############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TransView ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'TransView' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_TransView.c -o R_init_TransView.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bin_density.c -o bin_density.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c construct_dc.c -o construct_dc.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parse_sam.c -o parse_sam.o parse_sam.c: In function 'quality_check': parse_sam.c:161:75: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=] 161 | warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read)); | ~^ ~~~~~~~~~~~~~~~~~~~~~ | | | | int hts_pos_t {aka long long int} | %lld parse_sam.c:161:103: warning: format '%d' expects argument of type 'int', but argument 4 has type 'uint32_t *' {aka 'unsigned int *'} [-Wformat=] 161 | warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read)); | ~^ | | | int | %n parse_sam.c: In function 'print_readinfo': parse_sam.c:202:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=] 202 | printf("Pos %d\n",current_read->core.pos); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | int hts_pos_t {aka long long int} | %lld parse_sam.c:203:33: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=] 203 | printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int hts_pos_t {aka long long int} | %lld parse_sam.c: In function 'seq_density': parse_sam.c:314:61: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=] 314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n", | ~^ | | | int | %lld 315 | BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND, | ~~~~~~~~~~~~~~~~~~~~~~ | | | hts_pos_t {aka long long int} parse_sam.c:314:94: warning: format '%d' expects argument of type 'int', but argument 6 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=] 314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n", | ~^ | | | int | %lld 315 | BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND, 316 | current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hts_pos_t {aka long long int} gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c slice_dc.c -o slice_dc.o slice_dc.c: In function 'slice_dc': slice_dc.c:184:33: warning: 'slicep' may be used uninitialized [-Wmaybe-uninitialized] 184 | expand(slicep,new_vecp,rebuildc,wsize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ slice_dc.c:101:22: note: 'slicep' was declared here 101 | int *slicep= INTEGER_POINTER(slice); | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c visuals.c -o visuals.o gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-TransView/00new/TransView/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (TransView)