[pkg-bioc] svn commit r309 r309 - in /trunk/tools: buildDeps.list cran2deb.pl
egonw-guest at users.alioth.debian.org
egonw-guest at users.alioth.debian.org
Wed Aug 29 13:14:10 UTC 2007
Author: egonw-guest
Date: Wed Aug 29 13:14:10 2007
New Revision: 309
URL: http://svn.debian.org/wsvn/pkg-bioc/?sc=1&rev=309
Log:
Refactored the build deps into a flat file config file
Added:
trunk/tools/buildDeps.list (with props)
Modified:
trunk/tools/cran2deb.pl
Added: trunk/tools/buildDeps.list
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools/buildDeps.list?rev=309&op=file
==============================================================================
--- trunk/tools/buildDeps.list (added)
+++ trunk/tools/buildDeps.list Wed Aug 29 13:14:10 2007
@@ -0,0 +1,182 @@
+## Build Dependencies
+ade4TkGUI: r-cran-ade4
+adehabitat: r-cran-ade4, r-cran-gpclib
+arules: r-cran-matrix
+arm: r-cran-r2winbugs
+arrayImpute: r-cran-rgtk2, r-cran-vr
+aster: r-cran-trust
+bayesmix: r-cran-coda
+bma: r-cran-leaps
+boolean: r-cran-rgenoud
+cacheSweave: r-cran-digest
+Cairo: libgtk2.0-dev, libcairo2-dev, x-dev, libx11-dev, libxt-dev
+cairoDevice: libgtk2.0-dev
+clustTool: r-cran-rcmdr
+coin: r-cran-mvtnorm, r-cran-modeltools
+cyclones: r-cran-ncdf, r-cran-clim.pact
+debug: r-cran-mvbutils
+deal: r-cran-dynamicgraph
+distr: r-cran-setrng
+drfit: r-cran-rodbc
+flexclust: r-cran-lattice
+gamlss.tr: r-cran-vr
+gap: r-cran-genetics
+GDD: libgd2-xpm-dev
+Geneland: r-cran-randomfields
+GeneNet: r-cran-fdrtool
+GeneNT: r-cran-e1071,r-cran-genets,r-bioc-graph, r-bioc-rbgl
+GeneTS: r-cran-corpcor, r-cran-locfdr
+genetics: r-cran-gdata, r-cran-gtools, r-cran-combinat
+gmp: libgmp3-dev
+gsl: libgsl0-dev
+gstat: r-cran-sp
+gplots: r-cran-gtools, r-cran-gdata
+gWidgetsRGtk2: r-cran-gwidgets, r-cran-rgtk2
+hdf5: libhdf5-serial-dev, zlib1g-dev
+homals: r-cran-deldir
+iplots: r-cran-rjava
+laser: r-cran-ape
+LDheatmap: r-cran-genetics
+MarkedPointProcess: r-cran-randomfields
+Matching: r-cran-rgenoud
+MBA: libboost-graph-dev, libboost-dev
+MBESS: r-cran-vr, r-cran-gsl
+multinomrob: r-cran-mvtnorm
+ncdf: netcdfg-dev
+ncvar: r-cran-rnetcdf
+netCDF: netcdfg-dev
+orientlib: r-cran-scatterplot3d
+pcalg: r-bioc-graph
+pcurve: r-cran-vegan
+PKfit: r-cran-odesolve, r-cran-rgenoud
+plotAndPlayGTK: r-cran-rgtk2, r-cran-cairodevice, r-cran-lattice
+ProbForecastGOP: r-cran-randomfields
+quantchem: r-cran-outliers
+QRMlib: r-cran-vr, r-cran-hmisc, r-cran-lattice, r-cran-cluster
+R.cache: r-cran-r.oo, r-cran-r.utils
+R.huge: r-cran-r.oo, r-cran-r.utils
+R.matlab: r-cran-r.oo
+R.rsp: r-cran-r.oo
+R.utils: r-cran-r.oo
+ROptEst: r-cran-randvar
+RBGL: libboost-graph-dev, r-cran-cluster, r-bioc-ruuid, r-cran-graph
+rcurl: libcurl3-dev
+rgdal: libgdal1-dev, r-cran-abind, r-cran-pixmap, r-cran-lattice
+rimage: fftw-dev, libjpeg62-dev
+Rpad: r-cran-r2html
+rscalapack: lam-runtime, lam4-dev, refblas3-dev, blacs-lam-dev , scalapack-mpich-dev
+RSQLite: r-cran-dbi
+rtiff: libtiff4-dev
+SciViews: r-cran-r2html
+SensoMineR: r-cran-hopach, r-cran-ade4, r-cran-cluster
+SLmisc: r-cran-plotrix
+SoPhy: r-cran-randomfields, libtiff4-dev
+spatstat: r-cran-sm
+spdep: r-cran-maptools
+spgwr: r-cran-maptools
+Synth: r-cran-kernlab
+taskPR: lam4-dev
+trip: r-cran-lattice
+untb: r-cran-partitions
+verification: r-cran-fields, r-cran-waveslim
+vars: r-cran-nlme
+WeedMap: r-cran-randomfields
+
+# BioConductor
+adSplit: r-bioc-affy,r-bioc-multtest, r-bioc-biobase, r-bioc-go, r-bioc-kegg
+
+aCGH: r-bioc-multtest, r-cran-sma
+affy: r-bioc-biobase, r-bioc-affyio
+affycoretools: r-bioc-affy, r-cran-limma, r-bioc-gostats, r-bioc-biomart, r-bioc-gcrma,r-bioc-biobase, r-bioc-annotate, r-bioc-xtable, r-bioc-annaffy
+
+affyPLM: r-bioc-affy,r-bioc-gcrma
+affyQCReport: r-bioc-biobase, r-bioc-affy, r-bioc-simpleaffy
+altcdfenvs: r-bioc-affy
+AmpAffyExample: r-bioc-affy
+annaffy: r-bioc-go, r-bioc-kegg
+annotate: r-bioc-biobase
+AnnBuilder: r-cran-xml, r-bioc-biobase, r-bioc-annotate
+aroma.light: r-cran-r.oo
+arrayMagic: r-bioc-vsn, r-cran-limma, r-bioc-genefilter
+arrayQuality: r-bioc-hexbin, r-bioc-convert, r-bioc-lpe,r-cran-rcolorbrewer, r-cran-gridbase
+
+Aspell: libaspell-dev
+biomaRt: r-cran-rmysql, r-bioc-biobase, r-cran-xml
+biocViews: r-bioc-rbgl
+BufferedMatrixMethods: r-cran-bufferedmatrix
+cellHTS: r-bioc-prada
+convert: r-cran-limma, r-bioc-marray
+CORBA: libidl0
+cosmo: r-bioc-seqlogo
+cosmogui: r-bioc-tkwidgets, r-bioc-widgettools, r-bioc-dyndoc,r-bioc-cosmo, r-bioc-seqlogo, r-cran-grid
+
+ecolitk: r-bioc-affy, r-bioc-ecolileucine
+EBImage: libmagick++9-dev
+edd: r-bioc-golubesets, r-bioc-biobase, r-cran-vr, r-cran-xtable
+exonmap: r-bioc-affy, r-bioc-genefilter, r-bioc-rcolorbrewer, r-cran-rmysql (>= 0.5-11), r-cran-dbi, r-bioc-plier
+
+exprDB: libdb4.3-dev, r-bioc-biobase
+exprexternal: r-bioc-biobase, r-bioc-externalvector
+flowCore: r-bioc-biobase, r-cran-rrcov
+gcrma: r-bioc-matchprobes
+genarize: r-cran-xtable, r-cran-tkrplot
+geneplotter: r-bioc-biobase, r-bioc-annotate, r-cran-rcolorbrewer
+genefilter: r-bioc-biobase, r-cran-survival
+GeneTraffic: r-bioc-marray
+gff3Plotter: r-bioc-biobase, r-cran-gdd
+gocluster: r-bioc-biobase
+GGdata: r-bioc-ggtools
+GOstats: r-bioc-rbgl,r-bioc-category
+goTools: r-bioc-biobase, r-bioc-annotate, r-bioc-go
+graph: r-bioc-ruuid, r-cran-cluster
+gtkWidgets: r-bioc-dyndoc
+hexbin: r-bioc-marray, r-cran-cluster, r-cran-colorspace
+hopach: r-cran-cluster
+hypergraph: r-bioc-graph
+iSPlot: RGtk, gtkDevice
+iSNetwork: r-bioc-graph
+marray: r-bioc-biobase, r-cran-limma
+makecdfenv: r-bioc-biobase, r-bioc-affy
+matchprobes: r-bioc-affy
+mcrestimate: r-cran-e1071,r-cran-pamr, r-cran-randomforest, r-cran-rcolorbrewer
+
+multtest: r-bioc-biobase, r-cran-survival
+ontoTools: r-bioc-graph, r-cran-sparsem, r-bioc-go,r-bioc-biobase, r-bioc-annotate
+
+pcaMethods: r-cran-ellipse, r-cran-pls
+pkgDepTools: r-bioc-rbgl
+plier: r-bioc-affy
+prism: r-bioc-ebimage
+ppiData: r-bioc-rgraphviz
+prada: r-bioc-biobase, r-cran-rrcov, r-cran-rcolorbrewer
+process: r-bioc-icens
+pgUtils: r-bioc-rdbi
+Rgraphviz: r-bioc-graph, graphviz-dev, r-cran-rcolorbrewer, libgraphviz3-dev, libltdl3-dev
+
+rhdf5: libhdf5-serial-dev
+Rredland: librdf0-dev
+Ruuid: libglib1.2-dev, pkg-config
+SBMLR: r-cran-xml, r-cran-odesolve
+ScISI: r-bioc-apcomplex, r-bioc-go, r-bioc-gostats, r-bioc-graph, r-bioc-rbgl, r-bioc-rgraphviz, r-bioc-yeast, r-cran-xtable, r-bioc-geneplotter
+
+simplefilter: r-bioc-genefilter
+splicegear: r-bioc-biobase
+stam: r-cran-pamr
+stepNorm: r-bioc-marray
+tilingArray: r-cran-rcolorbrewer, r-bioc-biobase, r-cran-strucchange, r-cran-pixmap
+
+topGO: r-bioc-graph, r-bioc-annotate, r-bioc-go,r-cran-sparsem, r-bioc-biobase
+
+tkWidgets: r-bioc-widgettools, r-bioc-dyndoc
+vsn: r-bioc-biobase
+weaver: r-cran-digest
+webbioc: r-bioc-affy,r-cran-multtest, r-bioc-annaffy, r-bioc-vsn, r-bioc-gcrma
+
+widgetInvoke: r-cran-rgtk2
+
+## Omegahat
+CORBA: omniidl4
+RCurl: libcurl3-dev
+RSPython: python
+RwxWidgets: libwxgtk2.4-dev
+XML: libxml2-dev
Propchange: trunk/tools/buildDeps.list
------------------------------------------------------------------------------
svn:executable = *
Modified: trunk/tools/cran2deb.pl
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools/cran2deb.pl?rev=309&op=diff
==============================================================================
--- trunk/tools/cran2deb.pl (original)
+++ trunk/tools/cran2deb.pl Wed Aug 29 13:14:10 2007
@@ -25,7 +25,7 @@ Albrecht Gebhardt's script build-R-contr
http://www.math.uni-klu.ac.at/~agebhard/build-R-contrib-debs.pl
is gratefully acknowledged as a fairly complete starting point.
-Dirk Eddelbuettel, David Vernazobres, Steffen Möller
+Dirk Eddelbuettel, David Vernazobres, Steffen M�ller
=cut
@@ -90,7 +90,14 @@ $_system = $_config->system;
## DE 20 May 2007 need to set this or
## './cran2deb.pl --listRequiredDebianPackages '
## dies with an ugly error
-$installRequiredPackages = "echo"; ## provide a default
+$installRequiredPackages = "sudo"; ## provide a default
+
+sub trim($) {
+ my $string = shift;
+ $string =~ s/^\s*//;
+ $string =~ s/\s*$//;
+ return $string;
+}
sub readList($) {
my $list = shift;
@@ -101,8 +108,27 @@ sub readList($) {
if ($line =~ m/^#/) {
# skip comment line
} elsif ($line =~ m/(.*?):(.*)/) {
- $list{"$1"} = "$2";
- print "package: $1\nreason: " . $list{"$1"} . "\n";
+ $list{"$1"} = trim($2);
+ }
+ }
+ return %list;
+}
+
+sub readListList($) {
+ my $list = shift;
+ my %list = ();
+ open(FILE, "<../tools/$list") || die "Cannot open $list!\n";
+ while (<FILE>) {
+ my $line = $_;
+ if ($line =~ m/^#/) {
+ # skip comment line
+ } elsif ($line =~ m/(.*?):(.*)/) {
+ my @deps = split(/,/, $2);
+ for (my $i=(scalar @deps -1); $i>=0; $i--) {
+ $deps[$i] = trim($deps[$i]);
+ # print "package: $1 dep: '" . $deps[$i] . "'\n";
+ }
+ $list{"$1"} = [ @deps ];
}
}
return %list;
@@ -831,264 +857,7 @@ file.
=cut
-my %buildDeps = (
- ##ADaCGH => ["r-bioc-tilingarray"], no i386 version
- ade4TkGUI => ["r-cran-ade4"],
- adehabitat => [ "r-cran-ade4", "r-cran-gpclib" ],
- arules => ["r-cran-matrix"], ##
- arm => ["r-cran-r2winbugs"],
- arrayImpute => ["r-cran-rgtk2", "r-cran-vr"],
- aster => ["r-cran-trust"],
- bayesmix => ["r-cran-coda"],
- bma => ["r-cran-leaps"],
- boolean => ["r-cran-rgenoud"],
- cacheSweave => ["r-cran-digest"],
- Cairo => ["libgtk2.0-dev", "libcairo2-dev",
- "x-dev", "libx11-dev", "libxt-dev"],
- cairoDevice => ["libgtk2.0-dev"],
- clustTool => ["r-cran-rcmdr"],
- coin => [ "r-cran-mvtnorm", "r-cran-modeltools" ], ##
- cyclones => [ "r-cran-ncdf", "r-cran-clim.pact" ], ##
- debug => ["r-cran-mvbutils"],
- deal => ["r-cran-dynamicgraph"],
- distr => ["r-cran-setrng"],
- drfit => ["r-cran-rodbc"],
- flexclust => ["r-cran-lattice"],
- "gamlss.tr" => ["r-cran-vr"],
- gap => ["r-cran-genetics"], ##
- GDD => ["libgd2-xpm-dev"],
- Geneland => ["r-cran-randomfields"],
- GeneNet => ["r-cran-fdrtool"],
- GeneNT => [ "r-cran-e1071","r-cran-genets","r-bioc-graph",
- "r-bioc-rbgl" ],
- GeneTS => [ "r-cran-corpcor", "r-cran-locfdr" ],
- genetics => [ "r-cran-gdata", "r-cran-gtools", "r-cran-combinat" ], ##
- gmp => ["libgmp3-dev"],
- #gnomegui => ["libgtk2.0-dev","libgnome-dev","libglade2-dev","glade-2" ],
- gsl => ["libgsl0-dev"],
- gstat => ["r-cran-sp"],
- # in Debian gtkDevice => [ "libgtk1.2-dev","libglib1.2-dev","xlibs-dev"],
- gplots => [ "r-cran-gtools", "r-cran-gdata" ],
- gWidgetsRGtk2 => ["r-cran-gwidgets", "r-cran-rgtk2"],
- hdf5 => [ "libhdf5-serial-dev", "zlib1g-dev" ],
- homals => ["r-cran-deldir"],
- iplots => ["r-cran-rjava"],
- # in Debian its => ["r-cran-hmisc"],
- laser => ["r-cran-ape"],
- LDheatmap => ["r-cran-genetics"],
- # unbuildable, non-free: LogConcDEAD => ["r-cran-akima"],
- # in Debian!! lme4 => ["r-cran-matrix"],
- MarkedPointProcess => ["r-cran-randomfields"],
- Matching => ["r-cran-rgenoud"],
- MBA => ["libboost-graph-dev", "libboost-dev"],
- MBESS => ["r-cran-vr", "r-cran-gsl"],
- # in Debian mcmcpack => ["r-cran-coda"],
- multinomrob => ["r-cran-mvtnorm"],
- ncdf => ["netcdfg-dev"],
- ncvar => ["r-cran-rnetcdf"],
- netCDF => ["netcdfg-dev"],
- orientlib => ["r-cran-scatterplot3d"],
- pcalg => ["r-bioc-graph"],
- pcurve => ["r-cran-vegan"],
- PKfit => [ "r-cran-odesolve", "r-cran-rgenoud" ],
- plotAndPlayGTK => ["r-cran-rgtk2", "r-cran-cairodevice", "r-cran-lattice"],
- ProbForecastGOP => ["r-cran-randomfields"],
- quantchem => ["r-cran-outliers"],
- QRMlib => ["r-cran-vr", ## for spatial via fEcofin
- "r-cran-hmisc", "r-cran-lattice", "r-cran-cluster"],
- "R.cache" => [ "r-cran-r.oo", "r-cran-r.utils" ],
- "R.huge" => [ "r-cran-r.oo", "r-cran-r.utils"],
- "R.matlab" => ["r-cran-r.oo"],
- "R.rsp" => ["r-cran-r.oo"],
- "R.utils" => ["r-cran-r.oo"],
- RBGL => [ "libboost-graph-dev", "r-cran-cluster",
- "r-bioc-ruuid", "r-cran-graph" ],
- rcurl => ["libcurl3-dev"],
- rgdal => [ "libgdal1-dev", "r-cran-abind", "r-cran-pixmap",
- "r-cran-lattice" ],
- # in Debian RGtk2 => ["libgtk2.0-dev"],
- rimage => [ "fftw-dev", "libjpeg62-dev" ],
- # in Debian Rmpi => [ "lam-runtime", "lam4-dev" ],
- # in Debiam RMySQL => [ "libmysqlclient-dev", "r-cran-dbi" ],
-
- # RNetCDF => ["r-cran-udunits", "netcdfg-dev", "udunits"],
- # BioC RPgSQL => ["postgresql-dev"],
- # BioC RdbiPgSQL => ["r-cran-rdbi"],
- Rpad => ["r-cran-r2html"],
- # in Debian rpvm => ["pvm-dev"],
- # in Debian rquantlib => [ "libquantlib0-dev", "libboost-test-dev" ],
- rscalapack => [ "lam-runtime", "lam4-dev", "refblas3-dev",
- "blacs-lam-dev ", "scalapack-mpich-dev" ],
- # in Debian rsprng => [ "libsprng2-dev", "libgmp3-dev" ],
- RSQLite => ["r-cran-dbi"], ##
- rtiff => ["libtiff4-dev"], ##
- SciViews => ["r-cran-r2html"],
- SensoMineR => [ "r-cran-hopach", "r-cran-ade4", "r-cran-cluster" ],
- SLmisc => ["r-cran-plotrix"],
-
- # snow => ["pvm-dev"],
- SoPhy => ["r-cran-randomfields", "libtiff4-dev"],
- spatstat => ["r-cran-sm"],
- spdep => ["r-cran-maptools"],
- spgwr => ["r-cran-maptools"], ##
- Synth => ["r-cran-kernlab"],
- taskPR => ["lam4-dev"], ##
- trip => ["r-cran-lattice"],
- # in Debian tkrplot => [ "tcl8.4-dev", "tk8.4-dev", "xlibs-dev" ],
- # udunits => ["udunits"],
- # uroot => ["r-cran-tcltk"],
- untb => ["r-cran-partitions"],
- verification => [ "r-cran-fields", "r-cran-waveslim" ],
- vars => ["r-cran-nlme"],
- WeedMap => ["r-cran-randomfields"],
-
-
- # BioConductor
- adSplit => [
- "r-bioc-affy", "r-bioc-multtest",
- "r-bioc-biobase", "r-bioc-go",
- "r-bioc-kegg"
- ],
- aCGH => [ "r-bioc-multtest", "r-cran-sma" ],
- affy => [ "r-bioc-biobase", "r-bioc-affyio" ],
- affycoretools => [
- "r-bioc-affy", "r-cran-limma",
- "r-bioc-gostats", "r-bioc-biomart",
- "r-bioc-gcrma", "r-bioc-biobase",
- "r-bioc-annotate", "r-bioc-xtable",
- "r-bioc-annaffy"
- ],
- affyPLM => [ "r-bioc-affy", "r-bioc-gcrma" ],
- affyQCReport => [ "r-bioc-biobase", "r-bioc-affy", "r-bioc-simpleaffy" ],
- altcdfenvs => ["r-bioc-affy"],
- AmpAffyExample => ["r-bioc-affy"],
- annaffy => [ "r-bioc-go", "r-bioc-kegg" ],
- annotate => ["r-bioc-biobase"],
- AnnBuilder => [ "r-cran-xml", "r-bioc-biobase", "r-bioc-annotate" ],
- "aroma.light" => ["r-cran-r.oo"],
- arrayMagic => [ "r-bioc-vsn", "r-cran-limma", "r-bioc-genefilter" ],
- arrayQuality => [
- "r-bioc-hexbin", "r-bioc-convert",
- "r-bioc-lpe", "r-cran-rcolorbrewer",
- "r-cran-gridbase"
- ],
- Aspell => ["libaspell-dev"],
- biomaRt => [ "r-cran-rmysql", "r-bioc-biobase", "r-cran-xml" ],
- biocViews => ["r-bioc-rbgl"],
- BufferedMatrixMethods => ["r-cran-bufferedmatrix"],
- cellHTS => ["r-bioc-prada"],
- convert => [ "r-cran-limma", "r-bioc-marray" ],
- CORBA => ["libidl0"],
- cosmo => ["r-bioc-seqlogo"],
- cosmogui => [
- "r-bioc-tkwidgets", "r-bioc-widgettools",
- "r-bioc-dyndoc", "r-bioc-cosmo",
- "r-bioc-seqlogo", "r-cran-grid"
- ],
- ecolitk => [ "r-bioc-affy", "r-bioc-ecolileucine" ],
- EBImage => ["libmagick++9-dev"],
- edd =>
- [ "r-bioc-golubesets", "r-bioc-biobase", "r-cran-vr", "r-cran-xtable" ],
- exonmap => [
- "r-bioc-affy", "r-bioc-genefilter",
- "r-bioc-rcolorbrewer", "r-cran-rmysql (>= 0.5-11)",
- "r-cran-dbi", "r-bioc-plier"
- ],
- exprDB => [ "libdb4.3-dev", "r-bioc-biobase" ],
- exprexternal => [ "r-bioc-biobase", "r-bioc-externalvector" ],
- flowCore => [ "r-bioc-biobase", "r-cran-rrcov" ],
- gcrma => ["r-bioc-matchprobes"],
- genarize => [ "r-cran-xtable", "r-cran-tkrplot" ],
- geneplotter => [
- "r-bioc-biobase", # this is indirectly required, unclear if it should
- # be listed. Probably not.
- "r-bioc-annotate", "r-cran-rcolorbrewer"],
- genefilter => [ "r-bioc-biobase", "r-cran-survival" ],
- GeneTraffic => ["r-bioc-marray"],
- gff3Plotter => [ "r-bioc-biobase", "r-cran-gdd" ],
- gocluster => ["r-bioc-biobase"],
- GGdata => ["r-bioc-ggtools"],
- GOstats => [ "r-bioc-rbgl", "r-bioc-category" ],
- goTools => [ "r-bioc-biobase", "r-bioc-annotate", "r-bioc-go" ],
- gpls => [],
- graph => [ "r-bioc-ruuid", "r-cran-cluster" ],
- gtkWidgets => ["r-bioc-dyndoc"],
- hexbin => [ "r-bioc-marray", "r-cran-cluster", "r-cran-colorspace" ],
- hopach => ["r-cran-cluster"],
- hypergraph => ["r-bioc-graph"],
- iSPlot => [ "RGtk", "gtkDevice" ],
- iSNetwork => ["r-bioc-graph"],
- marray => [ "r-bioc-biobase", "r-cran-limma" ],
- makecdfenv => [ "r-bioc-biobase", "r-bioc-affy" ],
- matchprobes => ["r-bioc-affy"], # not in description
- mcrestimate => [
- "r-cran-e1071", "r-cran-pamr",
- "r-cran-randomforest", "r-cran-rcolorbrewer"
- ],
- multtest => [ "r-bioc-biobase", "r-cran-survival" ],
- ontoTools => [
- "r-bioc-graph", "r-cran-sparsem",
- "r-bioc-go", "r-bioc-biobase",
- "r-bioc-annotate"
- ],
- pcaMethods => [ "r-cran-ellipse", "r-cran-pls" ],
- pkgDepTools => ["r-bioc-rbgl"],
- plier => ["r-bioc-affy"],
- prism => ["r-bioc-ebimage"],
- ppiData => ["r-bioc-rgraphviz"],
- prada => [ "r-bioc-biobase", "r-cran-rrcov", "r-cran-rcolorbrewer" ],
- process => ["r-bioc-icens"],
- pgUtils => ["r-bioc-rdbi"],
- Rgraphviz => [
- "r-bioc-graph", "graphviz-dev", "r-cran-rcolorbrewer"
- , "libgraphviz3-dev", "libltdl3-dev" # requested by graphviz-dev
- # and for some reason it was
- # requested to have these specified
- # explicitly ?!?!
- ],
- rhdf5 => ["libhdf5-serial-dev"],
- Rredland => ["librdf0-dev"],
- Ruuid => [ "libglib1.2-dev", "pkg-config" ],
- SBMLR => [ "r-cran-xml", "r-cran-odesolve" ],
- ScISI => [
- "r-bioc-apcomplex", "r-bioc-go",
- "r-bioc-gostats", "r-bioc-graph",
- "r-bioc-rbgl", "r-bioc-rgraphviz",
- "r-bioc-yeast", "r-cran-xtable",
- "r-bioc-geneplotter"
- ],
- simplefilter => ["r-bioc-genefilter"],
- splicegear => ["r-bioc-biobase"],
- stam => ["r-cran-pamr"],
- stepNorm => ["r-bioc-marray"],
- tilingArray => [
- "r-cran-rcolorbrewer", "r-bioc-biobase",
- "r-cran-strucchange", "r-cran-pixmap"
- ],
- topGO => [
- "r-bioc-graph", "r-bioc-annotate",
- "r-bioc-go", "r-cran-sparsem",
- "r-bioc-biobase"
- ],
- tkWidgets => [ "r-bioc-widgettools", "r-bioc-dyndoc" ],
- twilight => [],
- vsn => ["r-bioc-biobase"],
- weaver => ["r-cran-digest"],
- webbioc => [
- "r-bioc-affy", "r-cran-multtest",
- "r-bioc-annaffy", "r-bioc-vsn",
- "r-bioc-gcrma"
- ],
- widgetInvoke => ["r-cran-rgtk2"],
-
- ## Omegahat
- CORBA => ["omniidl4"],
- RCurl => ["libcurl3-dev"], #|libcurl3-gnutls-dev|libcurl3-openssl-dev
- #RGtkExtra => ...
- RSPython => ["python"],
- RwxWidgets => ["libwxgtk2.4-dev"],
- XML => ["libxml2-dev"],
-);
+my %buildDeps = readListList("buildDeps.list");
=item Dependencies for the execution of the package
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