oligo 1.3.18
Benilton Carvalho
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo | | Last Changed Rev: 30606 / Revision: 30951 | | Last Changed Date: 2008-03-21 01:53:31 -0700 (Fri, 21 Mar 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | [ WARNINGS ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/oligo.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ASCII
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.3.18'
* 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
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'
justCRLMM: no visible binding for global variable 'maleIndex'
justCRLMM2: no visible binding for global variable 'maleIndex'
justCRLMMv2: no visible binding for global variable 'maleIndex'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'kind' and siglist 'AffyGeneSTPDInfo'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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
WARNING: There was 1 warning, see
/Users/biocbuild/bbs-2.2-bioc/meat/oligo.Rcheck/00check.log
for details
* Installing *source* package 'oligo' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -Wall -c baseProfile.c -o baseProfile.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -Wall -c basecontent.c -o basecontent.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -Wall -c rma2.c -o rma2.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -Wall -c rma_background2.c -o rma_background2.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -Wall -c rma_common.c -o rma_common.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma2.c -o rma2.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma2.c -o rma2.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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
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
PDInfo-methods text html latex
Sequences-methods text html latex
SnpQSet-class text html latex example
SnpQSet-methods text html latex
SnpSetExtensions-class text html latex example
basecontent text html latex example
boxplot text html latex
chromosome text html latex
crlmm text html latex example
featureIndex text html latex
featureNames-methods text html latex
genomeBuild text html latex
getCrlmmSummaries text html latex
getPlatformDesign text html latex
hist text html latex
image text html latex
internals text html latex
justSNPRMA text html latex example
kind text html latex
list.celfiles text html latex
manufacturer text html latex
nProbes text html latex
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
pmStrand text html latex
probeNames text html latex
read.celfiles text html latex
read.xysfiles text html latex
readSummaries text html latex
rma text html latex
sequenceDesignMatrix text html latex
snprma text html latex
snprmaSummaries text html latex
** building package indices ...
* DONE (oligo)