Package: edgeR

Version: 3.1.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_3.1.9.tar.gz

StartedAt: 2013-03-24 04:46:51 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 04:48:46 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 115.0 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 3.0.0 beta (2013-03-21 r62346)
* 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 '3.1.9'
* 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 ... [14s/14s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [13s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'edgeR-Tests.R' [9s/9s]
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 [10s/10s] 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 -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
   'edgeR.Rnw' 
** testing if installed package can be loaded
* DONE (edgeR)

name	user	system	elapsed
DGEList	0.038	0.003	0.052
WLEB	0.166	0.017	0.210
adjustedProfileLik	0.022	0.002	0.025
aveLogCPM	0.024	0.001	0.027
binomTest	0.015	0.000	0.020
calcNormFactors	0.019	0.001	0.020
camera.DGEList	0.367	0.009	0.433
commonCondLogLikDerDelta	0.090	0.001	0.106
condLogLikDerSize	0.012	0.001	0.014
cpm	0.014	0.001	0.015
cutWithMinN	0.019	0.001	0.023
dglmStdResid	0.102	0.006	0.130
dim	0.020	0.001	0.021
dispBinTrend	0.732	0.020	0.998
dispCoxReid	0.065	0.001	0.071
dispCoxReidInterpolateTagwise	0.075	0.003	0.089
dispCoxReidSplineTrend	1.247	0.016	1.414
edgeRUsersGuide	0.013	0.002	0.020
equalizeLibSizes	0.047	0.001	0.049
estimateCommonDisp	0.072	0.001	0.103
estimateDisp	0.412	0.006	0.486
estimateExonGenewisedisp	0.050	0.001	0.069
estimateGLMCommonDisp	0.137	0.004	0.172
estimateGLMTagwiseDisp	1.268	0.014	1.460
estimateGLMTrendedDisp	0.496	0.006	0.601
estimateTagwiseDisp	0.005	0.000	0.006
estimateTrendedDisp	1.141	0.022	1.304
exactTest	0.048	0.002	0.056
expandAsMatrix	0.007	0.001	0.008
getCounts	0.029	0.002	0.030
getPriorN	0.013	0.001	0.015
glmfit	0.109	0.004	0.134
gof	0.042	0.003	0.052
goodTuring	0.021	0.001	0.029
loessByCol	0.014	0.001	0.016
maPlot	0.034	0.002	0.038
maximizeInterpolant	0.011	0.001	0.015
maximizeQuadratic	0.012	0.000	0.012
meanvar	0.131	0.005	0.170
mglm	0.089	0.003	0.099
movingAverageByCol	0.012	0.001	0.013
plotBCV	0.963	0.013	1.120
plotExonUsage	0.025	0.003	0.033
plotMDS.DGEList	0.133	0.005	0.199
plotSmear	0.806	0.015	0.952
predFC	0.048	0.003	0.056
q2qnbinom	0.017	0.001	0.024
readDGE	0.007	0.002	0.009
roast.DGEList	0.319	0.017	0.353
spliceVariants	0.039	0.001	0.042
splitIntoGroups	0.016	0.000	0.022
subsetting	0.050	0.002	0.054
systematicSubset	0.009	0.001	0.012
thinCounts	0.008	0.001	0.010
topTags	0.058	0.004	0.064
weightedCondLogLikDerDelta	0.015	0.001	0.019
zscoreNBinom	0.007	0.001	0.008