############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL hapFabia ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘hapFabia’ ... ** this is package ‘hapFabia’ version ‘1.49.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c interfaceR.c -o interfaceR.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c split_sparse_matrixB.c -o split_sparse_matrixB.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c vcftoFABIAB.c -o vcftoFABIAB.o vcftoFABIAB.c: In function ‘vcftoFABIAB’: vcftoFABIAB.c:250:21: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 250 | snpName[0] = calloc((long) 50*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from vcftoFABIAB.c:2: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ vcftoFABIAB.c:258:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 258 | filter[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ vcftoFABIAB.c:266:18: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | qual[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ vcftoFABIAB.c:281:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 281 | format[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR gcc -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 gcc -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 gcc ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix mv ./commandLine/split_sparse_matrix ../inst/commandLine/ gcc -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 gcc -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 vcftoFABIAB.c: In function ‘vcftoFABIAB’: vcftoFABIAB.c:250:21: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 250 | snpName[0] = calloc((long) 50*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from vcftoFABIAB.c:2: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ vcftoFABIAB.c:258:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 258 | filter[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ vcftoFABIAB.c:266:18: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | qual[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ vcftoFABIAB.c:281:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 281 | format[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA mv ./commandLine/vcftoFABIA ../inst/commandLine/ installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-hapFabia/00new/hapFabia/libs ** R ** data ** 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 (hapFabia)