Package: affyio

Version: 1.6.0

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check affyio_1.6.0.tar.gz

RetCode: 0

Time: 40.9 seconds

Status: OK

CheckDir: affyio.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/affyio.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.6.0'
* 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 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
* creating affyio-Ex.R ... OK
* checking examples ... OK
* creating affyio-manual.tex ... OK
* checking affyio-manual.tex ... OK

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/affyio.Rcheck


---------- Making package affyio ------------

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************

  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making fread_functions.d from fread_functions.c
making read_abatch.d from read_abatch.c
making read_bpmap.d from read_bpmap.c
making read_cdf_xda.d from read_cdf_xda.c
making read_cdffile2.d from read_cdffile2.c
making read_celfile_generic.d from read_celfile_generic.c
making read_generic.d from read_generic.c
gcc-sjlj  -std=gnu99 -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc-sjlj  -std=gnu99 -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c read_abatch.c -o read_abatch.o
gcc-sjlj  -std=gnu99 -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:76: warning: unused variable 'version_number_int'
gcc-sjlj  -std=gnu99 -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c read_cdf_xda.c -o read_cdf_xda.o
read_cdf_xda.c: In function 'isPM':
read_cdf_xda.c:614: warning: implicit declaration of function 'toupper'
gcc-sjlj  -std=gnu99 -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:363: warning: 'token_ends_with' defined but not used
gcc-sjlj  -std=gnu99 -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'read_genericcel_file_intensities':
read_celfile_generic.c:591: warning: unused variable 'fread_err'
read_celfile_generic.c:589: warning: unused variable 'cur_index'
read_celfile_generic.c:588: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:641: warning: unused variable 'fread_err'
read_celfile_generic.c:639: warning: unused variable 'cur_index'
read_celfile_generic.c:638: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:695: warning: unused variable 'fread_err'
read_celfile_generic.c:693: warning: unused variable 'cur_index'
read_celfile_generic.c:692: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:757: warning: unused variable 'fread_err'
read_celfile_generic.c:755: warning: unused variable 'cur_index'
read_celfile_generic.c:754: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:849: warning: unused variable 'fread_err'
read_celfile_generic.c:843: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1488: warning: unused variable 'fread_err'
read_celfile_generic.c:1486: warning: unused variable 'cur_index'
read_celfile_generic.c:1485: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1539: warning: unused variable 'fread_err'
read_celfile_generic.c:1537: warning: unused variable 'cur_index'
read_celfile_generic.c:1536: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1593: warning: unused variable 'fread_err'
read_celfile_generic.c:1591: warning: unused variable 'cur_index'
read_celfile_generic.c:1590: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1658: warning: unused variable 'fread_err'
read_celfile_generic.c:1656: warning: unused variable 'cur_index'
read_celfile_generic.c:1655: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1750: warning: unused variable 'fread_err'
read_celfile_generic.c:1744: warning: unused variable 'j'
gcc-sjlj  -std=gnu99 -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c read_generic.c -o read_generic.o
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:389: warning: control reaches end of non-void function
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.1-bioc/R/include  -i affyio_res.rc -o affyio_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o affyio.dll affyio.def fread_functions.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_generic.o affyio_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin -Le:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -lz   -lR
  ... DLL made
  installing DLL
  installing R files
  preparing package affyio for lazy loading
  installing man source files
  installing indices
  installing help
 >>> 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-bioc\meat\affyio.Rcheck\00_pkg_src\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-bioc\meat\affyio.Rcheck\00_pkg_src\affyio\chm\affyio.chm, 19,567 bytes
Compression increased file by 2,051 bytes.
  adding MD5 sums

* DONE (affyio)