############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TCGAbiolinks_2.20.1.tar.gz && rm -rf TCGAbiolinks.buildbin-libdir && mkdir TCGAbiolinks.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.20.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks_2.20.1.zip && rm TCGAbiolinks_2.20.1.tar.gz TCGAbiolinks_2.20.1.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 31 6491k 31 2048k 0 0 3045k 0 0:00:02 --:--:-- 0:00:02 3044k 100 6491k 100 6491k 0 0 4234k 0 0:00:01 0:00:01 --:--:-- 4237k install for i386 * installing *source* package 'TCGAbiolinks' ... ** 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 'TCGAbiolinks' finding HTML links ... done BRCA_rnaseqv2 html GDCdownload html GDCprepare html GDCprepare_clinic html GDCquery html GDCquery_ATAC_seq html GDCquery_Maf html GDCquery_clinic html GeneSplitRegulon html GenesCutID html PCBC_stemSig html PanCancerAtlas_subtypes html TCGAVisualize_volcano html TCGA_MolecularSubtype html TCGAanalyze_Clustering html TCGAanalyze_DEA html TCGAanalyze_DEA_Affy html TCGAanalyze_DMC html TCGAanalyze_EA html TCGAanalyze_EAcomplete html TCGAanalyze_Filtering html TCGAanalyze_LevelTab html TCGAanalyze_Normalization html TCGAanalyze_Pathview html TCGAanalyze_Preprocessing html TCGAanalyze_Stemness html TCGAanalyze_SurvivalKM html TCGAanalyze_analyseGRN html TCGAanalyze_networkInference html TCGAanalyze_survival html TCGAbatch_Correction html TCGAbiolinks html TCGAprepare_Affy html TCGAquery_MatchedCoupledSampleTypes html TCGAquery_SampleTypes html TCGAquery_recount2 html TCGAquery_subtype html TCGAtumor_purity html TCGAvisualize_BarPlot html TCGAvisualize_EAbarplot html TCGAvisualize_Heatmap html TCGAvisualize_PCA html TCGAvisualize_SurvivalCoxNET html TCGAvisualize_meanMethylation html TCGAvisualize_oncoprint html TCGAvisualize_starburst html TabSubtypesCol_merged html Tumor.purity html UseRaw_afterFilter html batch.info html bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf html chol_maf html classification html clinBRCA html clinical.biotab html colDataPrepare html dataBRCA html dataDEGsFiltLevel html dataREAD html dataREAD_df html dmc.non.parametric html dmc.non.parametric.se html gaiaCNVplot html gbm.exp.harmonized html gbm.exp.legacy html geneInfo html geneInfoHT html get.GRCh.bioMart html getAdjacencyBiogrid html getDataCategorySummary html getGDCInfo html getGDCprojects html getGistic html getLinkedOmicsData html getMC3MAF html getManifest html getNbCases html getNbFiles html getProjectSummary html getResults html getSampleFilesSummary html getTSS html get_IDs html ggbiplot html gliomaClassifier html isServeOK html matchedMetExp html met.gbm.27k html msi_results html pancan2018 html splitAPICall html tabSurvKMcompleteDEGs 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 'TCGAbiolinks' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'TCGAbiolinks' as TCGAbiolinks_2.20.1.zip * DONE (TCGAbiolinks) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'TCGAbiolinks' successfully unpacked and MD5 sums checked