Package: limma

Version: 3.4.5

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings limma_3.4.5.tar.gz

StartedAt: 2010-10-04 17:35:45 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:37:34 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 108.8 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/limma.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* 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

* install options are ' --no-html'

* installing *source* package ‘limma’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/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-2.6-bioc/meat/limma.Rcheck/limma/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 ppc -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-2.6-bioc/meat/limma.Rcheck/limma/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -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 x86_64 -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-2.6-bioc/meat/limma.Rcheck/limma/libs/x86_64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (limma)

name	user	system	elapsed
LargeDataObject	0	0	0
PrintLayout	0.001	0.000	0.001
TestResults	0.001	0.000	0.000
alias2Symbol	3.619	0.192	3.885
arrayWeights	0.009	0.001	0.010
arrayWeightsQuick	0	0	0
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.002
avereps	0.002	0.001	0.003
backgroundcorrect	0.024	0.003	0.027
blockDiag	0.001	0.001	0.002
cbind	0.090	0.002	0.093
channel2M	0.003	0.001	0.002
classifytests	0.005	0.001	0.005
contrasts.fit	0.044	0.004	0.048
controlStatus	0.016	0.002	0.018
convest	2.645	0.016	2.670
dim	0.003	0.000	0.003
dupcor	0	0	0
ebayes	0.017	0.000	0.019
genas	0.136	0.003	0.139
geneSetTest	0.009	0.000	0.010
getSpacing	0.001	0.000	0.002
getlayout	0.001	0.000	0.001
heatdiagram	0.007	0.000	0.008
helpMethods	0	0	0
imageplot	0.048	0.005	0.055
intraspotCorrelation	0.001	0.000	0.000
isfullrank	0.002	0.000	0.002
isnumeric	0.002	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.003	0.001	0.005
lm.series	0.000	0.000	0.001
lmFit	2.555	0.021	2.600
lmscFit	0.012	0.002	0.014
loessfit	0.515	0.005	0.525
ma3x3	0.003	0.000	0.003
makeContrasts	0.002	0.000	0.002
makeunique	0.002	0.001	0.002
merge	0.014	0.001	0.015
mergeScansRG	0.001	0.000	0.000
modelMatrix	0.004	0.000	0.004
modifyWeights	0.001	0.001	0.001
neqc	0.000	0.000	0.001
normalizeMedianAbsValues	0.001	0.001	0.002
normalizeRobustSpline	0.003	0.001	0.005
normalizeWithinArrays	0.000	0.000	0.001
normalizebetweenarrays	0.005	0.000	0.005
normalizeprintorder	0.004	0.001	0.005
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0.000	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.019	0.001	0.020
plotMDS	0.020	0.001	0.021
plotRLDF	0.499	0.052	0.549
plotma	0.020	0.001	0.021
poolvar	0.002	0.000	0.002
printorder	0.025	0.009	0.035
printtipWeights	0.013	0.001	0.014
propexpr	0.000	0.000	0.001
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.000	0.003
qualwt	0.000	0.001	0.000
read.ilmn	0.001	0.000	0.000
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0.000	0.000	0.001
readgal	0.001	0.000	0.001
removeext	0.001	0.000	0.001
roast	0.122	0.011	0.134
romer	0.693	0.024	0.724
selectmodel	0.048	0.000	0.049
squeezeVar	0.001	0.000	0.002
strsplit2	0.001	0.001	0.001
subsetting	0.022	0.001	0.023
targetsA2C	0.011	0.000	0.011
topRomer	0	0	0
toptable	0	0	0
trigammainverse	0.000	0.001	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.050	0.001	0.051
volcanoplot	0	0	0
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.001	0.001