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This page was generated on 2021-06-21 12:05:40 -0400 (Mon, 21 Jun 2021).

CHECK results for mirIntegrator on riesling1

To the developers/maintainers of the mirIntegrator package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mirIntegrator.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1118/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mirIntegrator 1.23.0  (landing page)
Diana Diaz
Snapshot Date: 2021-06-20 14:50:05 -0400 (Sun, 20 Jun 2021)
URL: https://git.bioconductor.org/packages/mirIntegrator
Branch: master
Last Commit: 5cfa672
Last Changed Date: 2021-05-19 12:14:08 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'ROntoTools' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mirIntegrator
Version: 1.23.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mirIntegrator.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings mirIntegrator_1.23.0.tar.gz
StartedAt: 2021-06-21 01:10:09 -0400 (Mon, 21 Jun 2021)
EndedAt: 2021-06-21 01:13:19 -0400 (Mon, 21 Jun 2021)
EllapsedTime: 190.2 seconds
RetCode: 0
Status:   OK  
CheckDir: mirIntegrator.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mirIntegrator.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings mirIntegrator_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/mirIntegrator.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.23.0'
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/mirIntegrator.Rcheck/00check.log'
for details.



Installation output

mirIntegrator.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/mirIntegrator_1.23.0.tar.gz && rm -rf mirIntegrator.buildbin-libdir && mkdir mirIntegrator.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mirIntegrator.buildbin-libdir mirIntegrator_1.23.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL mirIntegrator_1.23.0.zip && rm mirIntegrator_1.23.0.tar.gz mirIntegrator_1.23.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1592k  100 1592k    0     0  7305k      0 --:--:-- --:--:-- --:--:-- 7339k

install for i386

* installing *source* package 'mirIntegrator' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mirIntegrator'
    finding HTML links ... done
    GSE43592_mRNA                           html  
    GSE43592_miRNA                          html  
    augmented_pathways                      html  
    integrate_mir                           html  
    kegg_pathways                           html  
    mirTarBase                              html  
    names_pathways                          html  
    pathways2pdf                            html  
    plot_augmented_pathway                  html  
    plot_change                             html  
    smallest_pathway                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'mirIntegrator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mirIntegrator' as mirIntegrator_1.23.0.zip
* DONE (mirIntegrator)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'mirIntegrator' successfully unpacked and MD5 sums checked

Tests output

mirIntegrator.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("mirIntegrator")

Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min



RUNIT TEST PROTOCOL -- Mon Jun 21 01:12:14 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mirIntegrator RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.20    0.37    5.56 

mirIntegrator.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("mirIntegrator")

Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min



RUNIT TEST PROTOCOL -- Mon Jun 21 01:12:20 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mirIntegrator RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.68    0.28    5.96 

Example timings

mirIntegrator.Rcheck/examples_i386/mirIntegrator-Ex.timings

nameusersystemelapsed
GSE43592_mRNA0.110.020.12
GSE43592_miRNA0.010.000.02
augmented_pathways0.390.010.40
integrate_mir1.500.061.57
kegg_pathways0.160.000.15
mirTarBase0.060.000.07
names_pathways000
pathways2pdf3.500.133.64
plot_augmented_pathway1.030.061.09
plot_change0.740.050.78
smallest_pathway0.360.010.38

mirIntegrator.Rcheck/examples_x64/mirIntegrator-Ex.timings

nameusersystemelapsed
GSE43592_mRNA0.090.000.09
GSE43592_miRNA0.000.020.02
augmented_pathways0.300.010.31
integrate_mir1.840.031.87
kegg_pathways0.110.020.13
mirTarBase0.030.020.05
names_pathways0.000.010.01
pathways2pdf2.960.143.09
plot_augmented_pathway1.000.031.04
plot_change0.920.000.92
smallest_pathway0.230.050.28