BioC 3.4: CHECK report for iCOBRA on morelia

Package: iCOBRA

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCOBRA_1.1.2.tar.gz

StartedAt: 2016-09-20 08:02:00 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:03:42 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 102.3 seconds

RetCode: 0

Status:  OK

CheckDir: iCOBRA.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 iCOBRA_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/iCOBRA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iCOBRA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iCOBRA’ version ‘1.1.2’
* 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 ‘iCOBRA’ can be installed ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 ‘iCOBRA’ ...
** 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 (iCOBRA)

name	user	system	elapsed
COBRAData	0.005	0.000	0.005
COBRAPerformance	0.005	0.000	0.005
COBRAPlot	0.002	0.000	0.002
COBRAapp	0.002	0.001	0.003
Extract	0.107	0.005	0.113
basemethods	0.332	0.006	0.337
calculate_adjp	0.012	0.001	0.013
calculate_performance	0.742	0.009	0.751
coerce	0.129	0.003	0.133
corr	0.023	0.001	0.025
deviation	0.497	0.004	0.501
facetted	0.080	0.006	0.086
fdrnbr	0.079	0.002	0.080
fdrnbrcurve	0.346	0.003	0.350
fdrtpr	0.071	0.001	0.071
fdrtprcurve	0.471	0.006	0.478
fpc	0.552	0.007	0.559
fpr	0.091	0.002	0.093
maxsplit	0.238	0.002	0.241
onlyshared	0.067	0.001	0.067
overlap	0.010	0.000	0.011
padj	0.007	0.001	0.008
plot_corr	0.230	0.005	0.234
plot_deviation	0.986	0.012	0.998
plot_fdrnbrcurve	0.918	0.007	0.947
plot_fdrtprcurve	0.902	0.008	0.912
plot_fpc	0.592	0.010	0.602
plot_fpr	0.248	0.002	0.251
plot_overlap	0.032	0.001	0.033
plot_roc	0.768	0.010	0.779
plot_scatter	0.953	0.012	0.973
plot_tpr	0.337	0.003	0.343
plot_upset	1.153	0.005	1.159
plotcolors	0.081	0.001	0.082
prepare_data_for_plot	0.794	0.009	0.802
pval	0.006	0.001	0.008
reorder_levels	0.000	0.000	0.001
roc	0.325	0.003	0.328
scatter	0.500	0.004	0.505
score	0.006	0.000	0.007
splv	0.180	0.007	0.186
stratiflevels	0.217	0.005	0.222
tpr	0.074	0.001	0.073
truth	0.007	0.000	0.008