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BioC 2.13: CHECK report for limma on moscato1

This page was generated on 2014-04-05 09:48:59 -0700 (Sat, 05 Apr 2014).

Package 395/750HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.18.13
Gordon Smyth
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/limma
Last Changed Rev: 86520 / Revision: 88450
Last Changed Date: 2014-02-17 18:15:35 -0800 (Mon, 17 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: limma
Version: 3.18.13
Command: rm -rf limma.buildbin-libdir && mkdir limma.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=limma.buildbin-libdir limma_3.18.13.tar.gz >limma-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=limma.buildbin-libdir --install="check:limma-install.out" --force-multiarch --no-vignettes --timings limma_3.18.13.tar.gz && mv limma.buildbin-libdir/* limma.Rcheck/ && rmdir limma.buildbin-libdir
StartedAt: 2014-04-05 04:49:33 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:51:55 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 142.1 seconds
RetCode: 0
Status:  OK  
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/limma.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.18.13'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'limma' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... OK
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/limma.buildbin-libdir/limma/libs/i386/limma.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/limma.buildbin-libdir/limma/libs/x64/limma.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [12s] OK
** running examples for arch 'x64' ... [12s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'limma-Tests.R' [2s]
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ... OK
 [2s] OK
** running tests for arch 'x64'
  Running 'limma-Tests.R' [2s]
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...631,636c631,636
<  Min.   :-5.88044   Min.   :-5.66985  
<  1st Qu.:-1.18483   1st Qu.:-1.57014  
<  Median :-0.21632   Median : 0.04823  
<  Mean   : 0.03487   Mean   :-0.05481  
<  3rd Qu.: 1.49669   3rd Qu.: 1.45113  
<  Max.   : 7.07324   Max.   : 6.19744  
---
>  Min.   :-5.85163   Min.   :-5.69877  
>  1st Qu.:-1.18482   1st Qu.:-1.55421  
>  Median :-0.21631   Median : 0.06267  
>  Mean   : 0.03613   Mean   :-0.05369  
>  3rd Qu.: 1.49673   3rd Qu.: 1.41900  
>  Max.   : 7.07528   Max.   : 6.28902  
647,651c647,651
< [1,] -1.1689588  4.5558123
< [2,]  0.8971363  0.3296544
< [3,]  2.8247439  1.4249960
< [4,] -1.8533240  0.4804851
< [5,]  1.9158459 -5.5087631
---
> [1,] -1.1623390  4.5343276
> [2,]  0.8971391  0.3495635
> [3,]  2.8247455  1.4459533
> [4,] -1.8533288  0.4894799
> [5,]  1.9158416 -5.5363732
662,666c662,666
< [1,] -1.1689588  4.5558123
< [2,]  0.8971363  0.3296544
< [3,]  2.8247439  1.4249960
< [4,] -1.8533240  0.4804851
< [5,]  1.9158459 -5.5087631
---
> [1,] -1.1623390  4.5343276
> [2,]  0.8971391  0.3495635
> [3,]  2.8247455  1.4459533
> [4,] -1.8533288  0.4894799
> [5,]  1.9158416 -5.5363732
994,995c994,995
< 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
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpmSAC8D\Rdiffa2fdcc06439c" "D:\biocbld\bbs-2.13-bioc\tmpdir\RtmpmSAC8D\Rdiffb2fdc1d1743e7"' had status 1 
 [2s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-2.13-bioc/meat/limma.Rcheck/00check.log'
for details.

limma.Rcheck/00install.out:


install for i386

* installing *source* package 'limma' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
gcc -m32 -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/limma.buildbin-libdir/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'limma' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
gcc -m64 -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/limma.buildbin-libdir/limma/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'limma' as limma_3.18.13.zip
* DONE (limma)

limma.Rcheck/examples_i386/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject000
PrintLayout0.020.000.02
TestResults000
alias2Symbol4.340.114.62
arrayWeights0.010.000.01
arrayWeightsQuick0.010.000.01
asMatrixWeights0.010.000.02
auROC0.030.000.03
avearrays0.020.000.02
avereps0.010.000.01
backgroundcorrect0.030.000.03
barcodeplot0.010.000.01
beadCountWeights0.010.000.01
blockDiag0.010.000.01
camera0.050.000.05
cbind0.050.000.05
channel2M0.030.000.03
classifytests0.020.000.02
contrastAsCoef0.030.000.03
contrasts.fit0.040.000.05
controlStatus0.020.000.01
dim0.020.000.01
dupcor000
ebayes0.140.000.14
fitGammaIntercept0.020.000.01
fitfdist0.020.000.01
genas0.200.010.22
geneSetTest0.020.000.01
getSpacing0.010.000.01
getlayout0.010.000.02
heatdiagram0.010.000.02
helpMethods0.000.020.01
imageplot0.080.000.08
intraspotCorrelation0.020.000.02
isfullrank0.040.000.03
isnumeric0.010.000.01
kooperberg0.010.000.01
limmaUsersGuide0.010.000.01
lm.series0.020.000.01
lmFit0.690.000.69
lmscFit0.050.000.05
loessfit0.150.010.18
ma3x30.030.000.03
makeContrasts0.050.000.05
makeunique0.130.000.12
merge0.030.000.03
mergeScansRG0.020.000.01
modelMatrix0.010.000.01
modifyWeights0.010.000.02
nec0.010.000.02
normalizeMedianAbsValues0.010.000.02
normalizeRobustSpline0.080.000.08
normalizeVSN0.380.080.56
normalizebetweenarrays0.030.000.04
normalizeprintorder0.020.000.02
normexpfit0.030.000.03
normexpfitcontrol0.030.000.03
normexpfitdetectionp0.010.000.01
normexpsignal0.020.000.02
plotDensities0.030.000.03
plotMDS0.150.000.15
plotRLDF0.320.000.33
plotma0.050.020.06
poolvar0.020.000.01
predFCm0.070.000.06
printorder0.000.010.01
printtipWeights0.010.000.01
propTrueNull0.010.000.02
propexpr000
protectMetachar000
qqt0.030.000.03
qualwt0.020.000.02
rankSumTestwithCorrelation0.030.000.03
read.ilmn0.010.000.02
read.maimages0.030.000.03
readImaGeneHeader0.020.000.01
readgal000
removeext000
roast0.080.000.08
romer0.340.000.34
selectmodel0.050.000.04
squeezeVar0.020.000.02
strsplit20.010.000.01
subsetting0.010.000.02
targetsA2C0.010.000.02
topRomer000
toptable000
trigammainverse0.010.000.01
trimWhiteSpace000
uniquegenelist0.020.000.01
unwrapdups0.010.000.02
venn0.050.000.05
volcanoplot000
weightedmedian0.010.000.02
zscore0.020.000.02

limma.Rcheck/examples_x64/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject0.010.000.02
PrintLayout000
TestResults0.020.000.01
alias2Symbol4.760.144.90
arrayWeights0.010.020.03
arrayWeightsQuick0.020.000.02
asMatrixWeights0.020.000.02
auROC0.020.000.02
avearrays0.020.000.02
avereps0.030.000.03
backgroundcorrect0.010.000.01
barcodeplot0.030.000.03
beadCountWeights0.020.000.02
blockDiag0.010.000.02
camera0.050.000.05
cbind0.040.000.05
channel2M0.020.000.02
classifytests0.010.000.02
contrastAsCoef0.030.000.03
contrasts.fit0.050.000.05
controlStatus0.030.000.03
dim0.030.000.03
dupcor0.140.000.15
ebayes0.050.000.04
fitGammaIntercept0.020.000.03
fitfdist000
genas0.230.000.23
geneSetTest0.040.000.03
getSpacing0.020.000.01
getlayout0.000.000.03
heatdiagram0.010.000.02
helpMethods0.020.000.01
imageplot0.070.000.08
intraspotCorrelation0.010.000.02
isfullrank0.030.000.03
isnumeric0.020.000.01
kooperberg0.010.000.02
limmaUsersGuide0.030.000.03
lm.series0.020.000.01
lmFit0.730.020.75
lmscFit0.030.000.03
loessfit0.150.020.17
ma3x30.010.000.01
makeContrasts0.010.000.02
makeunique0.010.000.02
merge0.010.000.01
mergeScansRG0.030.000.03
modelMatrix0.030.000.03
modifyWeights0.020.000.01
nec0.010.000.02
normalizeMedianAbsValues000
normalizeRobustSpline0.080.010.10
normalizeVSN0.390.030.49
normalizebetweenarrays0.030.000.03
normalizeprintorder000
normexpfit0.020.000.02
normexpfitcontrol0.020.000.02
normexpfitdetectionp0.020.000.01
normexpsignal0.020.000.01
plotDensities0.010.000.02
plotMDS0.040.000.04
plotRLDF0.460.000.45
plotma0.050.000.05
poolvar0.020.000.02
predFCm0.060.000.07
printorder0.010.000.01
printtipWeights0.030.000.03
propTrueNull0.030.000.03
propexpr0.010.000.01
protectMetachar0.010.000.01
qqt0.020.000.01
qualwt0.010.000.02
rankSumTestwithCorrelation0.030.000.04
read.ilmn0.020.000.02
read.maimages0.030.000.03
readImaGeneHeader0.010.000.02
readgal0.010.000.01
removeext0.020.000.02
roast0.090.000.09
romer0.30.00.3
selectmodel0.040.000.03
squeezeVar000
strsplit20.010.000.02
subsetting0.030.000.03
targetsA2C0.030.000.03
topRomer0.020.000.02
toptable0.010.000.02
trigammainverse0.030.000.03
trimWhiteSpace0.020.000.02
uniquegenelist0.020.000.02
unwrapdups000
venn0.060.000.06
volcanoplot000
weightedmedian000
zscore0.020.000.01