Package: oligo

Version: 0.99.18

Command: /loc/biocbuild/1.9d/R/bin/R CMD check oligo_0.99.18.tar.gz

RetCode: 1

Time: 15.4 seconds

Status: ERROR

CheckDir: oligo.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/oligo.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* 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 '/loc/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
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c basecontent.c -o basecontent.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c baseProfile.c -o baseProfile.o
baseProfile.c: In function `gcrma_getSeq2':
baseProfile.c:14: warning: unused variable `nx'
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1518: warning: unused variable `ind'
qnorm.c:1519: warning: unused variable `dimat'
qnorm.c:1523: warning: unused variable `ranks'
qnorm.c: In function `R_qnorm_using_target':
qnorm.c:1599: warning: unused variable `dim2'
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1591: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:114: warning: `min' defined but not used
qnorm.c:387: warning: `qnorm_c_old' defined but not used
qnorm.c:461: warning: `qnorm_robust_c_old' defined but not used
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c rma2.c -o rma2.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c rma_background2.c -o rma_background2.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c rma_common.c -o rma_common.o
gcc -shared -L/usr/local/lib64 -o oligo.so basecontent.o baseProfile.o qnorm.o rma2.o rma_background2.o rma_common.o -lz   
** R
Error in tools:::.install_package_code_files(".", "/loc/biocbuild/1.9d/Rpacks/oligo.Rcheck/oligo") : 
	
files in 'Collate' field missing from '/loc/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 '/loc/biocbuild/1.9d/Rpacks/oligo.Rcheck/oligo'