BioC 3.4: INSTALL report for affyio on moscato1

Package: affyio

Version: 1.43.0

Command: rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/affyio_1.43.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=affyio.buildbin-libdir --merge-multiarch affyio_1.43.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL affyio_1.43.0.zip && rm affyio_1.43.0.tar.gz affyio_1.43.0.zip

StartedAt: 2016-09-19 20:38:56 -0700 (Mon, 19 Sep 2016)

EndedAt: 2016-09-19 20:40:07 -0700 (Mon, 19 Sep 2016)

EllapsedTime: 71.1 seconds

RetCode: 0

Status:  OK

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###
### Running command:
###
###   rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/affyio_1.43.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=affyio.buildbin-libdir --merge-multiarch affyio_1.43.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL affyio_1.43.0.zip  && rm affyio_1.43.0.tar.gz affyio_1.43.0.zip
###
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install for i386

* installing *source* package 'affyio' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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 */
             ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_abatch.c -o read_abatch.o
read_abatch.c: In function 'read_cel_file_stddev':
read_abatch.c:735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
read_abatch.c: In function 'read_cel_file_npixels':
read_abatch.c:841:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
                    ^
read_abatch.c:841:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
read_abatch.c: In function 'read_gzcel_file_stddev':
read_abatch.c:1630:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
read_abatch.c: In function 'read_gzcel_file_npixels':
read_abatch.c:1735:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
                    ^
read_abatch.c:1735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:78:7: warning: unused variable 'version_number_int' [-Wunused-variable]
   int version_number_int;
       ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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){
            ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'read_genericcel_file_intensities':
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:708:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
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: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:815:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:813:10: warning: unused variable 'cur_index' [-Wunused-variable]
   size_t cur_index;
          ^
read_celfile_generic.c:812:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:877:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:875:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
read_celfile_generic.c:874:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0;
            ^
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:969:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:963:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
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:1712:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
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: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1820:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:1818:10: warning: unused variable 'cur_index' [-Wunused-variable]
   size_t cur_index;
          ^
read_celfile_generic.c:1817:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1885:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
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: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1977:7: 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;
               ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_clf.c -o read_clf.o
read_clf.c: In function 'read_clf_header':
read_clf.c:557:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
read_clf.c: At top level:
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){
            ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_generic.c -o read_generic.o
read_generic.c: In function 'decode_nvt_triplet':
read_generic.c:1606:8: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SEXP return_value;
        ^
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:2029:2: 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:1794:3: warning: 'tmp_sexp' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SET_VECTOR_ELT(return_value,0,tmp_sexp);
   ^
read_generic.c:1783:8: note: 'tmp_sexp' was declared here
   SEXP tmp_sexp, return_names;
        ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c: In function 'multichannel_determine_number_channels':
read_multichannel_celfile_generic.c:109:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:106:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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:105:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0, j=0, k=0;
       ^
read_multichannel_celfile_generic.c: In function 'multichannel_determine_channel_name':
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: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:161:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
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: In function 'read_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:223:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
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: In function 'read_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:280:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:278:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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: In function 'read_genericcel_file_npixels_multichannel':
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:341:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'generic_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:418:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:416:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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: In function 'generic_apply_masks_multichannel':
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: In function 'gzmultichannel_determine_number_channels':
read_multichannel_celfile_generic.c:664:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=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:660:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0, j=0, k=0;
       ^
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name':
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:717:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:714:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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:713:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0, j=0, k=0;
       ^
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:766:7: 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:763:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:822:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=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: In function 'gzread_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:884:7: 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:881:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel':
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:950:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel':
read_multichannel_celfile_generic.c:1055:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:1049:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'read_pgf_header':
read_pgf.c:901:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167:23: warning: unused variable 'temp_ptr' [-Wunused-variable]
   probeset_list_node *temp_ptr;
                       ^
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type
  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){
            ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o affyio.dll tmp.def 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 -LD:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/affyio.buildbin-libdir/affyio/libs/i386
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'affyio' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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 */
             ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_abatch.c -o read_abatch.o
read_abatch.c: In function 'read_cel_file_stddev':
read_abatch.c:735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
read_abatch.c: In function 'read_cel_file_npixels':
read_abatch.c:841:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
                    ^
read_abatch.c:841:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
read_abatch.c: In function 'read_gzcel_file_stddev':
read_abatch.c:1630:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
read_abatch.c: In function 'read_gzcel_file_npixels':
read_abatch.c:1735:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
                    ^
read_abatch.c:1735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
   double cur_mean, cur_stddev;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:110:18: warning: overflow in implicit constant conversion [-Woverflow]
     fseek(infile,-sizeof(float),SEEK_CUR);
                  ^
read_bpmap.c:78:7: warning: unused variable 'version_number_int' [-Wunused-variable]
   int version_number_int;
       ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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){
            ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'read_genericcel_file_intensities':
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:708:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
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: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:815:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:813:10: warning: unused variable 'cur_index' [-Wunused-variable]
   size_t cur_index;
          ^
read_celfile_generic.c:812:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:877:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:875:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
read_celfile_generic.c:874:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0;
            ^
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:969:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:963:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
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:1712:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
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: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1820:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_celfile_generic.c:1818:10: warning: unused variable 'cur_index' [-Wunused-variable]
   size_t cur_index;
          ^
read_celfile_generic.c:1817:15: warning: unused variable 'j' [-Wunused-variable]
   size_t i=0, j=0;
               ^
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1885:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
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: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1977:7: 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;
               ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_clf.c -o read_clf.o
read_clf.c: In function 'read_clf_header':
read_clf.c:557:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
read_clf.c: At top level:
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){
            ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_generic.c -o read_generic.o
read_generic.c: In function 'decode_nvt_triplet':
read_generic.c:1606:8: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SEXP return_value;
        ^
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:2029:2: 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:1794:3: warning: 'tmp_sexp' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SET_VECTOR_ELT(return_value,0,tmp_sexp);
   ^
read_generic.c:1783:8: note: 'tmp_sexp' was declared here
   SEXP tmp_sexp, return_names;
        ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c: In function 'multichannel_determine_number_channels':
read_multichannel_celfile_generic.c:109:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:106:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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:105:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0, j=0, k=0;
       ^
read_multichannel_celfile_generic.c: In function 'multichannel_determine_channel_name':
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: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:161:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
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: In function 'read_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:223:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
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: In function 'read_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:280:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:278:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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: In function 'read_genericcel_file_npixels_multichannel':
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:341:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'generic_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:418:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:416:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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: In function 'generic_apply_masks_multichannel':
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: In function 'gzmultichannel_determine_number_channels':
read_multichannel_celfile_generic.c:664:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=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:660:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0, j=0, k=0;
       ^
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name':
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:717:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:714:7: warning: unused variable 'cur_index' [-Wunused-variable]
   int cur_index;
       ^
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:713:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0, j=0, k=0;
       ^
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:766:7: 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:763:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:822:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=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: In function 'gzread_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:884:7: 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:881:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel':
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:950:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0, k=0;
            ^
read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel':
read_multichannel_celfile_generic.c:1055:7: warning: unused variable 'fread_err' [-Wunused-variable]
   int fread_err=0;
       ^
read_multichannel_celfile_generic.c:1049:12: warning: unused variable 'j' [-Wunused-variable]
   int i=0, j=0;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'read_pgf_header':
read_pgf.c:901:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167:23: warning: unused variable 'temp_ptr' [-Wunused-variable]
   probeset_list_node *temp_ptr;
                       ^
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type
  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){
            ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o affyio.dll tmp.def 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 -LD:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyio' as affyio_1.43.0.zip
* DONE (affyio)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'affyio' successfully unpacked and MD5 sums checked