BioC 2.13: CHECK report for edgeR on zin1

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

* 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.

* 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)

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