BioC 3.3: CHECK report for iCOBRA on morelia

Package: iCOBRA

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCOBRA_0.99.9.tar.gz

StartedAt: 2016-04-21 04:01:05 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:03:45 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 159.7 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_0.99.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/iCOBRA.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.9’
* 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 ... [5s/5s] 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 ... [23s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [67s/69s]
 [67s/70s] 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	0.008	0.000	0.008
COBRAPerformance	0.008	0.000	0.008
COBRAPlot	0.003	0.000	0.003
COBRAapp	0.003	0.000	0.003
Extract	0.180	0.010	0.192
basemethods	0.599	0.015	0.622
calculate_adjp	0.023	0.001	0.026
calculate_performance	1.304	0.015	1.352
coerce	0.165	0.005	0.177
corr	0.098	0.002	0.104
deviation	0.906	0.004	0.939
facetted	0.151	0.003	0.155
fdrnbr	0.136	0.003	0.140
fdrnbrcurve	0.518	0.002	0.522
fdrtpr	0.156	0.002	0.175
fdrtprcurve	0.562	0.007	0.585
fpc	0.616	0.003	0.669
fpr	0.185	0.002	0.198
maxsplit	0.299	0.003	0.324
onlyshared	0.178	0.001	0.191
overlap	0.020	0.001	0.022
padj	0.010	0.001	0.014
plot_corr	0.448	0.006	0.457
plot_deviation	1.582	0.012	1.821
plot_fdrnbrcurve	1.272	0.013	1.317
plot_fdrtprcurve	1.363	0.014	1.404
plot_fpc	0.987	0.004	1.054
plot_fpr	0.447	0.002	0.497
plot_overlap	0.057	0.002	0.060
plot_roc	1.086	0.006	1.134
plot_scatter	1.595	0.011	1.696
plot_tpr	0.494	0.006	0.507
plot_upset	2.014	0.006	2.269
plotcolors	0.127	0.003	0.135
prepare_data_for_plot	1.396	0.011	1.448
pval	0.024	0.002	0.029
reorder_levels	0.000	0.000	0.001
roc	0.630	0.003	0.645
scatter	0.990	0.007	1.019
score	0.010	0.001	0.012
splv	0.290	0.011	0.302
stratiflevels	0.364	0.011	0.383
tpr	0.127	0.002	0.142
truth	0.014	0.001	0.015