Package: edgeR

Version: 3.1.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.1.3.tar.gz

StartedAt: 2013-01-16 02:14:28 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:15:56 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 87.9 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/edgeR.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘3.1.3’
* 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 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 ... OK
* 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 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/usr/local/include    -fpic  -g -O2  -c cr_adjustment.cpp -o cr_adjustment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fmm_spline.c -o fmm_spline.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c lowess_by_col.cpp -o lowess_by_col.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c maximize_interpolant.cpp -o maximize_interpolant.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mglm_levenberg.cpp -o mglm_levenberg.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c simple_good_turing.cpp -o simple_good_turing.o
g++ -shared -L/usr/local/lib64 -o edgeR.so cr_adjustment.o fmm_spline.o lowess_by_col.o maximize_interpolant.o mglm_levenberg.o simple_good_turing.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/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
   ‘edgeR.Rnw’ 
** testing if installed package can be loaded

* DONE (edgeR)

name	user	system	elapsed
DGEList	0.028	0.004	0.033
adjustedProfileLik	0.032	0.000	0.030
aveLogCPM	0.004	0.004	0.006
bin.dispersion	2.668	0.008	2.682
binomTest	0.016	0.000	0.014
calcNormFactors	0.008	0.008	0.019
commonCondLogLikDerDelta	0.016	0.000	0.017
condLogLikDerSize	0.008	0.004	0.012
cpm	0.016	0.000	0.017
cutWithMinN	0.012	0.000	0.011
dglmStdResid	0.092	0.004	0.093
dim	0.012	0.004	0.018
dispBinTrend	1.268	0.000	1.269
dispCoxReid	0.104	0.004	0.107
dispCoxReidInterpolateTagwise	0.112	0.004	0.116
dispCoxReidSplineTrend	2.680	0.008	2.693
edgeRUsersGuide	0.008	0.004	0.011
equalizeLibSizes	0.040	0.004	0.044
estimateCommonDisp	0.052	0.004	0.056
estimateExonGenewisedisp	0.036	0.004	0.042
estimateGLMCommonDisp	0.316	0.004	0.321
estimateGLMTagwiseDisp	2.164	0.000	2.165
estimateGLMTrendedDisp	2.056	0.000	2.060
estimateTagwiseDisp	0.004	0.000	0.005
estimateTrendedDisp	1.168	0.000	1.172
exactTest	0.116	0.000	0.116
expandAsMatrix	0.008	0.000	0.009
getCounts	0.020	0.004	0.025
getPriorN	0.012	0.000	0.011
glmfit	0.160	0.004	0.165
gof	0.124	0.000	0.125
goodTuring	0.024	0.004	0.027
loessByCol	0.016	0.000	0.017
maPlot	0.028	0.000	0.027
maximizeInterpolant	0.008	0.000	0.010
maximizeQuadratic	0.008	0.000	0.008
meanvar	0.100	0.000	0.102
mglm	0.148	0.000	0.144
movingAverageByCol	0.008	0.000	0.009
plotBCV	0.957	0.000	0.954
plotExonUsage	0.016	0.000	0.017
plotMDS.DGEList	0.756	0.008	0.766
plotSmear	0.596	0.004	0.600
predFC	0.036	0.000	0.035
q2qnbinom	0.008	0.000	0.010
readDGE	0.008	0.000	0.007
spliceVariants	0.108	0.004	0.115
splitIntoGroups	0.012	0.000	0.012
subsetting	0.040	0.000	0.038
systematicSubset	0.004	0.000	0.005
thinCounts	0.004	0.000	0.004
topTags	0.040	0.000	0.041
weightedCondLogLikDerDelta	0.008	0.004	0.011
zscoreNBinom	0.008	0.000	0.005