affyio 1.18.0
Benjamin Milo Bolstad
| Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/affyio | | Last Changed Rev: 50293 / Revision: 54588 | | Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ OK ] | OK |
* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/affyio.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.18.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyio' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* installing *source* package 'affyio' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -c fread_functions.c -o fread_functions.o
fread_functions.c:300:13: warning: 'swap_uint_32' defined but not used
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -c read_abatch.c -o read_abatch.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -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
read_bpmap.c:78:7: warning: unused variable 'version_number_int'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -c read_cdf_xda.c -o read_cdf_xda.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364:12: warning: 'token_ends_with' defined but not used
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -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'
read_celfile_generic.c:708:7: warning: unused variable 'cur_index'
read_celfile_generic.c:707:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:760:7: warning: unused variable 'fread_err'
read_celfile_generic.c:758:7: warning: unused variable 'cur_index'
read_celfile_generic.c:757:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:814:7: warning: unused variable 'fread_err'
read_celfile_generic.c:812:7: warning: unused variable 'cur_index'
read_celfile_generic.c:811:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:876:7: warning: unused variable 'fread_err'
read_celfile_generic.c:874:7: warning: unused variable 'cur_index'
read_celfile_generic.c:873:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:968:7: warning: unused variable 'fread_err'
read_celfile_generic.c:962:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1714:7: warning: unused variable 'fread_err'
read_celfile_generic.c:1712:7: warning: unused variable 'cur_index'
read_celfile_generic.c:1711:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1765:7: warning: unused variable 'fread_err'
read_celfile_generic.c:1763:7: warning: unused variable 'cur_index'
read_celfile_generic.c:1762:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1819:7: warning: unused variable 'fread_err'
read_celfile_generic.c:1817:7: warning: unused variable 'cur_index'
read_celfile_generic.c:1816:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1884:7: warning: unused variable 'fread_err'
read_celfile_generic.c:1882:7: warning: unused variable 'cur_index'
read_celfile_generic.c:1881:12: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1976:7: warning: unused variable 'fread_err'
read_celfile_generic.c:1970:12: warning: unused variable 'j'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -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'
read_clf.c: At top level:
read_clf.c:292:12: warning: 'token_ends_with' defined but not used
read_clf.c:389:12: warning: 'IsCommentLine' defined but not used
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -c read_generic.c -o read_generic.o
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:399:1: warning: control reaches end of non-void function
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -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'
read_multichannel_celfile_generic.c:106:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:105:7: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'multichannel_determine_channel_name':
read_multichannel_celfile_generic.c:160:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:157:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:156:7: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:219:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:217:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:277:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:275:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:342:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:340:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'generic_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:417:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:415:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'generic_apply_masks_multichannel':
read_multichannel_celfile_generic.c:522:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:516:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_number_channels':
read_multichannel_celfile_generic.c:658:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:655:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:654:7: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name':
read_multichannel_celfile_generic.c:705:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:702:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:701:7: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:756:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:754:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:814:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:812:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:878:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:876:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:949:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:947:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel':
read_multichannel_celfile_generic.c:1053:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:1047:12: warning: unused variable 'j'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB -O2 -Wall -std=gnu99 -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'
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167:23: warning: unused variable 'temp_ptr'
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type
read_pgf.c: At top level:
read_pgf.c:363:12: warning: 'token_ends_with' defined but not used
x86_64-w64-mingw32-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 -lRzlib -LD:/biocbld/BBS-2˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-bioc/meat/affyio.Rcheck/affyio/libs/x64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (affyio)