############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL GenomicAlignments ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’ * installing *source* package ‘GenomicAlignments’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’ gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c cigar_utils.c -o cigar_utils.o cigar_utils.c: In function ‘cigar_ranges’: cigar_utils.c:676:30: warning: ‘f_elt’ may be used uninitialized [-Wmaybe-uninitialized] 676 | f_elt++; | ~~~~~^~ cigar_utils.c:593:41: note: ‘f_elt’ was declared here 593 | const int *flag_elt, *pos_elt, *f_elt; | ^~~~~ In function ‘drop_or_append_or_merge_range’, inlined from ‘parse_cigar_ranges’ at cigar_utils.c:221:4, inlined from ‘cigar_ranges’ at cigar_utils.c:660:12: cigar_utils.c:180:44: warning: ‘range_buf1’ may be used uninitialized [-Wmaybe-uninitialized] 180 | range_buf->b->elts[buf_nelt_minus_1]; | ~~~~~~~~~^~~ cigar_utils.c: In function ‘cigar_ranges’: cigar_utils.c:590:20: note: ‘range_buf1’ was declared here 590 | IntPairAE *range_buf1; | ^~~~~~~~~~ cigar_utils.c:674:37: warning: ‘breakpoint’ may be used uninitialized [-Wmaybe-uninitialized] 674 | *(breakpoint++) = IntPairAE_get_nelt(range_buf1); | ~~~~~~~~~~~^~~ cigar_utils.c:588:62: note: ‘breakpoint’ was declared here 588 | int cigar_len, space0, pos_len, f_is_NULL, ans_len, *breakpoint, | ^~~~~~~~~~ cigar_utils.c:542:25: warning: ‘ans_breakpoints’ may be used uninitialized [-Wmaybe-uninitialized] 542 | new_PartitioningByEnd("PartitioningByEnd", | ^~~~~~~~~~~~~~~~~~~~~ cigar_utils.c:587:19: note: ‘ans_breakpoints’ was declared here 587 | SEXP ans, ans_breakpoints, f_levels, cigar_elt; | ^~~~~~~~~~~~~~~ cigar_utils.c:626:29: warning: ‘flag_elt’ may be used uninitialized [-Wmaybe-uninitialized] 626 | if (*flag_elt == NA_INTEGER) { | ^~~~~~~~~ cigar_utils.c:593:20: note: ‘flag_elt’ was declared here 593 | const int *flag_elt, *pos_elt, *f_elt; | ^~~~~~~~ cigar_utils.c: In function ‘cigar_width’: cigar_utils.c:708:29: warning: ‘flag_elt’ may be used uninitialized [-Wmaybe-uninitialized] 708 | if (*flag_elt == NA_INTEGER) { | ^~~~~~~~~ cigar_utils.c:698:20: note: ‘flag_elt’ was declared here 698 | const int *flag_elt; | ^~~~~~~~ In function ‘narrow_cigar_string’, inlined from ‘cigar_narrow’ at cigar_utils.c:920:12: cigar_utils.c:879:39: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized] 879 | for (offset = Loffset; offset <= Roffset; offset += n) { | ~~~~~~~^~~~~~~~~~ cigar_utils.c: In function ‘cigar_narrow’: cigar_utils.c:854:22: note: ‘Roffset’ was declared here 854 | int Loffset, Roffset, buf_offset; | ^~~~~~~ In function ‘narrow_cigar_string’, inlined from ‘cigar_narrow’ at cigar_utils.c:920:12: cigar_utils.c:881:20: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized] 881 | if (offset == Loffset) | ^ cigar_utils.c: In function ‘cigar_narrow’: cigar_utils.c:854:13: note: ‘Loffset’ was declared here 854 | int Loffset, Roffset, buf_offset; | ^~~~~~~ In function ‘qnarrow_cigar_string’, inlined from ‘cigar_qnarrow’ at cigar_utils.c:1116:12: cigar_utils.c:1070:39: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized] 1070 | for (offset = Loffset; offset <= Roffset; offset += n) { | ~~~~~~~^~~~~~~~~~ cigar_utils.c: In function ‘cigar_qnarrow’: cigar_utils.c:1045:22: note: ‘Roffset’ was declared here 1045 | int Loffset, Roffset, buf_offset; | ^~~~~~~ In function ‘qnarrow_cigar_string’, inlined from ‘cigar_qnarrow’ at cigar_utils.c:1116:12: cigar_utils.c:1072:20: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized] 1072 | if (offset == Loffset) | ^ cigar_utils.c: In function ‘cigar_qnarrow’: cigar_utils.c:1045:13: note: ‘Loffset’ was declared here 1045 | int Loffset, Roffset, buf_offset; | ^~~~~~~ gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o coordinate_mapping_methods.c: In function ‘to_query’: coordinate_mapping_methods.c:64:26: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 64 | if (query_loc < 0 || n == 0) | ~~^~~~ coordinate_mapping_methods.c:17:7: note: ‘n’ was declared here 17 | int n, offset = 0, OPL, query_consumed = 0; | ^ coordinate_mapping_methods.c: In function ‘to_ref’: coordinate_mapping_methods.c:219:6: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 219 | if (n == 0) | ^ coordinate_mapping_methods.c:172:7: note: ‘n’ was declared here 172 | int n, offset = 0, OPL, query_consumed = 0; | ^ gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o gcc -shared -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments)