BioC 3.2: CHECK report for edgeR on perceval

Package: edgeR

Version: 3.11.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.11.2.tar.gz

StartedAt: 2015-08-24 00:21:48 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:23:16 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 87.8 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.11.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/edgeR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.11.2’
* 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 ... [12s/12s] 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 ... [17s/17s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 8.657  0.312   9.003
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [6s/6s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [6s/6s] 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

* installing *source* package ‘edgeR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_cr_adjust.cpp -o R_cr_adjust.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_levenberg.cpp -o R_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_loess_by_col.cpp -o R_loess_by_col.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_one_group.cpp -o R_one_group.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c adj_coxreid.cpp -o adj_coxreid.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fmm_spline.c -o fmm_spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_levenberg.cpp -o glm_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_one_group.cpp -o glm_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.cpp -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c interpolator.cpp -o interpolator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matvec_check.cpp -o matvec_check.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nbdev.cpp -o nbdev.o
llvm-g++-4.2 -arch x86_64 -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 -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/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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)

name	user	system	elapsed
DGEList	0.024	0.004	0.027
WLEB	0.088	0.005	0.094
adjustedProfileLik	0.011	0.001	0.013
aveLogCPM	0.003	0.000	0.003
binomTest	0.003	0.001	0.002
calcNormFactors	0.006	0.000	0.006
camera.DGEList	0.171	0.004	0.174
commonCondLogLikDerDelta	0.003	0.001	0.003
condLogLikDerSize	0.001	0.000	0.001
cpm	0.018	0.001	0.019
cutWithMinN	0.003	0.000	0.002
dglmStdResid	0.014	0.002	0.015
diffSpliceDGE	0.225	0.008	0.234
dim	0.003	0.000	0.004
dispBinTrend	0.521	0.004	0.526
dispCoxReid	0.03	0.00	0.03
dispCoxReidInterpolateTagwise	0.038	0.002	0.041
dispCoxReidSplineTrend	0.876	0.003	0.881
dropEmptyLevels	0.002	0.000	0.002
edgeRUsersGuide	0.003	0.001	0.003
equalizeLibSizes	0.021	0.001	0.022
estimateCommonDisp	0.029	0.001	0.030
estimateDisp	0.315	0.002	0.317
estimateExonGenewisedisp	0.017	0.000	0.018
estimateGLMCommonDisp	0.063	0.001	0.064
estimateGLMRobustDisp	0.714	0.001	0.714
estimateGLMTagwiseDisp	0.163	0.001	0.164
estimateGLMTrendedDisp	0.230	0.008	0.238
estimateTagwiseDisp	0.001	0.000	0.000
estimateTrendedDisp	0.416	0.012	0.428
exactTest	0.015	0.000	0.016
expandAsMatrix	0.001	0.000	0.001
getCounts	0.011	0.000	0.012
getPriorN	0.003	0.000	0.003
glmQLFTest	0.502	0.013	0.525
glmTreat	0.022	0.001	0.023
glmfit	0.047	0.001	0.048
goana	0.001	0.001	0.001
gof	0.015	0.000	0.015
goodTuring	0.011	0.001	0.013
loessByCol	0.002	0.000	0.003
maPlot	0.017	0.002	0.018
maximizeInterpolant	0.001	0.000	0.002
maximizeQuadratic	0.001	0.001	0.002
meanvar	0.072	0.004	0.077
mglm	0.010	0.001	0.010
movingAverageByCol	0.002	0.001	0.001
nbinomDeviance	0.001	0.000	0.001
plotBCV	0.627	0.012	0.638
plotExonUsage	0.008	0.001	0.009
plotMDS.DGEList	0.021	0.003	0.024
plotQLDisp	0.462	0.010	0.474
plotSmear	0.473	0.006	0.483
plotSpliceDGE	0	0	0
predFC	0.018	0.002	0.020
q2qnbinom	0.002	0.000	0.001
readDGE	0.001	0.000	0.001
roast.DGEList	0.208	0.002	0.211
romer.DGEList	8.657	0.312	9.003
spliceVariants	0.018	0.000	0.019
splitIntoGroups	0.003	0.001	0.004
subsetting	0.020	0.001	0.022
sumTechReps	0.001	0.000	0.002
systematicSubset	0.000	0.000	0.001
thinCounts	0.001	0.000	0.001
topSpliceDGE	0	0	0
topTags	0.031	0.003	0.033
validDGEList	0.003	0.000	0.003
weightedCondLogLikDerDelta	0.004	0.000	0.003
zscoreNBinom	0.001	0.000	0.001