BioC 3.2: CHECK report for edge on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings edge_2.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/edge.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ‘2.2.1’
* 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘edge.pdf’ from 452Kb to 345Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
apply_snm 13.215  0.073  13.281
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [9s/9s]
 [9s/9s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/edge.Rcheck/00check.log’
for details.

* installing *source* package ‘edge’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c edge-init.c -o edge-init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c edgeKLODP.c -o edgeKLODP.o
edgeKLODP.c: In function ‘odpScoreCluster’:
edgeKLODP.c:11:19: warning: ‘middle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   double *first, *middle;
                   ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o edge.so edge-init.o edgeKLODP.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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_jackstraw	2.085	0.008	2.091
apply_qvalue	0.757	0.008	0.765
apply_snm	13.215	0.073	13.281
apply_sva	2.537	0.020	2.559
betaCoef	0.401	0.000	0.402
build_models	0.428	0.000	0.429
build_study	0.446	0.000	0.446
deSet	0.834	0.000	0.834
edge	0	0	0
endotoxin	1.059	0.004	1.063
fitFull	0.441	0.000	0.442
fitNull	0.433	0.000	0.432
fit_models	0.437	0.000	0.438
fullMatrix	0.427	0.000	0.426
fullModel	0.669	0.000	0.672
gibson	0.934	0.000	0.939
individual	0.446	0.000	0.446
kidney	1.019	0.000	1.019
kl_clust	0.536	0.003	0.540
lrt	1.100	0.004	1.105
nullMatrix	0.425	0.000	0.425
nullModel	0.853	0.000	0.853
odp	1.909	0.004	1.937
qvalueObj	1.321	0.004	1.478
resFull	0.449	0.000	0.450
resNull	0.434	0.000	0.446
sType	0.450	0.000	0.449
show	1.221	0.000	1.222
summary	1.118	0.000	1.118

BioC 3.2: CHECK report for edge on zin1

Summary

Command output