affyio 1.22.0
Benjamin Milo Bolstad
| Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/affyio | | Last Changed Rev: 59920 / Revision: 64395 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
install for i386
* installing *source* package 'affyio' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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:733:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
read_abatch.c: In function 'read_cel_file_npixels':
read_abatch.c:839:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
read_abatch.c:839:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
read_abatch.c: In function 'read_gzcel_file_stddev':
read_abatch.c:1628:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
read_abatch.c: In function 'read_gzcel_file_npixels':
read_abatch.c:1733:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
read_abatch.c:1733:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
gcc -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -O3 -Wall -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
gcc -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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:710:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:708:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:707:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:760:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:758:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:757:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:814:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:812:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:811:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:876:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:874:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:873:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:968:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:962:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1714:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1712:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1711:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1765:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1763:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1762:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1819:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1817:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1816:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1884:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1882:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1881:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1976:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1970:12: warning: unused variable 'j' [-Wunused-variable]
gcc -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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:1594:1: warning: control reaches end of non-void function [-Wreturn-type]
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:411:1: warning: control reaches end of non-void function [-Wreturn-type]
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:1939:16: warning: 'return_value' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1704:17: warning: 'tmp_sexp' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1693:8: note: 'tmp_sexp' was declared here
gcc -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB -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 -shared -s -static-libgcc -o affyio.dll tmp.def fread_functions.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-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-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
add DLL 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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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:733:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
read_abatch.c: In function 'read_cel_file_npixels':
read_abatch.c:839:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
read_abatch.c:839:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
read_abatch.c: In function 'read_gzcel_file_stddev':
read_abatch.c:1628:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
read_abatch.c: In function 'read_gzcel_file_npixels':
read_abatch.c:1733:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable]
read_abatch.c:1733:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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:710:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:708:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:707:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:760:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:758:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:757:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:814:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:812:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:811:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:876:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:874:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:873:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:968:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:962:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1714:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1712:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1711:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1765:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1763:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1762:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1819:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1817:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1816:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1884:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1882:7: warning: unused variable 'cur_index' [-Wunused-variable]
read_celfile_generic.c:1881:12: warning: unused variable 'j' [-Wunused-variable]
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1976:7: warning: unused variable 'fread_err' [-Wunused-variable]
read_celfile_generic.c:1970:12: warning: unused variable 'j' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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:1594:1: warning: control reaches end of non-void function [-Wreturn-type]
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:411:1: warning: control reaches end of non-void function [-Wreturn-type]
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:1939:16: warning: 'return_value' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1704:17: warning: 'tmp_sexp' may be used uninitialized in this function [-Wuninitialized]
read_generic.c:1693:8: note: 'tmp_sexp' was declared here
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -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 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-2.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyio' as affyio_1.22.0.zip
* DONE (affyio)