BioC 3.0: CHECK report for edgeR on zin1

Package: edgeR

Version: 3.8.6

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.8.6.tar.gz

StartedAt: 2015-04-09 23:31:47 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:32:57 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 69.6 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.8.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/edgeR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘3.8.6’
* 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 ... [12s/12s] 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
'library' or 'require' calls in package code:
  ‘locfit’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
dispBinTrend: no visible global function definition for ‘ns’
dispCoxReidSplineTrend: no visible global function definition for ‘ns’
locfitByCol: no visible global function definition for ‘locfit.raw’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* 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/6s] 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
* DONE

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/edgeR.Rcheck/00check.log’
for details.

* installing *source* package ‘edgeR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_levenberg.cpp -o R_levenberg.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_one_group.cpp -o R_one_group.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c adj_coxreid.cpp -o adj_coxreid.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fmm_spline.c -o fmm_spline.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_levenberg.cpp -o glm_levenberg.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_one_group.cpp -o glm_one_group.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c interpolator.cpp -o interpolator.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matvec_check.cpp -o matvec_check.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nbdev.cpp -o nbdev.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o edgeR.so R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** 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	0.016	0.000	0.019
WLEB	0.092	0.004	0.096
adjustedProfileLik	0.044	0.000	0.045
aveLogCPM	0.004	0.000	0.002
binomTest	0.004	0.000	0.002
calcNormFactors	0.008	0.000	0.006
camera.DGEList	0.156	0.004	0.160
commonCondLogLikDerDelta	0.004	0.000	0.004
condLogLikDerSize	0.004	0.000	0.001
cpm	0.004	0.000	0.004
cutWithMinN	0.004	0.000	0.003
dglmStdResid	0.016	0.000	0.015
diffSpliceDGE	0.184	0.000	0.183
dim	0.004	0.000	0.003
dispBinTrend	0.608	0.004	0.614
dispCoxReid	0.032	0.000	0.030
dispCoxReidInterpolateTagwise	0.036	0.004	0.039
dispCoxReidSplineTrend	0.868	0.000	0.872
edgeRUsersGuide	0.004	0.000	0.003
equalizeLibSizes	0.020	0.000	0.021
estimateCommonDisp	0.028	0.000	0.029
estimateDisp	0.204	0.004	0.210
estimateExonGenewisedisp	0.016	0.004	0.020
estimateGLMCommonDisp	0.072	0.000	0.072
estimateGLMRobustDisp	0.712	0.000	0.712
estimateGLMTagwiseDisp	0.172	0.000	0.172
estimateGLMTrendedDisp	0.140	0.000	0.143
estimateTagwiseDisp	0.000	0.000	0.001
estimateTrendedDisp	0.452	0.004	0.456
exactTest	0.016	0.000	0.015
expandAsMatrix	0.004	0.000	0.001
getCounts	0.012	0.000	0.012
getPriorN	0.004	0.000	0.003
glmQLFTest	0.456	0.000	0.455
glmfit	0.048	0.000	0.048
goana	0.000	0.000	0.001
gof	0.012	0.000	0.012
goodTuring	0.012	0.000	0.009
loessByCol	0.004	0.000	0.003
maPlot	0.016	0.000	0.016
maximizeInterpolant	0.000	0.000	0.001
maximizeQuadratic	0.000	0.000	0.001
meanvar	0.068	0.000	0.068
mglm	0.008	0.000	0.008
movingAverageByCol	0.000	0.000	0.001
nbinomDeviance	0	0	0
plotBCV	0.572	0.000	0.577
plotExonUsage	0.008	0.000	0.007
plotMDS.DGEList	0.020	0.000	0.022
plotQLDisp	0.408	0.008	0.416
plotSmear	0.504	0.000	0.504
plotSpliceDGE	0	0	0
predFC	0.016	0.000	0.015
q2qnbinom	0.004	0.000	0.001
readDGE	0.000	0.000	0.001
roast.DGEList	0.152	0.004	0.157
spliceVariants	0.020	0.000	0.019
splitIntoGroups	0.004	0.000	0.003
subsetting	0.020	0.000	0.021
sumTechReps	0.000	0.000	0.001
systematicSubset	0	0	0
thinCounts	0	0	0
topSpliceDGE	0	0	0
topTags	0.028	0.000	0.027
treatDGE	0.020	0.000	0.023
validDGEList	0.000	0.000	0.003
weightedCondLogLikDerDelta	0.000	0.000	0.004
zscoreNBinom	0.000	0.000	0.001