BioC 3.3: CHECK report for edgeR on morelia

Package: edgeR

Version: 3.13.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.13.9.tar.gz

StartedAt: 2016-04-21 01:55:20 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 01:56:53 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 93.2 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.13.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/edgeR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.13.9’
* 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 ... [15s/15s] 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 ... [15s/15s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 6.419  0.134   6.728
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [6s/6s]
  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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_cr_adjust.cpp -o R_cr_adjust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_levenberg.cpp -o R_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_loess_by_col.cpp -o R_loess_by_col.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_one_group.cpp -o R_one_group.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c adj_coxreid.cpp -o adj_coxreid.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fmm_spline.c -o fmm_spline.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c glm_levenberg.cpp -o glm_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c glm_one_group.cpp -o glm_one_group.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c interpolator.cpp -o interpolator.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matvec_check.cpp -o matvec_check.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nbdev.cpp -o nbdev.o
clang++ -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 -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/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.003	0.024
WLEB	0.112	0.006	0.122
adjustedProfileLik	0.009	0.001	0.010
aveLogCPM	0.004	0.001	0.004
binomTest	0.003	0.000	0.003
calcNormFactors	0.006	0.001	0.006
camera.DGEList	0.216	0.004	0.220
commonCondLogLikDerDelta	0.007	0.000	0.007
condLogLikDerSize	0.001	0.001	0.001
cpm	0.004	0.000	0.005
cutWithMinN	0.002	0.000	0.002
dglmStdResid	0.016	0.001	0.017
diffSpliceDGE	0.117	0.004	0.120
dim	0.004	0.000	0.004
dispBinTrend	0.635	0.013	0.654
dispCoxReid	0.035	0.000	0.035
dispCoxReidInterpolateTagwise	0.046	0.002	0.049
dispCoxReidSplineTrend	1.049	0.007	1.108
dropEmptyLevels	0.002	0.000	0.002
edgeRUsersGuide	0.001	0.000	0.002
equalizeLibSizes	0.019	0.001	0.022
estimateCommonDisp	0.030	0.000	0.038
estimateDisp	0.330	0.003	0.334
estimateExonGenewisedisp	0.026	0.000	0.026
estimateGLMCommonDisp	0.071	0.000	0.072
estimateGLMRobustDisp	0.827	0.002	0.832
estimateGLMTagwiseDisp	0.248	0.003	0.252
estimateGLMTrendedDisp	0.167	0.001	0.169
estimateTagwiseDisp	0.036	0.001	0.037
estimateTrendedDisp	0.360	0.006	0.366
exactTest	0.018	0.001	0.018
expandAsMatrix	0.001	0.000	0.001
getCounts	0.018	0.001	0.019
getPriorN	0.003	0.000	0.003
gini	0.001	0.000	0.001
glmQLFTest	0.517	0.007	0.528
glmTreat	0.028	0.000	0.028
glmfit	0.053	0.001	0.054
goana	0.001	0.000	0.001
gof	0.013	0.000	0.013
goodTuring	0.006	0.001	0.006
loessByCol	0.003	0.000	0.003
maPlot	0.018	0.001	0.019
maximizeInterpolant	0.002	0.000	0.002
maximizeQuadratic	0.002	0.000	0.001
meanvar	0.076	0.003	0.080
mglm	0.011	0.001	0.011
movingAverageByCol	0.001	0.000	0.001
nbinomDeviance	0.001	0.000	0.001
plotBCV	0.460	0.009	0.474
plotExonUsage	0.009	0.001	0.010
plotMDS.DGEList	0.026	0.002	0.029
plotQLDisp	0.536	0.003	0.544
plotSmear	0.380	0.004	0.386
predFC	0.017	0.001	0.020
q2qnbinom	0.001	0.000	0.002
readDGE	0	0	0
roast.DGEList	0.196	0.002	0.198
romer.DGEList	6.419	0.134	6.728
spliceVariants	0.021	0.000	0.022
splitIntoGroups	0.004	0.000	0.004
subsetting	0.023	0.000	0.027
sumTechReps	0.001	0.000	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.001	0.000	0.001
topTags	0.029	0.001	0.032
validDGEList	0.002	0.000	0.003
weightedCondLogLikDerDelta	0.003	0.000	0.004
zscoreNBinom	0	0	0