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: 2013-03-25 02:15:20 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:17:07 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 106.6 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/edgeR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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/15s] 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 ... [12s/12s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'edgeR-Tests.R' [7s/7s]
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 [8s/8s] 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
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_levenberg.cpp -o R_levenberg.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_one_group.cpp -o R_one_group.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/interpolator.cpp -o core/interpolator.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c core/fmm_spline.c -o core/fmm_spline.o
g++ -arch i386 -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/i386 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -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/i386
** 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	0.039	0.010	0.049
WLEB	0.225	0.039	0.267
adjustedProfileLik	0.025	0.013	0.047
aveLogCPM	0.017	0.015	0.033
binomTest	0.013	0.010	0.023
calcNormFactors	0.019	0.007	0.026
camera.DGEList	0.362	0.034	0.397
commonCondLogLikDerDelta	0.011	0.008	0.021
condLogLikDerSize	0.007	0.006	0.013
cpm	0.014	0.009	0.023
cutWithMinN	0.010	0.006	0.017
dglmStdResid	0.102	0.016	0.121
dim	0.025	0.014	0.040
dispBinTrend	0.580	0.019	0.601
dispCoxReid	0.087	0.008	0.097
dispCoxReidInterpolateTagwise	0.053	0.008	0.062
dispCoxReidSplineTrend	0.921	0.012	0.934
edgeRUsersGuide	0.009	0.008	0.018
equalizeLibSizes	0.037	0.012	0.049
estimateCommonDisp	0.044	0.007	0.051
estimateDisp	0.353	0.014	0.368
estimateExonGenewisedisp	0.035	0.007	0.041
estimateGLMCommonDisp	0.133	0.009	0.143
estimateGLMTagwiseDisp	0.949	0.014	0.964
estimateGLMTrendedDisp	0.393	0.010	0.403
estimateTagwiseDisp	0.005	0.004	0.009
estimateTrendedDisp	1.148	0.039	1.190
exactTest	0.038	0.013	0.052
expandAsMatrix	0.009	0.008	0.017
getCounts	0.034	0.012	0.045
getPriorN	0.014	0.008	0.023
glmfit	0.125	0.025	0.152
gof	0.048	0.019	0.068
goodTuring	0.024	0.013	0.039
loessByCol	0.013	0.008	0.022
maPlot	0.041	0.011	0.053
maximizeInterpolant	0.011	0.007	0.018
maximizeQuadratic	0.011	0.007	0.019
meanvar	0.132	0.018	0.153
mglm	0.081	0.017	0.097
movingAverageByCol	0.008	0.007	0.015
plotBCV	1.108	0.055	1.165
plotExonUsage	0.027	0.012	0.045
plotMDS.DGEList	0.063	0.021	0.087
plotSmear	0.558	0.085	0.653
predFC	0.035	0.013	0.052
q2qnbinom	0.010	0.008	0.018
readDGE	0.007	0.005	0.013
roast.DGEList	0.245	0.028	0.273
spliceVariants	0.031	0.008	0.037
splitIntoGroups	0.051	0.008	0.060
subsetting	0.052	0.014	0.068
systematicSubset	0.007	0.007	0.014
thinCounts	0.007	0.006	0.013
topTags	0.043	0.016	0.060
weightedCondLogLikDerDelta	0.012	0.007	0.019
zscoreNBinom	0.005	0.005	0.010