BioC 3.1: CHECK report for edgeR on petty

Package: edgeR

Version: 3.10.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz

StartedAt: 2015-10-08 22:47:51 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:49:57 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 126.9 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/edgeR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.10.5’
* 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 ... [16s/19s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
romer.DGEList 11.815  0.312  12.139
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [9s/11s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [9s/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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘edgeR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_cr_adjust.cpp -o R_cr_adjust.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_levenberg.cpp -o R_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_loess_by_col.cpp -o R_loess_by_col.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_one_group.cpp -o R_one_group.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c adj_coxreid.cpp -o adj_coxreid.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fmm_spline.c -o fmm_spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_levenberg.cpp -o glm_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_one_group.cpp -o glm_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.cpp -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c interpolator.cpp -o interpolator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matvec_check.cpp -o matvec_check.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nbdev.cpp -o nbdev.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-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	0.021	0.001	0.022
WLEB	0.140	0.005	0.145
adjustedProfileLik	0.018	0.002	0.020
aveLogCPM	0.005	0.001	0.006
binomTest	0.004	0.000	0.004
calcNormFactors	0.01	0.00	0.01
camera.DGEList	0.285	0.005	0.290
commonCondLogLikDerDelta	0.009	0.000	0.009
condLogLikDerSize	0.002	0.000	0.002
cpm	0.005	0.001	0.007
cutWithMinN	0.005	0.000	0.005
dglmStdResid	0.023	0.002	0.025
diffSpliceDGE	0.173	0.005	0.179
dim	0.005	0.000	0.006
dispBinTrend	0.672	0.006	0.678
dispCoxReid	0.051	0.000	0.051
dispCoxReidInterpolateTagwise	0.054	0.004	0.057
dispCoxReidSplineTrend	1.267	0.003	1.271
dropEmptyLevels	0.002	0.001	0.002
edgeRUsersGuide	0.002	0.000	0.002
equalizeLibSizes	0.034	0.000	0.034
estimateCommonDisp	0.031	0.001	0.033
estimateDisp	0.431	0.002	0.434
estimateExonGenewisedisp	0.023	0.001	0.023
estimateGLMCommonDisp	0.101	0.000	0.102
estimateGLMRobustDisp	1.090	0.001	1.094
estimateGLMTagwiseDisp	0.289	0.001	0.291
estimateGLMTrendedDisp	0.218	0.001	0.220
estimateTagwiseDisp	0.000	0.000	0.001
estimateTrendedDisp	0.704	0.019	0.724
exactTest	0.023	0.001	0.023
expandAsMatrix	0.001	0.001	0.001
getCounts	0.017	0.000	0.016
getPriorN	0.004	0.000	0.004
glmQLFTest	0.682	0.007	0.699
glmTreat	0.041	0.001	0.043
glmfit	0.084	0.002	0.086
goana	0.001	0.000	0.001
gof	0.015	0.000	0.015
goodTuring	0.011	0.001	0.012
loessByCol	0.002	0.000	0.002
maPlot	0.027	0.002	0.033
maximizeInterpolant	0.003	0.000	0.002
maximizeQuadratic	0.002	0.000	0.002
meanvar	0.098	0.003	0.104
mglm	0.013	0.001	0.014
movingAverageByCol	0.002	0.000	0.002
nbinomDeviance	0.001	0.000	0.002
plotBCV	0.565	0.008	0.572
plotExonUsage	0.010	0.001	0.011
plotMDS.DGEList	0.039	0.002	0.042
plotQLDisp	0.744	0.008	0.773
plotSmear	0.516	0.005	0.522
predFC	0.026	0.002	0.028
q2qnbinom	0.003	0.000	0.003
readDGE	0.001	0.000	0.001
roast.DGEList	0.302	0.002	0.304
romer.DGEList	11.815	0.312	12.139
spliceVariants	0.028	0.001	0.028
splitIntoGroups	0.005	0.000	0.005
subsetting	0.029	0.001	0.031
sumTechReps	0.002	0.000	0.002
systematicSubset	0.001	0.001	0.002
thinCounts	0.001	0.000	0.002
topTags	0.037	0.002	0.039
validDGEList	0.004	0.001	0.005
weightedCondLogLikDerDelta	0.006	0.000	0.005
zscoreNBinom	0.001	0.000	0.001