BioC 3.5: CHECK report for iCOBRA on veracruz2

Package: iCOBRA

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCOBRA_1.4.0.tar.gz

StartedAt: 2017-08-16 04:10:26 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:12:41 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 135.2 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/iCOBRA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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 ‘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	0.142	0.002	0.153
COBRAPerformance	0.006	0.001	0.007
COBRAPlot	0.003	0.000	0.002
COBRAapp	0.002	0.001	0.004
Extract	0.367	0.008	0.386
basemethods	1.808	0.016	1.867
calculate_adjp	0.018	0.001	0.019
calculate_performance	1.075	0.014	1.130
coerce	0.264	0.004	0.272
corr	0.036	0.001	0.036
deviation	0.823	0.008	0.838
facetted	0.177	0.005	0.187
fdrnbr	0.091	0.002	0.095
fdrnbrcurve	0.380	0.002	0.393
fdrtpr	0.152	0.001	0.158
fdrtprcurve	0.382	0.003	0.399
fpc	0.548	0.002	0.566
fpr	0.083	0.001	0.089
maxsplit	0.404	0.002	0.426
onlyshared	0.084	0.001	0.088
overlap	0.089	0.001	0.089
padj	0.008	0.001	0.009
plot_corr	1.245	0.006	1.283
plot_deviation	3.449	0.017	3.560
plot_fdrnbrcurve	0.930	0.011	0.975
plot_fdrtprcurve	1.194	0.013	1.249
plot_fpc	0.809	0.004	0.843
plot_fpr	0.488	0.002	0.512
plot_overlap	0.038	0.001	0.039
plot_roc	0.955	0.010	0.993
plot_scatter	1.244	0.009	1.279
plot_tpr	0.383	0.004	0.395
plot_upset	2.646	0.008	2.715
plotcolors	0.108	0.002	0.110
prepare_data_for_plot	0.957	0.011	0.995
pval	0.018	0.001	0.019
reorder_levels	0.001	0.000	0.001
roc	0.491	0.005	0.503
scatter	0.620	0.002	0.633
score	0.009	0.000	0.009
splv	0.250	0.002	0.259
stratiflevels	0.274	0.003	0.285
tpr	0.093	0.004	0.096
truth	0.010	0.001	0.011