Multiple platform build/check report for BioC 3.11 - CHECK report for SBGNview on tokay2

Package: SBGNview

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SBGNview_1.2.0.tar.gz

StartedAt: 2020-10-17 07:56:59 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 08:05:38 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 519.6 seconds

RetCode: 0

Status: OK

CheckDir: SBGNview.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SBGNview_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SBGNview.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SBGNview/DESCRIPTION' ... OK
* this is package 'SBGNview' version '1.2.0'
* package encoding: UTF-8
* 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 'SBGNview' 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
SBGNview         15.43   1.77   18.42
sbgnNodes        16.20   0.54   16.75
print.SBGNview   10.59   0.13   10.75
downloadSbgnFile  8.78   0.35    9.13
changeIds         5.76   0.36    6.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
sbgnNodes        14.72   0.44   15.15
SBGNview         13.95   0.59   14.65
print.SBGNview    8.66   0.28    8.97
downloadSbgnFile  7.25   0.14    7.39
changeIds         5.06   0.09    5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SBGNview_1.2.0.tar.gz && rm -rf SBGNview.buildbin-libdir && mkdir SBGNview.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SBGNview.buildbin-libdir SBGNview_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SBGNview_1.2.0.zip && rm SBGNview_1.2.0.tar.gz SBGNview_1.2.0.zip
###
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  % 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  359k  100  359k    0     0  3111k      0 --:--:-- --:--:-- --:--:-- 3301k

install for i386

* installing *source* package 'SBGNview' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SBGNview'
    finding HTML links ... done
    SBGNview                                html  
    SBGNview.obj                            html  
    arc-class                               html  
    changeDataId                            html  
    changeIds                               html  
    downloadSbgnFile                        html  
    findPathways                            html  
    getMolList                              html  
    glyph-class                             html  
    highlightArcs                           html  
    highlightNodes                          html  
    highlightPath                           html  
    loadMappingTable                        html  
    mapped.ids                              html  
    outputFile-set                          html  
    outputFile                              html  
    pathways.info                           html  
    pathways.stat                           html  
    plus-.SBGNview                          html  
    print.SBGNview                          html  
    renderSbgn                              html  
    sbgnNodes                               html  
    spline.arc-class                        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 'SBGNview' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SBGNview' as SBGNview_1.2.0.zip
* DONE (SBGNview)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SBGNview' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library(testthat)
> library(SBGNview)
Loading required package: pathview

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Loading required package: SBGNview.data
> 
> test_check("SBGNview")
[1] "loading mapping file from data package"
[1] "hsa_ENTREZID_pathwayCommons"
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.84    1.59   18.42


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library(testthat)
> library(SBGNview)
Loading required package: pathview

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Loading required package: SBGNview.data
> 
> test_check("SBGNview")
[1] "loading mapping file from data package"
[1] "hsa_ENTREZID_pathwayCommons"
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.85    1.35   20.26

name	user	system	elapsed
SBGNview	15.43	1.77	18.42
changeDataId	0.05	0.01	0.07
changeIds	5.76	0.36	6.25
downloadSbgnFile	8.78	0.35	9.13
findPathways	0.11	0.01	0.12
getMolList	1.80	0.19	2.27
highlightArcs	0.05	0.00	0.05
highlightNodes	2.83	0.16	3.14
highlightPath	0.03	0.00	0.03
loadMappingTable	3.66	0.10	3.75
outputFile-set	0.01	0.01	0.03
outputFile	0.04	0.00	0.03
plus-.SBGNview	0.03	0.00	0.03
print.SBGNview	10.59	0.13	10.75
renderSbgn	0.05	0.00	0.05
sbgnNodes	16.20	0.54	16.75

name	user	system	elapsed
SBGNview	13.95	0.59	14.65
changeDataId	0.03	0.00	0.03
changeIds	5.06	0.09	5.16
downloadSbgnFile	7.25	0.14	7.39
findPathways	0.09	0.02	0.11
getMolList	1.77	0.03	1.80
highlightArcs	0.00	0.03	0.03
highlightNodes	3.08	0.11	3.19
highlightPath	0.01	0.00	0.01
loadMappingTable	3.17	0.05	3.22
outputFile-set	0.04	0.00	0.03
outputFile	0.03	0.00	0.03
plus-.SBGNview	0.03	0.00	0.03
print.SBGNview	8.66	0.28	8.97
renderSbgn	0.05	0.01	0.06
sbgnNodes	14.72	0.44	15.15

CHECK report for SBGNview on tokay2

Summary

Command output

Installation output

Tests output

Example timings