##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
   42 |     Rprintf("What?\n");
      |     ^~~~~~~
      |     dprintf
In file included from /usr/include/string.h:495,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:17:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:14:19: note: length computed here
   14 |     int length1 = strlen(text1);
      |                   ^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:18:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:15:19: note: length computed here
   15 |     int length2 = strlen(text2);
      |                   ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fltbam.c -o fltbam.o
fltbam.c:2:10: fatal error: sam.h: No such file or directory
    2 | #include "sam.h"
      |          ^~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.16-bioc/R/etc/Makeconf:169: fltbam.o] Error 1
ERROR: compilation failed for package ‘ArrayExpressHTS’
* removing ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/ArrayExpressHTS’