oligo 1.8.3
Benilton Carvalho
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/oligo | | Last Changed Rev: 41241 / Revision: 42512 | | Last Changed Date: 2009-08-19 19:22:00 -0700 (Wed, 19 Aug 2009) |
| wilson1 | 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 |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/oligo.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49419)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.8.3'
* 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 ... OK
* checking Rd files against version 2 parser ... 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
* Installing *source* package ‘oligo’ ...
** libs
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -c baseProfile.c -o baseProfile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -c basecontent.c -o basecontent.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -c rma2.c -o rma2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -c rma_background2.c -o rma_background2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -c rma_common.c -o rma_common.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -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 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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -g -O2 -c baseProfile.c -o baseProfile.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -g -O2 -c basecontent.c -o basecontent.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -g -O2 -c rma2.c -o rma2.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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 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)'.
** help
*** installing help indices
>>> Building/Updating help pages for package 'oligo'
Formats: text html latex example
IntensityMatrix-methods text html latex example
MAplot-methods text html latex
basecontent text html latex example
basicRMA text html latex example
boxplot text html latex
coordinates text html latex example
crlmm text html latex
getContainer text html latex
getCrlmmSummaries text html latex
getNgsColorsInfo text html latex
hist text html latex
image text html latex
justSNPRMA text html latex example
list.celfiles text html latex example
oligo-package text html latex
plotM-methods text html latex
read.celfiles text html latex example
read.xysfiles text html latex example
readSummaries text html latex
rma text html latex example
sequenceDesignMatrix text html latex example
snprma text html latex
** building package indices ...
* DONE (oligo)