############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/h5vc_2.28.0.tar.gz && rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=h5vc.buildbin-libdir h5vc_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL h5vc_2.28.0.zip && rm h5vc_2.28.0.tar.gz h5vc_2.28.0.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 246k 100 246k 0 0 719k 0 --:--:-- --:--:-- --:--:-- 721k install for i386 * installing *source* package 'h5vc' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tallyBAM.cpp -o tallyBAM.o tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^~~ tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^~~ tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)': tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ tallyBAM.cpp: At global scope: tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function] static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data) ^~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o h5vc.dll tmp.def bam.o bam_plbuf.o sam.o tallyBAM.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -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/h5vc.buildbin-libdir/00LOCK-h5vc/00new/h5vc/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' ** help *** installing help indices converting help for package 'h5vc' finding HTML links ... done applyTallies html batchTallies html binGenome html binnedAFs html callVariants html callVariantsFisher html callVariantsSingle html coverage html geom_h5vc html getSampleData html h5dapply html h5readBlock html h5vc-package html helpers html mergeTallies html mergeTallyFiles html mismatchPlot html mutationSpectrum html plotMutationSpectrum html prepareForHDF5 html prepareTallyFile html tallyBAM html tallyRanges html finding level-2 HTML links ... done writeReference html writeToTallyFile html ** building package indices ** installing vignettes 'h5vc.simple.genome.browser.Rmd' 'h5vc.tour.Rmd' ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'h5vc' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tallyBAM.cpp -o tallyBAM.o tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^~~ tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^~~ tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)': tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ tallyBAM.cpp: At global scope: tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function] static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data) ^~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o h5vc.dll tmp.def bam.o bam_plbuf.o sam.o tallyBAM.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -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/h5vc.buildbin-libdir/h5vc/libs/x64 ** testing if installed package can be loaded Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' * MD5 sums packaged installation of 'h5vc' as h5vc_2.28.0.zip * DONE (h5vc) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'h5vc' successfully unpacked and MD5 sums checked