BioC 2.6: CHECK report for limma on gewurz

Package: limma

Version: 3.4.5

Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings limma_3.4.5.tar.gz

StartedAt: 2010-10-04 17:26:20 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:27:49 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 88.3 seconds

RetCode: 0

Status: OK

CheckDir: limma.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/limma.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.4.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'limma' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 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 Rd contents ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...896,897c896,897
< mu+alpha    0.3333333 3.333333e-01  5.551115e-17
< mu+beta    -0.3333333 5.551115e-17  3.333333e-01
---
> mu+alpha    0.3333333  3.333333e-01 -1.821460e-17
> mu+beta    -0.3333333 -1.821460e-17  3.333333e-01
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'limma' ...
** libs
  making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -std=gnu99 -c normexp.c -o normexp.o
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153: warning: floating constant exceeds range of 'double'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/limma.Rcheck/limma/libs/x64
  ... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (limma)

name	user	system	elapsed
LargeDataObject	0	0	0
PrintLayout	0	0	0
TestResults	0	0	0
alias2Symbol	3.31	0.06	3.96
arrayWeights	0.02	0.00	0.02
arrayWeightsQuick	0	0	0
asMatrixWeights	0	0	0
auROC	0	0	0
avereps	0	0	0
backgroundcorrect	0.02	0.00	0.01
blockDiag	0	0	0
cbind	0.01	0.00	0.02
channel2M	0	0	0
classifytests	0	0	0
contrasts.fit	0.03	0.00	0.04
controlStatus	0.01	0.00	0.01
convest	2.05	0.00	2.05
dim	0	0	0
dupcor	0	0	0
ebayes	0.01	0.00	0.02
genas	0.08	0.02	0.09
geneSetTest	0.01	0.00	0.01
getSpacing	0	0	0
getlayout	0	0	0
heatdiagram	0	0	0
helpMethods	0	0	0
imageplot	0.06	0.00	0.07
intraspotCorrelation	0	0	0
isfullrank	0	0	0
isnumeric	0	0	0
kooperberg	0	0	0
limmaUsersGuide	0	0	0
lm.series	0	0	0
lmFit	1.78	0.03	1.82
lmscFit	0	0	0
loessfit	0.48	0.00	0.48
ma3x3	0	0	0
makeContrasts	0	0	0
makeunique	0	0	0
merge	0.02	0.00	0.02
mergeScansRG	0	0	0
modelMatrix	0	0	0
modifyWeights	0	0	0
neqc	0	0	0
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0	0	0
normalizeWithinArrays	0	0	0
normalizebetweenarrays	0.02	0.00	0.01
normalizeprintorder	0	0	0
normexpfit	0	0	0
normexpfitcontrol	0	0	0
normexpsignal	0	0	0
plotDensities	0.01	0.00	0.02
plotMDS	0.02	0.00	0.01
plotRLDF	0.56	0.00	0.56
plotma	0.02	0.00	0.02
poolvar	0	0	0
printorder	0.01	0.00	0.02
printtipWeights	0	0	0
propexpr	0	0	0
protectMetachar	0	0	0
qqt	0	0	0
qualwt	0	0	0
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeext	0	0	0
roast	0.10	0.00	0.09
romer	0.46	0.00	0.47
selectmodel	0.04	0.00	0.03
squeezeVar	0	0	0
strsplit2	0.01	0.00	0.02
subsetting	0	0	0
targetsA2C	0	0	0
topRomer	0	0	0
toptable	0	0	0
trigammainverse	0	0	0
trimWhiteSpace	0	0	0
uniquegenelist	0	0	0
unwrapdups	0	0	0
venn	0.04	0.00	0.05
volcanoplot	0	0	0
weightedmedian	0	0	0
zscore	0	0	0

Summary

Command output