BioC 3.5: INSTALL report for deepSNV on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL deepSNV
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* installing *source* package ‘deepSNV’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function ‘int bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t)’:
bam2R.cpp:69:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
bam2R.cpp: In function ‘int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)’:
bam2R.cpp:76:13: warning: unused variable ‘iter’ [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:79:6: warning: unused variable ‘c’ [-Wunused-variable]
  int c = 0;
      ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c betabinom.c -o betabinom.o
betabinom.c: In function ‘pbb’:
betabinom.c:27:9: warning: unused variable ‘log’ [-Wunused-variable]
  int i, log=0;
         ^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o deepSNV.so bam2R.o betabinom.o -L/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/R/library/deepSNV/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (deepSNV)
BioC 3.5: INSTALL report for deepSNV on malbec2

Summary

Command output
