############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/biovizBase_1.40.0.tar.gz && rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biovizBase.buildbin-libdir biovizBase_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL biovizBase_1.40.0.zip && rm biovizBase_1.40.0.tar.gz biovizBase_1.40.0.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 5 2135k 5 126k 0 0 531k 0 0:00:04 --:--:-- 0:00:04 531k 68 2135k 68 1457k 0 0 1187k 0 0:00:01 0:00:01 --:--:-- 1187k 100 2135k 100 2135k 0 0 1397k 0 0:00:01 0:00:01 --:--:-- 1396k install for i386 * installing *source* package 'biovizBase' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_biovizBase.c -o R_init_biovizBase.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bin_offsets.c -o bin_offsets.o bin_offsets.c: In function 'scan_bam_bin_offsets': bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign] if (strncmp(b, "BAI\1", 4)) ^ In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:34, from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39, from bin_offsets.h:1, from bin_offsets.c:3: C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:86:15: note: expected 'const char *' but argument is of type 'Rbyte *' {aka 'unsigned char *'} int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount); ^~~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.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/biovizBase.buildbin-libdir/00LOCK-biovizBase/00new/biovizBase/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 'biovizBase' finding HTML links ... done CRC html GCcontent html addStepping-method html aes-utils html biovizBase-package html colorBlindSafePal html containLetters html crc1.GeRL html crunch-method html darned_hg19_subset500 html estimateCoverage-method html flatGrl html genesymbol html getBioColor html getFormalNames html getGaps html getIdeoGR html getIdeogram html getScale html hg19Ideogram html hg19IdeogramCyto html ideo html ideoCyto html isIdeogram html isMatchedWithModel html isSimpleIdeogram html labs html maxGap-method html mold-method html finding level-2 HTML links ... done pileupAsGRanges html pileupGRangesAsVariantTable html plotColorLegend html scale html showColor html shrinkageFun-method html splitByFacets-method html strip_formula_dots html subsetArgsByFormals html transform html transformGRangesForEvenSpace 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 'biovizBase' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_biovizBase.c -o R_init_biovizBase.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bin_offsets.c -o bin_offsets.o bin_offsets.c: In function 'scan_bam_bin_offsets': bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign] if (strncmp(b, "BAI\1", 4)) ^ In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:34, from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39, from bin_offsets.h:1, from bin_offsets.c:3: C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:86:15: note: expected 'const char *' but argument is of type 'Rbyte *' {aka 'unsigned char *'} int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount); ^~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.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/biovizBase.buildbin-libdir/biovizBase/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'biovizBase' as biovizBase_1.40.0.zip * DONE (biovizBase) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'biovizBase' successfully unpacked and MD5 sums checked