BioC 3.2: CHECK report for edgeR on zin1

Package: edgeR

Version: 3.11.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.11.2.tar.gz

StartedAt: 2015-08-23 23:31:43 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:32:42 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 58.6 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.11.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/edgeR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [8s/9s] 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 ... [13s/13s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 6.744      0   6.743
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [4s/4s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [4s/4s] 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
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_levenberg.cpp -o R_levenberg.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_one_group.cpp -o R_one_group.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c adj_coxreid.cpp -o adj_coxreid.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fmm_spline.c -o fmm_spline.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_levenberg.cpp -o glm_levenberg.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_one_group.cpp -o glm_one_group.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c interpolator.cpp -o interpolator.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matvec_check.cpp -o matvec_check.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nbdev.cpp -o nbdev.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/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/home/biocbuild/bbs-3.2-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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	0.017	0.000	0.018
WLEB	0.064	0.012	0.076
adjustedProfileLik	0.008	0.004	0.009
aveLogCPM	0.000	0.000	0.002
binomTest	0.002	0.000	0.002
calcNormFactors	0.006	0.000	0.006
camera.DGEList	0.136	0.000	0.137
commonCondLogLikDerDelta	0.003	0.000	0.002
condLogLikDerSize	0.000	0.000	0.001
cpm	0.003	0.000	0.003
cutWithMinN	0.002	0.000	0.002
dglmStdResid	0.018	0.000	0.018
diffSpliceDGE	0.163	0.000	0.168
dim	0.003	0.000	0.003
dispBinTrend	0.472	0.000	0.480
dispCoxReid	0.030	0.000	0.029
dispCoxReidInterpolateTagwise	0.036	0.000	0.036
dispCoxReidSplineTrend	0.766	0.000	0.766
dropEmptyLevels	0.001	0.000	0.002
edgeRUsersGuide	0.002	0.000	0.003
equalizeLibSizes	0.018	0.000	0.017
estimateCommonDisp	0.024	0.000	0.024
estimateDisp	0.237	0.000	0.237
estimateExonGenewisedisp	0.014	0.000	0.015
estimateGLMCommonDisp	0.065	0.000	0.065
estimateGLMRobustDisp	0.679	0.000	0.701
estimateGLMTagwiseDisp	0.147	0.000	0.147
estimateGLMTrendedDisp	0.170	0.000	0.174
estimateTagwiseDisp	0.000	0.000	0.001
estimateTrendedDisp	0.388	0.004	0.429
exactTest	0.009	0.000	0.012
expandAsMatrix	0.000	0.000	0.001
getCounts	0.009	0.000	0.009
getPriorN	0.002	0.000	0.002
glmQLFTest	0.459	0.000	0.464
glmTreat	0.022	0.000	0.021
glmfit	0.075	0.000	0.075
goana	0.000	0.000	0.001
gof	0.010	0.000	0.009
goodTuring	0.008	0.000	0.008
loessByCol	0.002	0.000	0.003
maPlot	0.016	0.000	0.015
maximizeInterpolant	0.001	0.000	0.001
maximizeQuadratic	0.000	0.000	0.001
meanvar	0.053	0.000	0.053
mglm	0.007	0.000	0.006
movingAverageByCol	0.000	0.000	0.001
nbinomDeviance	0.001	0.000	0.000
plotBCV	0.413	0.000	0.413
plotExonUsage	0.007	0.000	0.007
plotMDS.DGEList	0.02	0.00	0.02
plotQLDisp	0.424	0.004	0.428
plotSmear	0.377	0.000	0.378
plotSpliceDGE	0	0	0
predFC	0.012	0.000	0.011
q2qnbinom	0.001	0.000	0.001
readDGE	0.000	0.000	0.001
roast.DGEList	0.133	0.000	0.135
romer.DGEList	6.744	0.000	6.743
spliceVariants	0.014	0.000	0.014
splitIntoGroups	0.003	0.000	0.002
subsetting	0.017	0.000	0.017
sumTechReps	0.001	0.000	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.000	0.000	0.001
topSpliceDGE	0.001	0.000	0.000
topTags	0.019	0.000	0.019
validDGEList	0.002	0.000	0.001
weightedCondLogLikDerDelta	0.002	0.000	0.003
zscoreNBinom	0.001	0.000	0.000