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Package 12/319HostnameOS / ArchBUILDCHECKBUILD BIN
affyio 1.12.0
Benjamin Milo Bolstad
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/affyio
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: affyio
Version: 1.12.0
Command: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD check --no-vignettes affyio_1.12.0.tar.gz
StartedAt: 2009-10-20 16:01:08 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 16:01:39 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 30.6 seconds
RetCode: 0
Status: OK
CheckDir: affyio.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/affyio.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.12.0'
* 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 name space can be loaded with stated dependencies ... 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 files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... OK
* checking examples ... OK
* 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
  making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c read_abatch.c -o read_abatch.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:78: warning: unused variable 'version_number_int'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c read_cdf_xda.c -o read_cdf_xda.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364: warning: 'token_ends_with' defined but not used
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -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:697: warning: unused variable 'fread_err'
read_celfile_generic.c:695: warning: unused variable 'cur_index'
read_celfile_generic.c:694: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:747: warning: unused variable 'fread_err'
read_celfile_generic.c:745: warning: unused variable 'cur_index'
read_celfile_generic.c:744: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:801: warning: unused variable 'fread_err'
read_celfile_generic.c:799: warning: unused variable 'cur_index'
read_celfile_generic.c:798: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:863: warning: unused variable 'fread_err'
read_celfile_generic.c:861: warning: unused variable 'cur_index'
read_celfile_generic.c:860: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:955: warning: unused variable 'fread_err'
read_celfile_generic.c:949: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1689: warning: unused variable 'fread_err'
read_celfile_generic.c:1687: warning: unused variable 'cur_index'
read_celfile_generic.c:1686: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1740: warning: unused variable 'fread_err'
read_celfile_generic.c:1738: warning: unused variable 'cur_index'
read_celfile_generic.c:1737: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1794: warning: unused variable 'fread_err'
read_celfile_generic.c:1792: warning: unused variable 'cur_index'
read_celfile_generic.c:1791: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1859: warning: unused variable 'fread_err'
read_celfile_generic.c:1857: warning: unused variable 'cur_index'
read_celfile_generic.c:1856: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1951: warning: unused variable 'fread_err'
read_celfile_generic.c:1945: warning: unused variable 'j'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c read_clf.c -o read_clf.o
read_clf.c: In function 'read_clf_header':
read_clf.c:557: warning: unused variable 'i'
read_clf.c: At top level:
read_clf.c:292: warning: 'token_ends_with' defined but not used
read_clf.c:389: warning: 'IsCommentLine' defined but not used
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c read_generic.c -o read_generic.o
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:399: warning: control reaches end of non-void function
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB       -O3 -Wall  -std=gnu99 -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'read_pgf_header':
read_pgf.c:901: warning: unused variable 'i'
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167: warning: unused variable 'temp_ptr'
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265: warning: assignment from incompatible pointer type
read_pgf.c: At top level:
read_pgf.c:363: warning: 'token_ends_with' defined but not used
gcc -shared -s -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_pgf.o -lRzlib -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
  ... done
** R
** preparing package for lazy loading
** help
*** installing help indices
 >>> Building/Updating help pages for package 'affyio'
     Formats: text html latex example chm 
  check.cdf.type                    text    html    latex           chm
  read.cdffile.list                 text    html    latex           chm
  read.celfile                      text    html    latex           chm
  read.celfile.header               text    html    latex           chm
  read.celfile.probeintensity.matri text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\BBS-2~1.4-B\meat\AFFYIO~1.RCH\00_PKG~1\affyio\chm\affyio.chm


Compile time: 0 minutes, 0 seconds
6	Topics
11	Local links
0	Internet links
1	Graphic


Created e:\biocbld\BBS-2~1.4-B\meat\AFFYIO~1.RCH\00_PKG~1\affyio\chm\affyio.chm, 19,631 bytes
Compression increased file by 1,980 bytes.
** building package indices ...
** MD5 sums
* DONE (affyio)