############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TransView ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘TransView’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_TransView.c -o R_init_TransView.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bin_density.c -o bin_density.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c construct_dc.c -o construct_dc.o In file included from construct_dc.c:23: In file included from ./parse_sam.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/sam.h:33: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/hts.h:36: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/hts_log.h:76:1: warning: '__format__' attribute argument not supported: Rprintf [-Wignored-attributes] HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/hts_defs.h:101:53: note: expanded from macro 'HTS_FORMAT' #define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first))) ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c parse_sam.c -o parse_sam.o parse_sam.c:161:88: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] 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)); ~~ ^~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:161:133: warning: format specifies type 'int' but the argument has type 'uint32_t *' (aka 'unsigned int *') [-Wformat] 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)); ~~ ^~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:23:23: note: expanded from macro 'bam1_cigar' #define bam1_cigar(b) (bam_get_cigar((b))) ^~~~~~~~~~~~~~~~~~~~ parse_sam.c:202:20: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] printf("Pos %d\n",current_read->core.pos); ~~ ^~~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:203:47: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat] printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:315:18: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND, ^~~~~~~~~~~~~~~~~~~~~~ parse_sam.c:316:6: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat] current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c slice_dc.c -o slice_dc.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c visuals.c -o visuals.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o TransView.so R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-TransView/00new/TransView/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TransView)