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Package 199/658HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 3.1.9
Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 74597 / Revision: 74756
Last Changed Date: 2013-03-19 21:41:13 -0700 (Tue, 19 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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

Command output

* 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

edgeR.Rcheck/00install.out:

* 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)

edgeR.Rcheck/edgeR-Ex.timings:

nameusersystemelapsed
DGEList0.0380.0030.052
WLEB0.1660.0170.210
adjustedProfileLik0.0220.0020.025
aveLogCPM0.0240.0010.027
binomTest0.0150.0000.020
calcNormFactors0.0190.0010.020
camera.DGEList0.3670.0090.433
commonCondLogLikDerDelta0.0900.0010.106
condLogLikDerSize0.0120.0010.014
cpm0.0140.0010.015
cutWithMinN0.0190.0010.023
dglmStdResid0.1020.0060.130
dim0.0200.0010.021
dispBinTrend0.7320.0200.998
dispCoxReid0.0650.0010.071
dispCoxReidInterpolateTagwise0.0750.0030.089
dispCoxReidSplineTrend1.2470.0161.414
edgeRUsersGuide0.0130.0020.020
equalizeLibSizes0.0470.0010.049
estimateCommonDisp0.0720.0010.103
estimateDisp0.4120.0060.486
estimateExonGenewisedisp0.0500.0010.069
estimateGLMCommonDisp0.1370.0040.172
estimateGLMTagwiseDisp1.2680.0141.460
estimateGLMTrendedDisp0.4960.0060.601
estimateTagwiseDisp0.0050.0000.006
estimateTrendedDisp1.1410.0221.304
exactTest0.0480.0020.056
expandAsMatrix0.0070.0010.008
getCounts0.0290.0020.030
getPriorN0.0130.0010.015
glmfit0.1090.0040.134
gof0.0420.0030.052
goodTuring0.0210.0010.029
loessByCol0.0140.0010.016
maPlot0.0340.0020.038
maximizeInterpolant0.0110.0010.015
maximizeQuadratic0.0120.0000.012
meanvar0.1310.0050.170
mglm0.0890.0030.099
movingAverageByCol0.0120.0010.013
plotBCV0.9630.0131.120
plotExonUsage0.0250.0030.033
plotMDS.DGEList0.1330.0050.199
plotSmear0.8060.0150.952
predFC0.0480.0030.056
q2qnbinom0.0170.0010.024
readDGE0.0070.0020.009
roast.DGEList0.3190.0170.353
spliceVariants0.0390.0010.042
splitIntoGroups0.0160.0000.022
subsetting0.0500.0020.054
systematicSubset0.0090.0010.012
thinCounts0.0080.0010.010
topTags0.0580.0040.064
weightedCondLogLikDerDelta0.0150.0010.019
zscoreNBinom0.0070.0010.008