############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/AneuFinder_1.20.0.tar.gz && rm -rf AneuFinder.buildbin-libdir && mkdir AneuFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AneuFinder.buildbin-libdir AneuFinder_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL AneuFinder_1.20.0.zip && rm AneuFinder_1.20.0.tar.gz AneuFinder_1.20.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 187k 100 187k 0 0 803k 0 --:--:-- --:--:-- --:--:-- 806k install for i386 * installing *source* package 'AneuFinder' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loghmm.cpp -o loghmm.o loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.buildbin-libdir/00LOCK-AneuFinder/00new/AneuFinder/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'AneuFinder' finding HTML links ... done AneuFinder-package html Aneufinder html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.buildbin-libdir/00LOCK-AneuFinder/00new/AneuFinder/help/Aneufinder.html finding level-2 HTML links ... done DNAcopy.findCNVs html HMM.findCNVs html aneuBiHMM html aneuHMM html annotateBreakpoints html bam2GRanges html bed2GRanges html bi.edivisive.findCNVs html biDNAcopy.findCNVs html biHMM.findCNVs html binReads html binned.data html binning html blacklist html clusterByQuality html clusterHMMs html collapseBins html colors html compareMethods html compareModels html consensusSegments html correctGC html edivisive.findCNVs html estimateComplexity html export html filterSegments html findCNVs html findCNVs.strandseq html findHotspots html fixedWidthBins html getBreakpoints html getDistinctColors html getQC html getSCEcoordinates html heatmapAneuploidies html heatmapGenomewide html heatmapGenomewideClusters html hotspotter html hotspotter.variable html importBed html initializeStates html karyotypeMeasures html loadFromFiles html mergeStrandseqFiles html plot.GRanges html plot.GRangesList html plot.aneuBiHMM html plot.aneuHMM html plot.character html plotHeterogeneity html plotHistogram html plotKaryogram html plotProfile html plot_pca html print.aneuBiHMM html print.aneuHMM html qualityControl html readConfig html refineBreakpoints html simulateReads html subsetByCNVprofile html transCoord html variableWidthBins html writeConfig html zinbinom 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 'AneuFinder' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loghmm.cpp -o loghmm.o loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.buildbin-libdir/AneuFinder/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'AneuFinder' as AneuFinder_1.20.0.zip * DONE (AneuFinder) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'AneuFinder' successfully unpacked and MD5 sums checked