BioC 3.5: CHECK report for limma on tokay2

Package: limma

Version: 3.32.10

Command: rm -rf limma.buildbin-libdir limma.Rcheck && mkdir limma.buildbin-libdir limma.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=limma.buildbin-libdir limma_3.32.10.tar.gz >limma.Rcheck\00install.out 2>&1 && cp limma.Rcheck\00install.out limma-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=limma.buildbin-libdir --install="check:limma-install.out" --force-multiarch --no-vignettes --timings limma_3.32.10.tar.gz

StartedAt: 2017-10-18 00:55:02 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:57:19 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 136.8 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf limma.buildbin-libdir limma.Rcheck && mkdir limma.buildbin-libdir limma.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=limma.buildbin-libdir limma_3.32.10.tar.gz >limma.Rcheck\00install.out 2>&1 && cp limma.Rcheck\00install.out limma-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=limma.buildbin-libdir --install="check:limma-install.out" --force-multiarch --no-vignettes --timings limma_3.32.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/limma.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.32.10'
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/limma.buildbin-libdir/limma/libs/i386/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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'limma-Tests.R'
  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.   :-5.82498   Min.   :-5.69877  
<  1st Qu.:-1.19140   1st Qu.:-1.55421  
<  Median :-0.19318   Median : 0.06267  
<  Mean   : 0.08691   Mean   :-0.05369  
<  3rd Qu.: 1.48646   3rd Qu.: 1.41900  
<  Max.   : 7.16195   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,] -1.0618269  4.5343276
< [2,]  0.8507603  0.3495635
< [3,]  2.7703696  1.4459533
< [4,] -1.8511286  0.4894799
< [5,]  1.9180276 -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,] -1.0618269  4.5343276
< [2,]  0.8507603  0.3495635
< [3,]  2.7703696  1.4459533
< [4,] -1.8511286  0.4894799
< [5,]  1.9180276 -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 -1.464215e-16
< mu+beta    -0.3333333 -1.464215e-16  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 "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\Rtmpaaa5Dk\Rdiffa27c86fb71bc" "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\Rtmpaaa5Dk\Rdiffb27c855b11096"' had status 1 
 OK
** running tests for arch 'x64' ...
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ... OK
 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

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/limma.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'limma' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c weighted_lowess.c -o weighted_lowess.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o limma.dll tmp.def init.o normexp.o weighted_lowess.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c weighted_lowess.c -o weighted_lowess.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o limma.dll tmp.def init.o normexp.o weighted_lowess.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/limma.buildbin-libdir/limma/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'limma' as limma_3.32.10.zip
* DONE (limma)

name	user	system	elapsed
LargeDataObject	0	0	0
PrintLayout	0	0	0
TestResults	0	0	0
alias2Symbol	3.68	0.08	4.52
arrayWeights	0	0	0
arrayWeightsQuick	0	0	0
asMatrixWeights	0.03	0.00	0.03
auROC	0.05	0.00	0.05
avearrays	0	0	0
avereps	0	0	0
backgroundcorrect	0.15	0.00	0.14
barcodeplot	0.44	0.00	0.44
beadCountWeights	0	0	0
blockDiag	0	0	0
camera	0.43	0.01	0.43
cbind	0.01	0.00	0.02
changelog	0	0	0
channel2M	0	0	0
classifytests	0.06	0.00	0.06
contrastAsCoef	0.02	0.00	0.02
contrasts.fit	0.23	0.00	0.23
controlStatus	0.02	0.00	0.02
coolmap	0.45	0.00	0.45
cumOverlap	0	0	0
detectionPValue	0	0	0
diffSplice	0	0	0
dim	0.02	0.00	0.02
dupcor	0.78	0.00	0.78
ebayes	0.03	0.00	0.03
fitGammaIntercept	0	0	0
fitfdist	0	0	0
fitmixture	0.02	0.00	0.01
genas	0.39	0.00	0.39
geneSetTest	0	0	0
getSpacing	0.01	0.00	0.02
getlayout	0	0	0
goana	0	0	0
heatdiagram	0	0	0
helpMethods	0	0	0
ids2indices	0	0	0
imageplot	0.08	0.00	0.07
intraspotCorrelation	0	0	0
isfullrank	0	0	0
isnumeric	0	0	0
kooperberg	0	0	0
limmaUsersGuide	0	0	0
lm.series	0	0	0
lmFit	0.42	0.02	0.44
lmscFit	0	0	0
loessfit	0.08	0.00	0.08
logcosh	0.00	0.00	0.02
ma3x3	0.03	0.00	0.03
makeContrasts	0.08	0.00	0.08
makeunique	0	0	0
mdplot	0.06	0.00	0.06
merge	0.11	0.00	0.11
mergeScansRG	0	0	0
modelMatrix	0.03	0.00	0.03
modifyWeights	0	0	0
nec	0	0	0
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0.03	0.00	0.04
normalizeVSN	0.53	0.03	0.81
normalizebetweenarrays	0	0	0
normalizeprintorder	0	0	0
normexpfit	0	0	0
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.00	0.02	0.01
normexpsignal	0	0	0
plotDensities	0	0	0
plotExons	0	0	0
plotMD	0.05	0.00	0.05
plotMDS	0.04	0.00	0.05
plotRLDF	0.02	0.00	0.01
plotSplice	0	0	0
plotWithHighlights	0.01	0.00	0.02
plotma	0.03	0.01	0.05
poolvar	0	0	0
predFCm	0.04	0.00	0.03
printorder	0	0	0
printtipWeights	0	0	0
propTrueNull	0	0	0
propexpr	0	0	0
protectMetachar	0	0	0
qqt	0	0	0
qualwt	0	0	0
rankSumTestwithCorrelation	0.06	0.00	0.07
read.idat	0	0	0
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeBatchEffect	0.02	0.00	0.01
removeext	0	0	0
roast	0.12	0.00	0.12
romer	0.04	0.00	0.03
selectmodel	0.01	0.00	0.02
squeezeVar	0	0	0
strsplit2	0	0	0
subsetting	0	0	0
targetsA2C	0.02	0.00	0.01
topGO	0	0	0
topRomer	0	0	0
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0	0	0
trigammainverse	0	0	0
trimWhiteSpace	0	0	0
uniquegenelist	0	0	0
unwrapdups	0	0	0
venn	0.42	0.00	0.42
volcanoplot	0	0	0
weightedLowess	0.02	0.00	0.01
weightedmedian	0	0	0
zscore	0	0	0

name	user	system	elapsed
LargeDataObject	0	0	0
PrintLayout	0	0	0
TestResults	0	0	0
alias2Symbol	3.48	0.06	3.55
arrayWeights	0	0	0
arrayWeightsQuick	0	0	0
asMatrixWeights	0.02	0.00	0.01
auROC	0.01	0.00	0.02
avearrays	0	0	0
avereps	0	0	0
backgroundcorrect	0.09	0.00	0.10
barcodeplot	0.35	0.00	0.34
beadCountWeights	0	0	0
blockDiag	0	0	0
camera	0.42	0.00	0.42
cbind	0	0	0
changelog	0	0	0
channel2M	0	0	0
classifytests	0.06	0.00	0.07
contrastAsCoef	0.02	0.00	0.01
contrasts.fit	0.22	0.00	0.22
controlStatus	0.01	0.00	0.02
coolmap	0.35	0.02	0.36
cumOverlap	0	0	0
detectionPValue	0	0	0
diffSplice	0	0	0
dim	0.01	0.00	0.01
dupcor	0.88	0.00	0.88
ebayes	0.03	0.00	0.03
fitGammaIntercept	0	0	0
fitfdist	0	0	0
fitmixture	0	0	0
genas	0.19	0.00	0.19
geneSetTest	0.02	0.00	0.02
getSpacing	0	0	0
getlayout	0	0	0
goana	0	0	0
heatdiagram	0	0	0
helpMethods	0.01	0.00	0.01
ids2indices	0	0	0
imageplot	0.03	0.00	0.03
intraspotCorrelation	0	0	0
isfullrank	0	0	0
isnumeric	0	0	0
kooperberg	0	0	0
limmaUsersGuide	0	0	0
lm.series	0	0	0
lmFit	0.37	0.00	0.37
lmscFit	0	0	0
loessfit	0.08	0.00	0.08
logcosh	0	0	0
ma3x3	0.03	0.00	0.03
makeContrasts	0.05	0.00	0.05
makeunique	0	0	0
mdplot	0.06	0.00	0.06
merge	0.06	0.00	0.06
mergeScansRG	0	0	0
modelMatrix	0.04	0.00	0.04
modifyWeights	0	0	0
nec	0	0	0
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0.02	0.00	0.02
normalizeVSN	0.68	0.09	0.89
normalizebetweenarrays	0	0	0
normalizeprintorder	0	0	0
normexpfit	0	0	0
normexpfitcontrol	0	0	0
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0	0	0
plotExons	0	0	0
plotMD	0.05	0.00	0.05
plotMDS	0.04	0.00	0.05
plotRLDF	0.02	0.00	0.01
plotSplice	0	0	0
plotWithHighlights	0.02	0.00	0.02
plotma	0.03	0.00	0.03
poolvar	0	0	0
predFCm	0.03	0.00	0.03
printorder	0	0	0
printtipWeights	0	0	0
propTrueNull	0.01	0.00	0.02
propexpr	0	0	0
protectMetachar	0	0	0
qqt	0	0	0
qualwt	0	0	0
rankSumTestwithCorrelation	0.05	0.00	0.05
read.idat	0	0	0
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeBatchEffect	0.02	0.00	0.02
removeext	0.01	0.00	0.02
roast	0.11	0.00	0.11
romer	0.03	0.00	0.03
selectmodel	0.02	0.00	0.01
squeezeVar	0	0	0
strsplit2	0	0	0
subsetting	0.01	0.00	0.02
targetsA2C	0	0	0
topGO	0	0	0
topRomer	0	0	0
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.02	0.00	0.01
trigammainverse	0	0	0
trimWhiteSpace	0	0	0
uniquegenelist	0	0	0
unwrapdups	0	0	0
venn	0.44	0.00	0.44
volcanoplot	0	0	0
weightedLowess	0.06	0.00	0.06
weightedmedian	0	0	0
zscore	0.02	0.00	0.02