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: 2017-10-18 03:03:55 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:05:35 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 99.6 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 3.4.2 (2017-09-28)
* 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 5.396  0.074   5.616
* 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	0.060	0.001	0.063
WLEB	0.352	0.005	0.372
addPriorCount	0.002	0.000	0.002
adjustedProfileLik	0.024	0.002	0.026
aveLogCPM	0.032	0.001	0.035
binomTest	0.002	0.000	0.002
calcNormFactors	0.056	0.000	0.057
camera.DGEList	0.995	0.018	1.050
commonCondLogLikDerDelta	0.054	0.001	0.056
condLogLikDerSize	0.001	0.000	0.001
cpm	0.019	0.000	0.024
cutWithMinN	0.003	0.001	0.002
decidetestsDGE	0.142	0.001	0.146
dglmStdResid	0.029	0.002	0.030
diffSpliceDGE	0.081	0.004	0.085
dim	0.003	0.000	0.003
dispBinTrend	0.670	0.006	0.697
dispCoxReid	0.026	0.000	0.026
dispCoxReidInterpolateTagwise	0.029	0.001	0.031
dispCoxReidSplineTrend	0.786	0.006	0.818
dropEmptyLevels	0.001	0.000	0.001
edgeRUsersGuide	0.002	0.000	0.002
equalizeLibSizes	0.014	0.001	0.016
estimateCommonDisp	0.110	0.002	0.122
estimateDisp	0.434	0.003	0.452
estimateExonGenewisedisp	0.086	0.001	0.091
estimateGLMCommonDisp	0.056	0.001	0.058
estimateGLMRobustDisp	0.913	0.005	0.952
estimateGLMTagwiseDisp	0.156	0.001	0.160
estimateGLMTrendedDisp	0.139	0.002	0.145
estimateTagwiseDisp	0.118	0.001	0.122
estimateTrendedDisp	0.271	0.005	0.282
exactTest	0.097	0.001	0.100
expandAsMatrix	0.001	0.001	0.001
getCounts	0.011	0.000	0.011
getPriorN	0.003	0.000	0.002
gini	0.001	0.000	0.001
glmQLFTest	0.554	0.008	0.578
glmTreat	0.038	0.000	0.039
glmfit	0.036	0.000	0.039
goana	0.000	0.000	0.001
gof	0.008	0.000	0.008
goodTuring	0.006	0.001	0.006
loessByCol	0.002	0.001	0.003
maPlot	0.015	0.001	0.017
makeCompressedMatrix	0.005	0.002	0.012
maximizeInterpolant	0.001	0.000	0.001
maximizeQuadratic	0.001	0.000	0.001
meanvar	0.322	0.003	0.334
mglm	0.007	0.000	0.007
movingAverageByCol	0.001	0.000	0.001
nbinomDeviance	0.002	0.000	0.001
plotBCV	0.465	0.006	0.483
plotExonUsage	0.007	0.001	0.008
plotMDS.DGEList	0.054	0.001	0.061
plotQLDisp	0.401	0.005	0.416
plotSmear	0.476	0.005	0.496
predFC	0.014	0.001	0.016
q2qnbinom	0.002	0.000	0.001
readDGE	0	0	0
roast.DGEList	0.613	0.004	0.630
romer.DGEList	5.396	0.074	5.616
scaleOffset	0.001	0.000	0.001
spliceVariants	0.067	0.001	0.068
splitIntoGroups	0.003	0.001	0.004
subsetting	0.047	0.001	0.049
sumTechReps	0.000	0.000	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.001	0.000	0.001
topTags	0.021	0.001	0.025
validDGEList	0.001	0.000	0.002
weightedCondLogLikDerDelta	0.011	0.001	0.011
zscoreNBinom	0.001	0.000	0.001