############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL hapFabia ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘hapFabia’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interfaceR.c -o interfaceR.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c split_sparse_matrixB.c -o split_sparse_matrixB.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vcftoFABIAB.c -o vcftoFABIAB.o vcftoFABIAB.c: In function ‘getdelimS’: vcftoFABIAB.c:50:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 50 | if (ch == EOF) | ^~ vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 54 | while (idx > *linebufsz - 2) { | ^~~~~ In file included from /usr/include/string.h:495, from vcftoFABIAB.c:3: In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:394:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:382:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:372:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:362:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:352:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:342:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:332:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR gcc -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 -Wall gcc -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 -Wall 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 -Wall gcc -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 -Wall vcftoFABIAB.c: In function ‘getdelimS’: vcftoFABIAB.c:50:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 50 | if (ch == EOF) | ^~ vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 54 | while (idx > *linebufsz - 2) { | ^~~~~ In file included from /usr/include/string.h:495, from vcftoFABIAB.c:3: In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:394:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:382:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:372:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:362:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:352:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:342:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:332:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA mv ./commandLine/vcftoFABIA ../inst/commandLine/ installing to /home/biocbuild/bbs-3.13-bioc/R/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)