BioC 3.3: CHECK report for iCOBRA on oaxaca

Package: iCOBRA

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iCOBRA_1.0.2.tar.gz

StartedAt: 2016-10-13 02:49:11 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:51:33 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 141.6 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_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/iCOBRA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.2’
* 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	0.007	0.000	0.007
COBRAPerformance	0.006	0.001	0.007
COBRAPlot	0.003	0.000	0.004
COBRAapp	0.003	0.001	0.004
Extract	0.165	0.009	0.174
basemethods	0.502	0.008	0.511
calculate_adjp	0.016	0.001	0.017
calculate_performance	1.077	0.013	1.091
coerce	0.166	0.004	0.169
corr	0.037	0.002	0.038
deviation	0.756	0.006	0.763
facetted	0.124	0.003	0.127
fdrnbr	0.129	0.003	0.132
fdrnbrcurve	0.517	0.002	0.527
fdrtpr	0.110	0.002	0.112
fdrtprcurve	0.491	0.002	0.495
fpc	0.571	0.002	0.588
fpr	0.100	0.001	0.102
maxsplit	0.280	0.002	0.285
onlyshared	0.121	0.002	0.124
overlap	0.022	0.001	0.022
padj	0.009	0.001	0.009
plot_corr	0.440	0.003	0.444
plot_deviation	1.414	0.012	1.434
plot_fdrnbrcurve	1.180	0.006	1.190
plot_fdrtprcurve	1.010	0.014	1.042
plot_fpc	0.931	0.007	0.940
plot_fpr	0.395	0.004	0.399
plot_overlap	0.048	0.002	0.050
plot_roc	0.919	0.007	0.927
plot_scatter	1.402	0.010	1.420
plot_tpr	0.372	0.002	0.377
plot_upset	1.676	0.005	1.684
plotcolors	0.116	0.001	0.117
prepare_data_for_plot	1.220	0.006	1.227
pval	0.008	0.001	0.008
reorder_levels	0.000	0.000	0.001
roc	0.554	0.003	0.562
scatter	0.873	0.006	0.879
score	0.009	0.001	0.010
splv	0.239	0.004	0.244
stratiflevels	0.301	0.002	0.304
tpr	0.094	0.001	0.095
truth	0.010	0.001	0.011