BioC 3.2: CHECK report for edge on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edge_2.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/edge.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘edge’ version ‘2.1.0’
* 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 ‘edge’ can be installed ... [16s/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 loading without being on the library search path ... OK
* checking 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 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 ... [54s/60s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
apply_snm 17.646  1.328  19.451
apply_sva  3.535  0.257   5.045
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/13s]
 [11s/13s] 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

Status: OK

* installing *source* package ‘edge’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c edge-init.c -o edge-init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c edgeKLODP.c -o edgeKLODP.o
clang -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 -o edge.so edge-init.o edgeKLODP.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/edge.Rcheck/edge/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edge)

name	user	system	elapsed
apply_qvalue	1.484	0.023	1.522
apply_snm	17.646	1.328	19.451
apply_sva	3.535	0.257	5.045
betaCoef	0.617	0.003	0.622
build_models	0.634	0.007	0.641
build_study	0.655	0.003	0.658
deSet	1.204	0.005	1.210
edge	0	0	0
endotoxin	1.166	0.058	1.338
fitFull	0.590	0.010	0.601
fitNull	0.658	0.005	0.720
fit_models	0.701	0.009	0.745
fullMatrix	0.595	0.004	0.600
fullModel	0.955	0.004	0.960
gibson	1.253	0.058	1.314
individual	0.551	0.002	1.658
kidney	1.388	0.080	1.468
kl_clust	0.752	0.019	0.772
lrt	1.353	0.075	1.433
nullMatrix	0.652	0.017	0.676
nullModel	1.302	0.011	1.320
odp	2.236	0.250	3.432
qvalueObj	1.239	0.079	1.322
resFull	0.475	0.007	0.484
resNull	0.548	0.004	0.551
sType	0.568	0.003	0.572
show	1.258	0.082	1.348
summary	1.265	0.080	1.359

BioC 3.2: CHECK report for edge on oaxaca

Summary

Command output