############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/deepSNV_1.40.0.tar.gz && rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deepSNV.buildbin-libdir deepSNV_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.40.0.zip && rm deepSNV_1.40.0.tar.gz deepSNV_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 18 1241k 18 230k 0 0 612k 0 0:00:02 --:--:-- 0:00:02 613k 100 1241k 100 1241k 0 0 1074k 0 0:00:01 0:00:01 --:--:-- 1075k install for i386 * installing *source* package 'deepSNV' ... ** using staged installation ** libs "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 bam2R.cpp -o bam2R.o bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)': bam2R.cpp:97:13: warning: unused variable 'iter' [-Wunused-variable] hts_itr_t *iter = NULL; ^~~~ bam2R.cpp:100:6: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ "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 betabinom.c -o betabinom.o betabinom.c: In function 'pbb': betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable] int i, log=0; ^~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.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/deepSNV.buildbin-libdir/00LOCK-deepSNV/00new/deepSNV/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'deepSNV' finding HTML links ... done Extract-methods html RCC html RF html bam2R html betabinLRT html bf2Vcf html finding level-2 HTML links ... done consensusSequence-methods html control-methods html coordinates-methods html counts html dbetabinom html deepSNV-class html deepSNV-methods html deepSNV-package html estimateDirichlet-methods html estimateDispersion-methods html estimateRho html loadAllData html makePrior html manhattanPlot html mcChunk html normalize-methods html p.combine html p.val-methods html pbetabinom html phiX html pi html plot.deepSNV html qvals2Vcf html repeatMask-methods html shearwater html show-deepSNV-method html summary-methods html test-methods html trueSNVs 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 'deepSNV' ... ** libs "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 bam2R.cpp -o bam2R.o bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)': bam2R.cpp:97:13: warning: unused variable 'iter' [-Wunused-variable] hts_itr_t *iter = NULL; ^~~~ bam2R.cpp:100:6: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ "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 betabinom.c -o betabinom.o betabinom.c: In function 'pbb': betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable] int i, log=0; ^~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.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/deepSNV.buildbin-libdir/deepSNV/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'deepSNV' as deepSNV_1.40.0.zip * DONE (deepSNV) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'deepSNV' successfully unpacked and MD5 sums checked