BioC 3.5: BUILD BIN report for affyio on veracruz2

Package: affyio

Version: 1.46.0

Command: rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R affyio.buildbin-libdir

StartedAt: 2017-10-18 10:32:36 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:32:46 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 9.5 seconds

RetCode: 0

Status:  OK

PackageFile: affyio_1.46.0.tgz

PackageFileSize: 89.61 KiB

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###
### Running command:
###
###   rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R affyio.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyio.buildbin-libdir affyio_1.46.0.tar.gz'
>>>>>>> 

* installing *source* package ‘affyio’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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... /usr/bin/grep
checking for egrep... /usr/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: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c fread_functions.c -o fread_functions.o
fread_functions.c:300:13: warning: unused function 'swap_uint_32' [-Wunused-function]
static void swap_uint_32(unsigned int *tni4)              /* 4 byte integer numbers */
            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c init_package.c -o init_package.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_abatch.c -o read_abatch.o
read_abatch.c:683:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
    if (cur_x < 0 || cur_x >= chip_dim_rows){
        ˜˜˜˜˜ ^ ˜
read_abatch.c:687:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
    if (cur_y < 0 || cur_y >= chip_dim_rows){
        ˜˜˜˜˜ ^ ˜
read_abatch.c:1582:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
    if (cur_x < 0 || cur_x >= chip_dim_rows){
        ˜˜˜˜˜ ^ ˜
read_abatch.c:1586:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
    if (cur_y < 0 || cur_y >= chip_dim_rows){
        ˜˜˜˜˜ ^ ˜
read_abatch.c:4369:9: warning: unused variable 'Current_intensity' [-Wunused-variable]
   SEXP Current_intensity;
        ^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_bpmap.c -o read_bpmap.o
read_bpmap.c:78:7: warning: unused variable 'version_number_int' [-Wunused-variable]
  int version_number_int;
      ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_cdf_xda.c -o read_cdf_xda.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364:12: warning: unused function 'token_ends_with' [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
           ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c:708:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:711:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:709:10: warning: unused variable 'cur_index' [-Wunused-variable]
  size_t cur_index;
         ^
read_celfile_generic.c:761:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:759:10: warning: unused variable 'cur_index' [-Wunused-variable]
  size_t cur_index;
         ^
read_celfile_generic.c:758:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:815:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:812:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:813:10: warning: unused variable 'cur_index' [-Wunused-variable]
  size_t cur_index;
         ^
read_celfile_generic.c:877:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:874:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0;
           ^
read_celfile_generic.c:875:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_celfile_generic.c:963:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:969:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:1712:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:1715:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:1713:10: warning: unused variable 'cur_index' [-Wunused-variable]
  size_t cur_index;
         ^
read_celfile_generic.c:1766:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:1764:10: warning: unused variable 'cur_index' [-Wunused-variable]
  size_t cur_index;
         ^
read_celfile_generic.c:1763:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:1820:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:1817:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:1818:10: warning: unused variable 'cur_index' [-Wunused-variable]
  size_t cur_index;
         ^
read_celfile_generic.c:1883:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_celfile_generic.c:1882:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0;
           ^
read_celfile_generic.c:1885:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_celfile_generic.c:1971:15: warning: unused variable 'j' [-Wunused-variable]
  size_t i=0, j=0;
              ^
read_celfile_generic.c:1977:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
28 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_clf.c -o read_clf.o
read_clf.c:557:7: warning: unused variable 'i' [-Wunused-variable]
  int i;
      ^
read_clf.c:292:12: warning: unused function 'token_ends_with' [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
           ^
read_clf.c:389:12: warning: unused function 'IsCommentLine' [-Wunused-function]
static int IsCommentLine(char *buffer){
           ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_generic.c -o read_generic.o
read_generic.c:1287:42: warning: variable 'temp32' is uninitialized when used here [-Wuninitialized]
    Rprintf("Its a float  value is %f\n",temp32);
                                         ^˜˜˜˜˜
read_generic.c:1277:13: note: initialize the variable 'temp32' to silence this warning
  int temp32;
            ^
             = 0
read_generic.c:1683:10: warning: variable 'return_value' is uninitialized when used here [-Wuninitialized]
  return(return_value);
         ^˜˜˜˜˜˜˜˜˜˜˜
read_generic.c:1606:20: note: initialize the variable 'return_value' to silence this warning
  SEXP return_value;
                   ^
                    = NULL
read_generic.c:1787:7: warning: variable 'tmp_sexp' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if (my_data_group->data_group_name.len > 0){
      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
read_generic.c:1794:33: note: uninitialized use occurs here
  SET_VECTOR_ELT(return_value,0,tmp_sexp);
                                ^˜˜˜˜˜˜˜
read_generic.c:1787:3: note: remove the 'if' if its condition is always true
  if (my_data_group->data_group_name.len > 0){
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
read_generic.c:1783:16: note: initialize the variable 'tmp_sexp' to silence this warning
  SEXP tmp_sexp, return_names;
               ^
                = NULL
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c:106:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:105:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0, j=0, k=0;
      ^
read_multichannel_celfile_generic.c:109:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:105:17: warning: unused variable 'k' [-Wunused-variable]
  int i=0, j=0, k=0;
                ^
read_multichannel_celfile_generic.c:165:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:162:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:161:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0, j=0, k=0;
      ^
read_multichannel_celfile_generic.c:161:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:173:20: warning: unused variable 'my_data_set' [-Wunused-variable]
  generic_data_set my_data_set;
                   ^
read_multichannel_celfile_generic.c:221:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:220:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:223:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:280:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:277:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:278:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:341:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:344:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:342:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:416:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:418:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:415:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:522:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:516:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0;
           ^
read_multichannel_celfile_generic.c:660:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0, j=0, k=0;
      ^
read_multichannel_celfile_generic.c:661:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:660:17: warning: unused variable 'k' [-Wunused-variable]
  int i=0, j=0, k=0;
                ^
read_multichannel_celfile_generic.c:664:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:713:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0, j=0, k=0;
      ^
read_multichannel_celfile_generic.c:714:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:725:20: warning: unused variable 'my_data_set' [-Wunused-variable]
  generic_data_set my_data_set;
                   ^
read_multichannel_celfile_generic.c:713:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:717:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:764:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:766:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:763:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:820:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:819:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:822:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:882:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:884:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:881:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:950:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, k=0;
           ^
read_multichannel_celfile_generic.c:953:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
read_multichannel_celfile_generic.c:951:7: warning: unused variable 'cur_index' [-Wunused-variable]
  int cur_index;
      ^
read_multichannel_celfile_generic.c:1049:12: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0;
           ^
read_multichannel_celfile_generic.c:1055:7: warning: unused variable 'fread_err' [-Wunused-variable]
  int fread_err=0;
      ^
46 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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  -Wall -g -O2  -c read_pgf.c -o read_pgf.o
read_pgf.c:901:7: warning: unused variable 'i' [-Wunused-variable]
  int i;
      ^
read_pgf.c:1167:23: warning: unused variable 'temp_ptr' [-Wunused-variable]
  probeset_list_node *temp_ptr;
                      ^
read_pgf.c:1265:28: warning: incompatible pointer types assigning to 'probeset_list_node *' from 'struct probeset_list_node *' [-Wincompatible-pointer-types]
        my_pgf->probesets->current= my_pgf->probesets->current->next;
                                  ^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
read_pgf.c:363:12: warning: unused function 'token_ends_with' [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
           ^
4 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/affyio.buildbin-libdir/affyio/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affyio)


>>>>>>> 
>>>>>>> FIXING LINKS FOR affyio.buildbin-libdir/affyio/libs//affyio.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "affyio.buildbin-libdir/affyio/libs//affyio.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "affyio.buildbin-libdir/affyio/libs//affyio.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "affyio.buildbin-libdir/affyio/libs//affyio.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "affyio.buildbin-libdir/affyio/libs//affyio.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "affyio.buildbin-libdir/affyio/libs//affyio.so"