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Package 323/479HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.17.2
Benilton Carvalho
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo
Last Changed Rev: 56179 / Revision: 56603
Last Changed Date: 2011-06-14 14:36:25 -0700 (Tue, 14 Jun 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: oligo
Version: 1.17.2
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch oligo_1.17.2.tar.gz
StartedAt: 2011-07-07 02:56:18 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 03:00:46 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 267.9 seconds
RetCode: 0
Status:  OK  
CheckDir: oligo.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/oligo.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.17.2'
* 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 installed package size ... 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 ... OK
* 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 for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

oligo.Rcheck/00install.out:

* installing *source* package 'oligo' ...
** libs
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c DABG.c -o DABG.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c LESN.c -o LESN.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c PLM_avg_log.c -o PLM_avg_log.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c PLM_biweight.c -o PLM_biweight.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c PLM_log_avg.c -o PLM_log_avg.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c PLM_medianPM.c -o PLM_medianPM.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function 'gzread_one_xys':
ParserGzXYS.c:74:54: warning: unused variable 'token'
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c ParserXYS.c -o ParserXYS.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c SCAB.c -o SCAB.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c baseProfile.c -o baseProfile.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c basecontent.c -o basecontent.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c common_types.c -o common_types.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c idealmismatch.c -o idealmismatch.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c lm_threestep.c -o lm_threestep.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c preprocess.c -o preprocess.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma_PLM.c -o rma_PLM.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i'
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c scaling.c -o scaling.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c threestep.c -o threestep.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c threestep_common.c -o threestep_common.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c threestep_summary.c -o threestep_summary.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c transfns.c -o transfns.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/bbs-2.9-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 DABG.o LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o ParserGzXYS.o ParserXYS.o SCAB.o baseProfile.o basecontent.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o mas5calls.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rma2.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o trimmed.o -LE:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lgfortran -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRblas -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/oligo.Rcheck/oligo/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Loading package bit1.1-7

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit

Loading package ff2.2-2
- getOption("fftempdir")=="E:/biocbld/bbs-2.9-bioc/tmpdir/RtmpWkrU3L"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system

Creating a generic function for "boxplot" from package "graphics" in package "oligo"
Creating a generic function for "summary" from package "base" in package "oligo"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'V1Overview.Rnw' 
   'V2NExpression.Rnw' 
   'V3AffySnpGenotype.Rnw' 
   'V4Experimental.Rnw' 
   'V5ExonGene.Rnw' 
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
================================================================================
Welcome to oligo version 1.17.2
================================================================================

* DONE (oligo)

oligo.Rcheck/oligo-Ex.timings:

nameusersystemelapsed
Index-methods000
IntensityMatrix-methods2.600.083.57
MAplot-methods3.190.013.25
basecontent000
basicPLM6.810.057.01
basicRMA6.780.056.90
colors000
coordinates000
fitPLM10.82 0.1211.26
justSNPRMA000
list.xysfiles000
paCalls000
preprocessTools36.69 0.0536.89
read.celfiles17.72 0.2522.65
read.xysfiles1.830.041.89
rma-methods5.090.115.20
sequenceDesignMatrix0.020.000.02