BioC 3.2: CHECK report for edgeR on linux1.bioconductor.org

Package: edgeR

Version: 3.12.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.12.0.tar.gz

StartedAt: 2015-10-27 03:09:44 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:10:46 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 62.1 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_3.12.0.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 ‘3.12.0’
* 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 ... [7s/7s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 7.946      0   7.947
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [5s/5s]
  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	0.014	0.000	0.014
WLEB	0.054	0.004	0.057
adjustedProfileLik	0.007	0.000	0.007
aveLogCPM	0.002	0.000	0.002
binomTest	0.001	0.000	0.002
calcNormFactors	0.006	0.000	0.006
camera.DGEList	0.12	0.00	0.12
commonCondLogLikDerDelta	0.002	0.000	0.002
condLogLikDerSize	0	0	0
cpm	0.002	0.000	0.002
cutWithMinN	0.002	0.000	0.002
dglmStdResid	0.015	0.000	0.016
diffSpliceDGE	0.078	0.000	0.078
dim	0.002	0.000	0.002
dispBinTrend	0.388	0.000	0.388
dispCoxReid	0.021	0.000	0.021
dispCoxReidInterpolateTagwise	0.026	0.004	0.030
dispCoxReidSplineTrend	0.761	0.000	0.762
dropEmptyLevels	0.002	0.000	0.002
edgeRUsersGuide	0.002	0.000	0.002
equalizeLibSizes	0.024	0.000	0.025
estimateCommonDisp	0.028	0.000	0.028
estimateDisp	0.335	0.000	0.336
estimateExonGenewisedisp	0.019	0.000	0.020
estimateGLMCommonDisp	0.081	0.000	0.082
estimateGLMRobustDisp	0.625	0.000	0.625
estimateGLMTagwiseDisp	0.132	0.000	0.131
estimateGLMTrendedDisp	0.105	0.000	0.105
estimateTagwiseDisp	0	0	0
estimateTrendedDisp	0.351	0.000	0.351
exactTest	0.015	0.000	0.015
expandAsMatrix	0.000	0.000	0.001
getCounts	0.011	0.000	0.011
getPriorN	0.002	0.000	0.002
glmQLFTest	0.565	0.000	0.566
glmTreat	0.027	0.000	0.028
glmfit	0.054	0.000	0.055
goana	0.000	0.000	0.001
gof	0.013	0.000	0.012
goodTuring	0.01	0.00	0.01
loessByCol	0.003	0.000	0.003
maPlot	0.019	0.000	0.019
maximizeInterpolant	0.002	0.000	0.002
maximizeQuadratic	0.001	0.000	0.001
meanvar	0.066	0.004	0.070
mglm	0.009	0.000	0.009
movingAverageByCol	0.001	0.000	0.001
nbinomDeviance	0.001	0.000	0.001
plotBCV	0.402	0.000	0.401
plotExonUsage	0.006	0.000	0.006
plotMDS.DGEList	0.017	0.000	0.018
plotQLDisp	0.496	0.000	0.496
plotSmear	0.337	0.000	0.337
predFC	0.011	0.000	0.012
q2qnbinom	0.001	0.000	0.001
readDGE	0.000	0.000	0.001
roast.DGEList	0.122	0.000	0.121
romer.DGEList	7.946	0.000	7.947
spliceVariants	0.02	0.00	0.02
splitIntoGroups	0.003	0.000	0.003
subsetting	0.023	0.000	0.023
sumTechReps	0.001	0.000	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.001	0.000	0.001
topTags	0.024	0.004	0.028
validDGEList	0.002	0.000	0.002
weightedCondLogLikDerDelta	0.003	0.000	0.003
zscoreNBinom	0	0	0