############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL pwalign ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘pwalign’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_pairwiseAlignment.c -o R_init_pairwiseAlignment.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align_utils.c -o align_utils.o align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned': align_utils.c:234:78: warning: 'indelStartPattern' may be used uninitialized [-Wmaybe-uninitialized] 234 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:223:21: note: 'indelStartPattern' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:240:55: warning: 'indelWidthPattern' may be used uninitialized [-Wmaybe-uninitialized] 240 | for (k = 0; k < indelWidthPattern; k++) { | ~~^~~~~~~~~~~~~~~~~~~ align_utils.c:223:40: note: 'indelWidthPattern' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:233:63: warning: 'indelStartSubject' may be used uninitialized [-Wmaybe-uninitialized] 233 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) { | ~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:223:59: note: 'indelStartSubject' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:252:42: warning: 'indelWidthSubject' may be used uninitialized [-Wmaybe-uninitialized] 252 | jPattern += indelWidthSubject; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:223:78: note: 'indelWidthSubject' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o pwalign.so Biostrings_stubs.o IRanges_stubs.o R_init_pairwiseAlignment.o S4Vectors_stubs.o XVector_stubs.o align_pairwiseAlignment.o align_utils.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-pwalign/00new/pwalign/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘insertion’ in package ‘pwalign’ Creating a new generic function for ‘deletion’ in package ‘pwalign’ Creating a new generic function for ‘unaligned’ in package ‘pwalign’ Creating a new generic function for ‘aligned’ in package ‘pwalign’ Creating a new generic function for ‘indel’ in package ‘pwalign’ Creating a new generic function for ‘nindel’ in package ‘pwalign’ Creating a new generic function for ‘PairwiseAlignments’ in package ‘pwalign’ Creating a new generic function for ‘alignedPattern’ in package ‘pwalign’ Creating a new generic function for ‘alignedSubject’ in package ‘pwalign’ Creating a new generic function for ‘PairwiseAlignmentsSingleSubject’ in package ‘pwalign’ Creating a new generic function for ‘nedit’ in package ‘pwalign’ Creating a new generic function for ‘mismatchTable’ in package ‘pwalign’ Creating a new generic function for ‘mismatchSummary’ in package ‘pwalign’ Creating a new generic function for ‘compareStrings’ in package ‘pwalign’ Creating a new generic function for ‘pid’ in package ‘pwalign’ Creating a new generic function for ‘pairwiseAlignment’ in package ‘pwalign’ Creating a new generic function for ‘stringDist’ in package ‘pwalign’ ** 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 (pwalign)