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BioC 3.5: CHECK report for mirIntegrator on tokay2

This page was generated on 2017-10-18 14:24:54 -0400 (Wed, 18 Oct 2017).

Package 827/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mirIntegrator 1.6.0
Diana Diaz
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/mirIntegrator
Branch: RELEASE_3_5
Last Commit: adab11e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


mirIntegrator.Rcheck/00install.out:


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)

mirIntegrator.Rcheck/examples_i386/mirIntegrator-Ex.timings:

nameusersystemelapsed
GSE43592_mRNA0.170.020.19
GSE43592_miRNA0.000.010.01
augmented_pathways0.870.030.90
integrate_mir3.500.083.58
kegg_pathways0.30.00.3
mirTarBase0.080.000.08
names_pathways000
pathways2pdf5.820.145.97
plot_augmented_pathway2.000.082.07
plot_change2.580.022.60
smallest_pathway0.550.000.54

mirIntegrator.Rcheck/examples_x64/mirIntegrator-Ex.timings:

nameusersystemelapsed
GSE43592_mRNA0.140.010.16
GSE43592_miRNA0.020.000.01
augmented_pathways0.860.020.88
integrate_mir3.660.053.72
kegg_pathways0.280.000.28
mirTarBase0.120.010.14
names_pathways000
pathways2pdf6.670.136.84
plot_augmented_pathway2.250.042.31
plot_change2.080.052.12
smallest_pathway0.470.000.47