############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf beadarray.buildbin-libdir && mkdir beadarray.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=beadarray.buildbin-libdir beadarray_2.46.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'beadarray' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BASH.c -o BASH.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HULK.c -o HULK.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c determiningGridPositions.c -o determiningGridPositions.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 196 | 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] 196 | if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){ | ~~~^~~~~~~~~~~~ findAllOutliers.c: In function 'findAllOutliers': findAllOutliers.c:246:13: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized] 246 | free(status->validInds); | ~~~~~~^~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 88 | #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] 135 | #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] 244 | #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2) | imageProcessing.c:251: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 251 | #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2) | gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/meat/beadarray.buildbin-libdir/00LOCK-beadarray/00new/beadarray/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * MD5 sums packaged installation of 'beadarray' as beadarray_2.46.0.zip * DONE (beadarray)