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: 2017-10-18 04:55:46 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:58:02 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 135.9 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 3.4.2 (2017-09-28)
* 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	0.148	0.001	0.154
COBRAPerformance	0.006	0.001	0.007
COBRAPlot	0.003	0.001	0.004
COBRAapp	0.003	0.001	0.003
Extract	0.362	0.012	0.381
basemethods	1.839	0.023	1.930
calculate_adjp	0.016	0.001	0.018
calculate_performance	1.074	0.013	1.118
coerce	0.270	0.005	0.283
corr	0.033	0.002	0.035
deviation	0.705	0.005	0.739
facetted	0.107	0.003	0.118
fdrnbr	0.105	0.002	0.109
fdrnbrcurve	0.450	0.004	0.470
fdrtpr	0.093	0.004	0.099
fdrtprcurve	0.395	0.003	0.418
fpc	0.543	0.004	0.557
fpr	0.079	0.004	0.085
maxsplit	0.393	0.006	0.414
onlyshared	0.090	0.001	0.094
overlap	0.017	0.001	0.018
padj	0.009	0.001	0.010
plot_corr	1.265	0.009	1.312
plot_deviation	3.689	0.027	3.874
plot_fdrnbrcurve	1.047	0.010	1.098
plot_fdrtprcurve	1.127	0.011	1.164
plot_fpc	0.911	0.012	0.956
plot_fpr	0.393	0.003	0.408
plot_overlap	0.038	0.002	0.040
plot_roc	0.869	0.007	0.899
plot_scatter	1.367	0.010	1.418
plot_tpr	0.366	0.003	0.377
plot_upset	2.689	0.017	2.790
plotcolors	0.099	0.002	0.103
prepare_data_for_plot	1.016	0.011	1.063
pval	0.012	0.001	0.013
reorder_levels	0.001	0.000	0.001
roc	0.476	0.004	0.494
scatter	0.732	0.004	0.758
score	0.009	0.000	0.010
splv	0.272	0.001	0.279
stratiflevels	0.302	0.002	0.310
tpr	0.087	0.002	0.090
truth	0.013	0.001	0.013