Package: affyio

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check affyio_1.6.0.tar.gz

RetCode: 0

Time: 27.9 seconds

Status: OK

CheckDir: affyio.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/Users/biocbuild/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 for sufficient/correct file permissions ... 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 *source* package 'affyio' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_abatch.c -o read_abatch.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -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-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -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-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:363: warning: 'token_ends_with' defined but not used
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -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-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -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
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affyio.so fread_functions.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_generic.o -lz   -F/Library/Frameworks/R.framework/.. -framework R 
** R
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'affyio'
     Formats: text html latex example 
  check.cdf.type                    text    html    latex
  read.cdffile.list                 text    html    latex
  read.celfile                      text    html    latex
  read.celfile.header               text    html    latex
  read.celfile.probeintensity.matri text    html    latex
** building package indices ...
* DONE (affyio)