BioC 2.12: CHECK report for edgeR on george2

Package: edgeR

Version: 3.2.4

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.2.4.tar.gz

StartedAt: 2013-10-09 01:32:07 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:34:09 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 122.0 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/edgeR.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.2.4’
* 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 ... [15s/16s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [15s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [10s/10s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [10s/11s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘edgeR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -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-2.12-bioc/R/include -DNDEBUG -I./core -I.  -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-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_levenberg.cpp -o R_levenberg.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_one_group.cpp -o R_one_group.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -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-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c core/interpolator.cpp -o core/interpolator.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -c core/fmm_spline.c -o core/fmm_spline.o
g++ -shared -L/usr/local/lib -o edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** data
** 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	0.048	0.004	0.054
WLEB	0.176	0.016	0.194
adjustedProfileLik	0.036	0.008	0.044
aveLogCPM	0.028	0.000	0.028
binomTest	0.020	0.000	0.022
calcNormFactors	0.028	0.000	0.028
camera.DGEList	0.348	0.000	0.351
commonCondLogLikDerDelta	0.028	0.000	0.028
condLogLikDerSize	0.016	0.000	0.016
cpm	0.024	0.000	0.020
cutWithMinN	0.02	0.00	0.02
dglmStdResid	0.120	0.004	0.122
dim	0.028	0.000	0.031
dispBinTrend	1.156	0.008	1.166
dispCoxReid	0.116	0.000	0.116
dispCoxReidInterpolateTagwise	0.092	0.000	0.094
dispCoxReidSplineTrend	1.540	0.004	1.541
edgeRUsersGuide	0.020	0.000	0.018
equalizeLibSizes	0.076	0.000	0.080
estimateCommonDisp	0.080	0.004	0.084
estimateDisp	0.620	0.000	0.626
estimateExonGenewisedisp	0.060	0.000	0.061
estimateGLMCommonDisp	0.208	0.016	0.225
estimateGLMTagwiseDisp	0.432	0.004	0.438
estimateGLMTrendedDisp	0.360	0.000	0.359
estimateTagwiseDisp	0.008	0.000	0.012
estimateTrendedDisp	1.528	0.000	1.528
exactTest	0.060	0.000	0.062
expandAsMatrix	0.028	0.004	0.032
getCounts	0.048	0.000	0.044
getPriorN	0.016	0.000	0.014
glmfit	0.124	0.000	0.122
gof	0.06	0.00	0.06
goodTuring	0.028	0.000	0.029
loessByCol	0.016	0.000	0.018
maPlot	0.036	0.000	0.036
maximizeInterpolant	0.024	0.000	0.021
maximizeQuadratic	0.016	0.004	0.015
meanvar	0.152	0.008	0.160
mglm	0.140	0.000	0.136
movingAverageByCol	0.012	0.000	0.011
plotBCV	1.124	0.000	1.126
plotExonUsage	0.156	0.000	0.160
plotMDS.DGEList	0.080	0.000	0.079
plotSmear	1.028	0.008	1.040
predFC	0.060	0.004	0.064
q2qnbinom	0.024	0.004	0.024
readDGE	0.012	0.000	0.017
roast.DGEList	0.344	0.004	0.353
spliceVariants	0.216	0.000	0.218
splitIntoGroups	0.024	0.000	0.025
subsetting	0.076	0.004	0.079
systematicSubset	0.016	0.000	0.017
thinCounts	0.020	0.000	0.016
topTags	0.116	0.004	0.115
weightedCondLogLikDerDelta	0.032	0.004	0.032
zscoreNBinom	0.004	0.000	0.007