############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL XVector ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘XVector’ ... ** 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 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function ‘RDS_extract_subarray’: RDS_random_access.c:796:25: warning: unused variable ‘ans’ [-Wunused-variable] 796 | SEXP subscript, ans; | ^~~ RDS_random_access.c:793:18: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable] 793 | SEXPTYPE x_type; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_XVector.c -o R_init_XVector.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedDouble_class.c -o SharedDouble_class.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedInteger_class.c -o SharedInteger_class.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedRaw_class.c -o SharedRaw_class.o SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’: SharedRaw_class.c:396:20: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable] 396 | SEXP dest, src_tag; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedVector_class.c -o SharedVector_class.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XDouble_class.c -o XDouble_class.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XInteger_class.c -o XInteger_class.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRawList_comparison.c -o XRawList_comparison.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRaw_class.c -o XRaw_class.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVectorList_class.c -o XVectorList_class.o XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’: XVectorList_class.c:459:17: warning: ‘lkup_length’ may be used uninitialized [-Wmaybe-uninitialized] 459 | _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 | (char *) dest.ptr, dest.length, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 461 | src->elts, CharAE_get_nelt(src), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 | lkup0, lkup_length); | ~~~~~~~~~~~~~~~~~~~ XVectorList_class.c:434:13: note: ‘lkup_length’ was declared here 434 | int lkup_length, nelt, i; | ^~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_class.c -o XVector_class.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c io_utils.c -o io_utils.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c slice_methods.c -o slice_methods.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c vector_copy.c -o vector_copy.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c view_summarization_methods.c -o view_summarization_methods.o view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’: view_summarization_methods.c:219:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized] 219 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:208:19: note: ‘cur_min’ was declared here 208 | int xlen, cur_min, which_min, i, x; | ^~~~~~~ view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’: view_summarization_methods.c:246:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized] 246 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:235:16: note: ‘cur_min’ was declared here 235 | double cur_min, x; | ^~~~~~~ view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’: view_summarization_methods.c:269:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized] 269 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:258:19: note: ‘cur_max’ was declared here 258 | int xlen, cur_max, which_max, i, x; | ^~~~~~~ view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’: view_summarization_methods.c:296:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized] 296 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:285:16: note: ‘cur_max’ was declared here 285 | double cur_max, x; | ^~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -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-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (XVector)