############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TransView ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘TransView’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_TransView.c -o R_init_TransView.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam_plbuf.c -o bam_plbuf.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bin_density.c -o bin_density.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c construct_dc.c -o construct_dc.o In file included from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/hts.h:36, from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/sam.h:33, from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/samtools-1.7-compat.h:5, from parse_sam.h:4, from construct_dc.c:23: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/hts_log.h:76:1: warning: ‘Rprintf’ is an unrecognized format function type [-Wformat=] 76 | HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); | ^~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -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 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 int} | %ld 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 | %ls 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 int’} [-Wformat=] 202 | printf("Pos %d\n",current_read->core.pos); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | int hts_pos_t {aka long int} | %ld parse_sam.c:203:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘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 int} | %ld 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 int’} [-Wformat=] 314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n", | ~^ | | | int | %ld 315 | BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND, | ~~~~~~~~~~~~~~~~~~~~~~ | | | hts_pos_t {aka 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 int’} [-Wformat=] 314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n", | ~^ | | | int | %ld 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 int} gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c visuals.c -o visuals.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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)