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Package 233/353HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.10.4
Benilton Carvalho
Snapshot Date: 2010-04-02 23:28:25 -0700 (Fri, 02 Apr 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/oligo
Last Changed Rev: 45393 / Revision: 45705
Last Changed Date: 2010-03-22 04:28:58 -0700 (Mon, 22 Mar 2010)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: oligo
Version: 1.10.4
Command: /Library/Frameworks/R.framework/Versions/2.10/Resources/bin/R CMD check --no-vignettes oligo_1.10.4.tar.gz
StartedAt: 2010-04-03 06:29:17 -0700 (Sat, 03 Apr 2010)
EndedAt: 2010-04-03 06:32:30 -0700 (Sat, 03 Apr 2010)
EllapsedTime: 192.3 seconds
RetCode: 0
Status: OK
CheckDir: oligo.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/oligo.Rcheck'
* using R version 2.10.1 Patched (2009-12-14 r50738)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.10.4'
* 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 for sufficient/correct file permissions ... 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 name space can be loaded with stated dependencies ... 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 ... NOTE
prepare_Rd: basecontent.Rd:14-15: Dropping empty section \details
* 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 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
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c rma2.c -o rma2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so ParserXYS.o baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c ParserXYS.c -o ParserXYS.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c baseProfile.c -o baseProfile.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c basecontent.c -o basecontent.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma2.c -o rma2.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma_background2.c -o rma_background2.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma_common.c -o rma_common.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c trimmed.c -o trimmed.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so ParserXYS.o baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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)'.

Creating a new generic function for "boxplot" in "oligo"
** help
*** installing help indices
** building package indices ...
* DONE (oligo)