmodelFinder"
   "PoMoS"
+  "PopGenReport"
   "PredictABEL"
   "PrevMap"
   "ProbForecastGOP"
@@ -57,6 +71,7 @@
   "R2STATS"
   "RHRV"
   "RNCEP"
+  "RQDA"
   "RSDA"
   "RSurvey"
   "RandomFields"
@@ -102,6 +117,8 @@
   "SPACECAP"
   "SRRS"
   "SSDforR"
+  "STEPCAM"
+  "SYNCSA"
   "Simile"
   "SimpleTable"
   "StatDA"
@@ -118,17 +135,26 @@
   "accrual"
   "ade4TkGUI"
   "adehabitat"
+  "analogue"
+  "analogueExtra"
   "aplpack"
   "aqfig"
   "arf3DS4"
   "asbio"
+  "bayesDem"
+  "betapart"
+  "betaper"
   "bio_infer"
+  "bipartite"
   "biplotbootGUI"
+  "blender"
   "cairoDevice"
   "cncaGUI"
+  "cocorresp"
   "confidence"
   "constrainedKriging"
   "cpa"
+  "dave"
   "debug"
   "detrendeR"
   "dgmb"
@@ -144,33 +170,53 @@
   "fgui"
   "fisheyeR"
   "fit4NM"
+  "forams"
   "forensim"
   "fscaret"
   "gWidgets2RGtk2"
   "gWidgets2tcltk"
+  "gWidgetsRGtk2"
   "gWidgetstcltk"
   "gcmr"
   "geoR"
   "geoRglm"
+  "geomorph"
   "georob"
   "gnm"
   "gsubfn"
+  "iBUGS"
+  "iDynoR"
   "ic50"
   "in2extRemes"
   "iplots"
+  "isopam"
   "likeLTD"
+  "loe"
   "logmult"
+  "memgene"
+  "metacom"
   "migui"
   "miniGUI"
   "mixsep"
   "mlDNA"
+  "mpmcorrelogram"
   "mritc"
   "multgee"
   "multibiplotGUI"
+  "nodiv"
   "onemap"
+  "palaeoSig"
+  "paleoMAS"
   "pbatR"
+  "pez"
+  "phylotools"
+  "picante"
   "playwith"
   "plotSEMM"
+  "plsRbeta"
+  "plsRglm"
+  "pmg"
+  "poppr"
   "powerpkg"
   "prefmod"
   "qtbase"
@@ -178,27 +224,47 @@
   "qtutils"
   "r4ss"
   "rAverage"
+  "rareNMtests"
+  "recluster"
   "relax"
   "relimp"
   "reportRx"
+  "reshapeGUI"
+  "rgl"
+  "rich"
   "ringscale"
+  "rioja"
   "ripa"
   "rite"
   "rnbn"
   "rriskDistributions"
   "rsgcc"
   "sdcMicroGUI"
+  "sharpshootR"
+  "simba"
+  "soundecology"
+  "spacodiR"
   "spatsurv"
   "sqldf"
+  "statcheck"
   "stosim"
+  "strvalidator"
   "stylo"
   "svDialogstcltk"
   "svIDE"
   "svSocket"
   "svWidgets"
+  "tcltk2"
   "titan"
   "tkrgl"
+  "tkrplot"
+  "tmap"
+  "tspmeta"
   "twiddler"
   "vcdExtra"
+  "vegan"
+  "vegan3d"
+  "vegclust"
   "x12GUI"
+  "xergm"
 ]

pkgs/development/r-modules/packages-with-native-build-inputs.nix

@@ -2,6 +2,7 @@ pkgs: {
   # sort -t '=' -k 2
   RAppArmor = [ pkgs.apparmor ];
   SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
+  curl = [ pkgs.curl pkgs.openldap ];
   Rssa = [ pkgs.fftw ];
   fftw = [ pkgs.fftw ];
   fftwtools = [ pkgs.fftw ];

pkgs/development/r-modules/patches/dbarts.patch

@@ -1,12 +0,0 @@
-diff -ru -x '*~' dbarts_orig/src/Makevars.in dbarts/src/Makevars.in
---- dbarts_orig/src/Makevars.in	2014-07-01 02:30:57.000000000 +0900
-+++ dbarts/src/Makevars.in	2014-10-25 19:25:58.910704279 +0900
-@@ -6,7 +6,7 @@
- 
- PKG_CPPFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
- PKG_CPPXXFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
--PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) dbarts/libdbarts.a external/libexternal.a @PTHREAD_LIBS@ 
-+PKG_LIBS=dbarts/libdbarts.a external/libexternal.a $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @PTHREAD_LIBS@ 
- 
- .PHONY: all dbarts/libdbarts.a external/libexternal.a clean
- 

pkgs/development/r-modules/patches/openssl.patch

@@ -1,28 +1,30 @@
 diff -ru -x '*~' openssl_orig/configure openssl/configure
---- openssl_orig/configure	2014-10-18 08:14:15.000000000 +0900
+--- openssl_orig/configure	2014-11-08 02:32:33.000000000 +0900
-+++ openssl/configure	2014-11-03 15:05:25.122906126 +0900
++++ openssl/configure	2014-11-29 20:57:19.919495325 +0900
-@@ -1,23 +1 @@
+@@ -4,14 +4,15 @@
--# Check for include
+ # if present, hence this script is not really required. On CRAN, we use
--if [ ! -e /usr/include/openssl/rand.h ]
+ # the $OPENSSL_INCLUDES variable; elsewhere we assume to the standard
--then
+ # linux location: /usr/include/openssl.
--  echo "openssl/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
+-if [ -z "$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
--# Not linux. Probably OSX.
++# if [ ! -e $OPENSSL_INCLUDES/openssl/rand.h ]; then
--if [ ! -e /sbin/ldconfig ]
++#   echo "File $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
--then
++#   exit 1
--  exit 0
++# fi
--fi
--
--# looks like unix
--LIBFILE=$(/sbin/ldconfig -p | egrep -ohm1 " [-_a-zA-Z0-9/]*/libssl[0-9]*.so$")
--
--if [ -z "$LIBFILE" ]
--then
--  echo "libssl.so not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
--  exit 1
--fi
--
--echo "PKG_LIBS= -L"$(dirname $LIBFILE)" -lssl -lcrypto" > src/Makevars
 +echo "PKG_LIBS= -L"${OPENSSL_HOME}/lib" -lssl -lcrypto" > src/Makevars
+\ No newline at end of file