############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/beadarray_2.44.0.tar.gz && rm -rf beadarray.buildbin-libdir && mkdir beadarray.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=beadarray.buildbin-libdir beadarray_2.44.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL beadarray_2.44.0.zip && rm beadarray_2.44.0.tar.gz beadarray_2.44.0.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 29 1320k 29 392k 0 0 698k 0 0:00:01 --:--:-- 0:00:01 698k 100 1320k 100 1320k 0 0 1071k 0 0:00:01 0:00:01 --:--:-- 1072k install for i386 * installing *source* package 'beadarray' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BASH.c -o BASH.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HULK.c -o HULK.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c determiningGridPositions.c -o determiningGridPositions.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findAllOutliers.c -o findAllOutliers.o findAllOutliers.c: In function 'findBeadStatus': findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wmaybe-uninitialized] if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){ ~~~~~~^~~ findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized] if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){ ~~~^~~~~~~~~~~~ findAllOutliers.c: In function 'findAllOutliers': findAllOutliers.c:226:20: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized] beadStatusStruct *status; ^~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c imageProcessing.c -o imageProcessing.o imageProcessing.c: In function 'illuminaBackground': imageProcessing.c:88: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function 'medianBackground': imageProcessing.c:135: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function 'illuminaSharpen': imageProcessing.c:244: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2) imageProcessing.c:251: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2) C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.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/beadarray.buildbin-libdir/00LOCK-beadarray/00new/beadarray/libs/i386 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'beadarray' finding HTML links ... done BASH html BASHCompact html BASHDiffuse html BASHExtended html GEO html GEOtemplate html HULK html addFeatureData html annotationInterface html backgroundCorrectSingleSection html beadarray-package html beadarrayUsersGuide html boxplot html calculateDetection html calculateOutlierStats html checkRegistration html class-BeadLevelList html class-ExpressionSetIllumina html class-beadLevelData html class-beadRegistrationData html class-illuminaChannel html class-limmaResults html combine html controlProbeDetection html convertBeadLevelList html createTargetsFile html deprecatedFunctions html dim html expressionQCPipeline html generateNeighbours html getBeadData html identifyControlBeads html illuminaOutlierMethod html imageProcessing html imageplot html insertBeadData html insertSectionData html limmaDE html makeControlProfile html makeQCTable html maplots html medianNormalise html metrics html noOutlierMethod html normaliseIllumina html numBeads html outlierplot html platformSigs html plotBeadIntensities html plotBeadLocations html plotChipLayout html plotMAXY html plotTIFF html poscontPlot html processSwathData html quickSummary html readBeadSummaryData html readIdatFiles html readIllumina html readLocsFile html readTIFF html sampleSheet html sectionNames html setWeights html show html showArrayMask html squeezedVarOutlierMethod html summarize html transformationFunctions html weightsOutlierMethod 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 'beadarray' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BASH.c -o BASH.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HULK.c -o HULK.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c determiningGridPositions.c -o determiningGridPositions.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findAllOutliers.c -o findAllOutliers.o findAllOutliers.c: In function 'findBeadStatus': findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wmaybe-uninitialized] if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){ ~~~~~~^~~ findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized] if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){ ~~~^~~~~~~~~~~~ findAllOutliers.c: In function 'findAllOutliers': findAllOutliers.c:226:20: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized] beadStatusStruct *status; ^~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c imageProcessing.c -o imageProcessing.o imageProcessing.c: In function 'illuminaBackground': imageProcessing.c:88: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function 'medianBackground': imageProcessing.c:135: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function 'illuminaSharpen': imageProcessing.c:244: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2) imageProcessing.c:251: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2) C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.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/beadarray.buildbin-libdir/beadarray/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'beadarray' as beadarray_2.44.0.zip * DONE (beadarray) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'beadarray' successfully unpacked and MD5 sums checked