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Package 250/462HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.9.2
Gordon Smyth
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limma
Last Changed Rev: 55291 / Revision: 55359
Last Changed Date: 2011-05-05 20:32:59 -0700 (Thu, 05 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

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

Command output

* 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

limma.Rcheck/00install.out:

* 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)

limma.Rcheck/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject000
PrintLayout000
TestResults000
alias2Symbol2.680.113.37
arrayWeights000
arrayWeightsQuick000
asMatrixWeights000
auROC000
avearrays000
avereps000
backgroundcorrect0.010.000.01
blockDiag000
cbind0.020.000.02
channel2M000
classifytests0.010.000.01
contrasts.fit0.030.000.03
controlStatus0.020.000.02
convest2.660.002.67
dim000
dupcor000
ebayes0.010.000.02
genas0.100.000.12
geneSetTest0.010.000.02
getSpacing000
getlayout000
heatdiagram000
helpMethods000
imageplot0.100.000.09
intraspotCorrelation000
isfullrank000
isnumeric000
kooperberg000
limmaUsersGuide0.010.000.02
lm.series000
lmFit1.590.001.65
lmscFit000
loessfit0.450.000.45
ma3x3000
makeContrasts000
makeunique000
merge000
mergeScansRG0.020.000.02
modelMatrix000
modifyWeights000
nec000
normalizeMedianAbsValues000
normalizeRobustSpline000
normalizeVSN0.470.000.47
normalizebetweenarrays0.000.020.01
normalizeprintorder000
normexpfit000
normexpfitcontrol000
normexpfitdetectionp000
normexpsignal000
plotDensities000
plotMDS0.010.000.02
plotRLDF0.570.000.56
plotma0.010.000.02
poolvar000
printorder0.020.000.01
printtipWeights000
propexpr000
protectMetachar000
qqt000
qualwt000
read.ilmn000
read.maimages000
readImaGeneHeader000
readgal000
removeext000
roast0.070.000.06
romer0.460.000.47
selectmodel0.040.000.03
squeezeVar000
strsplit2000
subsetting000
targetsA2C0.010.000.02
topRomer000
toptable000
trigammainverse000
trimWhiteSpace000
uniquegenelist000
unwrapdups000
venn0.050.000.04
volcanoplot000
weightedmedian000
zscore000