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BioC 3.0: CHECK report for affyio on moscato1

This page was generated on 2015-04-10 09:43:01 -0700 (Fri, 10 Apr 2015).

Package 21/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyio 1.34.0
Benjamin Milo Bolstad
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/affyio
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: affyio
Version: 1.34.0
Command: rm -rf affyio.buildbin-libdir affyio.Rcheck && mkdir affyio.buildbin-libdir affyio.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyio.buildbin-libdir affyio_1.34.0.tar.gz >affyio.Rcheck\00install.out 2>&1 && cp affyio.Rcheck\00install.out affyio-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=affyio.buildbin-libdir --install="check:affyio-install.out" --force-multiarch --no-vignettes --timings affyio_1.34.0.tar.gz
StartedAt: 2015-04-09 22:24:39 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:25:35 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 55.3 seconds
RetCode: 0
Status:  OK  
CheckDir: affyio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyio.buildbin-libdir affyio.Rcheck && mkdir affyio.buildbin-libdir affyio.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyio.buildbin-libdir affyio_1.34.0.tar.gz >affyio.Rcheck\00install.out 2>&1 && cp affyio.Rcheck\00install.out affyio-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=affyio.buildbin-libdir --install="check:affyio-install.out" --force-multiarch --no-vignettes --timings affyio_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/affyio.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.34.0'
* 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 ... OK
* 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 'D:/biocbld/bbs-3.0-bioc/meat/affyio.buildbin-libdir/affyio/libs/i386/affyio.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64/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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/affyio.Rcheck/00check.log'
for details.

affyio.Rcheck/00install.out:


install for i386

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

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


** libs
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
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]
read_abatch.c:841:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
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]
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]
read_abatch.c:1735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_celfile_generic.c:709:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:708:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:761:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:759:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:758:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:815:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:813:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:812:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:877:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:875:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:874:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:969:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:963:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1715:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1713:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1712:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1766:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1764:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1763:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1820:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1818:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1817:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1885:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1883:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1882:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1977:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1971:15: warning: unused variable 'j' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_clf.c: At top level:
read_clf.c:292:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
read_clf.c:389:12: warning: 'IsCommentLine' defined but not used [-Wunused-function]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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 [-Wuninitialized]
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:2029:16: warning: 'return_value' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1794:17: warning: 'tmp_sexp' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1783:8: note: 'tmp_sexp' was declared here
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_multichannel_celfile_generic.c:106:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:105:17: warning: unused variable 'k' [-Wunused-variable]
read_multichannel_celfile_generic.c:105:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:165:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_multichannel_celfile_generic.c:162:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:161:12: warning: unused variable 'j' [-Wunused-variable]
read_multichannel_celfile_generic.c:161:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:221:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:220:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:278:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:277:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:342:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:341:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:416:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:415:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:516:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:661:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:660:17: warning: unused variable 'k' [-Wunused-variable]
read_multichannel_celfile_generic.c:660:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:717:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_multichannel_celfile_generic.c:714:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:713:12: warning: unused variable 'j' [-Wunused-variable]
read_multichannel_celfile_generic.c:713:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:764:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:763:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:820:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:819:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:882:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:881:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:951:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:950:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:1049:12: warning: unused variable 'j' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167:23: warning: unused variable 'temp_ptr' [-Wunused-variable]
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type [enabled by default]
read_pgf.c: At top level:
read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
gcc -m32 -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-3.0-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-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
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
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]
read_abatch.c:841:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
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]
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]
read_abatch.c:1735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:110:5: warning: overflow in implicit constant conversion [-Woverflow]
read_bpmap.c:78:7: warning: unused variable 'version_number_int' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_celfile_generic.c:709:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:708:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:761:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:759:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:758:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:815:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:813:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:812:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:877:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:875:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:874:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:969:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:963:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1715:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1713:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1712:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1766:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1764:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1763:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1820:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1818:10: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1817:15: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1885:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1883:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1882:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1977:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1971:15: warning: unused variable 'j' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_clf.c: At top level:
read_clf.c:292:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
read_clf.c:389:12: warning: 'IsCommentLine' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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 [-Wuninitialized]
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:2029:16: warning: 'return_value' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1794:17: warning: 'tmp_sexp' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1783:8: note: 'tmp_sexp' was declared here
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_multichannel_celfile_generic.c:106:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:105:17: warning: unused variable 'k' [-Wunused-variable]
read_multichannel_celfile_generic.c:105:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:165:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_multichannel_celfile_generic.c:162:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:161:12: warning: unused variable 'j' [-Wunused-variable]
read_multichannel_celfile_generic.c:161:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:221:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:220:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:278:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:277:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:342:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:341:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:416:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:415:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:516:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:661:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:660:17: warning: unused variable 'k' [-Wunused-variable]
read_multichannel_celfile_generic.c:660:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:717:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_multichannel_celfile_generic.c:714:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:713:12: warning: unused variable 'j' [-Wunused-variable]
read_multichannel_celfile_generic.c:713:7: warning: unused variable 'i' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:764:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:763:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:820:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:819:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:882:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:881:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:951:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_multichannel_celfile_generic.c:950:12: warning: unused variable 'j' [-Wunused-variable]
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]
read_multichannel_celfile_generic.c:1049:12: warning: unused variable 'j' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/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]
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167:23: warning: unused variable 'temp_ptr' [-Wunused-variable]
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type [enabled by default]
read_pgf.c: At top level:
read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
gcc -m64 -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-3.0-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyio' as affyio_1.34.0.zip
* DONE (affyio)