BioC 2.9: CHECK report for limma on moscato1

Package: limma

Version: 3.9.11

Command: mkdir limma.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=limma.buildbin-libdir limma_3.9.11.tar.gz >limma-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=limma.buildbin-libdir --install="check:limma-install.out" --force-multiarch --no-vignettes --timings limma_3.9.11.tar.gz && mv limma.buildbin-libdir/* limma.Rcheck/ && rmdir limma.buildbin-libdir

StartedAt: 2011-07-07 05:29:21 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:31:52 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 150.7 seconds

RetCode: 0

Status: OK

CheckDir: limma.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* 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 '3.9.11'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'marray'
* checking tests ...
** running tests for arch 'i386'
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ... OK
 OK
** running tests for arch 'x64'
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...920,921c920,921
< 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  9.280771e-17
> mu+beta    -0.3333333 9.280771e-17  3.333333e-01
 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


install for i386

* installing *source* package 'limma' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/limma.buildbin-libdir/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

add DLL for x64

* installing *source* package 'limma' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -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'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/limma.buildbin-libdir/limma/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'limma' as limma_3.9.11.zip

* DONE (limma)

name	user	system	elapsed
LargeDataObject	0	0	0
PrintLayout	0	0	0
TestResults	0	0	0
alias2Symbol	2.54	0.08	2.76
arrayWeights	0.02	0.00	0.02
arrayWeightsQuick	0	0	0
asMatrixWeights	0	0	0
auROC	0	0	0
avearrays	0	0	0
avereps	0	0	0
backgroundcorrect	0.02	0.00	0.02
blockDiag	0	0	0
cbind	0	0	0
channel2M	0	0	0
classifytests	0.01	0.00	0.01
contrasts.fit	0.03	0.00	0.03
controlStatus	0	0	0
convest	1.42	0.00	1.42
dim	0.02	0.00	0.02
dupcor	0	0	0
ebayes	0	0	0
genas	0.08	0.00	0.08
geneSetTest	0	0	0
getSpacing	0	0	0
getlayout	0	0	0
heatdiagram	0	0	0
helpMethods	0	0	0
imageplot	0.06	0.00	0.06
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	1.33	0.00	1.62
lmscFit	0	0	0
loessfit	0.45	0.00	0.45
ma3x3	0	0	0
makeContrasts	0	0	0
makeunique	0	0	0
merge	0.02	0.00	0.02
mergeScansRG	0	0	0
modelMatrix	0	0	0
modifyWeights	0	0	0
nec	0	0	0
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0.00	0.02	0.01
normalizeVSN	0.40	0.05	0.84
normalizebetweenarrays	0	0	0
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	0.02	0.00	0.01
plotRLDF	0.44	0.00	0.44
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	0.01	0.00	0.02
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	0.05	0.00	0.04
romer	0.42	0.00	0.43
selectmodel	0.03	0.00	0.03
squeezeVar	0	0	0
strsplit2	0	0	0
subsetting	0.02	0.00	0.01
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	0.03	0.02	0.05
volcanoplot	0	0	0
weightedmedian	0	0	0
zscore	0	0	0

Summary

Command output