BioC 3.1: CHECK report for edgeR on zin2

Package: edgeR

Version: 3.10.5

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz

StartedAt: 2015-10-09 00:48:10 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:49:43 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 92.6 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘3.10.5’
* 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/14s] 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/19s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 6.648      0   10.04
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [4s/6s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [4s/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
g++ -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c interpolator.cpp -o interpolator.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nbdev.cpp -o nbdev.o
g++ -shared -L/home/biocbuild/bbs-3.1-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-3.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	0.016	0.000	0.027
WLEB	0.067	0.000	0.073
adjustedProfileLik	0.008	0.000	0.008
aveLogCPM	0.002	0.000	0.002
binomTest	0.002	0.000	0.002
calcNormFactors	0.006	0.000	0.006
camera.DGEList	0.143	0.000	0.180
commonCondLogLikDerDelta	0.002	0.000	0.002
condLogLikDerSize	0.001	0.000	0.001
cpm	0.003	0.000	0.003
cutWithMinN	0.002	0.000	0.002
dglmStdResid	0.017	0.000	0.018
diffSpliceDGE	0.085	0.000	0.085
dim	0.003	0.000	0.003
dispBinTrend	0.454	0.003	0.627
dispCoxReid	0.028	0.000	0.049
dispCoxReidInterpolateTagwise	0.038	0.002	0.079
dispCoxReidSplineTrend	0.779	0.004	1.169
dropEmptyLevels	0.002	0.000	0.001
edgeRUsersGuide	0.002	0.000	0.001
equalizeLibSizes	0.018	0.000	0.018
estimateCommonDisp	0.018	0.004	0.022
estimateDisp	0.238	0.000	0.270
estimateExonGenewisedisp	0.014	0.000	0.014
estimateGLMCommonDisp	0.06	0.00	0.06
estimateGLMRobustDisp	0.621	0.001	0.938
estimateGLMTagwiseDisp	0.156	0.000	0.207
estimateGLMTrendedDisp	0.130	0.000	0.211
estimateTagwiseDisp	0.001	0.000	0.001
estimateTrendedDisp	0.376	0.004	0.590
exactTest	0.011	0.000	0.011
expandAsMatrix	0.000	0.000	0.001
getCounts	0.008	0.000	0.024
getPriorN	0.002	0.000	0.002
glmQLFTest	0.410	0.004	0.557
glmTreat	0.014	0.003	0.019
glmfit	0.04	0.00	0.04
goana	0.000	0.000	0.001
gof	0.01	0.00	0.01
goodTuring	0.008	0.000	0.008
loessByCol	0.002	0.000	0.003
maPlot	0.012	0.004	0.015
maximizeInterpolant	0.001	0.000	0.001
maximizeQuadratic	0.001	0.000	0.001
meanvar	0.055	0.004	0.098
mglm	0.008	0.000	0.020
movingAverageByCol	0	0	0
nbinomDeviance	0.001	0.000	0.001
plotBCV	0.432	0.000	0.596
plotExonUsage	0.006	0.001	0.019
plotMDS.DGEList	0.020	0.000	0.036
plotQLDisp	0.460	0.000	0.665
plotSmear	0.394	0.000	0.703
predFC	0.013	0.000	0.024
q2qnbinom	0.001	0.000	0.001
readDGE	0	0	0
roast.DGEList	0.142	0.000	0.300
romer.DGEList	6.648	0.000	10.040
spliceVariants	0.014	0.000	0.014
splitIntoGroups	0.003	0.000	0.002
subsetting	0.015	0.000	0.014
sumTechReps	0.001	0.000	0.001
systematicSubset	0	0	0
thinCounts	0.001	0.000	0.001
topTags	0.021	0.000	0.019
validDGEList	0.001	0.000	0.002
weightedCondLogLikDerDelta	0.003	0.000	0.006
zscoreNBinom	0.001	0.000	0.001