############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL h5vc ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'h5vc' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tallyBAM.cpp -o tallyBAM.o tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable] 47 | int len = nttable->end - nttable->beg; | ^~~ tallyBAM.cpp: In function 'int pileup_func(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable] 96 | int len = nttable->end - nttable->beg; | ^~~ tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)': tallyBAM.cpp:140:13: warning: unused variable 'c' [-Wunused-variable] 140 | int c = 0; | ^ tallyBAM.cpp: At global scope: tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function] 43 | static int pileup_func_old(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data) | ^~~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -s -static-libgcc -o h5vc.dll tmp.def bam_plbuf.o tallyBAM.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-h5vc/00new/h5vc/libs/x64 ** 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 ** building package indices ** installing vignettes ** 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 * DONE (h5vc)