Package: edgeR

Version: 3.1.9

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.1.9.tar.gz

StartedAt: 2013-03-25 01:21:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:23:57 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 127.3 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 3.0.0 beta (2013-03-19 r62328)
* 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 ‘3.1.9’
* 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 ... [14s/15s] 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’ [11s/11s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [12s/12s] 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
   ‘edgeR.Rnw’ 
** testing if installed package can be loaded
* DONE (edgeR)

name	user	system	elapsed
DGEList	0.040	0.000	0.043
WLEB	0.188	0.000	0.187
adjustedProfileLik	0.048	0.000	0.048
aveLogCPM	0.020	0.000	0.021
binomTest	0.020	0.000	0.019
calcNormFactors	0.020	0.004	0.024
camera.DGEList	0.316	0.012	0.325
commonCondLogLikDerDelta	0.016	0.004	0.020
condLogLikDerSize	0.012	0.004	0.017
cpm	0.016	0.008	0.024
cutWithMinN	0.012	0.008	0.019
dglmStdResid	0.108	0.008	0.115
dim	0.024	0.000	0.027
dispBinTrend	0.828	0.008	0.838
dispCoxReid	0.212	0.004	0.217
dispCoxReidInterpolateTagwise	0.112	0.004	0.116
dispCoxReidSplineTrend	1.452	0.016	1.469
edgeRUsersGuide	0.020	0.000	0.018
equalizeLibSizes	0.056	0.000	0.058
estimateCommonDisp	0.072	0.000	0.073
estimateDisp	0.620	0.008	0.629
estimateExonGenewisedisp	0.056	0.004	0.062
estimateGLMCommonDisp	0.196	0.004	0.202
estimateGLMTagwiseDisp	1.420	0.004	1.422
estimateGLMTrendedDisp	0.58	0.00	0.58
estimateTagwiseDisp	0.012	0.000	0.010
estimateTrendedDisp	1.284	0.000	1.443
exactTest	0.180	0.000	0.214
expandAsMatrix	0.008	0.000	0.011
getCounts	0.032	0.000	0.033
getPriorN	0.016	0.000	0.018
glmfit	0.152	0.004	0.167
gof	0.064	0.000	0.066
goodTuring	0.028	0.000	0.032
loessByCol	0.02	0.00	0.02
maPlot	0.040	0.000	0.039
maximizeInterpolant	0.020	0.000	0.017
maximizeQuadratic	0.016	0.000	0.020
meanvar	0.284	0.004	0.365
mglm	0.100	0.004	0.104
movingAverageByCol	0.012	0.000	0.013
plotBCV	1.044	0.004	1.053
plotExonUsage	0.048	0.000	0.048
plotMDS.DGEList	0.076	0.000	0.077
plotSmear	1.040	0.004	1.046
predFC	0.184	0.000	0.186
q2qnbinom	0.024	0.000	0.031
readDGE	0.012	0.000	0.013
roast.DGEList	0.344	0.020	0.367
spliceVariants	0.044	0.004	0.049
splitIntoGroups	0.012	0.020	0.032
subsetting	0.056	0.024	0.082
systematicSubset	0.020	0.000	0.019
thinCounts	0.020	0.004	0.025
topTags	0.104	0.000	0.100
weightedCondLogLikDerDelta	0.024	0.004	0.029
zscoreNBinom	0.008	0.000	0.011