BioC 2.13: CHECK report for edgeR on zin1
This page was generated on 2014-04-05 09:47:40 -0700 (Sat, 05 Apr 2014).
edgeR 3.4.2 Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/edgeR | Last Changed Rev: 83948 / Revision: 88450 | Last Changed Date: 2013-12-05 07:55:15 -0800 (Thu, 05 Dec 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
Package: edgeR |
Version: 3.4.2 |
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.4.2.tar.gz |
StartedAt: 2014-04-05 00:56:50 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 00:57:47 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 57.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: edgeR.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/edgeR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.4.2’
* 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 ... [7s/7s] 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 ... NOTE
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘edgeR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘edgeR-Tests.R’ [5s/5s]
Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
[5s/5s] 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/edgeR.Rcheck/00check.log’
for details.
edgeR.Rcheck/00install.out:
* installing *source* package ‘edgeR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c R_levenberg.cpp -o R_levenberg.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c R_one_group.cpp -o R_one_group.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c core/interpolator.cpp -o core/interpolator.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./core -I. -I/usr/local/include -fpic -g -O2 -Wall -c core/fmm_spline.c -o core/fmm_spline.o
g++ -shared -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/home/biocbuild/bbs-2.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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)
edgeR.Rcheck/edgeR-Ex.timings:
name | user | system | elapsed
|
DGEList | 0.020 | 0.004 | 0.024 |
|
WLEB | 0.140 | 0.004 | 0.143 |
|
adjustedProfileLik | 0.012 | 0.004 | 0.015 |
|
aveLogCPM | 0.004 | 0.000 | 0.006 |
|
binomTest | 0.008 | 0.000 | 0.005 |
|
calcNormFactors | 0.040 | 0.000 | 0.043 |
|
camera.DGEList | 0.176 | 0.008 | 0.185 |
|
commonCondLogLikDerDelta | 0.012 | 0.000 | 0.011 |
|
condLogLikDerSize | 0.008 | 0.000 | 0.006 |
|
cpm | 0.012 | 0.000 | 0.009 |
|
cutWithMinN | 0.008 | 0.000 | 0.008 |
|
dglmStdResid | 0.060 | 0.000 | 0.061 |
|
dim | 0.048 | 0.000 | 0.050 |
|
dispBinTrend | 0.604 | 0.000 | 0.605 |
|
dispCoxReid | 0.036 | 0.000 | 0.036 |
|
dispCoxReidInterpolateTagwise | 0.040 | 0.004 | 0.044 |
|
dispCoxReidSplineTrend | 0.692 | 0.000 | 0.692 |
|
edgeRUsersGuide | 0.004 | 0.000 | 0.006 |
|
equalizeLibSizes | 0.024 | 0.004 | 0.028 |
|
estimateCommonDisp | 0.032 | 0.000 | 0.033 |
|
estimateDisp | 0.240 | 0.000 | 0.243 |
|
estimateExonGenewisedisp | 0.020 | 0.000 | 0.021 |
|
estimateGLMCommonDisp | 0.080 | 0.000 | 0.079 |
|
estimateGLMTagwiseDisp | 0.196 | 0.004 | 0.200 |
|
estimateGLMTrendedDisp | 0.168 | 0.000 | 0.169 |
|
estimateTagwiseDisp | 0.004 | 0.000 | 0.003 |
|
estimateTrendedDisp | 0.696 | 0.000 | 0.694 |
|
exactTest | 0.02 | 0.00 | 0.02 |
|
expandAsMatrix | 0.004 | 0.000 | 0.003 |
|
getCounts | 0.012 | 0.000 | 0.013 |
|
getPriorN | 0.004 | 0.000 | 0.006 |
|
glmfit | 0.060 | 0.000 | 0.061 |
|
gof | 0.060 | 0.000 | 0.061 |
|
goodTuring | 0.012 | 0.000 | 0.012 |
|
loessByCol | 0.004 | 0.004 | 0.006 |
|
maPlot | 0.020 | 0.000 | 0.019 |
|
maximizeInterpolant | 0.004 | 0.000 | 0.005 |
|
maximizeQuadratic | 0.004 | 0.000 | 0.004 |
|
meanvar | 0.068 | 0.000 | 0.068 |
|
mglm | 0.044 | 0.000 | 0.047 |
|
movingAverageByCol | 0.004 | 0.000 | 0.004 |
|
plotBCV | 0.596 | 0.000 | 0.596 |
|
plotExonUsage | 0.056 | 0.000 | 0.054 |
|
plotMDS.DGEList | 0.032 | 0.000 | 0.031 |
|
plotSmear | 0.492 | 0.000 | 0.493 |
|
predFC | 0.020 | 0.000 | 0.022 |
|
q2qnbinom | 0.004 | 0.000 | 0.004 |
|
readDGE | 0.000 | 0.000 | 0.003 |
|
roast.DGEList | 0.176 | 0.012 | 0.189 |
|
spliceVariants | 0.020 | 0.000 | 0.022 |
|
splitIntoGroups | 0.008 | 0.000 | 0.007 |
|
subsetting | 0.024 | 0.004 | 0.028 |
|
systematicSubset | 0.004 | 0.000 | 0.003 |
|
thinCounts | 0.004 | 0.000 | 0.004 |
|
topTags | 0.032 | 0.000 | 0.033 |
|
weightedCondLogLikDerDelta | 0.004 | 0.004 | 0.007 |
|
zscoreNBinom | 0.004 | 0.000 | 0.004 |
|