Package: limma

Version: 3.9.2

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings limma_3.9.2.tar.gz

StartedAt: 2011-05-09 14:18:58 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:20:51 -0700 (Mon, 09 May 2011)

EllapsedTime: 112.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: limma.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.9.2'
* 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 installed package size ... 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 ... WARNING
Undocumented arguments in documentation object 'plotMDS'
  'xlab' 'ylab'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: 'sma'
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'marray'
* checking tests ...
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ... OK
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck/00check.log'
for details

* installing *source* package 'limma' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c normexp.c -o normexp.o
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153:3: warning: floating constant exceeds range of 'double'
gcc -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'limma.Rnw' 
** 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	2.68	0.11	3.37
arrayWeights	0	0	0
arrayWeightsQuick	0	0	0
asMatrixWeights	0	0	0
auROC	0	0	0
avearrays	0	0	0
avereps	0	0	0
backgroundcorrect	0.01	0.00	0.01
blockDiag	0	0	0
cbind	0.02	0.00	0.02
channel2M	0	0	0
classifytests	0.01	0.00	0.01
contrasts.fit	0.03	0.00	0.03
controlStatus	0.02	0.00	0.02
convest	2.66	0.00	2.67
dim	0	0	0
dupcor	0	0	0
ebayes	0.01	0.00	0.02
genas	0.10	0.00	0.12
geneSetTest	0.01	0.00	0.02
getSpacing	0	0	0
getlayout	0	0	0
heatdiagram	0	0	0
helpMethods	0	0	0
imageplot	0.10	0.00	0.09
intraspotCorrelation	0	0	0
isfullrank	0	0	0
isnumeric	0	0	0
kooperberg	0	0	0
limmaUsersGuide	0.01	0.00	0.02
lm.series	0	0	0
lmFit	1.59	0.00	1.65
lmscFit	0	0	0
loessfit	0.45	0.00	0.45
ma3x3	0	0	0
makeContrasts	0	0	0
makeunique	0	0	0
merge	0	0	0
mergeScansRG	0.02	0.00	0.02
modelMatrix	0	0	0
modifyWeights	0	0	0
nec	0	0	0
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0	0	0
normalizeVSN	0.47	0.00	0.47
normalizebetweenarrays	0.00	0.02	0.01
normalizeprintorder	0	0	0
normexpfit	0	0	0
normexpfitcontrol	0	0	0
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0	0	0
plotMDS	0.01	0.00	0.02
plotRLDF	0.57	0.00	0.56
plotma	0.01	0.00	0.02
poolvar	0	0	0
printorder	0.02	0.00	0.01
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	0.07	0.00	0.06
romer	0.46	0.00	0.47
selectmodel	0.04	0.00	0.03
squeezeVar	0	0	0
strsplit2	0	0	0
subsetting	0	0	0
targetsA2C	0.01	0.00	0.02
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	0.05	0.00	0.04
volcanoplot	0	0	0
weightedmedian	0	0	0
zscore	0	0	0