BioC 3.4: CHECK report for iCOBRA on malbec1

Package: iCOBRA

Version: 1.2.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.2.0.tar.gz

StartedAt: 2017-04-14 23:16:18 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:18:06 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 107.5 seconds

RetCode: 0

Status:  OK

CheckDir: iCOBRA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/iCOBRA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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	0.008	0.000	0.008
COBRAPerformance	0.008	0.000	0.007
COBRAPlot	0.004	0.000	0.002
COBRAapp	0.004	0.000	0.003
Extract	0.116	0.004	0.120
basemethods	0.332	0.008	0.341
calculate_adjp	0.012	0.000	0.013
calculate_performance	0.704	0.000	0.701
coerce	0.144	0.000	0.146
corr	0.028	0.000	0.025
deviation	0.432	0.000	0.433
facetted	0.112	0.000	0.110
fdrnbr	0.096	0.000	0.095
fdrnbrcurve	0.380	0.004	0.386
fdrtpr	0.144	0.000	0.142
fdrtprcurve	0.312	0.004	0.317
fpc	0.304	0.000	0.307
fpr	0.124	0.000	0.126
maxsplit	0.160	0.008	0.167
onlyshared	0.072	0.000	0.072
overlap	0.012	0.000	0.011
padj	0.012	0.000	0.008
plot_corr	0.348	0.004	0.355
plot_deviation	1.064	0.000	1.066
plot_fdrnbrcurve	0.788	0.000	0.789
plot_fdrtprcurve	0.828	0.000	0.828
plot_fpc	0.572	0.000	0.573
plot_fpr	0.376	0.000	0.376
plot_overlap	0.032	0.000	0.035
plot_roc	0.608	0.000	0.606
plot_scatter	0.932	0.000	0.931
plot_tpr	0.324	0.000	0.322
plot_upset	1.624	0.000	1.628
plotcolors	0.076	0.000	0.078
prepare_data_for_plot	0.680	0.000	0.681
pval	0.008	0.000	0.009
reorder_levels	0.000	0.000	0.001
roc	0.332	0.000	0.335
scatter	0.472	0.000	0.473
score	0.008	0.000	0.008
splv	0.208	0.000	0.208
stratiflevels	0.280	0.000	0.279
tpr	0.064	0.000	0.062
truth	0.008	0.000	0.008