Package: oligo

Version: 0.99.18

Command: D:\biocbld\1.9d\R\bin\R.exe 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 'D:/biocbld/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 'D:/biocbld/1.9d/Rpacks/oligo.Rcheck/00install.out' for details.

installing R.css in D:/biocbld/1.9d/Rpacks/oligo.Rcheck


---------- Making package oligo ------------

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

  adding build stamp to DESCRIPTION
  making DLL ...
making baseProfile.d from baseProfile.c
making basecontent.d from basecontent.c
making qnorm.d from qnorm.c
making rma2.d from rma2.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
gcc  -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include  -Wall -O2 -std=gnu99   -c baseProfile.c -o baseProfile.o
baseProfile.c: In function `gcrma_getSeq2':
baseProfile.c:14: warning: unused variable `nx'
gcc  -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include  -Wall -O2 -std=gnu99   -c basecontent.c -o basecontent.o
gcc  -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include  -Wall -O2 -std=gnu99   -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  -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include  -Wall -O2 -std=gnu99   -c rma2.c -o rma2.o
gcc  -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include  -Wall -O2 -std=gnu99   -c rma_background2.c -o rma_background2.o
gcc  -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include  -Wall -O2 -std=gnu99   -c rma_common.c -o rma_common.o
windres --include-dir d:/biocbld/1.9d/R/include  -i oligo_res.rc -o oligo_res.o
gcc  -shared -s  -o oligo.dll oligo.def baseProfile.o basecontent.o qnorm.o rma2.o rma_background2.o rma_common.o oligo_res.o  -Ld:/biocbld/1.9d/R/bin   -lR
  ... DLL made
  installing DLL
  installing R files
Error in tools:::.install_package_code_files(".", "D:/biocbld/1.9d/Rpacks/oligo.Rcheck/oligo") : 
	
files in 'Collate' field missing from 'D:/biocbld/1.9d/Rpacks/oligo.Rcheck/00_pkg_src/oligo/R':
  methods-SnpCallSetPlus.R
Execution halted
make[2]: *** [D:/biocbld/1.9d/Rpacks/oligo.Rcheck/oligo/R/oligo] Error 1
make[1]: *** [all] Error 2
make: *** [pkg-oligo] Error 2
*** Installation of oligo failed ***

Removing 'D:/biocbld/1.9d/Rpacks/oligo.Rcheck/oligo'