Package: oligo

Version: 0.99.18

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check oligo_0.99.18.tar.gz

RetCode: 1

Time: 11.5 seconds

Status: ERROR

CheckDir: oligo.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/Users/biocbuild/1.9d/Rpacks/oligo.Rcheck'
* using R version 2.4.0 alpha (2006-09-07 r39185)
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '0.99.18'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from
pdn pkgname designname
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'oligo' can be installed ... ERROR
Installation failed.
See '/Users/biocbuild/1.9d/Rpacks/oligo.Rcheck/00install.out' for details.

* Installing *source* package 'oligo' ...
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 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c baseProfile.c -o baseProfile.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c basecontent.c -o basecontent.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c qnorm.c -o qnorm.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c rma2.c -o rma2.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c rma_background2.c -o rma_background2.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c rma_common.c -o rma_common.o
gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so baseProfile.o basecontent.o qnorm.o rma2.o rma_background2.o rma_common.o -lz   -L/Library/Frameworks/R.framework/Resources/lib/i386 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/i386/libRblas.dylib
** R
Error in tools:::.install_package_code_files(".", "/Users/biocbuild/1.9d/Rpacks/oligo.Rcheck/oligo") : 
	
files in 'Collate' field missing from '/Users/biocbuild/1.9d/Rpacks/oligo.Rcheck/00_pkg_src/oligo/R':
  methods-SnpCallSetPlus.R
Execution halted
ERROR: unable to collate files for package 'oligo'
** Removing '/Users/biocbuild/1.9d/Rpacks/oligo.Rcheck/oligo'