Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: INSTALL report for affyio on moscato1

This page was generated on 2016-04-23 10:15:12 -0700 (Sat, 23 Apr 2016).

Package 23/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyio 1.40.0
Benjamin Milo Bolstad
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/affyio
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyio
Version: 1.40.0
Command: rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.2/bioc/src/contrib/affyio_1.40.0.tar.gz && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --library=affyio.buildbin-libdir --merge-multiarch affyio_1.40.0.tar.gz && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL affyio_1.40.0.zip && rm affyio_1.40.0.tar.gz affyio_1.40.0.zip
StartedAt: 2016-04-22 18:02:21 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 18:04:40 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 138.8 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.2/bioc/src/contrib/affyio_1.40.0.tar.gz && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --library=affyio.buildbin-libdir --merge-multiarch affyio_1.40.0.tar.gz && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL affyio_1.40.0.zip  && rm affyio_1.40.0.tar.gz affyio_1.40.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  104k  100  104k    0     0   507k      0 --:--:-- --:--:-- --:--:--  512k

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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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 [-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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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:110:5: 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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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 [-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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/r-compiling/local/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]
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-3.2-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyio' as affyio_1.40.0.zip
* DONE (affyio)
* installing to library 'D:/biocbld/bbs-3.2-bioc/R/library'
package 'affyio' successfully unpacked and MD5 sums checked