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Package 259/389HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.12.2
Benilton Carvalho
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/oligo
Last Changed Rev: 48736 / Revision: 49923
Last Changed Date: 2010-08-10 03:10:00 -0700 (Tue, 10 Aug 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: oligo
Version: 1.12.2
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings oligo_1.12.2.tar.gz
StartedAt: 2010-10-04 19:17:18 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 19:20:42 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 203.4 seconds
RetCode: 0
Status:  OK  
CheckDir: oligo.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/oligo.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.12.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligo' 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
alleleSetFrom: no visible global function definition for 'finalizer<-'
ffSubset: no visible global function definition for 'vmode'
fitAffySnpMixture2: no visible global function definition for 'ff'
fitAffySnpMixture2: no visible global function definition for
  'ffvecapply'
fitAffySnpMixture2: no visible binding for global variable 'i1'
fitAffySnpMixture2: no visible binding for global variable 'i2'
rmaBgCorrectLDSmaster: no visible global function definition for
  'clone'
smartReadCEL: no visible global function definition for 'filename'
smartReadXYS: no visible global function definition for 'filename'
snpGenderCall: no visible global function definition for 'is.ff'
snprma2: no visible global function definition for 'finalizer<-'
normalizeToTarget,ff_matrix: no visible global function definition for
  'clone'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

oligo.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'oligo' ...
** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function 'read_one_xys':
ParserXYS.c:105: warning: unused variable 'token'
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c baseProfile.c -o baseProfile.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c basecontent.c -o basecontent.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c trimmed.c -o trimmed.o
gcc -shared -s -static-libgcc -o oligo.dll tmp.def ParserXYS.o baseProfile.o basecontent.o chipbackground.o rma2.o rma_common.o trimmed.o -lRzlib -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/oligo.Rcheck/oligo/libs
  ... done
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

================================================================================
Welcome to oligoClasses version 1.10.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
in method for 'backgroundCorrect' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'normalize' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'normalizeToTarget' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'summarize' with signature '"ff_matrix"': no definition for class "ff_matrix"
Creating a new generic function for "boxplot" in "oligo"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligo version 1.12.2
================================================================================

* DONE (oligo)

oligo.Rcheck/oligo-Ex.timings:

nameusersystemelapsed
Index-methods000
IntensityMatrix-methods3.310.077.31
basecontent000
basicRMA6.760.016.81
colors0.000.020.01
coordinates000
justSNPRMA000
list.xysfiles000
preprocessTools36.64 0.1236.80
read.celfiles19.89 0.4925.42
read.xysfiles2.810.092.91
rma-methods6.470.116.62
sequenceDesignMatrix0.020.000.02