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Package 20/479HostnameOS / ArchBUILDCHECKBUILD BIN
affyio 1.21.2
Benjamin Milo Bolstad
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyio
Last Changed Rev: 56148 / Revision: 56603
Last Changed Date: 2011-06-13 14:27:18 -0700 (Mon, 13 Jun 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: affyio
Version: 1.21.2
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch affyio_1.21.2.tar.gz
StartedAt: 2011-07-07 01:38:45 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 01:39:26 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 41.2 seconds
RetCode: 0
Status:  OK  
CheckDir: affyio.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/affyio.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* 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 '1.21.2'
* 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 installed package size ... 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

affyio.Rcheck/00install.out:

* 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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB         -O2 -Wall  -std=gnu99 -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
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:411:1: warning: control reaches end of non-void function
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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:105:17: warning: unused variable 'k'
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:173:20: warning: unused variable 'my_data_set'
read_multichannel_celfile_generic.c:165:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:162:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:161:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c:161:7: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:223:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:221:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:220:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:280:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:278:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:277:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:344:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:342:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:341:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'generic_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:418:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:416:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:415:12: warning: unused variable 'j'
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:664:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:661:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:660:17: warning: unused variable 'k'
read_multichannel_celfile_generic.c:660:7: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name':
read_multichannel_celfile_generic.c:725:20: warning: unused variable 'my_data_set'
read_multichannel_celfile_generic.c:717:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:714:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:713:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c:713:7: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:766:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:764:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:763:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:822:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:820:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:819:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:884:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:882:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:881:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:953:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:951:7: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:950:12: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel':
read_multichannel_celfile_generic.c:1055:7: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:1049:12: warning: unused variable 'j'
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-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 -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-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)