BioC 3.5: CHECK report for affyio on tokay2

Package: affyio

Version: 1.46.0

Command: rm -rf affyio.buildbin-libdir affyio.Rcheck && mkdir affyio.buildbin-libdir affyio.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyio.buildbin-libdir affyio_1.46.0.tar.gz >affyio.Rcheck\00install.out 2>&1 && cp affyio.Rcheck\00install.out affyio-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=affyio.buildbin-libdir --install="check:affyio-install.out" --force-multiarch --no-vignettes --timings affyio_1.46.0.tar.gz

StartedAt: 2017-08-15 21:54:54 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:55:50 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 56.4 seconds

RetCode: 0

Status:  OK

CheckDir: affyio.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   rm -rf affyio.buildbin-libdir affyio.Rcheck && mkdir affyio.buildbin-libdir affyio.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyio.buildbin-libdir affyio_1.46.0.tar.gz >affyio.Rcheck\00install.out 2>&1 && cp affyio.Rcheck\00install.out affyio-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=affyio.buildbin-libdir --install="check:affyio-install.out" --force-multiarch --no-vignettes --timings affyio_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/affyio.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.46.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'affyio' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
read.celfile.header: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/affyio.buildbin-libdir/affyio/libs/i386/affyio.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/affyio.Rcheck/00check.log'
for details.

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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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 -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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 -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyio' as affyio_1.46.0.zip
* DONE (affyio)