BioC 2.12: CHECK report for edgeR on petty

Package: edgeR

Version: 3.2.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_3.2.4.tar.gz

StartedAt: 2013-10-08 22:15:21 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:17:31 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 130.4 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/edgeR.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '3.2.4'
* 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 ... [15s/17s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable 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 examples ... [14s/14s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'edgeR-Tests.R' [11s/11s]
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 [11s/11s] 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 vignettes ... 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./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -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./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -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./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -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./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c R_levenberg.cpp -o R_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -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./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c R_one_group.cpp -o R_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -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./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c core/adj_coxreid.cpp -o core/adj_coxreid.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c core/glm_levenberg.cpp -o core/glm_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c core/glm_one_group.cpp -o core/glm_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c core/interpolator.cpp -o core/interpolator.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c core/fmm_spline.c -o core/fmm_spline.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_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.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-2.12-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** data
** 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	0.050	0.002	0.051
WLEB	0.261	0.022	0.301
adjustedProfileLik	0.024	0.002	0.026
aveLogCPM	0.018	0.001	0.019
binomTest	0.017	0.000	0.019
calcNormFactors	0.019	0.001	0.020
camera.DGEList	0.362	0.012	0.383
commonCondLogLikDerDelta	0.015	0.000	0.017
condLogLikDerSize	0.008	0.000	0.009
cpm	0.015	0.001	0.025
cutWithMinN	0.080	0.001	0.082
dglmStdResid	0.109	0.009	0.119
dim	0.021	0.001	0.022
dispBinTrend	1.271	0.035	1.314
dispCoxReid	0.077	0.001	0.081
dispCoxReidInterpolateTagwise	0.082	0.004	0.087
dispCoxReidSplineTrend	1.534	0.025	1.583
edgeRUsersGuide	0.013	0.001	0.019
equalizeLibSizes	0.120	0.002	0.122
estimateCommonDisp	0.063	0.002	0.065
estimateDisp	0.519	0.007	0.526
estimateExonGenewisedisp	0.054	0.001	0.055
estimateGLMCommonDisp	0.152	0.003	0.156
estimateGLMTagwiseDisp	0.416	0.009	0.426
estimateGLMTrendedDisp	0.336	0.010	0.346
estimateTagwiseDisp	0.005	0.000	0.006
estimateTrendedDisp	1.531	0.032	1.572
exactTest	0.043	0.001	0.044
expandAsMatrix	0.006	0.001	0.007
getCounts	0.031	0.001	0.031
getPriorN	0.014	0.001	0.015
glmfit	0.137	0.003	0.143
gof	0.055	0.001	0.056
goodTuring	0.023	0.001	0.024
loessByCol	0.015	0.000	0.016
maPlot	0.038	0.002	0.040
maximizeInterpolant	0.010	0.001	0.010
maximizeQuadratic	0.010	0.001	0.011
meanvar	0.144	0.006	0.153
mglm	0.085	0.001	0.086
movingAverageByCol	0.009	0.001	0.009
plotBCV	1.162	0.020	1.187
plotExonUsage	0.021	0.001	0.023
plotMDS.DGEList	0.057	0.002	0.060
plotSmear	0.855	0.015	0.874
predFC	0.045	0.003	0.051
q2qnbinom	0.015	0.000	0.015
readDGE	0.006	0.000	0.007
roast.DGEList	0.367	0.004	0.382
spliceVariants	0.047	0.001	0.049
splitIntoGroups	0.015	0.000	0.016
subsetting	0.156	0.001	0.161
systematicSubset	0.006	0.001	0.007
thinCounts	0.006	0.001	0.006
topTags	0.056	0.003	0.061
weightedCondLogLikDerDelta	0.011	0.001	0.012
zscoreNBinom	0.004	0.000	0.004