BioC 3.4: CHECK report for iCOBRA on zin1

Package: iCOBRA

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.1.2.tar.gz

StartedAt: 2016-09-20 08:00:27 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:02:03 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 96.1 seconds

RetCode: 0

Status:  OK

CheckDir: iCOBRA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iCOBRA_1.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.1.2’
* 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	0.008	0.000	0.005
COBRAPerformance	0.004	0.000	0.005
COBRAPlot	0.004	0.000	0.002
COBRAapp	0.004	0.000	0.002
Extract	0.12	0.00	0.12
basemethods	0.360	0.004	0.364
calculate_adjp	0.016	0.000	0.015
calculate_performance	0.784	0.000	0.781
coerce	0.152	0.000	0.153
corr	0.028	0.000	0.028
deviation	0.520	0.000	0.522
facetted	0.092	0.000	0.091
fdrnbr	0.092	0.000	0.089
fdrnbrcurve	0.360	0.000	0.362
fdrtpr	0.076	0.000	0.078
fdrtprcurve	0.364	0.004	0.369
fpc	0.364	0.000	0.363
fpr	0.120	0.000	0.121
maxsplit	0.192	0.000	0.193
onlyshared	0.076	0.000	0.079
overlap	0.012	0.000	0.014
padj	0.008	0.000	0.007
plot_corr	0.264	0.000	0.263
plot_deviation	1.048	0.000	1.048
plot_fdrnbrcurve	0.784	0.000	0.784
plot_fdrtprcurve	0.848	0.000	0.850
plot_fpc	0.596	0.000	0.607
plot_fpr	0.332	0.000	0.331
plot_overlap	0.036	0.000	0.036
plot_roc	0.616	0.000	0.614
plot_scatter	0.924	0.000	0.922
plot_tpr	0.284	0.000	0.283
plot_upset	1.276	0.000	1.277
plotcolors	0.096	0.000	0.099
prepare_data_for_plot	0.840	0.000	0.838
pval	0.008	0.000	0.009
reorder_levels	0	0	0
roc	0.376	0.004	0.379
scatter	0.612	0.000	0.614
score	0.008	0.000	0.011
splv	0.196	0.000	0.197
stratiflevels	0.24	0.00	0.24
tpr	0.072	0.000	0.072
truth	0.004	0.004	0.009