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Package 209/389 | Hostname | OS / Arch | BUILD | CHECK | BUILD BIN | ||||
limma 3.4.5 Gordon Smyth
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |||||
liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK | |||||
gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK | |||||
pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
Package: limma |
Version: 3.4.5 |
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.4.5.tar.gz |
StartedAt: 2010-10-04 18:20:14 -0700 (Mon, 04 Oct 2010) |
EndedAt: 2010-10-04 18:21:30 -0700 (Mon, 04 Oct 2010) |
EllapsedTime: 75.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: limma.Rcheck |
Warnings: 0 |
* checking for working pdflatex ... OK * using log directory '/loc/home/biocbuild/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 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 ... 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
limma.Rcheck/00install.out:
* install options are ' --no-html' * installing *source* package 'limma' ... ** libs gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o normexp.c: In function 'fit_saddle_nelder_mead': normexp.c:153: warning: floating constant exceeds range of 'double' gcc -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/limma.Rcheck/limma/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (limma)
limma.Rcheck/limma-Ex.timings:
name | user | system | elapsed | |
LargeDataObject | 0 | 0 | 0 | |
PrintLayout | 0 | 0 | 0 | |
TestResults | 0.000 | 0.000 | 0.001 | |
alias2Symbol | 2.852 | 0.100 | 3.097 | |
arrayWeights | 0.004 | 0.000 | 0.003 | |
arrayWeightsQuick | 0 | 0 | 0 | |
asMatrixWeights | 0.000 | 0.000 | 0.001 | |
auROC | 0.000 | 0.004 | 0.000 | |
avereps | 0.000 | 0.000 | 0.002 | |
backgroundcorrect | 0.016 | 0.000 | 0.019 | |
blockDiag | 0.000 | 0.000 | 0.001 | |
cbind | 0.008 | 0.000 | 0.009 | |
channel2M | 0.000 | 0.000 | 0.002 | |
classifytests | 0.004 | 0.000 | 0.003 | |
contrasts.fit | 0.048 | 0.000 | 0.048 | |
controlStatus | 0.008 | 0.000 | 0.009 | |
convest | 2.356 | 0.000 | 2.357 | |
dim | 0.000 | 0.000 | 0.002 | |
dupcor | 0 | 0 | 0 | |
ebayes | 0.012 | 0.000 | 0.013 | |
genas | 0.076 | 0.008 | 0.082 | |
geneSetTest | 0.008 | 0.000 | 0.006 | |
getSpacing | 0.000 | 0.000 | 0.001 | |
getlayout | 0 | 0 | 0 | |
heatdiagram | 0.000 | 0.000 | 0.002 | |
helpMethods | 0 | 0 | 0 | |
imageplot | 0.032 | 0.000 | 0.034 | |
intraspotCorrelation | 0 | 0 | 0 | |
isfullrank | 0.000 | 0.000 | 0.001 | |
isnumeric | 0.000 | 0.000 | 0.001 | |
kooperberg | 0 | 0 | 0 | |
limmaUsersGuide | 0.000 | 0.000 | 0.002 | |
lm.series | 0 | 0 | 0 | |
lmFit | 1.824 | 0.012 | 1.836 | |
lmscFit | 0.004 | 0.000 | 0.004 | |
loessfit | 0.596 | 0.004 | 0.646 | |
ma3x3 | 0.000 | 0.000 | 0.001 | |
makeContrasts | 0.000 | 0.000 | 0.001 | |
makeunique | 0.000 | 0.000 | 0.001 | |
merge | 0.008 | 0.000 | 0.009 | |
mergeScansRG | 0.000 | 0.000 | 0.001 | |
modelMatrix | 0.000 | 0.000 | 0.002 | |
modifyWeights | 0.000 | 0.000 | 0.001 | |
neqc | 0 | 0 | 0 | |
normalizeMedianAbsValues | 0.000 | 0.000 | 0.001 | |
normalizeRobustSpline | 0.000 | 0.000 | 0.002 | |
normalizeWithinArrays | 0 | 0 | 0 | |
normalizebetweenarrays | 0.000 | 0.000 | 0.003 | |
normalizeprintorder | 0.000 | 0.000 | 0.002 | |
normexpfit | 0.004 | 0.000 | 0.002 | |
normexpfitcontrol | 0 | 0 | 0 | |
normexpsignal | 0 | 0 | 0 | |
plotDensities | 0.004 | 0.004 | 0.005 | |
plotMDS | 0.012 | 0.000 | 0.015 | |
plotRLDF | 0.668 | 0.008 | 0.676 | |
plotma | 0.012 | 0.000 | 0.014 | |
poolvar | 0.000 | 0.000 | 0.001 | |
printorder | 0.012 | 0.004 | 0.017 | |
printtipWeights | 0.000 | 0.000 | 0.003 | |
propexpr | 0.000 | 0.000 | 0.001 | |
protectMetachar | 0.000 | 0.000 | 0.001 | |
qqt | 0.004 | 0.000 | 0.001 | |
qualwt | 0 | 0 | 0 | |
read.ilmn | 0 | 0 | 0 | |
read.maimages | 0 | 0 | 0 | |
readImaGeneHeader | 0 | 0 | 0 | |
readgal | 0 | 0 | 0 | |
removeext | 0.000 | 0.000 | 0.001 | |
roast | 0.092 | 0.000 | 0.092 | |
romer | 0.492 | 0.000 | 0.493 | |
selectmodel | 0.028 | 0.000 | 0.030 | |
squeezeVar | 0.000 | 0.000 | 0.001 | |
strsplit2 | 0.000 | 0.000 | 0.001 | |
subsetting | 0.004 | 0.000 | 0.003 | |
targetsA2C | 0.008 | 0.000 | 0.007 | |
topRomer | 0 | 0 | 0 | |
toptable | 0.000 | 0.000 | 0.001 | |
trigammainverse | 0 | 0 | 0 | |
trimWhiteSpace | 0 | 0 | 0 | |
uniquegenelist | 0 | 0 | 0 | |
unwrapdups | 0 | 0 | 0 | |
venn | 0.040 | 0.004 | 0.045 | |
volcanoplot | 0 | 0 | 0 | |
weightedmedian | 0 | 0 | 0 | |
zscore | 0.000 | 0.004 | 0.000 | |