| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:39:20 -0400 (Tue, 09 Apr 2019).
| Package 1127/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ORFik 1.3.13 Kornel Labun
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: ORFik |
| Version: 1.3.13 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ORFik_1.3.13.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.3.13.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ORFik_1.3.13.zip && rm ORFik_1.3.13.tar.gz ORFik_1.3.13.zip |
| StartedAt: 2019-04-08 20:05:32 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 20:09:02 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 211.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ORFik_1.3.13.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.3.13.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ORFik_1.3.13.zip && rm ORFik_1.3.13.tar.gz ORFik_1.3.13.zip
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install for i386
* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)':
findORFsHelpers.cpp:212:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < uorfSize/2; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0;i < xSize; i++){
^
pmapFromTranscripts.cpp:155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < indexSize; i++){
^
pmapFromTranscripts.cpp:161:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 1; i < indexSize; i++){
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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
ORFik-package html
addCdsOnLeaderEnds html
addNewTSSOnLeaders html
allFeaturesHelper html
finding level-2 HTML links ... done
asTX html
assignAnnotations html
assignFirstExonsStartSite html
assignLastExonsStopSite html
assignTSSByCage html
bedToGR html
changePointAnalysis html
checkRFP html
checkRNA html
codonSumsPerGroup html
computeFeatures html
computeFeaturesCage html
convertToOneBasedRanges html
coverageGroupings html
coverageHeatMap html
coveragePerTiling html
coverageScorings html
defineIsoform html
defineTrailer html
detectRibosomeShifts html
disengagementScore html
distToCds html
distToTSS html
downstreamFromPerGroup html
downstreamN html
downstreamOfPerGroup html
entropy html
extendLeaders html
extendsTSSexons html
filterCage html
filterTranscripts html
findFa html
findMapORFs html
findMaxPeaks html
findNewTSS html
findORFs html
findORFsFasta html
firstEndPerGroup html
firstExonPerGroup html
firstStartPerGroup html
floss html
fpkm html
fpkm_calc html
fractionLength html
fread.bed html
gSort html
gcContent html
groupGRangesBy html
groupings html
hasHits html
initiationScore html
insideOutsideORF html
is.ORF html
is.gr_or_grl html
is.grl html
isInFrame html
isOverlapping html
isPeriodic html
kozakSequenceScore html
lastExonEndPerGroup html
lastExonPerGroup html
lastExonStartPerGroup html
loadRegion html
loadTxdb html
longestORFs html
makeExonRanks html
makeORFNames html
mapToGRanges html
matchNaming html
metaWindow html
numCodons html
numExonsPerGroup html
orfID html
orfScore html
overlapsToCoverage html
pSitePlot html
parseCigar html
pmapFromTranscriptF html
rankOrder html
readWidths html
reassignTSSbyCage html
reassignTxDbByCage html
reduceKeepAttr html
remakeTxdbExonIds html
removeMetaCols html
removeTxdbExons html
removeTxdbTranscripts html
restrictTSSByUpstreamLeader html
ribosomeReleaseScore html
ribosomeStallingScore html
savePlot html
scaledWindowPositions html
seqnamesPerGroup html
shiftFootprints html
sortPerGroup html
startCodons html
startDefinition html
startRegion html
startRegionCoverage html
startRegionString html
startSites html
stopCodons html
stopDefinition html
stopSites html
strandBool html
strandPerGroup html
subsetCoverage html
subsetToFrame html
tile1 html
translationalEff html
txNames html
txSeqsFromFa html
uORFSearchSpace html
uniqueGroups html
uniqueOrder html
unlistGrl html
updateTxdbRanks html
updateTxdbStartSites html
upstreamFromPerGroup html
upstreamOfPerGroup html
validGRL html
validSeqlevels html
widthPerGroup html
windowCoveragePlot html
windowPerGroup html
windowPerReadLength html
windowPerTranscript 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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)':
findORFsHelpers.cpp:212:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < uorfSize/2; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0;i < xSize; i++){
^
pmapFromTranscripts.cpp:155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < indexSize; i++){
^
pmapFromTranscripts.cpp:161:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 1; i < indexSize; i++){
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ORFik' as ORFik_1.3.13.zip
* DONE (ORFik)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ORFik' successfully unpacked and MD5 sums checked