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BioC 3.4: CHECK report for edgeR on morelia

This page was generated on 2016-09-21 03:50:10 -0700 (Wed, 21 Sep 2016).

Package 358/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edgeR 3.15.2
Yunshun Chen , Aaron Lun , Mark Robinson , Davis McCarthy , Gordon Smyth
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 119042 / Revision: 121152
Last Changed Date: 2016-06-29 18:47:59 -0700 (Wed, 29 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 3.15.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.15.2.tar.gz
StartedAt: 2016-09-20 05:59:46 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:00:47 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 61.1 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_3.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/edgeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘3.15.2’
* 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 ‘edgeR’ 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-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: 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-3.4-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
DGEList0.0120.0010.012
WLEB0.0210.0010.021
adjustedProfileLik0.0060.0010.007
aveLogCPM0.0010.0000.002
binomTest0.0030.0010.003
calcNormFactors0.0060.0000.005
camera.DGEList0.1120.0020.114
commonCondLogLikDerDelta0.0030.0000.002
condLogLikDerSize0.0000.0000.001
cpm0.0020.0000.003
cutWithMinN0.0020.0000.002
dglmStdResid0.0110.0010.011
diffSpliceDGE0.0710.0020.073
dim0.0040.0000.003
dispBinTrend0.4730.0070.481
dispCoxReid0.0200.0010.020
dispCoxReidInterpolateTagwise0.0260.0010.028
dispCoxReidSplineTrend0.6490.0030.653
dropEmptyLevels0.0010.0000.001
edgeRUsersGuide0.0010.0000.001
equalizeLibSizes0.0130.0010.014
estimateCommonDisp0.0170.0000.017
estimateDisp0.2470.0010.248
estimateExonGenewisedisp0.0130.0000.013
estimateGLMCommonDisp0.0780.0010.079
estimateGLMRobustDisp0.4850.0040.489
estimateGLMTagwiseDisp0.1180.0040.122
estimateGLMTrendedDisp0.1050.0010.106
estimateTagwiseDisp0.0310.0020.032
estimateTrendedDisp0.2310.0050.236
exactTest0.0090.0000.009
expandAsMatrix000
getCounts0.0060.0000.007
getPriorN0.0020.0000.001
gini0.0000.0000.001
glmQLFTest0.3370.0060.369
glmTreat0.0180.0010.019
glmfit0.0310.0000.031
goana0.0000.0000.001
gof0.0070.0000.007
goodTuring0.0050.0000.005
loessByCol0.0010.0000.002
maPlot0.0120.0010.012
maximizeInterpolant0.0010.0000.001
maximizeQuadratic0.0010.0000.001
meanvar0.0430.0010.046
mglm0.0050.0000.005
movingAverageByCol0.0010.0000.001
nbinomDeviance0.0010.0000.001
plotBCV0.4080.0110.428
plotExonUsage0.0050.0010.010
plotMDS.DGEList0.0140.0000.015
plotQLDisp0.3220.0020.326
plotSmear0.2270.0020.231
predFC0.0100.0010.012
q2qnbinom0.0010.0000.001
readDGE000
roast.DGEList0.1420.0000.142
romer.DGEList4.2440.1104.354
spliceVariants0.0170.0000.017
splitIntoGroups0.0030.0000.004
subsetting0.0200.0010.021
sumTechReps0.0010.0000.001
systematicSubset0.0000.0000.001
thinCounts0.0000.0010.001
topTags0.0250.0030.029
validDGEList0.0030.0010.003
weightedCondLogLikDerDelta0.0030.0000.004
zscoreNBinom0.0000.0010.001