BioC 3.4: CHECK report for edgeR on morelia

Package: edgeR

Version: 3.16.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.16.5.tar.gz

StartedAt: 2017-04-15 01:25:21 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:26:51 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 90.2 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_3.16.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/edgeR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘3.16.5’
* 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 ... 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 6.154  0.113   6.377
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ...283c283
<  0.1423  0.1618  0.1788  0.1863  0.2015  0.2692 
---
>  0.1766  0.1789  0.1814  0.1846  0.1870  0.2119 
291c291
<  0.1423  0.1605  0.1783  0.1867  0.2031  0.2740 
---
>  0.1766  0.1789  0.1814  0.1846  0.1870  0.2119 
 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_add_prior_count.cpp -o R_add_prior_count.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_add_repeat_matrices.cpp -o R_add_repeat_matrices.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_ave_log_cpm.cpp -o R_ave_log_cpm.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_calculate_cpm.cpp -o R_calculate_cpm.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_check_counts.cpp -o R_check_counts.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_check_poisson_bound.cpp -o R_check_poisson_bound.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_compute_apl.cpp -o R_compute_apl.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_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_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_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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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 -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 add_prior.cpp -o add_prior.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_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/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-3.4-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	0.018	0.001	0.020
WLEB	0.031	0.001	0.032
adjustedProfileLik	0.015	0.001	0.015
aveLogCPM	0.005	0.000	0.005
binomTest	0.003	0.000	0.003
calcNormFactors	0.006	0.000	0.006
camera.DGEList	0.198	0.003	0.201
commonCondLogLikDerDelta	0.005	0.000	0.004
condLogLikDerSize	0.001	0.000	0.001
cpm	0.004	0.000	0.005
cutWithMinN	0.003	0.000	0.003
dglmStdResid	0.018	0.001	0.020
diffSpliceDGE	0.072	0.003	0.076
dim	0.004	0.001	0.004
dispBinTrend	0.666	0.005	0.672
dispCoxReid	0.037	0.001	0.038
dispCoxReidInterpolateTagwise	0.036	0.001	0.038
dispCoxReidSplineTrend	1.065	0.006	1.097
dropEmptyLevels	0.001	0.000	0.001
edgeRUsersGuide	0.001	0.000	0.002
equalizeLibSizes	0.016	0.000	0.017
estimateCommonDisp	0.027	0.001	0.028
estimateDisp	0.298	0.002	0.301
estimateExonGenewisedisp	0.021	0.001	0.022
estimateGLMCommonDisp	0.076	0.000	0.076
estimateGLMRobustDisp	0.880	0.003	0.885
estimateGLMTagwiseDisp	0.207	0.000	0.207
estimateGLMTrendedDisp	0.176	0.000	0.177
estimateTagwiseDisp	0.038	0.001	0.039
estimateTrendedDisp	0.370	0.011	0.382
exactTest	0.015	0.000	0.016
expandAsMatrix	0.001	0.001	0.001
getCounts	0.013	0.000	0.013
getPriorN	0.002	0.000	0.002
gini	0.001	0.000	0.001
glmQLFTest	0.389	0.006	0.427
glmTreat	0.033	0.000	0.033
glmfit	0.048	0.000	0.050
goana	0.001	0.001	0.000
gof	0.01	0.00	0.01
goodTuring	0.006	0.001	0.007
loessByCol	0.003	0.000	0.002
maPlot	0.019	0.002	0.020
makeCompressedMatrix	0.006	0.002	0.008
maximizeInterpolant	0.001	0.000	0.002
maximizeQuadratic	0.001	0.000	0.000
meanvar	0.056	0.002	0.060
mglm	0.008	0.001	0.009
movingAverageByCol	0.001	0.000	0.002
nbinomDeviance	0.001	0.000	0.002
plotBCV	0.511	0.008	0.522
plotExonUsage	0.010	0.000	0.011
plotMDS.DGEList	0.028	0.001	0.030
plotQLDisp	0.371	0.008	0.380
plotSmear	0.408	0.009	0.435
predFC	0.019	0.001	0.021
q2qnbinom	0.002	0.001	0.002
readDGE	0.001	0.000	0.001
roast.DGEList	0.194	0.005	0.199
romer.DGEList	6.154	0.113	6.377
scaleOffset	0.001	0.000	0.001
spliceVariants	0.021	0.000	0.021
splitIntoGroups	0.004	0.001	0.004
subsetting	0.023	0.001	0.024
sumTechReps	0.001	0.000	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.001	0.000	0.001
topTags	0.027	0.001	0.028
validDGEList	0.002	0.000	0.003
weightedCondLogLikDerDelta	0.004	0.001	0.004
zscoreNBinom	0.000	0.000	0.001