BioC 3.3: CHECK report for edgeR on zin2

Package: edgeR

Version: 3.14.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.14.0.tar.gz

StartedAt: 2016-10-13 01:36:43 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:37:50 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 67.3 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/edgeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘3.14.0’
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 5.003  0.004   5.033
* 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

* installing *source* package ‘edgeR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c interpolator.cpp -o interpolator.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nbdev.cpp -o nbdev.o
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.017
WLEB	0.071	0.000	0.072
adjustedProfileLik	0.009	0.000	0.008
aveLogCPM	0.003	0.000	0.003
binomTest	0.002	0.000	0.002
calcNormFactors	0.001	0.004	0.004
camera.DGEList	0.142	0.004	0.146
commonCondLogLikDerDelta	0.004	0.000	0.005
condLogLikDerSize	0.001	0.000	0.001
cpm	0.000	0.004	0.004
cutWithMinN	0.002	0.000	0.001
dglmStdResid	0.013	0.000	0.013
diffSpliceDGE	0.089	0.000	0.092
dim	0.002	0.000	0.002
dispBinTrend	0.455	0.004	0.459
dispCoxReid	0.025	0.000	0.025
dispCoxReidInterpolateTagwise	0.036	0.000	0.037
dispCoxReidSplineTrend	0.764	0.000	0.913
dropEmptyLevels	0.002	0.000	0.001
edgeRUsersGuide	0.001	0.000	0.002
equalizeLibSizes	0.019	0.000	0.020
estimateCommonDisp	0.03	0.00	0.03
estimateDisp	0.255	0.000	0.256
estimateExonGenewisedisp	0.016	0.000	0.016
estimateGLMCommonDisp	0.073	0.000	0.073
estimateGLMRobustDisp	0.626	0.004	0.640
estimateGLMTagwiseDisp	0.157	0.000	0.164
estimateGLMTrendedDisp	0.124	0.000	0.124
estimateTagwiseDisp	0.040	0.000	0.042
estimateTrendedDisp	0.312	0.000	0.312
exactTest	0.012	0.000	0.012
expandAsMatrix	0.000	0.000	0.001
getCounts	0.011	0.000	0.011
getPriorN	0.003	0.000	0.002
gini	0.001	0.000	0.001
glmQLFTest	0.459	0.000	0.471
glmTreat	0.023	0.000	0.023
glmfit	0.041	0.000	0.042
goana	0.001	0.000	0.000
gof	0.01	0.00	0.01
goodTuring	0.006	0.000	0.007
loessByCol	0.003	0.000	0.003
maPlot	0.016	0.000	0.017
maximizeInterpolant	0.001	0.000	0.001
maximizeQuadratic	0.001	0.000	0.001
meanvar	0.072	0.000	0.071
mglm	0.008	0.000	0.007
movingAverageByCol	0.001	0.000	0.001
nbinomDeviance	0.000	0.000	0.001
plotBCV	0.460	0.000	0.459
plotExonUsage	0.007	0.000	0.007
plotMDS.DGEList	0.021	0.000	0.021
plotQLDisp	0.459	0.000	0.458
plotSmear	0.386	0.003	0.391
predFC	0.012	0.000	0.012
q2qnbinom	0.001	0.000	0.000
readDGE	0.000	0.000	0.001
roast.DGEList	0.129	0.000	0.128
romer.DGEList	5.003	0.004	5.033
spliceVariants	0.013	0.000	0.013
splitIntoGroups	0.002	0.000	0.003
subsetting	0.014	0.000	0.015
sumTechReps	0.001	0.000	0.000
systematicSubset	0.001	0.000	0.001
thinCounts	0	0	0
topTags	0.014	0.004	0.018
validDGEList	0.002	0.000	0.002
weightedCondLogLikDerDelta	0.003	0.000	0.003
zscoreNBinom	0.000	0.000	0.001