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Package 224/419HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.6.9
Gordon Smyth
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/limma
Last Changed Rev: 51155 / Revision: 54281
Last Changed Date: 2010-11-30 19:05:51 -0800 (Tue, 30 Nov 2010)
lamb2 Linux (openSUSE 11.2) / 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 

Summary

Package: limma
Version: 3.6.9
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.6.9.tar.gz
StartedAt: 2011-03-31 06:28:06 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:30:36 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 150.5 seconds
RetCode: 0
Status:  OK 
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/limma.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.6.9’
* 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 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 package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

limma.Rcheck/00install.out:

* installing *source* package ‘limma’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c normexp.c -o normexp.o
normexp.c: In function ‘fit_saddle_nelder_mead’:
normexp.c:153: warning: floating constant exceeds range of ‘double’
normexp.c:167: warning: ISO C forbids passing argument 9 of ‘nmmin’ between function pointer and ‘void *’
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o limma.so normexp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/limma.Rcheck/limma/libs/i386
** 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:

nameusersystemelapsed
LargeDataObject000
PrintLayout0.0010.0000.001
TestResults000
alias2Symbol3.6780.1733.954
arrayWeights0.0100.0010.011
arrayWeightsQuick0.0000.0000.001
asMatrixWeights0.0010.0000.001
auROC0.0010.0000.002
avearrays0.0020.0000.002
avereps0.0020.0000.002
backgroundcorrect0.0140.0010.015
blockDiag0.0010.0000.001
cbind0.0120.0020.014
channel2M0.0020.0000.003
classifytests0.0160.0010.016
contrasts.fit0.0380.0030.041
controlStatus0.0120.0000.014
convest2.5930.0172.653
dim0.0030.0000.003
dupcor0.0010.0000.001
ebayes0.0160.0010.017
genas0.1300.0060.156
geneSetTest0.0090.0010.009
getSpacing0.0010.0000.002
getlayout0.0000.0000.001
heatdiagram0.0080.0010.009
helpMethods0.0000.0000.001
imageplot0.0470.0050.052
intraspotCorrelation0.0000.0010.000
isfullrank0.0010.0000.001
isnumeric0.0020.0010.002
kooperberg0.0000.0000.001
limmaUsersGuide0.0030.0010.005
lm.series0.0010.0000.000
lmFit2.3190.0232.401
lmscFit0.0130.0010.015
loessfit0.4860.0050.508
ma3x30.0020.0010.003
makeContrasts0.0020.0000.002
makeunique0.0020.0000.002
merge0.0110.0010.012
mergeScansRG0.0000.0010.001
modelMatrix0.0040.0000.004
modifyWeights0.0010.0010.002
nec000
neqc000
normalizeMedianAbsValues0.0010.0000.001
normalizeRobustSpline0.0040.0010.004
normalizeVSN0.6630.0350.725
normalizeWithinArrays0.0000.0000.001
normalizebetweenarrays0.0040.0000.005
normalizeprintorder0.0040.0010.005
normexpfit0.0030.0000.003
normexpfitcontrol0.0000.0000.001
normexpsignal000
plotDensities0.0190.0010.021
plotMDS0.0200.0040.023
plotRLDF0.5970.0310.655
plotma0.0190.0010.020
poolvar0.0020.0010.002
printorder0.0230.0090.032
printtipWeights0.0130.0010.014
propexpr000
protectMetachar0.0000.0000.001
qqt0.0020.0000.003
qualwt0.0010.0010.001
read.ilmn000
read.maimages0.0010.0000.000
readImaGeneHeader0.0000.0010.000
readgal000
removeext0.0000.0000.001
roast0.1140.0130.129
romer0.6310.0090.658
selectmodel0.0380.0010.038
squeezeVar0.0020.0000.002
strsplit20.0010.0010.002
subsetting0.0070.0010.007
targetsA2C0.010.000.01
topRomer0.0010.0000.000
toptable000
trigammainverse0.0010.0000.000
trimWhiteSpace0.0010.0010.000
uniquegenelist0.0010.0000.001
unwrapdups0.0010.0010.002
venn0.0480.0010.049
volcanoplot0.0010.0000.000
weightedmedian0.0010.0000.001
zscore0.0010.0010.001