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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: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.9.2.tar.gz
StartedAt: 2011-05-09 13:02:02 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 13:03:44 -0700 (Mon, 09 May 2011)
EllapsedTime: 102.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: limma.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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 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’ ...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

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck/00check.log’
for details

limma.Rcheck/00install.out:

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck/limma/libs
** 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
alias2Symbol2.8120.0642.915
arrayWeights0.0040.0040.005
arrayWeightsQuick000
asMatrixWeights0.0000.0000.001
auROC000
avearrays0.0000.0000.001
avereps0.0000.0000.001
backgroundcorrect0.0240.0000.026
blockDiag0.0040.0000.001
cbind0.0080.0000.007
channel2M0.0000.0000.001
classifytests0.0040.0000.003
contrasts.fit0.0280.0000.026
controlStatus0.0080.0000.008
convest3.1720.0043.178
dim0.0000.0000.001
dupcor000
ebayes0.0080.0000.011
genas0.0920.0000.092
geneSetTest0.0040.0000.006
getSpacing0.0000.0000.001
getlayout000
heatdiagram0.0040.0000.004
helpMethods000
imageplot0.0280.0040.034
intraspotCorrelation000
isfullrank000
isnumeric0.0000.0000.001
kooperberg000
limmaUsersGuide0.0200.0000.021
lm.series000
lmFit1.5800.0081.599
lmscFit0.0040.0000.005
loessfit0.6160.0000.619
ma3x30.0000.0000.002
makeContrasts0.0000.0000.001
makeunique0.0000.0000.001
merge0.0080.0000.007
mergeScansRG000
modelMatrix0.0040.0000.002
modifyWeights0.0000.0000.001
nec0.0000.0000.001
normalizeMedianAbsValues0.0000.0000.001
normalizeRobustSpline0.0000.0000.002
normalizeVSN0.4040.0160.420
normalizebetweenarrays0.0040.0000.002
normalizeprintorder000
normexpfit0.0040.0000.002
normexpfitcontrol000
normexpfitdetectionp0.0000.0000.001
normexpsignal000
plotDensities000
plotMDS0.0120.0000.015
plotRLDF0.7680.0160.787
plotma0.0120.0000.013
poolvar0.0000.0000.001
printorder0.0120.0040.016
printtipWeights0.0000.0000.001
propexpr000
protectMetachar0.0000.0000.001
qqt0.0040.0000.002
qualwt000
read.ilmn000
read.maimages0.0040.0000.001
readImaGeneHeader000
readgal000
removeext000
roast0.0600.0000.059
romer0.5000.0000.498
selectmodel0.0520.0000.052
squeezeVar0.0040.0000.001
strsplit20.0000.0000.001
subsetting0.0040.0000.004
targetsA2C0.0080.0000.006
topRomer000
toptable000
trigammainverse000
trimWhiteSpace000
uniquegenelist0.0000.0000.001
unwrapdups000
venn0.0320.0000.032
volcanoplot000
weightedmedian000
zscore000