BioC 2.14: CHECK report for edgeR on petty

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 21:48:38 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:50:49 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 131.2 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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


* 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-darwin10.8.0 (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 ... [18s/18s] 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 ... [13s/13s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [8s/8s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [9s/9s] 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_cr_adjust.cpp -o R_cr_adjust.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_levenberg.cpp -o R_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_loess_by_col.cpp -o R_loess_by_col.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_one_group.cpp -o R_one_group.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c adj_coxreid.cpp -o adj_coxreid.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fmm_spline.c -o fmm_spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_levenberg.cpp -o glm_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_one_group.cpp -o glm_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c interpolator.cpp -o interpolator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matvec_check.cpp -o matvec_check.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nbdev.cpp -o nbdev.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -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	0.030	0.002	0.032
WLEB	0.229	0.013	0.244
adjustedProfileLik	0.016	0.002	0.019
aveLogCPM	0.004	0.001	0.005
binomTest	0.005	0.001	0.005
calcNormFactors	0.011	0.001	0.012
camera.DGEList	0.434	0.009	0.443
commonCondLogLikDerDelta	0.007	0.000	0.007
condLogLikDerSize	0.001	0.000	0.002
cpm	0.007	0.001	0.008
cutWithMinN	0.005	0.001	0.006
dglmStdResid	0.028	0.003	0.032
dim	0.007	0.002	0.008
dispBinTrend	1.200	0.010	1.214
dispCoxReid	0.061	0.001	0.062
dispCoxReidInterpolateTagwise	0.064	0.003	0.067
dispCoxReidSplineTrend	1.820	0.006	1.842
edgeRUsersGuide	0.005	0.001	0.006
equalizeLibSizes	0.033	0.001	0.033
estimateCommonDisp	0.047	0.001	0.048
estimateDisp	0.473	0.003	0.479
estimateExonGenewisedisp	0.035	0.001	0.037
estimateGLMCommonDisp	0.119	0.000	0.121
estimateGLMRobustDisp	1.402	0.002	1.409
estimateGLMTagwiseDisp	0.365	0.001	0.367
estimateGLMTrendedDisp	0.311	0.002	0.313
estimateTagwiseDisp	0.001	0.000	0.001
estimateTrendedDisp	0.871	0.009	0.882
exactTest	0.027	0.000	0.028
expandAsMatrix	0.001	0.000	0.001
getCounts	0.022	0.001	0.023
getPriorN	0.005	0.001	0.006
glmfit	0.099	0.001	0.100
gof	0.021	0.001	0.021
goodTuring	0.014	0.001	0.016
loessByCol	0.003	0.000	0.004
maPlot	0.030	0.002	0.033
maximizeInterpolant	0.002	0.000	0.003
maximizeQuadratic	0.006	0.000	0.008
meanvar	0.110	0.004	0.123
mglm	0.019	0.000	0.021
movingAverageByCol	0.001	0.000	0.002
nbinomDeviance	0.002	0.001	0.002
plotBCV	1.030	0.009	1.043
plotExonUsage	0.014	0.002	0.016
plotMDS.DGEList	0.044	0.003	0.049
plotSmear	0.643	0.008	0.653
predFC	0.029	0.002	0.032
q2qnbinom	0.003	0.000	0.003
readDGE	0.001	0.000	0.001
roast.DGEList	0.351	0.003	0.354
spliceVariants	0.034	0.000	0.035
splitIntoGroups	0.005	0.000	0.006
subsetting	0.043	0.001	0.045
sumTechReps	0.002	0.000	0.002
systematicSubset	0.001	0.001	0.002
thinCounts	0.001	0.000	0.002
topTags	0.049	0.002	0.051
validDGEList	0.005	0.001	0.005
weightedCondLogLikDerDelta	0.006	0.001	0.007
zscoreNBinom	0.001	0.000	0.001