cran-packages: updated sources
This commit is contained in:
taku0
Peter Simons
parent
2532844fb5
commit
4647743ed7
@ -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
|
||||
]
|
||||
|
||||
@ -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}";
|
||||
|
||||
@ -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"
|
||||
]
|
||||
|
||||
@ -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 ];
|
||||
|
||||
@ -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
|
||||
|
||||
@ -1,28 +1,30 @@
|
||||
diff -ru -x '*~' openssl_orig/configure openssl/configure
|
||||
--- openssl_orig/configure 2014-10-18 08:14:15.000000000 +0900
|
||||
+++ openssl/configure 2014-11-03 15:05:25.122906126 +0900
|
||||
@@ -1,23 +1 @@
|
||||
-# Check for include
|
||||
-if [ ! -e /usr/include/openssl/rand.h ]
|
||||
-then
|
||||
- echo "openssl/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
|
||||
--- 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 $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
|
||||
- exit 1
|
||||
-fi
|
||||
-
|
||||
-# Not linux. Probably OSX.
|
||||
-if [ ! -e /sbin/ldconfig ]
|
||||
-then
|
||||
- exit 0
|
||||
-fi
|
||||
-
|
||||
-# looks like unix
|
||||
-LIBFILE=$(/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
|
||||
+# # 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
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
Loading…
Reference in New Issue
Block a user