Package: limma

Version: 3.10.3

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.10.3.tar.gz

StartedAt: 2012-03-24 02:08:10 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:10:33 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 143.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: limma.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.10.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... WARNING
Codoc mismatches from documentation object 'normalizeCyclicLoess':
normalizeCyclicLoess
  Code: function(x, weights = NULL, span = 0.7, iterations = 3, method
                 = "fast")
  Docs: function(x, weights = NULL, span = 0.7, iterations = 3, method
                 = "pairs")
  Mismatches in argument default values:
    Name: 'method' Code: "fast" Docs: "pairs"

Codoc mismatches from documentation object 'normalizeBetweenArrays':
normalizeBetweenArrays
  Code: function(object, method = NULL, targets = NULL, cyclic.method =
                 "fast", ...)
  Docs: function(object, method = NULL, targets = NULL, cyclic.method =
                 "pairs", ...)
  Mismatches in argument default values:
    Name: 'cyclic.method' Code: "fast" Docs: "pairs"

* 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... 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
  '/Users/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck/00check.log'
for details

* installing *source* package 'limma' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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-2.9-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)

name	user	system	elapsed
LargeDataObject	0.000	0.000	0.001
PrintLayout	0	0	0
TestResults	0	0	0
alias2Symbol	6.856	0.245	7.758
arrayWeights	0.003	0.001	0.005
arrayWeightsQuick	0	0	0
asMatrixWeights	0.001	0.000	0.002
auROC	0.001	0.001	0.002
avearrays	0.002	0.000	0.002
avereps	0.001	0.000	0.001
backgroundcorrect	0.012	0.001	0.013
blockDiag	0.001	0.000	0.001
cbind	0.009	0.001	0.009
channel2M	0.003	0.000	0.002
classifytests	0.003	0.001	0.004
contrasts.fit	0.037	0.006	0.113
controlStatus	0.028	0.002	0.030
convest	2.842	0.020	2.926
dim	0.002	0.001	0.003
dupcor	0	0	0
ebayes	0.018	0.002	0.020
genas	0.092	0.001	0.094
geneSetTest	0.011	0.002	0.013
getSpacing	0.000	0.000	0.001
getlayout	0	0	0
heatdiagram	0.003	0.001	0.004
helpMethods	0	0	0
imageplot	0.064	0.005	0.070
intraspotCorrelation	0	0	0
isfullrank	0.001	0.000	0.002
isnumeric	0.001	0.001	0.001
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.002	0.001	0.003
lm.series	0.000	0.000	0.001
lmFit	1.134	0.021	1.201
lmscFit	0.004	0.001	0.005
loessfit	0.764	0.007	0.800
ma3x3	0.002	0.001	0.002
makeContrasts	0.001	0.000	0.001
makeunique	0.001	0.001	0.002
merge	0.009	0.001	0.009
mergeScansRG	0	0	0
modelMatrix	0.002	0.001	0.005
modifyWeights	0.001	0.000	0.001
nec	0.000	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.003	0.000	0.003
normalizeVSN	0.629	0.047	0.685
normalizebetweenarrays	0.004	0.001	0.004
normalizeprintorder	0	0	0
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.000	0.000	0.001
plotMDS	0.037	0.003	0.040
plotRLDF	0.672	0.028	0.724
plotma	0.022	0.003	0.027
poolvar	0.001	0.000	0.001
printorder	0.018	0.009	0.027
printtipWeights	0.001	0.001	0.000
propexpr	0.001	0.000	0.000
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.001	0.004
qualwt	0.000	0.000	0.001
read.ilmn	0	0	0
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0.000	0.000	0.001
removeext	0.001	0.000	0.000
roast	0.058	0.005	0.064
romer	0.539	0.011	0.562
selectmodel	0.031	0.000	0.034
squeezeVar	0.001	0.000	0.002
strsplit2	0.001	0.001	0.001
subsetting	0.006	0.001	0.007
targetsA2C	0.008	0.001	0.009
topRomer	0	0	0
toptable	0	0	0
trigammainverse	0.001	0.000	0.000
trimWhiteSpace	0	0	0
uniquegenelist	0.000	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.039	0.002	0.051
volcanoplot	0	0	0
weightedmedian	0.001	0.000	0.000
zscore	0.001	0.000	0.002