BioC 3.6: CHECK report for iCOBRA on veracruz1

Package: iCOBRA

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCOBRA_1.5.0.tar.gz

StartedAt: 2017-08-16 04:25:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:28:09 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 132.9 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.5.0’
* 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	0.151	0.003	0.155
COBRAPerformance	0.006	0.001	0.007
COBRAPlot	0.003	0.000	0.003
COBRAapp	0.003	0.001	0.004
Extract	0.389	0.007	0.398
basemethods	1.834	0.018	1.941
calculate_adjp	0.015	0.001	0.016
calculate_performance	1.035	0.010	1.064
coerce	0.268	0.004	0.286
corr	0.037	0.001	0.038
deviation	0.767	0.004	0.790
facetted	0.179	0.001	0.185
fdrnbr	0.095	0.003	0.098
fdrnbrcurve	0.371	0.002	0.383
fdrtpr	0.160	0.001	0.162
fdrtprcurve	0.411	0.005	0.427
fpc	0.514	0.003	0.536
fpr	0.080	0.001	0.081
maxsplit	0.396	0.002	0.412
onlyshared	0.102	0.001	0.103
overlap	0.086	0.001	0.092
padj	0.007	0.000	0.008
plot_corr	1.111	0.004	1.159
plot_deviation	3.490	0.013	3.619
plot_fdrnbrcurve	0.933	0.011	0.973
plot_fdrtprcurve	1.092	0.006	1.126
plot_fpc	0.875	0.005	0.908
plot_fpr	0.416	0.006	0.433
plot_overlap	0.044	0.002	0.048
plot_roc	0.913	0.009	0.939
plot_scatter	1.164	0.010	1.208
plot_tpr	0.359	0.002	0.373
plot_upset	2.679	0.007	2.765
plotcolors	0.101	0.000	0.110
prepare_data_for_plot	1.011	0.008	1.055
pval	0.099	0.002	0.111
reorder_levels	0.000	0.000	0.001
roc	0.432	0.003	0.444
scatter	0.647	0.004	0.682
score	0.008	0.000	0.008
splv	0.228	0.002	0.240
stratiflevels	0.282	0.001	0.296
tpr	0.083	0.002	0.089
truth	0.014	0.001	0.014