BioC 3.3: CHECK report for edge on morelia

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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_2.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/edge.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘2.3.0’
* 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 ... [11s/11s] 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 ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
apply_snm 12.48  1.033  13.649
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [8s/8s]
 [8s/8s] 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-3.3-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_jackstraw	2.132	0.045	2.181
apply_qvalue	0.820	0.026	0.848
apply_snm	12.480	1.033	13.649
apply_sva	2.595	0.163	2.846
betaCoef	0.501	0.015	0.515
build_models	0.351	0.002	0.353
build_study	0.457	0.001	0.457
deSet	0.714	0.002	0.717
edge	0	0	0
endotoxin	0.977	0.057	1.034
fitFull	0.347	0.004	0.351
fitNull	0.350	0.002	0.353
fit_models	0.394	0.024	0.418
fullMatrix	0.351	0.005	0.356
fullModel	0.556	0.004	0.560
gibson	0.779	0.041	0.820
individual	0.361	0.006	0.367
kidney	0.871	0.061	0.932
kl_clust	0.444	0.014	0.459
lrt	1.077	0.079	1.157
nullMatrix	0.378	0.005	0.383
nullModel	0.792	0.008	0.799
odp	1.339	0.163	1.502
qvalueObj	0.836	0.059	0.894
resFull	0.326	0.006	0.332
resNull	0.356	0.014	0.369
sType	0.346	0.009	0.355
show	0.833	0.063	0.898
summary	0.776	0.057	0.833

BioC 3.3: CHECK report for edge on morelia

Summary

Command output