oligo 1.4.0
Benilton Carvalho
| Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/oligo | | Last Changed Rev: 31430 / Revision: 34573 | | Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | [ OK ] | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | 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 |
* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/oligo.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.4.0'
* 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 ... NOTE
justCRLMM: no visible binding for global variable 'maleIndex'
justCRLMM2: no visible binding for global variable 'maleIndex'
justCRLMMv2: no visible binding for global variable 'maleIndex'
LLR2conf: no visible binding for global variable 'HmzK3'
LLR2conf: no visible binding for global variable 'lm1'
LLR2conf: no visible binding for global variable 'HmzK2'
LLR2conf: no visible binding for global variable 'HtzK3'
LLR2conf: no visible binding for global variable 'lm2'
LLR2conf: no visible binding for global variable 'HtzK2'
LLR2conf: no visible binding for global variable 'SNRK'
LLR2conf: no visible binding for global variable 'SNRlm'
* checking Rd files ... 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
* creating oligo-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating oligo-manual.tex ... OK
* checking oligo-manual.tex using pdflatex ... OK
* Installing *source* package 'oligo' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o oligo.so basecontent.o baseProfile.o rma2.o rma_background2.o rma_common.o trimmed.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
Loading required package: oligoClasses
** help
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>>> Building/Updating help pages for package 'oligo'
Formats: text html latex example
DBPDInfo-class text html latex example
FeatureSet-class text html latex example
FeatureSetExtensions-class text html latex example
Index-methods text html latex
IntensityMatrix-methods text html latex
MAplot-methods text html latex
PDInfo-class text html latex example
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hist text html latex
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internals text html latex
justSNPRMA text html latex example
kind text html latex
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manufacturer text html latex
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ncol text html latex
oligo-package text html latex example
platform text html latex
platformDesign-class text html latex example
plotDensity text html latex
pmAllele text html latex
pmPosition text html latex
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rma text html latex
sequenceDesignMatrix text html latex
snprma text html latex
snprmaSummaries text html latex
** building package indices ...
* DONE (oligo)