BioC 3.0: CHECK report for edgeR on perceval

Package: edgeR

Version: 3.8.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_3.8.6.tar.gz

StartedAt: 2015-04-10 01:04:24 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:06:01 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 96.8 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_3.8.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/edgeR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [13s/16s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/10s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [6s/6s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [7s/7s] 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/edgeR.Rcheck/00check.log’
for details.

* installing *source* package ‘edgeR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_levenberg.cpp -o R_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_one_group.cpp -o R_one_group.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c adj_coxreid.cpp -o adj_coxreid.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fmm_spline.c -o fmm_spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_levenberg.cpp -o glm_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glm_one_group.cpp -o glm_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.cpp -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c interpolator.cpp -o interpolator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matvec_check.cpp -o matvec_check.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nbdev.cpp -o nbdev.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/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-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	0.018	0.001	0.020
WLEB	0.134	0.010	0.145
adjustedProfileLik	0.010	0.001	0.011
aveLogCPM	0.003	0.000	0.003
binomTest	0.003	0.001	0.003
calcNormFactors	0.007	0.002	0.009
camera.DGEList	0.201	0.007	0.208
commonCondLogLikDerDelta	0.005	0.001	0.005
condLogLikDerSize	0.001	0.000	0.002
cpm	0.004	0.001	0.006
cutWithMinN	0.003	0.001	0.003
dglmStdResid	0.024	0.001	0.026
diffSpliceDGE	0.253	0.008	0.292
dim	0.004	0.000	0.005
dispBinTrend	0.728	0.009	0.743
dispCoxReid	0.036	0.002	0.038
dispCoxReidInterpolateTagwise	0.041	0.002	0.043
dispCoxReidSplineTrend	1.021	0.008	1.042
edgeRUsersGuide	0.003	0.001	0.005
equalizeLibSizes	0.025	0.001	0.025
estimateCommonDisp	0.027	0.000	0.027
estimateDisp	0.261	0.003	0.265
estimateExonGenewisedisp	0.021	0.000	0.022
estimateGLMCommonDisp	0.071	0.001	0.073
estimateGLMRobustDisp	0.847	0.002	0.853
estimateGLMTagwiseDisp	0.205	0.000	0.205
estimateGLMTrendedDisp	0.164	0.001	0.169
estimateTagwiseDisp	0.000	0.000	0.001
estimateTrendedDisp	0.559	0.011	0.579
exactTest	0.018	0.001	0.019
expandAsMatrix	0.001	0.000	0.001
getCounts	0.015	0.000	0.016
getPriorN	0.003	0.000	0.003
glmQLFTest	0.529	0.008	0.546
glmfit	0.062	0.001	0.064
goana	0.001	0.001	0.001
gof	0.016	0.001	0.016
goodTuring	0.012	0.002	0.048
loessByCol	0.002	0.001	0.003
maPlot	0.018	0.002	0.024
maximizeInterpolant	0.001	0.001	0.001
maximizeQuadratic	0.002	0.000	0.001
meanvar	0.181	0.005	0.209
mglm	0.009	0.000	0.009
movingAverageByCol	0.001	0.001	0.001
nbinomDeviance	0.001	0.000	0.001
plotBCV	0.653	0.016	0.681
plotExonUsage	0.011	0.001	0.039
plotMDS.DGEList	0.028	0.004	0.086
plotQLDisp	0.476	0.007	0.531
plotSmear	0.569	0.005	0.611
plotSpliceDGE	0.000	0.000	0.001
predFC	0.017	0.001	0.030
q2qnbinom	0.002	0.001	0.002
readDGE	0.001	0.000	0.000
roast.DGEList	0.177	0.003	0.180
spliceVariants	0.022	0.000	0.023
splitIntoGroups	0.003	0.000	0.004
subsetting	0.023	0.001	0.024
sumTechReps	0.001	0.001	0.001
systematicSubset	0.001	0.000	0.001
thinCounts	0.001	0.001	0.001
topSpliceDGE	0.001	0.000	0.000
topTags	0.028	0.003	0.031
treatDGE	0.028	0.001	0.029
validDGEList	0.003	0.000	0.003
weightedCondLogLikDerDelta	0.004	0.000	0.004
zscoreNBinom	0.001	0.000	0.001