Multiple platform build/check report for BioC 3.6 - INSTALL report for affyio on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL affyio
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* installing to library ‘/home/biocbuild/bbs-3.6-bioc/R/library’
* installing *source* package ‘affyio’ ...
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 for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: Enabling threading for affyio
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c fread_functions.c -o fread_functions.o
fread_functions.c:300:13: warning: ‘swap_uint_32’ defined but not used [-Wunused-function]
 static void swap_uint_32(unsigned int *tni4)              /* 4 byte integer numbers */
             ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c init_package.c -o init_package.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_abatch.c -o read_abatch.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_bpmap.c -o read_bpmap.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_cdf_xda.c -o read_cdf_xda.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function]
 static int token_ends_with(char *token, char *ends_in){
            ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_celfile_generic.c -o read_celfile_generic.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_clf.c -o read_clf.o
read_clf.c:292:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function]
 static int token_ends_with(char *token, char *ends_in){
            ^
read_clf.c:389:12: warning: ‘IsCommentLine’ defined but not used [-Wunused-function]
 static int IsCommentLine(char *buffer){
            ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_generic.c -o read_generic.o
read_generic.c: In function ‘decode_nvt_triplet’:
read_generic.c:1684:9: warning: ‘return_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return(return_value);
         ^
read_generic.c: In function ‘Read_Generic_R_List’:
read_generic.c:2030:2: warning: ‘return_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  SET_VECTOR_ELT(VECTOR_ELT(temp_sxp2,2),i,generic_data_set_rows_R_List(&my_data_set, i));
  ^
read_generic.c:1795:3: warning: ‘tmp_sexp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   SET_VECTOR_ELT(return_value,0,tmp_sexp);
   ^
read_generic.c:1784:8: note: ‘tmp_sexp’ was declared here
   SEXP tmp_sexp, return_names;
        ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/usr/local/include  -g -O2   -fpic  -g -O2  -Wall -c read_pgf.c -o read_pgf.o
read_pgf.c: In function ‘pgf_count_probeset_types’:
read_pgf.c:1265:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  my_pgf->probesets->current= my_pgf->probesets->current->next;
                            ^
read_pgf.c: At top level:
read_pgf.c:363:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function]
 static int token_ends_with(char *token, char *ends_in){
            ^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/R/library/affyio/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affyio)
INSTALL report for affyio on malbec1

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