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: 2017-08-15 23:53:35 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:55:25 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 110.1 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 3.4.1 (2017-06-30)
* 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	0.124	0.000	0.123
COBRAPerformance	0.004	0.000	0.004
COBRAPlot	0.000	0.000	0.002
COBRAapp	0.000	0.000	0.003
Extract	0.276	0.004	0.280
basemethods	1.340	0.000	1.337
calculate_adjp	0.012	0.000	0.014
calculate_performance	0.652	0.000	0.653
coerce	0.264	0.000	0.265
corr	0.024	0.000	0.025
deviation	0.428	0.000	0.429
facetted	0.084	0.000	0.081
fdrnbr	0.140	0.004	0.144
fdrnbrcurve	0.244	0.004	0.248
fdrtpr	0.084	0.004	0.086
fdrtprcurve	0.312	0.000	0.315
fpc	0.372	0.000	0.375
fpr	0.064	0.000	0.066
maxsplit	0.308	0.000	0.306
onlyshared	0.124	0.000	0.127
overlap	0.112	0.000	0.115
padj	0.012	0.000	0.012
plot_corr	0.964	0.000	0.965
plot_deviation	2.684	0.012	2.699
plot_fdrnbrcurve	0.684	0.004	0.685
plot_fdrtprcurve	0.900	0.000	0.903
plot_fpc	0.656	0.000	0.654
plot_fpr	0.308	0.000	0.308
plot_overlap	0.040	0.000	0.038
plot_roc	0.648	0.000	0.649
plot_scatter	0.964	0.004	0.969
plot_tpr	0.376	0.000	0.380
plot_upset	1.960	0.000	1.983
plotcolors	0.076	0.000	0.075
prepare_data_for_plot	0.788	0.000	0.788
pval	0.004	0.000	0.008
reorder_levels	0	0	0
roc	0.288	0.000	0.287
scatter	0.440	0.000	0.439
score	0.008	0.000	0.007
splv	0.280	0.008	0.287
stratiflevels	0.204	0.000	0.203
tpr	0.060	0.000	0.059
truth	0.008	0.000	0.007