############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'ORFik' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c findORFsHelpers.cpp -o findORFsHelpers.o findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::__cxx11::string&, std::__cxx11::string, std::__cxx11::string, int)': findORFsHelpers.cpp:214:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < uorfSize/2; i++) { ~~^~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c findOrfs.cpp -o findOrfs.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c findOrfsFasta.cpp -o findOrfsFasta.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const char&, bool)': pmapFromTranscripts.cpp:151:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i = 0;i < xSize; i++){ ~~^~~~~~~ pmapFromTranscripts.cpp:155:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i = 0; i < indexSize; i++){ ~~^~~~~~~~~~~ pmapFromTranscripts.cpp:161:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i = 1; i < indexSize; i++){ ~~^~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pmapToTranscripts.cpp -o pmapToTranscripts.o pmapToTranscripts.cpp: In function 'void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)': pmapToTranscripts.cpp:22:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable] int currentWidth = 0; ^~~~~~~~~~~~ pmapToTranscripts.cpp: In function 'void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)': pmapToTranscripts.cpp:68:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable] int currentWidth = 0; ^~~~~~~~~~~~ pmapToTranscripts.cpp: In function 'Rcpp::List pmapToTranscriptsCPP(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const char&, const std::vector&)': pmapToTranscripts.cpp:126:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i = 0;i < xSize; i++){ // Width per exon in x ~~^~~~~~~ pmapToTranscripts.cpp:130:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i = 0; i < indexSize; i++){ // Width per exon in tx ~~^~~~~~~~~~~ pmapToTranscripts.cpp:136:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i = 1; i < indexSize; i++){ ~~^~~~~~~~~~~ pmapToTranscripts.cpp:147:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 1; i < 2 * xSize; i = i + 2) { ~~^~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ORFik/00new/ORFik/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ORFik' finding HTML links ... done DEG.analysis html DEG.plot.static html DTEG.analysis html finding level-2 HTML links ... done DTEG.plot html ORFik-package html ORFik.template.experiment html ORFik.template.experiment.zf html ORFikQC html QC_count_tables html QCfolder-experiment-method html QCfolder html QCplots html QCreport html QCstats html QCstats.plot html RiboQC.plot html STAR.align.folder html STAR.align.single html STAR.allsteps.multiQC html STAR.index html STAR.install html STAR.multiQC html STAR.remove.crashed.genome html TOP.Motif.ecdf html addCdsOnLeaderEnds html addNewTSSOnLeaders html alignmentFeatureStatistics html allFeaturesHelper html appendZeroes html artificial.orfs html asTX html assignAnnotations html assignFirstExonsStartSite html assignLastExonsStopSite html assignTSSByCage html bamVarName html bamVarNamePicker html batchNames html bedToGR html cellLineNames html changePointAnalysis html checkRFP html checkRNA html codonSumsPerGroup html collapse.by.scores html collapse.fastq html collapseDuplicatedReads-GAlignmentPairs-method html collapseDuplicatedReads-GAlignments-method html collapseDuplicatedReads-GRanges-method html collapseDuplicatedReads html combn.pairs html computeFeatures html computeFeaturesCage html conditionNames html config html config.exper html config.save html convertLibs html convertToOneBasedRanges html correlation.plots html countOverlapsW html countTable html countTable_regions html coverageByTranscriptW html coverageGroupings html coverageHeatMap html coveragePerTiling html coverageScorings html create.experiment html defineIsoform html defineTrailer html design-experiment-method html detectRibosomeShifts html disengagementScore html distToCds html distToTSS html download.SRA html download.SRA.metadata html download.ebi html downstreamFromPerGroup html downstreamN html downstreamOfPerGroup html entropy html envExp-experiment-method html envExp-set-experiment-method html envExp-set html envExp html exists.ftp.dir.fast html exists.ftp.file.fast html experiment-class html experiment.colors html export.bed12 html export.bedo html export.bedoc html export.bigWig html export.ofst-GAlignmentPairs-method html export.ofst-GAlignments-method html export.ofst-GRanges-method html export.ofst html export.wiggle html extendLeaders html extendTrailers html extendsTSSexons html filepath html filterCage html filterExtremePeakGenes html filterTranscripts html filterUORFs html fimport html findFa html findFromPath html findLibrariesInFolder html findMapORFs html findMaxPeaks html findNGSPairs html findNewTSS html findORFs html findORFsFasta html findPeaksPerGene html findUORFs html find_url_ebi html find_url_ebi_safe html firstEndPerGroup html firstExonPerGroup html firstStartPerGroup html flankPerGroup html floss html footprints.analysis html fpkm html fpkm_calc html fractionLength html fractionNames html fread.bed html gSort html gcContent html getGAlignments html getGAlignmentsPairs html getGRanges html getGenomeAndAnnotation html getGtfPathFromTxdb html getNGenesCoverage html getWeights html get_genome_fasta html get_genome_gtf html get_noncoding_rna html get_phix_genome html get_silva_rRNA html groupGRangesBy html groupings html hasHits html heatMapL html heatMapRegion html heatMap_single html import.bedo html import.bedoc html import.ofst html importGtfFromTxdb html inhibitorNames html initiationScore html insideOutsideORF html install.fastp html install.sratoolkit html is.ORF html is.gr_or_grl html is.grl html is.range html isInFrame html isOverlapping html isPeriodic html kozakHeatmap html kozakSequenceScore html kozak_IR_ranking html lastExonEndPerGroup html lastExonPerGroup html lastExonStartPerGroup html libNames html libraryTypes html list.experiments html list.genomes html loadRegion html loadRegions html loadTranscriptType html loadTxdb html longestORFs html mainNames html makeExonRanks html makeORFNames html makeSummarizedExperimentFromBam html makeTxdbFromGenome html mapToGRanges html matchColors html matchNaming html matchSeqStyle html mergeFastq html metaWindow html name-experiment-method html name html nrow-experiment-method html numCodons html numExonsPerGroup html optimizeReads html optimizedTranscriptLengths html optimized_txdb_path html orfFrameDistributions html orfID html orfScore html organism-experiment-method html outputLibs html pSitePlot html pasteDir html pcaExperiment html percentage_to_ratio html plotHelper html pmapFromTranscriptF html pmapToTranscriptF html prettyScoring html pseudo.transform html rankOrder html read.experiment html readBam html readBigWig html readLengthTable html readWidths html readWig html reassignTSSbyCage html reassignTxDbByCage html reduceKeepAttr html regionPerReadLength html remakeTxdbExonIds html remove.experiments html remove.file_ext html removeMetaCols html removeORFsWithSameStartAsCDS html removeORFsWithSameStopAsCDS html removeORFsWithStartInsideCDS html removeORFsWithinCDS html removeTxdbExons html removeTxdbTranscripts html rename.SRA.files html repNames html restrictTSSByUpstreamLeader html revElementsF html reverseMinusStrandPerGroup html ribosomeReleaseScore html ribosomeStallingScore html rnaNormalize html save.experiment html savePlot html scaledWindowPositions html scoreSummarizedExperiment html seqnamesPerGroup html shiftFootprints html shiftFootprintsByExperiment html shiftPlots html shifts.load html show-experiment-method html simpleLibs html sortPerGroup html splitIn3Tx html stageNames html startCodons html startDefinition html startRegion html startRegionCoverage html startRegionString html startSites html stopCodons html stopDefinition html stopRegion html stopSites html strandBool html strandPerGroup html subsetCoverage html subsetToFrame html te.plot html te.table html te_rna.plot html tile1 html tissueNames html topMotif html transcriptWindow html transcriptWindow1 html transcriptWindowPer html translationalEff html trim_detection html trimming.table html txNames html txNamesToGeneNames html txSeqsFromFa html uORFSearchSpace html uniqueGroups html uniqueOrder html unlistGrl html updateTxdbRanks html updateTxdbStartSites html upstreamFromPerGroup html upstreamOfPerGroup html validGRL html validSeqlevels html validateExperiments html widthPerGroup html windowCoveragePlot html windowPerGroup html windowPerReadLength html windowPerTranscript html xAxisScaler html yAxisScaler 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 * DONE (ORFik) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'deepSNV' is missing or broken done