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Package 364/671HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.16.2
Gordon Smyth
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/limma
Last Changed Rev: 76024 / Revision: 76155
Last Changed Date: 2013-04-25 01:20:22 -0700 (Thu, 25 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: limma
Version: 3.16.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.16.2.tar.gz
StartedAt: 2013-05-01 07:27:04 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 07:29:40 -0700 (Wed, 01 May 2013)
EllapsedTime: 155.4 seconds
RetCode: 0
Status:  OK 
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/limma.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.16.2'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'limma' can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package 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
* 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 ... 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [22s/23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 8.615  0.264   9.194
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'limma-Tests.R' [3s/3s]
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...588,592c588,592
< 0%   -0.78835384 -0.788312144 -0.79410956 -2.04434053 -2.0438088 -10.9766130
< 25%  -0.18340154 -0.183595325 -0.17340349 -0.59321065 -0.5863777  -0.7816385
< 50%  -0.11492924 -0.123303508 -0.04476096  0.05874864  0.0827054  -0.2577724
< 75%   0.01507921 -0.006825877  0.14015263  0.56010750  0.5606874   0.4406875
< 100%  0.21653837  0.193234186 11.47140874  2.57936026  2.5816432   2.5397022
---
> 0%   -0.78835384 -0.78097895 -0.78367166 -2.04434053 -2.04315267 -11.5610680
> 25%  -0.18340154 -0.18907787 -0.15525721 -0.59321065 -0.59309327  -0.8249477
> 50%  -0.11492924 -0.12136183 -0.03316003  0.05874864  0.08898459  -0.2466309
> 75%   0.01507921 -0.01000344  0.13229151  0.56010750  0.56606786   0.4502908
> 100%  0.21653837  0.21604173 11.69912073  2.57936026  2.56259812   2.5149556
630,635c630,635
<  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  
646,650c646,650
< [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
661,665c661,665
< [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
981,982c981,982
< 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
 [3s/3s] 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

limma.Rcheck/00install.out:

* installing *source* package 'limma' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c normexp.c -o normexp.o
normexp.c:153:20: warning: magnitude of floating-point constant too large for type 'double'; maximum is 1.797693134862316E+308 [-Wliteral-range]
  double abstol = -1e500; // infinity
                   ^
normexp.c:167:78: warning: passing 'void (*)()' to parameter of type 'void *' converts between void pointer and function pointer [-Wpedantic]
  nmmin(3, par, parsOut, Fmin, normexp_m2loglik_saddle, fail, abstol, intol, &ex, alpha, beta, gamma, trace, fncount, maxit);
                                                                             ^˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Applic.h:69:51: note: passing argument to parameter 'ex' here
           int *fail, double abstol, double intol, void *ex,
                                                         ^
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.12-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limma)

limma.Rcheck/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject0.0080.0010.009
PrintLayout0.0100.0020.013
TestResults0.0090.0010.010
alias2Symbol8.6150.2649.194
arrayWeights0.3010.0060.312
arrayWeightsQuick0.0380.0050.044
asMatrixWeights0.0340.0040.039
auROC0.0360.0030.038
avearrays0.0340.0020.037
avereps0.0380.0030.041
backgroundcorrect0.0480.0030.051
barcodeplot0.0650.0040.070
blockDiag0.0340.0020.036
camera0.1240.0050.130
cbind0.0830.0050.091
channel2M0.0510.0010.053
classifytests0.0400.0030.045
contrasts.fit0.1290.0030.137
controlStatus0.0590.0010.061
dim0.0840.0010.085
dupcor0.0260.0050.032
ebayes0.0880.0100.099
fitGammaIntercept0.0360.0030.039
fitfdist0.0350.0020.037
genas0.2160.0160.239
geneSetTest0.0520.0030.054
getSpacing0.0340.0010.037
getlayout0.0180.0000.019
heatdiagram0.0550.0020.058
helpMethods0.0200.0020.023
imageplot0.0820.0070.093
intraspotCorrelation0.0350.0030.039
isfullrank0.0620.0020.074
isnumeric0.0560.0010.059
kooperberg0.0340.0030.037
limmaUsersGuide0.0210.0020.024
lm.series0.0320.0030.035
lmFit1.1070.0581.207
lmscFit0.0510.0050.055
loessfit0.1180.0060.126
ma3x30.0400.0040.046
makeContrasts0.0570.0050.062
makeunique0.0200.0030.025
merge0.0580.0050.063
mergeScansRG0.0360.0040.040
modelMatrix0.0410.0050.046
modifyWeights0.0200.0030.022
nec0.0370.0040.041
normalizeMedianAbsValues0.0200.0020.022
normalizeRobustSpline0.1490.0110.164
normalizeVSN0.6680.0620.753
normalizebetweenarrays0.0430.0040.048
normalizeprintorder0.0460.0020.050
normexpfit0.0210.0030.023
normexpfitcontrol0.0350.0020.038
normexpfitdetectionp0.0740.0030.078
normexpsignal0.0200.0020.023
plotDensities0.0910.0070.099
plotMDS0.0930.0040.097
plotRLDF0.4910.0230.572
plotma0.1340.0050.154
poolvar0.0410.0080.051
predFCm0.1190.0130.133
printorder0.0280.0120.040
printtipWeights0.0550.0070.063
propTrueNull0.0410.0070.049
propexpr0.0230.0040.029
protectMetachar0.0230.0050.029
qqt0.0430.0060.053
qualwt0.0200.0040.024
rankSumTestwithCorrelation0.0470.0080.057
read.ilmn0.0410.0040.045
read.maimages0.0380.0050.042
readImaGeneHeader0.0200.0030.022
readgal0.0190.0030.022
removeext0.0350.0030.039
roast0.1510.0070.158
romer0.6060.0610.675
selectmodel0.0860.0080.097
squeezeVar0.0220.0040.027
strsplit20.0410.0050.047
subsetting0.0500.0060.057
targetsA2C0.0500.0040.074
topRomer0.0190.0020.021
toptable0.0190.0030.021
trigammainverse0.0380.0040.051
trimWhiteSpace0.0180.0020.022
uniquegenelist0.0380.0050.044
unwrapdups0.0220.0040.025
venn0.0900.0070.098
volcanoplot0.0330.0030.036
weightedmedian0.0200.0030.023
zscore0.0240.0040.027