BioC 3.5: CHECK report for iCOBRA on oaxaca

Package: iCOBRA

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCOBRA_1.3.0.tar.gz

StartedAt: 2017-03-04 04:28:42 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:31:03 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 140.5 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/iCOBRA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.3.0’
* 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	0.116	0.003	0.118
COBRAPerformance	0.005	0.001	0.005
COBRAPlot	0.002	0.000	0.001
COBRAapp	0.002	0.000	0.003
Extract	0.394	0.005	0.398
basemethods	2.002	0.020	2.024
calculate_adjp	0.019	0.001	0.020
calculate_performance	1.218	0.017	1.236
coerce	0.315	0.007	0.322
corr	0.103	0.003	0.106
deviation	0.847	0.003	0.850
facetted	0.132	0.003	0.135
fdrnbr	0.113	0.002	0.115
fdrnbrcurve	0.567	0.008	0.577
fdrtpr	0.127	0.003	0.131
fdrtprcurve	0.564	0.004	0.568
fpc	0.427	0.003	0.431
fpr	0.172	0.003	0.177
maxsplit	0.341	0.003	0.350
onlyshared	0.127	0.001	0.130
overlap	0.020	0.001	0.021
padj	0.082	0.001	0.084
plot_corr	1.497	0.005	1.510
plot_deviation	4.325	0.017	4.369
plot_fdrnbrcurve	1.026	0.020	1.050
plot_fdrtprcurve	1.332	0.009	1.348
plot_fpc	0.860	0.009	0.870
plot_fpr	0.389	0.002	0.392
plot_overlap	0.043	0.001	0.044
plot_roc	0.986	0.010	0.996
plot_scatter	1.392	0.006	1.399
plot_tpr	0.341	0.002	0.345
plot_upset	2.766	0.009	2.777
plotcolors	0.096	0.001	0.098
prepare_data_for_plot	1.006	0.008	1.014
pval	0.009	0.002	0.010
reorder_levels	0.001	0.000	0.001
roc	0.593	0.006	0.599
scatter	0.661	0.006	0.667
score	0.007	0.001	0.008
splv	0.265	0.005	0.270
stratiflevels	0.327	0.003	0.331
tpr	0.099	0.003	0.102
truth	0.011	0.000	0.012