BioC 3.5: CHECK report for mirIntegrator on tokay2

Package: mirIntegrator

Version: 1.6.0

Command: rm -rf mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && mkdir mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mirIntegrator.buildbin-libdir mirIntegrator_1.6.0.tar.gz >mirIntegrator.Rcheck\00install.out 2>&1 && cp mirIntegrator.Rcheck\00install.out mirIntegrator-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=mirIntegrator.buildbin-libdir --install="check:mirIntegrator-install.out" --force-multiarch --no-vignettes --timings mirIntegrator_1.6.0.tar.gz

StartedAt: 2017-10-18 01:24:30 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:28:13 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 222.6 seconds

RetCode: 0

Status:  OK

CheckDir: mirIntegrator.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && mkdir mirIntegrator.buildbin-libdir mirIntegrator.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mirIntegrator.buildbin-libdir mirIntegrator_1.6.0.tar.gz >mirIntegrator.Rcheck\00install.out 2>&1 && cp mirIntegrator.Rcheck\00install.out mirIntegrator-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=mirIntegrator.buildbin-libdir --install="check:mirIntegrator-install.out" --force-multiarch --no-vignettes --timings mirIntegrator_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/mirIntegrator.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mirIntegrator/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mirIntegrator' version '1.6.0'
* 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 whether package 'mirIntegrator' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
integrate_mir : isGraphNEL: no visible global function definition for
  'is'
pathways2pdf: no visible global function definition for 'pdf'
pathways2pdf: no visible global function definition for 'par'
pathways2pdf: no visible global function definition for 'graphics.off'
plotLines: no visible binding for global variable 'x'
plotLines: no visible binding for global variable 'y'
plotLines: no visible binding for global variable 'pathways_set'
plotPathway2Colors: no visible global function definition for 'legend'
plot_change: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  complete.cases graphics.off is legend par pathways_set pdf x y
Consider adding
  importFrom("grDevices", "graphics.off", "pdf")
  importFrom("graphics", "legend", "par")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
pathways2pdf 5.82   0.14    5.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
pathways2pdf 6.67   0.13    6.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/mirIntegrator.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'mirIntegrator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'mirIntegrator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mirIntegrator' as mirIntegrator_1.6.0.zip
* DONE (mirIntegrator)

name	user	system	elapsed
GSE43592_mRNA	0.17	0.02	0.19
GSE43592_miRNA	0.00	0.01	0.01
augmented_pathways	0.87	0.03	0.90
integrate_mir	3.50	0.08	3.58
kegg_pathways	0.3	0.0	0.3
mirTarBase	0.08	0.00	0.08
names_pathways	0	0	0
pathways2pdf	5.82	0.14	5.97
plot_augmented_pathway	2.00	0.08	2.07
plot_change	2.58	0.02	2.60
smallest_pathway	0.55	0.00	0.54

name	user	system	elapsed
GSE43592_mRNA	0.14	0.01	0.16
GSE43592_miRNA	0.02	0.00	0.01
augmented_pathways	0.86	0.02	0.88
integrate_mir	3.66	0.05	3.72
kegg_pathways	0.28	0.00	0.28
mirTarBase	0.12	0.01	0.14
names_pathways	0	0	0
pathways2pdf	6.67	0.13	6.84
plot_augmented_pathway	2.25	0.04	2.31
plot_change	2.08	0.05	2.12
smallest_pathway	0.47	0.00	0.47