############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GenomicAlignments ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GenomicAlignments’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cigar_utils.c -o cigar_utils.o In file included from /home/biocbuild/R/R/include/Rdefines.h:41, from GenomicAlignments.h:1, from cigar_utils.c:1: In function ‘make_CompressedIRangesList’, inlined from ‘cigar_ranges’ at cigar_utils.c:680:2: cigar_utils.c:534:25: warning: ‘range_buf1’ may be used uninitialized [-Wmaybe-uninitialized] 534 | new_IRanges_from_IntPairAE("IRanges", range_buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ 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: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:656:29: warning: ‘f_elt’ may be used uninitialized [-Wmaybe-uninitialized] 656 | if (*f_elt == NA_INTEGER) | ^~~~~~ cigar_utils.c:593:41: note: ‘f_elt’ was declared here 593 | const int *flag_elt, *pos_elt, *f_elt; | ^~~~~ In function ‘make_CompressedIRangesList’, inlined from ‘cigar_ranges’ at cigar_utils.c:680:2: cigar_utils.c:542:25: warning: ‘ans_breakpoints’ may be used uninitialized [-Wmaybe-uninitialized] 542 | new_PartitioningByEnd("PartitioningByEnd", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | breakpoints, NULL)); | ~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ cigar_utils.c: In function ‘cigar_ranges’: cigar_utils.c:587:19: note: ‘ans_breakpoints’ was declared here 587 | SEXP ans, ans_breakpoints, f_levels, cigar_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:872:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized] 872 | if (Roffset < 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 ‘narrow_cigar_string’, inlined from ‘cigar_narrow’ at cigar_utils.c:920:12: cigar_utils.c:872:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized] 872 | if (Roffset < Loffset) { | ^ 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 ‘qnarrow_cigar_string’, inlined from ‘cigar_qnarrow’ at cigar_utils.c:1116:12: cigar_utils.c:1063:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized] 1063 | if (Roffset < Loffset) { | ^ cigar_utils.c: In function ‘cigar_qnarrow’: cigar_utils.c:1045:13: note: ‘Loffset’ 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:1063:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized] 1063 | if (Roffset < Loffset) { | ^ cigar_utils.c: In function ‘cigar_qnarrow’: cigar_utils.c:1045:22: note: ‘Roffset’ was declared here 1045 | int Loffset, Roffset, buf_offset; | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o 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; | ^ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o In function ‘unsafe_overlap_encoding’, inlined from ‘overlap_encoding’ at encodeOverlaps_methods.c:209:2: encodeOverlaps_methods.c:182:9: warning: ‘out_nelt0’ may be used uninitialized [-Wmaybe-uninitialized] 182 | CharAE_delete_at(out, out_nelt0, j1 * nrow); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ encodeOverlaps_methods.c: In function ‘overlap_encoding’: encodeOverlaps_methods.c:99:13: note: ‘out_nelt0’ was declared here 99 | int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej, | ^~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -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 -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/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)