##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL hapFabia
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘hapFabia’ ...
** 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/usr/local/include -fpic -g -O2 -Wall -c interfaceR.c -o interfaceR.o
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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) {
| ^~~~~
vcftoFABIAB.c: In function ‘vcftoFABIAB’:
vcftoFABIAB.c:394:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
394 | strncat(format[j],Iformat,19);
| ^
vcftoFABIAB.c:382:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
382 | strncat(info[j],Iinfo,190);
| ^
vcftoFABIAB.c:372:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
372 | strncat(filter[j],Ifilter,19);
| ^
vcftoFABIAB.c:362:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
362 | strncat(qual[j],Iqual,19);
| ^
vcftoFABIAB.c:352:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
352 | strncat(minor[j],Iminor,190);
| ^
vcftoFABIAB.c:342:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
342 | strncat(major[j],Imajor,190);
| ^
vcftoFABIAB.c:332:19: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
332 | strncat(snpName[j],IsnpName,49);
| ^
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-3.20-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.20-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) {
| ^~~~~
vcftoFABIAB.c: In function ‘vcftoFABIAB’:
vcftoFABIAB.c:394:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
394 | strncat(format[j],Iformat,19);
| ^
vcftoFABIAB.c:382:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
382 | strncat(info[j],Iinfo,190);
| ^
vcftoFABIAB.c:372:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
372 | strncat(filter[j],Ifilter,19);
| ^
vcftoFABIAB.c:362:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
362 | strncat(qual[j],Iqual,19);
| ^
vcftoFABIAB.c:352:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
352 | strncat(minor[j],Iminor,190);
| ^
vcftoFABIAB.c:342:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
342 | strncat(major[j],Imajor,190);
| ^
vcftoFABIAB.c:332:19: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
332 | strncat(snpName[j],IsnpName,49);
| ^
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-3.20-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)
