############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TRONCO_2.24.0.tar.gz && rm -rf TRONCO.buildbin-libdir && mkdir TRONCO.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TRONCO.buildbin-libdir TRONCO_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TRONCO_2.24.0.zip && rm TRONCO_2.24.0.tar.gz TRONCO_2.24.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 270k 100 270k 0 0 474k 0 --:--:-- --:--:-- --:--:-- 475k install for i386 * installing *source* package 'TRONCO' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'TRONCO' finding HTML links ... done AND html OR html TCGA.map.clinical.data html TCGA.multiple.samples html TCGA.remove.multiple.samples html TCGA.shorten.barcodes html XOR html aCML html annotate.description html annotate.stages html as.adj.matrix html as.alterations html as.bootstrap.scores html as.colors html as.conditional.probs html as.confidence html as.description html as.events html as.events.in.patterns html as.events.in.sample html as.gene html as.genes html as.genes.in.patterns html as.genotypes html as.hypotheses html as.joint.probs html as.kfold.eloss html as.kfold.posterr html as.kfold.prederr html as.marginal.probs html as.models html as.parameters html as.pathway html as.patterns html as.samples html as.selective.advantage.relations html as.stages html as.types html as.types.in.patterns html cbio.query html change.color html consolidate.data html crc_gistic html crc_maf html crc_plain html delete.event html delete.gene html delete.hypothesis html delete.model html delete.pattern html delete.samples html delete.type html duplicates html ebind html enforce.numeric html enforce.string html events.selection html export.graphml html export.mutex html export.nbs.input html extract.MAF.HuGO.Entrez.map html genes.table.report html has.duplicates html has.model html has.stages html hypothesis.add html hypothesis.add.group html hypothesis.add.homologous html import.GISTIC html import.MAF html import.genotypes html import.model html import.mutex.groups html intersect.datasets html is.compliant html join.events html join.types html keysToNames html maf html muts html nameToKey html nevents html ngenes html nhypotheses html npatterns html nsamples html ntypes html oncoprint html oncoprint.cbio html order.frequency html pathway.visualization html pheatmap html rank.recurrents html rename.gene html rename.type html samples.selection html sbind html ssplit html stage html test_dataset html test_dataset_no_hypos html test_model html test_model_kfold html trim html tronco.bootstrap html tronco.caprese html tronco.capri html tronco.chowliu html tronco.edmonds html tronco.gabow html tronco.kfold.eloss html tronco.kfold.posterr html tronco.kfold.prederr html tronco.pattern.plot html tronco.plot html tronco.prim html view html which.samples html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'TRONCO' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'TRONCO' as TRONCO_2.24.0.zip * DONE (TRONCO) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'TRONCO' successfully unpacked and MD5 sums checked