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BioC 3.0: CHECK report for limma on moscato1

This page was generated on 2015-04-10 09:43:07 -0700 (Fri, 10 Apr 2015).

Package 483/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
limma 3.22.7
Gordon Smyth
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/limma
Last Changed Rev: 101920 / Revision: 102249
Last Changed Date: 2015-04-05 15:05:28 -0700 (Sun, 05 Apr 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: limma
Version: 3.22.7
Command: rm -rf limma.buildbin-libdir limma.Rcheck && mkdir limma.buildbin-libdir limma.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=limma.buildbin-libdir limma_3.22.7.tar.gz >limma.Rcheck\00install.out 2>&1 && cp limma.Rcheck\00install.out limma-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=limma.buildbin-libdir --install="check:limma-install.out" --force-multiarch --no-vignettes --timings limma_3.22.7.tar.gz
StartedAt: 2015-04-10 02:34:13 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:36:56 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 163.2 seconds
RetCode: 0
Status:  OK  
CheckDir: limma.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf limma.buildbin-libdir limma.Rcheck && mkdir limma.buildbin-libdir limma.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=limma.buildbin-libdir limma_3.22.7.tar.gz >limma.Rcheck\00install.out 2>&1 && cp limma.Rcheck\00install.out limma-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=limma.buildbin-libdir --install="check:limma-install.out" --force-multiarch --no-vignettes --timings limma_3.22.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/limma.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '3.22.7'
* 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 ... NOTE
'library' or 'require' call to 'GO.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 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-3.0-bioc/meat/limma.buildbin-libdir/limma/libs/i386/limma.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-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, nor the system RNG.
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' ... [8s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
alias2Symbol 5.16   0.01    5.18
** running examples for arch 'x64' ... [11s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
alias2Symbol 6.46   0.16    6.62
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'limma-Tests.R' [8s]
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...595,599c595,599
< 0%   -0.78835384 -0.687432210 -0.78957137 -0.75758558 -0.63778292
< 25%  -0.18340154 -0.179683572 -0.18979269 -0.16363329 -0.38064318
< 50%  -0.11492924 -0.114796040 -0.12087983 -0.07318718 -0.15971879
< 75%   0.01507921 -0.008145125 -0.01857508  0.03656491  0.07839396
< 100%  0.21653837  0.145106033  0.19214597  0.23710498  0.51836274
---
> 0%   -0.78835384 -0.687432210 -0.78957137 -0.76756060 -0.63778292
> 25%  -0.18340154 -0.179683572 -0.18979269 -0.16773223 -0.38064318
> 50%  -0.11492924 -0.114796040 -0.12087983 -0.07185314 -0.15971879
> 75%   0.01507921 -0.008145125 -0.01857508  0.04030634  0.07839396
> 100%  0.21653837  0.145106033  0.19214597  0.21417361  0.51836274
602,606c602,606
< 0%   -2.04434053 -2.05132680 -2.02404318 -2.09602100 -2.22280633
< 25%  -0.59321065 -0.57200209 -0.58975649 -0.58142533 -0.71037756
< 50%   0.05874864  0.04514326  0.08335198 -0.01037007  0.06785517
< 75%   0.56010750  0.55124530  0.57618740  0.55704748  0.65383830
< 100%  2.57936026  2.64549799  2.57549257  2.38180448  2.28648835
---
> 0%   -2.04434053 -2.05132680 -2.02404318 -2.101242874 -2.22280633
> 25%  -0.59321065 -0.57200209 -0.58975649 -0.577887481 -0.71037756
> 50%   0.05874864  0.04514326  0.08335198 -0.001769806  0.06785517
> 75%   0.56010750  0.55124530  0.57618740  0.561454370  0.65383830
> 100%  2.57936026  2.64549799  2.57549257  2.402324533  2.28648835
644,649c644,649
<  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  
---
>  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  
660,664c660,664
< [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
---
> [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
675,679c675,679
< [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
---
> [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
1007,1008c1007,1008
< mu+alpha    0.3333333 3.333333e-01  9.280771e-17
< mu+beta    -0.3333333 9.280771e-17  3.333333e-01
---
> mu+alpha    0.3333333 3.333333e-01  5.551115e-17
> mu+beta    -0.3333333 5.551115e-17  3.333333e-01
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.0-bioc\tmpdir\RtmpairP2H\Rdiffa122c5f075db9" "D:\biocbld\bbs-3.0-bioc\tmpdir\RtmpairP2H\Rdiffb122c6d4d5e4f"' had status 1 
 [8s] OK
** running tests for arch 'x64' ...
  Running 'limma-Tests.R' [9s]
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ... OK
 [10s] 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
* DONE

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c weighted_lowess.c -o weighted_lowess.o
gcc -m32 -shared -s -static-libgcc -o limma.dll tmp.def normexp.o weighted_lowess.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-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-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c weighted_lowess.c -o weighted_lowess.o
gcc -m64 -shared -s -static-libgcc -o limma.dll tmp.def normexp.o weighted_lowess.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/limma.buildbin-libdir/limma/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'limma' as limma_3.22.7.zip
* DONE (limma)

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

nameusersystemelapsed
LargeDataObject000
PrintLayout000
TestResults000
alias2Symbol5.160.015.18
arrayWeights000
arrayWeightsQuick000
asMatrixWeights000
auROC000
avearrays000
avereps0.020.000.01
backgroundcorrect000
barcodeplot0.030.000.03
beadCountWeights0.010.000.02
blockDiag000
camera0.130.000.12
cbind0.010.000.02
changelog000
channel2M000
classifytests000
contrastAsCoef0.020.000.02
contrasts.fit0.010.000.01
controlStatus0.020.000.02
diffSplice000
dim0.020.000.01
dupcor000
ebayes0.010.000.02
fitGammaIntercept000
fitfdist000
genas0.260.000.28
geneSetTest000
getSpacing000
getlayout000
goana.MArrayLM000
goana000
heatdiagram000
helpMethods000
ids2indices000
imageplot0.060.000.06
intraspotCorrelation000
isfullrank000
isnumeric000
kooperberg000
limmaUsersGuide0.000.020.02
lm.series000
lmFit0.550.000.54
lmscFit000
loessfit0.010.000.02
ma3x3000
makeContrasts000
makeunique000
merge0.020.000.02
mergeScansRG000
modelMatrix000
modifyWeights000
nec000
normalizeMedianAbsValues000
normalizeRobustSpline0.030.000.03
normalizeVSN0.320.030.36
normalizebetweenarrays000
normalizeprintorder000
normexpfit000
normexpfitcontrol000
normexpfitdetectionp000
normexpsignal000
plot0.020.000.01
plotDensities000
plotExons000
plotMDS0.020.000.01
plotRLDF0.280.000.28
plotSplice000
plotma0.030.000.04
poolvar000
predFCm0.030.000.03
printorder0.020.000.01
printtipWeights000
propTrueNull000
propexpr000
protectMetachar0.010.000.02
qqt000
qualwt000
rankSumTestwithCorrelation000
read.idat000
read.ilmn000
read.maimages000
readImaGeneHeader000
readgal000
removeBatchEffect000
removeext000
roast0.150.000.16
romer0.020.000.02
selectmodel0.010.000.02
squeezeVar000
strsplit2000
subsetting000
targetsA2C0.020.000.01
topGO000
topRomer000
topSplice000
toptable000
tricubeMovingAverage000
trigammainverse0.010.000.02
trimWhiteSpace000
uniquegenelist000
unwrapdups000
venn0.030.000.03
volcanoplot000
weightedLowess0.020.000.01
weightedmedian000
zscore000

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

nameusersystemelapsed
LargeDataObject000
PrintLayout000
TestResults000
alias2Symbol6.460.166.62
arrayWeights0.020.000.01
arrayWeightsQuick000
asMatrixWeights000
auROC000
avearrays000
avereps000
backgroundcorrect0.020.000.01
barcodeplot0.230.010.25
beadCountWeights000
blockDiag000
camera0.050.000.05
cbind000
changelog0.010.000.01
channel2M000
classifytests0.020.000.02
contrastAsCoef000
contrasts.fit0.020.000.01
controlStatus0.010.000.01
diffSplice000
dim0.020.000.02
dupcor000
ebayes0.010.000.01
fitGammaIntercept000
fitfdist000
genas0.190.020.20
geneSetTest000
getSpacing000
getlayout000
goana.MArrayLM000
goana0.020.000.01
heatdiagram000
helpMethods000
ids2indices000
imageplot0.280.000.28
intraspotCorrelation000
isfullrank000
isnumeric000
kooperberg000
limmaUsersGuide000
lm.series000
lmFit0.860.010.87
lmscFit000
loessfit0.020.000.02
ma3x3000
makeContrasts000
makeunique000
merge0.010.000.01
mergeScansRG000
modelMatrix000
modifyWeights000
nec000
normalizeMedianAbsValues000
normalizeRobustSpline0.030.000.03
normalizeVSN0.500.020.53
normalizebetweenarrays000
normalizeprintorder000
normexpfit000
normexpfitcontrol000
normexpfitdetectionp0.020.000.02
normexpsignal000
plot0.010.000.01
plotDensities000
plotExons000
plotMDS0.020.000.02
plotRLDF0.060.000.06
plotSplice000
plotma0.170.010.19
poolvar000
predFCm0.010.000.02
printorder0.020.000.01
printtipWeights000
propTrueNull000
propexpr000
protectMetachar000
qqt000
qualwt000
rankSumTestwithCorrelation0.010.000.02
read.idat000
read.ilmn000
read.maimages000
readImaGeneHeader000
readgal000
removeBatchEffect0.020.000.01
removeext000
roast0.040.000.05
romer0.030.000.03
selectmodel0.020.000.02
squeezeVar000
strsplit20.020.000.01
subsetting000
targetsA2C000
topGO000
topRomer000
topSplice000
toptable000
tricubeMovingAverage000
trigammainverse000
trimWhiteSpace000
uniquegenelist000
unwrapdups0.020.000.01
venn0.030.000.03
volcanoplot000
weightedLowess000
weightedmedian000
zscore000