BioC 3.5: CHECK report for edgeR on veracruz2

Package: edgeR

Version: 3.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.18.1.tar.gz

StartedAt: 2017-08-16 02:18:26 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:20:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 96.9 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_3.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/edgeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.18.1’
* 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 ‘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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
romer.DGEList 5.095  0.108   5.345
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ...95c95
< 0.02428 0.36369 0.55662 0.54319 0.78889 1.00000 
---
> 0.02428 0.36370 0.55660 0.54320 0.78890 1.00000 
98c98
< 0.02428 0.36369 0.55662 0.54319 0.78889 1.00000 
---
> 0.02428 0.36370 0.55660 0.54320 0.78890 1.00000 
270c270
< 0.09353 0.11082 0.15463 0.19006 0.23050 0.52006 
---
> 0.09353 0.11080 0.15460 0.19010 0.23050 0.52010 
421c421
< 0.05545 0.09511 0.11623 0.11014 0.13329 0.16861 
---
> 0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
425c425
< 0.04203 0.08586 0.11280 0.11010 0.12369 0.37408 
---
> 0.04203 0.08586 0.11280 0.11010 0.12370 0.37410 
429c429
< 0.05545 0.09511 0.11623 0.11014 0.13329 0.16861 
---
> 0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
 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   -fPIC  -Wall -g -O2  -c R_add_prior_count.cpp -o R_add_prior_count.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_add_repeat_matrices.cpp -o R_add_repeat_matrices.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_calculate_cpm.cpp -o R_calculate_cpm.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_check_counts.cpp -o R_check_counts.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_compute_apl.cpp -o R_compute_apl.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -g -O2  -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_levenberg.cpp -o R_levenberg.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -g -O2  -c add_prior.cpp -o add_prior.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c adj_coxreid.cpp -o adj_coxreid.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fmm_spline.c -o fmm_spline.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c glm_levenberg.cpp -o glm_levenberg.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c interpolator.cpp -o interpolator.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matvec_check.cpp -o matvec_check.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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_add_prior_count.o R_add_repeat_matrices.o R_ave_log_cpm.o R_calculate_cpm.o R_check_counts.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_get_one_way_fitted.o R_initialize_levenberg.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 add_prior.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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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	0.062	0.000	0.065
WLEB	0.354	0.006	0.376
addPriorCount	0.001	0.000	0.001
adjustedProfileLik	0.019	0.002	0.021
aveLogCPM	0.029	0.000	0.029
binomTest	0.002	0.001	0.002
calcNormFactors	0.057	0.000	0.057
camera.DGEList	0.989	0.015	1.040
commonCondLogLikDerDelta	0.051	0.000	0.051
condLogLikDerSize	0.001	0.000	0.001
cpm	0.020	0.001	0.021
cutWithMinN	0.002	0.000	0.002
decidetestsDGE	0.150	0.001	0.153
dglmStdResid	0.027	0.000	0.028
diffSpliceDGE	0.080	0.003	0.088
dim	0.003	0.000	0.003
dispBinTrend	0.608	0.003	0.627
dispCoxReid	0.02	0.00	0.02
dispCoxReidInterpolateTagwise	0.030	0.001	0.032
dispCoxReidSplineTrend	0.750	0.004	0.785
dropEmptyLevels	0.001	0.000	0.002
edgeRUsersGuide	0.002	0.000	0.002
equalizeLibSizes	0.016	0.000	0.016
estimateCommonDisp	0.106	0.004	0.111
estimateDisp	0.406	0.003	0.415
estimateExonGenewisedisp	0.083	0.000	0.086
estimateGLMCommonDisp	0.050	0.001	0.050
estimateGLMRobustDisp	0.858	0.002	0.886
estimateGLMTagwiseDisp	0.177	0.000	0.187
estimateGLMTrendedDisp	0.145	0.000	0.147
estimateTagwiseDisp	0.116	0.000	0.116
estimateTrendedDisp	0.241	0.005	0.256
exactTest	0.096	0.001	0.100
expandAsMatrix	0.000	0.000	0.001
getCounts	0.01	0.00	0.01
getPriorN	0.003	0.000	0.002
gini	0.001	0.000	0.001
glmQLFTest	0.520	0.007	0.543
glmTreat	0.038	0.001	0.040
glmfit	0.037	0.001	0.038
goana	0.001	0.000	0.001
gof	0.01	0.00	0.01
goodTuring	0.008	0.000	0.009
loessByCol	0.002	0.001	0.002
maPlot	0.014	0.001	0.015
makeCompressedMatrix	0.006	0.002	0.008
maximizeInterpolant	0.001	0.000	0.001
maximizeQuadratic	0.000	0.001	0.001
meanvar	0.306	0.001	0.328
mglm	0.007	0.000	0.008
movingAverageByCol	0.001	0.000	0.002
nbinomDeviance	0.002	0.000	0.001
plotBCV	0.512	0.004	0.534
plotExonUsage	0.006	0.001	0.007
plotMDS.DGEList	0.053	0.001	0.054
plotQLDisp	0.359	0.007	0.378
plotSmear	0.455	0.005	0.474
predFC	0.013	0.001	0.013
q2qnbinom	0.002	0.000	0.002
readDGE	0.000	0.000	0.001
roast.DGEList	0.574	0.001	0.583
romer.DGEList	5.095	0.108	5.345
scaleOffset	0.001	0.000	0.001
spliceVariants	0.053	0.002	0.056
splitIntoGroups	0.002	0.000	0.003
subsetting	0.038	0.000	0.039
sumTechReps	0.001	0.000	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.001	0.000	0.001
topTags	0.024	0.000	0.024
validDGEList	0.002	0.000	0.002
weightedCondLogLikDerDelta	0.013	0.000	0.012
zscoreNBinom	0.001	0.000	0.000