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| Package 136/214 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
oligo1.0.2Benilton CarvalhoLast Changed Date: 2007-04-25 11:40:29 -0700 Last Changed Rev: 24277 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | |
| wellington | Linux (SUSE 9.2) | i686 | OK | WARNINGS | ||
| churchill | Solaris 2.9 | sparc | OK | WARNINGS | ||
| lemming | Windows Server 2003 (32-bit) | x64 | OK | WARNINGS | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | WARNINGS | OK | |
| derby | Mac OS X (10.4.9) | i686 | OK | [ WARNINGS ] |
| Package: oligo |
| Version: 1.0.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check oligo_1.0.2.tar.gz |
| RetCode: 0 |
| Time: 85.7 seconds |
| Status: WARNINGS |
| CheckDir: oligo.Rcheck |
| Warnings: 1 |
* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.0-bioc/meat/oligo.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.0.2'
* 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'crlmm':
crlmm
Code: function(object, correction = NULL, recalibrate = TRUE,
minPforCalls = c(0.5, 0.1, 0.5), verbose = TRUE,
correctionFile = NULL)
Docs: function(object, correction = NULL, recalibrate = TRUE,
minLLRforCalls = c(25, 5, 25), verbose = TRUE,
correctionFile = NULL)
Argument names in code not in docs:
minPforCalls
Argument names in docs not in code:
minLLRforCalls
Mismatches in argument names:
Position: 4 Code: minPforCalls Docs: minLLRforCalls
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... 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
* creating oligo-manual.tex ... OK
* checking oligo-manual.tex ... OK
WARNING: There was 1 warning, see
/Users/biocbuild/bbs-2.0-bioc/meat/oligo.Rcheck/00check.log
for details
oligo.Rcheck/00install.out:
* Installing *source* package 'oligo' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=nocona -c M_estimator2.c -o M_estimator2.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=nocona -c baseProfile.c -o baseProfile.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=nocona -c basecontent.c -o basecontent.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so M_estimator2.o baseProfile.o basecontent.o -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c M_estimator2.c -o M_estimator2.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c baseProfile.c -o baseProfile.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c basecontent.c -o basecontent.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so M_estimator2.o baseProfile.o basecontent.o -F/Library/Frameworks/R.framework/.. -framework R
** R
** inst
** save image
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: affyio
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: BufferedMatrix
Loading required package: BufferedMatrixMethods
** help
>>> 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 example
IntensityMatrix-methods text html latex example
PDInfo-class text html latex example
PDInfo-methods text html latex example
Sequences-methods text html latex example
SnpCallSet-methods text html latex example
SnpCopyNumberSet-methods text html latex example
SnpQSet-class text html latex example
SnpQSet-methods text html latex example
SnpSetExtensions-class text html latex example
basecontent text html latex example
boxplot text html latex example
chromosome text html latex example
crlmm text html latex example
featureIndex text html latex example
genomeBuild text html latex example
getPlatformDesign text html latex example
hist text html latex example
image text html latex example
internals text html latex example
kind text html latex example
list.celfiles text html latex example
manufacturer text html latex example
nProbes text html latex example
ncol text html latex example
oligo-package text html latex example
platform text html latex example
platformDesign-class text html latex example
plotDensity text html latex example
pmAllele text html latex example
pmPosition text html latex example
pmStrand text html latex example
probeNames text html latex example
read.celfiles text html latex example
read.xysfiles text html latex example
rma text html latex example
sequenceDesignMatrix text html latex example
snprma text html latex example
snprmaSummaries text html latex example
** building package indices ...
* DONE (oligo)