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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ORFik_1.14.7.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.14.7.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ORFik_1.14.7.zip && rm ORFik_1.14.7.tar.gz ORFik_1.14.7.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
37 1346k 37 500k 0 0 1030k 0 0:00:01 --:--:-- 0:00:01 1030k
100 1346k 100 1346k 0 0 1392k 0 --:--:-- --:--:-- --:--:-- 1392k
install for i386
* installing *source* package 'ORFik' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 'unsigned int'} [-Wsign-compare]
for (int i = 0; i < uorfSize/2; i++) {
~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfs.cpp -o findOrfs.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfsFasta.cpp -o findOrfsFasta.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)':
pmapFromTranscripts.cpp:151:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka '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 '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 'unsigned int'} [-Wsign-compare]
for(auto i = 1; i < indexSize; i++){
~~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)':
pmapToTranscripts.cpp:126:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka '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 '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 '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 'unsigned int'} [-Wsign-compare]
for (auto i = 1; i < 2 * xSize; i = i + 2) {
~~^~~~~~~~~~~
C:/rtools40/mingw32/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/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ORFik.buildbin-libdir/00LOCK-ORFik/00new/ORFik/libs/i386
** 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
install for x64
* installing *source* package 'ORFik' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfs.cpp -o findOrfs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfsFasta.cpp -o findOrfsFasta.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, 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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)':
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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ORFik' as ORFik_1.14.7.zip
* DONE (ORFik)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ORFik' successfully unpacked and MD5 sums checked
