##############################################################################
##############################################################################
###
### 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)