BioC 3.5: CHECK report for iCOBRA on malbec2

Package: iCOBRA

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.4.0.tar.gz

StartedAt: 2017-10-18 00:04:21 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:06:21 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 119.8 seconds

RetCode: 0

Status:  OK

CheckDir: iCOBRA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/iCOBRA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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	0.108	0.000	0.110
COBRAPerformance	0.004	0.000	0.005
COBRAPlot	0.004	0.000	0.001
COBRAapp	0.000	0.000	0.002
Extract	0.260	0.004	0.260
basemethods	1.296	0.004	1.300
calculate_adjp	0.012	0.000	0.014
calculate_performance	0.648	0.000	0.646
coerce	0.264	0.000	0.264
corr	0.028	0.000	0.026
deviation	0.416	0.000	0.416
facetted	0.144	0.004	0.146
fdrnbr	0.072	0.000	0.072
fdrnbrcurve	0.248	0.000	0.247
fdrtpr	0.084	0.000	0.083
fdrtprcurve	0.376	0.000	0.376
fpc	0.276	0.000	0.276
fpr	0.060	0.000	0.061
maxsplit	0.288	0.000	0.290
onlyshared	0.08	0.00	0.08
overlap	0.012	0.000	0.011
padj	0.008	0.000	0.007
plot_corr	0.944	0.000	0.943
plot_deviation	2.632	0.004	2.636
plot_fdrnbrcurve	0.668	0.000	0.670
plot_fdrtprcurve	0.888	0.000	0.889
plot_fpc	0.624	0.000	0.625
plot_fpr	0.300	0.004	0.303
plot_overlap	0.036	0.000	0.036
plot_roc	0.640	0.000	0.639
plot_scatter	0.976	0.000	0.975
plot_tpr	0.276	0.000	0.275
plot_upset	1.988	0.000	2.004
plotcolors	0.084	0.000	0.083
prepare_data_for_plot	0.644	0.000	0.641
pval	0.008	0.000	0.008
reorder_levels	0.000	0.000	0.001
roc	0.312	0.000	0.310
scatter	0.484	0.000	0.483
score	0.008	0.000	0.007
splv	0.208	0.004	0.215
stratiflevels	0.296	0.000	0.298
tpr	0.064	0.000	0.061
truth	0.008	0.000	0.008