BioC 2.14: CHECK report for edgeR on morelia

Package: edgeR

Version: 3.6.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_3.6.8.tar.gz

StartedAt: 2014-10-07 22:35:16 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:36:34 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 78.0 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 --no-multiarch edgeR_3.6.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/edgeR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.6.8’
* 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 ... [13s/13s] 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 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 ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [5s/5s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [5s/5s] 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

* 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 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/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 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-2.14-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	0.017	0.002	0.019
WLEB	0.107	0.007	0.115
adjustedProfileLik	0.008	0.001	0.009
aveLogCPM	0.002	0.000	0.002
binomTest	0.002	0.001	0.002
calcNormFactors	0.007	0.000	0.007
camera.DGEList	0.207	0.004	0.210
commonCondLogLikDerDelta	0.004	0.000	0.005
condLogLikDerSize	0.001	0.000	0.001
cpm	0.005	0.000	0.004
cutWithMinN	0.003	0.000	0.003
dglmStdResid	0.014	0.002	0.016
dim	0.003	0.000	0.004
dispBinTrend	0.691	0.007	0.699
dispCoxReid	0.038	0.000	0.038
dispCoxReidInterpolateTagwise	0.037	0.001	0.039
dispCoxReidSplineTrend	1.026	0.007	1.034
edgeRUsersGuide	0.002	0.001	0.003
equalizeLibSizes	0.017	0.000	0.018
estimateCommonDisp	0.025	0.001	0.025
estimateDisp	0.243	0.002	0.246
estimateExonGenewisedisp	0.017	0.000	0.017
estimateGLMCommonDisp	0.067	0.001	0.067
estimateGLMRobustDisp	0.788	0.001	0.790
estimateGLMTagwiseDisp	0.223	0.001	0.225
estimateGLMTrendedDisp	0.164	0.001	0.165
estimateTagwiseDisp	0	0	0
estimateTrendedDisp	0.480	0.006	0.487
exactTest	0.015	0.000	0.016
expandAsMatrix	0.001	0.000	0.001
getCounts	0.012	0.000	0.013
getPriorN	0.003	0.000	0.003
glmfit	0.061	0.001	0.062
gof	0.012	0.000	0.012
goodTuring	0.009	0.001	0.009
loessByCol	0.003	0.001	0.003
maPlot	0.018	0.001	0.020
maximizeInterpolant	0.001	0.001	0.001
maximizeQuadratic	0.003	0.000	0.004
meanvar	0.060	0.002	0.065
mglm	0.011	0.000	0.011
movingAverageByCol	0.001	0.000	0.001
nbinomDeviance	0.001	0.000	0.001
plotBCV	0.534	0.005	0.541
plotExonUsage	0.009	0.001	0.010
plotMDS.DGEList	0.027	0.011	0.038
plotSmear	0.391	0.007	0.401
predFC	0.017	0.001	0.019
q2qnbinom	0.002	0.000	0.002
readDGE	0.001	0.000	0.001
roast.DGEList	0.202	0.003	0.218
spliceVariants	0.022	0.000	0.023
splitIntoGroups	0.003	0.000	0.004
subsetting	0.028	0.001	0.030
sumTechReps	0.001	0.000	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.001	0.001	0.001
topTags	0.029	0.001	0.031
validDGEList	0.004	0.000	0.004
weightedCondLogLikDerDelta	0.004	0.001	0.004
zscoreNBinom	0.001	0.000	0.001