BioC 3.6: CHECK report for edgeR on veracruz1

Package: edgeR

Version: 3.19.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.19.3.tar.gz

StartedAt: 2017-08-16 02:32:19 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:33:47 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 87.4 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_3.19.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘3.19.3’
* 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
* 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 
393c393
< [1,] 8.295172 8.338525 8.284484
---
> x 8.295172 8.338525 8.284484
395,397c395
< [1] "CompressedMatrix"
< attr(,"Dims")
< [1] 5 3
---
> [1] "compressedMatrix"
402d399
< 995 more rows ...
424c421
< 0.05545 0.09511 0.11623 0.11014 0.13329 0.16861 
---
> 0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
428c425
< 0.04203 0.08586 0.11280 0.11010 0.12369 0.37408 
---
> 0.04203 0.08586 0.11280 0.11010 0.12370 0.37410 
432c429
< 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-3.6-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	0.046	0.001	0.048
WLEB	0.300	0.004	0.318
addPriorCount	0.002	0.001	0.002
adjustedProfileLik	0.023	0.001	0.025
aveLogCPM	0.022	0.000	0.023
binomTest	0.002	0.000	0.002
calcNormFactors	0.037	0.000	0.037
camera.DGEList	0.819	0.013	0.844
cbind	0.000	0.000	0.001
commonCondLogLikDerDelta	0.041	0.001	0.042
condLogLikDerSize	0.001	0.000	0.000
cpm	0.019	0.001	0.019
cutWithMinN	0.001	0.000	0.001
decidetestsDGE	0.130	0.001	0.138
dglmStdResid	0.025	0.000	0.026
diffSpliceDGE	0.059	0.002	0.063
dim	0.002	0.000	0.002
dispBinTrend	0.594	0.002	0.631
dispCoxReid	0.027	0.000	0.028
dispCoxReidInterpolateTagwise	0.018	0.001	0.019
dispCoxReidSplineTrend	0.732	0.005	0.770
dropEmptyLevels	0.001	0.001	0.002
edgeRUsersGuide	0.001	0.000	0.001
equalizeLibSizes	0.014	0.001	0.015
estimateCommonDisp	0.100	0.002	0.105
estimateDisp	0.399	0.002	0.425
estimateExonGenewisedisp	0.088	0.001	0.089
estimateGLMCommonDisp	0.051	0.001	0.054
estimateGLMRobustDisp	0.760	0.002	0.782
estimateGLMTagwiseDisp	0.154	0.000	0.159
estimateGLMTrendedDisp	0.115	0.001	0.128
estimateTagwiseDisp	0.082	0.001	0.082
estimateTrendedDisp	0.230	0.004	0.240
exactTest	0.074	0.000	0.074
expandAsMatrix	0.001	0.000	0.001
getCounts	0.01	0.00	0.01
getPriorN	0.003	0.001	0.002
gini	0.001	0.000	0.001
glmQLFTest	0.480	0.007	0.498
glmTreat	0.041	0.001	0.041
glmfit	0.033	0.000	0.035
goana	0.001	0.000	0.001
gof	0.01	0.00	0.01
goodTuring	0.005	0.001	0.005
loessByCol	0.002	0.000	0.002
maPlot	0.016	0.001	0.016
makeCompressedMatrix	0.005	0.002	0.006
maximizeInterpolant	0.000	0.000	0.001
maximizeQuadratic	0.001	0.000	0.002
meanvar	0.297	0.002	0.301
mglm	0.004	0.000	0.005
movingAverageByCol	0.001	0.000	0.000
nbinomDeviance	0.001	0.000	0.001
plotBCV	0.455	0.006	0.477
plotExonUsage	0.006	0.000	0.006
plotMDS.DGEList	0.038	0.001	0.039
plotQLDisp	0.289	0.004	0.323
plotSmear	0.406	0.006	0.432
predFC	0.015	0.001	0.017
q2qnbinom	0.001	0.000	0.001
readDGE	0.001	0.000	0.001
roast.DGEList	0.465	0.002	0.482
romer.DGEList	4.544	0.097	4.820
scaleOffset	0.001	0.000	0.001
spliceVariants	0.050	0.001	0.050
splitIntoGroups	0.002	0.000	0.003
subsetting	0.038	0.001	0.044
sumTechReps	0.000	0.000	0.001
systematicSubset	0.001	0.001	0.000
thinCounts	0.000	0.000	0.001
topTags	0.015	0.001	0.016
validDGEList	0.002	0.000	0.002
weightedCondLogLikDerDelta	0.008	0.000	0.009
zscoreNBinom	0.000	0.000	0.001