BioC 3.3: CHECK report for edgeR on linux2.bioconductor.org

Package: edgeR

Version: 3.13.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.13.0.tar.gz

StartedAt: 2015-10-27 03:34:06 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:35:05 -0400 (Tue, 27 Oct 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-3.3-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/edgeR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘3.13.0’
* 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 ... [8s/8s] 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 ... [11s/11s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 5.066      0   5.066
* 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
 [6s/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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -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  -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  -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  -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  -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  -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  -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  -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  -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  -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  -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  -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  -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  -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c interpolator.cpp -o interpolator.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -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  -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	0.020	0.000	0.021
WLEB	0.100	0.003	0.103
adjustedProfileLik	0.006	0.000	0.007
aveLogCPM	0.002	0.000	0.002
binomTest	0.002	0.000	0.002
calcNormFactors	0.004	0.000	0.004
camera.DGEList	0.116	0.000	0.116
commonCondLogLikDerDelta	0.002	0.000	0.003
condLogLikDerSize	0.000	0.004	0.001
cpm	0.000	0.000	0.002
cutWithMinN	0.002	0.000	0.002
dglmStdResid	0.01	0.00	0.01
diffSpliceDGE	0.081	0.000	0.081
dim	0.001	0.000	0.002
dispBinTrend	0.460	0.008	0.467
dispCoxReid	0.031	0.000	0.031
dispCoxReidInterpolateTagwise	0.046	0.000	0.046
dispCoxReidSplineTrend	0.649	0.000	0.654
dropEmptyLevels	0.000	0.000	0.001
edgeRUsersGuide	0.001	0.000	0.001
equalizeLibSizes	0.014	0.000	0.015
estimateCommonDisp	0.016	0.004	0.020
estimateDisp	0.202	0.000	0.202
estimateExonGenewisedisp	0.011	0.000	0.010
estimateGLMCommonDisp	0.051	0.000	0.052
estimateGLMRobustDisp	0.508	0.000	0.509
estimateGLMTagwiseDisp	0.127	0.000	0.126
estimateGLMTrendedDisp	0.1	0.0	0.1
estimateTagwiseDisp	0	0	0
estimateTrendedDisp	0.317	0.000	0.318
exactTest	0.009	0.000	0.009
expandAsMatrix	0.001	0.004	0.001
getCounts	0.003	0.000	0.006
getPriorN	0.001	0.000	0.001
glmQLFTest	0.339	0.004	0.342
glmTreat	0.015	0.000	0.016
glmfit	0.034	0.000	0.035
goana	0.001	0.000	0.000
gof	0.009	0.000	0.009
goodTuring	0.009	0.000	0.008
loessByCol	0.003	0.000	0.002
maPlot	0.013	0.000	0.012
maximizeInterpolant	0.001	0.000	0.001
maximizeQuadratic	0.001	0.000	0.000
meanvar	0.043	0.000	0.043
mglm	0.005	0.000	0.006
movingAverageByCol	0.001	0.000	0.000
nbinomDeviance	0.000	0.000	0.001
plotBCV	0.348	0.000	0.350
plotExonUsage	0.005	0.000	0.006
plotMDS.DGEList	0.016	0.000	0.016
plotQLDisp	0.399	0.000	0.400
plotSmear	0.436	0.000	0.437
predFC	0.016	0.000	0.017
q2qnbinom	0.002	0.000	0.001
readDGE	0.000	0.000	0.001
roast.DGEList	0.216	0.000	0.216
romer.DGEList	5.066	0.000	5.066
spliceVariants	0.011	0.000	0.011
splitIntoGroups	0.001	0.000	0.001
subsetting	0.013	0.000	0.013
sumTechReps	0.001	0.000	0.001
systematicSubset	0	0	0
thinCounts	0.001	0.000	0.001
topTags	0.017	0.000	0.017
validDGEList	0.001	0.000	0.001
weightedCondLogLikDerDelta	0.002	0.000	0.002
zscoreNBinom	0	0	0