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r-modules: fix evaluation and minor cleanups

This commit is contained in:
Peter Simons 2015-01-21 17:10:16 +01:00
parent 0e214778de
commit 7fa0fa6450
1 changed files with 2 additions and 24 deletions
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26
pkgs/development/r-modules/default.nix
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@ -221,7 +221,6 @@ let
libamtrack = [ pkgs.gsl ]; libamtrack = [ pkgs.gsl ];
mixcat = [ pkgs.gsl ]; mixcat = [ pkgs.gsl ];
outbreaker = [ pkgs.gsl ]; outbreaker = [ pkgs.gsl ];
#pcaPA = [ pkgs.gsl ];
ridge = [ pkgs.gsl ]; ridge = [ pkgs.gsl ];
simplexreg = [ pkgs.gsl ]; simplexreg = [ pkgs.gsl ];
stsm = [ pkgs.gsl ]; stsm = [ pkgs.gsl ];
@ -283,10 +282,6 @@ let
PopGenome = [ pkgs.zlib ]; PopGenome = [ pkgs.zlib ];
RJaCGH = [ pkgs.zlib ]; RJaCGH = [ pkgs.zlib ];
RcppCNPy = [ pkgs.zlib ]; RcppCNPy = [ pkgs.zlib ];
#Rniftilib = [ pkgs.zlib ];
#WhopGenome = [ pkgs.zlib ];
#devEMF = [ pkgs.zlib ];
#gdsfmt = [ pkgs.zlib ];
rbamtools = [ pkgs.zlib ]; rbamtools = [ pkgs.zlib ];
rmatio = [ pkgs.zlib ]; rmatio = [ pkgs.zlib ];
RVowpalWabbit = [ pkgs.zlib pkgs.boost ]; RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
@ -311,7 +306,6 @@ let
gmatrix = [ pkgs.cudatoolkit ]; gmatrix = [ pkgs.cudatoolkit ];
WideLM = [ pkgs.cudatoolkit ]; WideLM = [ pkgs.cudatoolkit ];
RCurl = [ pkgs.curl ]; RCurl = [ pkgs.curl ];
#Rgnuplot = [ pkgs.gnuplot ];
R2SWF = [ pkgs.pkgconfig ]; R2SWF = [ pkgs.pkgconfig ];
RGtk2 = [ pkgs.pkgconfig ]; RGtk2 = [ pkgs.pkgconfig ];
RProtoBuf = [ pkgs.pkgconfig ]; RProtoBuf = [ pkgs.pkgconfig ];
@ -393,7 +387,6 @@ let
"LS2Wstat" "LS2Wstat"
"MAR1" "MAR1"
"MTurkR" "MTurkR"
#"MVPARTwrap"
"MareyMap" "MareyMap"
"MergeGUI" "MergeGUI"
"Meth27QC" "Meth27QC"
@ -405,8 +398,6 @@ let
"PBSadmb" "PBSadmb"
"PBSmodelling" "PBSmodelling"
"PCPS" "PCPS"
#"PKmodelFinder"
#"PoMoS"
"PopGenReport" "PopGenReport"
"PredictABEL" "PredictABEL"
"PrevMap" "PrevMap"
@ -432,7 +423,6 @@ let
"RcmdrPlugin_KMggplot2" "RcmdrPlugin_KMggplot2"
"RcmdrPlugin_MA" "RcmdrPlugin_MA"
"RcmdrPlugin_MPAStats" "RcmdrPlugin_MPAStats"
#"RcmdrPlugin_NMBU"
"RcmdrPlugin_ROC" "RcmdrPlugin_ROC"
"RcmdrPlugin_SCDA" "RcmdrPlugin_SCDA"
"RcmdrPlugin_SLC" "RcmdrPlugin_SLC"
@ -474,7 +464,6 @@ let
"TestScorer" "TestScorer"
"VIMGUI" "VIMGUI"
"VecStatGraphs3D" "VecStatGraphs3D"
#"VisuClust"
"WMCapacity" "WMCapacity"
"accrual" "accrual"
"ade4TkGUI" "ade4TkGUI"
@ -622,6 +611,8 @@ let
# Packages which cannot be installed due to lack of dependencies or other reasons. # Packages which cannot be installed due to lack of dependencies or other reasons.
brokenPackages = [ # sort -t '#' -k 2 brokenPackages = [ # sort -t '#' -k 2
"metabolomics" # depends on broken crmn
"retistruct" # depends on broken RImageJROI
"CARrampsOcl" # depends on OpenCL "CARrampsOcl" # depends on OpenCL
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED! "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
"alm" # jsonlite.so: undefined symbol: XXX "alm" # jsonlite.so: undefined symbol: XXX
@ -644,7 +635,6 @@ let
"rmongodb" # jsonlite.so: undefined symbol: XXX "rmongodb" # jsonlite.so: undefined symbol: XXX
"rnoaa" # jsonlite.so: undefined symbol: XXX "rnoaa" # jsonlite.so: undefined symbol: XXX
"RSiteCatalyst" # jsonlite.so: undefined symbol: XXX "RSiteCatalyst" # jsonlite.so: undefined symbol: XXX
#"RSocrata" # jsonlite.so: undefined symbol: XXX
"rsunlight" # jsonlite.so: undefined symbol: XXX "rsunlight" # jsonlite.so: undefined symbol: XXX
"rWBclimate" # jsonlite.so: undefined symbol: XXX "rWBclimate" # jsonlite.so: undefined symbol: XXX
"SGP" # jsonlite.so: undefined symbol: XXX "SGP" # jsonlite.so: undefined symbol: XXX
@ -722,7 +712,6 @@ let
"gRapHD" # requires graph "gRapHD" # requires graph
"msSurv" # requires graph "msSurv" # requires graph
"PairViz" # requires graph "PairViz" # requires graph
#"ddepn" # requires graph, and genefilter
"iRefR" # requires graph, and RBGL "iRefR" # requires graph, and RBGL
"pcalg" # requires graph, and RBGL "pcalg" # requires graph, and RBGL
"protiq" # requires graph, and RBGL "protiq" # requires graph, and RBGL
@ -765,7 +754,6 @@ let
"metaMA" # requires limma "metaMA" # requires limma
"plmDE" # requires limma "plmDE" # requires limma
"SQDA" # requires limma "SQDA" # requires limma
#"RPPanalyzer" # requires limma, and Biobase
"PerfMeas" # requires limma, graph, and RBGL "PerfMeas" # requires limma, graph, and RBGL
"rLindo" # requires LINDO API "rLindo" # requires LINDO API
"magma" # requires MAGMA "magma" # requires MAGMA
@ -802,7 +790,6 @@ let
"crmn" # requires pcaMethods, and Biobase "crmn" # requires pcaMethods, and Biobase
"imputeLCMD" # requires pcaMethods, and impute "imputeLCMD" # requires pcaMethods, and impute
"MEET" # requires pcaMethods, and seqLogo "MEET" # requires pcaMethods, and seqLogo
#"SigTree" # requires phyloseq
"saps" # requires piano, and survcomp "saps" # requires piano, and survcomp
"smart" # requires PMA "smart" # requires PMA
"surveillance" # requires polyCub "surveillance" # requires polyCub
@ -823,7 +810,6 @@ let
"PKgraph" # requires rggobi "PKgraph" # requires rggobi
"SeqGrapheR" # requires rggobi "SeqGrapheR" # requires rggobi
"branchLars" # requires Rgraphviz "branchLars" # requires Rgraphviz
#"gcExplorer" # requires Rgraphviz
"hasseDiagram" # requires Rgraphviz "hasseDiagram" # requires Rgraphviz
"hpoPlot" # requires Rgraphviz "hpoPlot" # requires Rgraphviz
"strum" # requires Rgraphviz "strum" # requires Rgraphviz
@ -891,7 +877,6 @@ let
"rsig" # requires survcomp "rsig" # requires survcomp
"leapp" # requires sva "leapp" # requires sva
"ttScreening" # requires sva, and limma "ttScreening" # requires sva, and limma
#"ENA" # requires WGCNA
"GOGANPA" # requires WGCNA "GOGANPA" # requires WGCNA
"nettools" # requires WGCNA "nettools" # requires WGCNA
"rneos" # requires XMLRPC "rneos" # requires XMLRPC
@ -1067,13 +1052,6 @@ let
qtpaint = old.qtpaint.override { hydraPlatforms = stdenv.lib.platforms.none; }; qtpaint = old.qtpaint.override { hydraPlatforms = stdenv.lib.platforms.none; };
bamboo = old.bamboo.override { hydraPlatforms = stdenv.lib.platforms.none; }; bamboo = old.bamboo.override { hydraPlatforms = stdenv.lib.platforms.none; };
# Obsolete package that I keep around temporarily because some
# existing code depends on it.
Defaults = derive {
name="Defaults";
version="1.1-1";
sha256="0ikgd5mswlky327pzp09cz93bn3mq7qnybq1r64y19c2brbax00d";
};
}; };
in in
self self