BioC 3.2: CHECK report for edgeR on zin1

Package: edgeR

Version: 3.12.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.12.1.tar.gz

StartedAt: 2016-04-23 00:16:55 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:17:55 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 60.6 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_3.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/edgeR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘3.12.1’
* 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 ... [9s/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 6.601      0   6.607
* 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
 [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

* 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	0.018	0.000	0.018
WLEB	0.078	0.000	0.078
adjustedProfileLik	0.009	0.000	0.009
aveLogCPM	0.003	0.000	0.003
binomTest	0.004	0.000	0.004
calcNormFactors	0.006	0.000	0.006
camera.DGEList	0.154	0.000	0.154
commonCondLogLikDerDelta	0.003	0.000	0.003
condLogLikDerSize	0.000	0.000	0.001
cpm	0.001	0.001	0.003
cutWithMinN	0.01	0.00	0.01
dglmStdResid	0.012	0.000	0.012
diffSpliceDGE	0.089	0.004	0.092
dim	0.002	0.000	0.003
dispBinTrend	0.455	0.000	0.454
dispCoxReid	0.026	0.000	0.026
dispCoxReidInterpolateTagwise	0.033	0.000	0.036
dispCoxReidSplineTrend	0.755	0.000	0.754
dropEmptyLevels	0.001	0.000	0.001
edgeRUsersGuide	0.001	0.000	0.001
equalizeLibSizes	0.017	0.000	0.018
estimateCommonDisp	0.025	0.000	0.024
estimateDisp	0.246	0.000	0.247
estimateExonGenewisedisp	0.015	0.000	0.014
estimateGLMCommonDisp	0.063	0.000	0.064
estimateGLMRobustDisp	0.685	0.000	0.696
estimateGLMTagwiseDisp	0.179	0.000	0.179
estimateGLMTrendedDisp	0.132	0.000	0.132
estimateTagwiseDisp	0	0	0
estimateTrendedDisp	0.402	0.003	0.405
exactTest	0.012	0.001	0.011
expandAsMatrix	0.001	0.000	0.001
getCounts	0.008	0.000	0.008
getPriorN	0.002	0.000	0.002
glmQLFTest	0.445	0.004	0.449
glmTreat	0.018	0.004	0.022
glmfit	0.047	0.000	0.046
goana	0.001	0.000	0.001
gof	0.012	0.000	0.011
goodTuring	0.009	0.000	0.009
loessByCol	0.003	0.000	0.002
maPlot	0.017	0.000	0.018
maximizeInterpolant	0.002	0.000	0.001
maximizeQuadratic	0.001	0.000	0.001
meanvar	0.06	0.00	0.06
mglm	0.012	0.003	0.013
movingAverageByCol	0.000	0.000	0.001
nbinomDeviance	0.000	0.001	0.000
plotBCV	0.467	0.000	0.467
plotExonUsage	0.007	0.000	0.007
plotMDS.DGEList	0.022	0.000	0.022
plotQLDisp	0.485	0.000	0.484
plotSmear	0.391	0.003	0.396
predFC	0.014	0.001	0.013
q2qnbinom	0.001	0.000	0.001
readDGE	0.001	0.000	0.000
roast.DGEList	0.141	0.000	0.141
romer.DGEList	6.601	0.000	6.607
spliceVariants	0.013	0.000	0.014
splitIntoGroups	0.003	0.000	0.003
subsetting	0.015	0.000	0.014
sumTechReps	0.001	0.000	0.001
systematicSubset	0.001	0.000	0.000
thinCounts	0.001	0.000	0.001
topTags	0.019	0.000	0.018
validDGEList	0.001	0.000	0.002
weightedCondLogLikDerDelta	0.003	0.000	0.002
zscoreNBinom	0	0	0