BioC 3.3: CHECK report for iCOBRA on zin2

Package: iCOBRA

Version: 1.0.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.0.2.tar.gz

StartedAt: 2016-10-13 03:17:42 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:19:25 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 103.0 seconds

RetCode: 0

Status:  OK

CheckDir: iCOBRA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/iCOBRA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.2’
* 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	0.006	0.000	0.006
COBRAPerformance	0.005	0.000	0.006
COBRAPlot	0.003	0.000	0.002
COBRAapp	0.003	0.000	0.003
Extract	0.132	0.004	0.139
basemethods	0.398	0.008	0.409
calculate_adjp	0.017	0.000	0.017
calculate_performance	0.893	0.000	0.892
coerce	0.173	0.000	0.172
corr	0.032	0.000	0.032
deviation	0.598	0.004	0.600
facetted	0.104	0.000	0.104
fdrnbr	0.104	0.000	0.104
fdrnbrcurve	0.404	0.004	0.408
fdrtpr	0.099	0.000	0.098
fdrtprcurve	0.407	0.000	0.408
fpc	0.407	0.000	0.410
fpr	0.135	0.000	0.135
maxsplit	0.231	0.000	0.231
onlyshared	0.092	0.004	0.096
overlap	0.010	0.000	0.014
padj	0.01	0.00	0.01
plot_corr	0.296	0.000	0.295
plot_deviation	1.174	0.000	1.174
plot_fdrnbrcurve	0.850	0.000	0.849
plot_fdrtprcurve	0.901	0.000	0.901
plot_fpc	0.757	0.004	0.760
plot_fpr	0.288	0.000	0.288
plot_overlap	0.043	0.000	0.042
plot_roc	0.767	0.000	0.767
plot_scatter	1.043	0.004	1.047
plot_tpr	0.279	0.000	0.278
plot_upset	1.357	0.000	1.356
plotcolors	0.094	0.000	0.094
prepare_data_for_plot	0.913	0.000	0.912
pval	0.008	0.000	0.008
reorder_levels	0.000	0.000	0.001
roc	0.381	0.000	0.380
scatter	0.651	0.000	0.651
score	0.008	0.000	0.008
splv	0.201	0.000	0.200
stratiflevels	0.228	0.004	0.233
tpr	0.074	0.000	0.073
truth	0.009	0.000	0.009