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_2.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/edge.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.1.0’
* 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 ... [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 344Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/43s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
apply_snm 13.907  0.099  14.159
* 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_qvalue	1.218	0.004	1.221
apply_snm	13.907	0.099	14.159
apply_sva	2.725	0.028	2.837
betaCoef	0.470	0.000	0.469
build_models	0.442	0.000	0.441
build_study	0.441	0.000	0.441
deSet	0.832	0.000	0.831
edge	0.001	0.000	0.000
endotoxin	1.184	0.004	1.188
fitFull	0.474	0.004	0.477
fitNull	0.471	0.000	0.471
fit_models	0.469	0.004	0.473
fullMatrix	0.435	0.008	0.443
fullModel	0.682	0.000	0.681
gibson	0.990	0.000	0.989
individual	0.438	0.000	0.455
kidney	1.225	0.000	1.290
kl_clust	0.612	0.000	0.624
lrt	1.223	0.004	1.244
nullMatrix	0.407	0.000	0.407
nullModel	0.985	0.000	0.994
odp	1.908	0.000	1.993
qvalueObj	1.206	0.000	1.219
resFull	0.485	0.000	0.507
resNull	0.48	0.00	0.48
sType	0.470	0.004	0.470
show	1.196	0.004	1.201
summary	1.129	0.000	1.128

BioC 3.2: CHECK report for edge on zin1

Summary

Command output