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BioC 3.1: CHECK report for edgeR on morelia

This page was generated on 2015-10-09 09:38:54 -0700 (Fri, 09 Oct 2015).

Package 292/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edgeR 3.10.5
Yunshun Chen , Aaron Lun , Mark Robinson , Davis McCarthy , Gordon Smyth
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/edgeR
Last Changed Rev: 109338 / Revision: 109384
Last Changed Date: 2015-10-07 17:40:28 -0700 (Wed, 07 Oct 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: edgeR
Version: 3.10.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz
StartedAt: 2015-10-09 01:30:50 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:32:13 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 82.6 seconds
RetCode: 0
Status:  OK 
CheckDir: edgeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/edgeR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.10.5’
* 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 ‘edgeR’ can be installed ... [12s/13s] 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
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/15s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
romer.DGEList 7.56  0.499   8.063
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [5s/5s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [5s/5s] 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: OK

edgeR.Rcheck/00install.out:

* installing *source* package ‘edgeR’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_cr_adjust.cpp -o R_cr_adjust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_levenberg.cpp -o R_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_loess_by_col.cpp -o R_loess_by_col.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_one_group.cpp -o R_one_group.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c adj_coxreid.cpp -o adj_coxreid.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fmm_spline.c -o fmm_spline.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c glm_levenberg.cpp -o glm_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c glm_one_group.cpp -o glm_one_group.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c interpolator.cpp -o interpolator.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matvec_check.cpp -o matvec_check.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nbdev.cpp -o nbdev.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o edgeR.so R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/edgeR.Rcheck/edgeR/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 (edgeR)

edgeR.Rcheck/edgeR-Ex.timings:

nameusersystemelapsed
DGEList0.0180.0060.023
WLEB0.0780.0060.083
adjustedProfileLik0.0080.0010.008
aveLogCPM0.0020.0000.002
binomTest0.0030.0000.003
calcNormFactors0.0060.0000.006
camera.DGEList0.1580.0190.176
commonCondLogLikDerDelta0.0060.0000.006
condLogLikDerSize0.0020.0010.002
cpm0.0040.0020.006
cutWithMinN0.0020.0000.003
dglmStdResid0.0140.0010.015
diffSpliceDGE0.0940.0170.111
dim0.0030.0000.004
dispBinTrend0.5030.0120.516
dispCoxReid0.0330.0000.034
dispCoxReidInterpolateTagwise0.0310.0030.034
dispCoxReidSplineTrend0.9040.0561.026
dropEmptyLevels0.0020.0000.002
edgeRUsersGuide0.0020.0000.002
equalizeLibSizes0.0200.0010.021
estimateCommonDisp0.0210.0010.021
estimateDisp0.2180.0020.220
estimateExonGenewisedisp0.0140.0000.014
estimateGLMCommonDisp0.0620.0000.062
estimateGLMRobustDisp0.5730.0050.578
estimateGLMTagwiseDisp0.1720.0000.172
estimateGLMTrendedDisp0.1490.0220.171
estimateTagwiseDisp000
estimateTrendedDisp0.3580.0090.367
exactTest0.0130.0000.014
expandAsMatrix000
getCounts0.0070.0000.007
getPriorN0.0020.0000.002
glmQLFTest0.3720.0090.424
glmTreat0.0170.0000.017
glmfit0.0440.0010.046
goana0.0010.0000.000
gof0.0090.0000.009
goodTuring0.0090.0000.010
loessByCol0.0030.0010.003
maPlot0.0180.0010.020
maximizeInterpolant0.0010.0000.002
maximizeQuadratic0.0010.0010.002
meanvar0.0590.0040.064
mglm0.0060.0010.007
movingAverageByCol0.0010.0000.001
nbinomDeviance0.0010.0000.000
plotBCV0.4080.0120.420
plotExonUsage0.0080.0010.010
plotMDS.DGEList0.0220.0010.022
plotQLDisp0.3560.0020.359
plotSmear0.2530.0040.259
predFC0.0110.0000.013
q2qnbinom0.0010.0000.002
readDGE0.0000.0000.001
roast.DGEList0.1440.0020.145
romer.DGEList7.5600.4998.063
spliceVariants0.0200.0030.024
splitIntoGroups0.0040.0000.004
subsetting0.0260.0070.033
sumTechReps0.0020.0010.002
systematicSubset0.0010.0000.001
thinCounts0.0010.0010.001
topTags0.0260.0030.030
validDGEList0.0020.0000.003
weightedCondLogLikDerDelta0.0030.0000.003
zscoreNBinom0.0010.0000.001