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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1809/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SBGNview 1.14.0  (landing page)
Weijun Luo
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SBGNview
git_branch: RELEASE_3_17
git_last_commit: e64acdb
git_last_commit_date: 2023-04-25 11:11:01 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for SBGNview on kjohnson2


To the developers/maintainers of the SBGNview package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SBGNview
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SBGNview.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SBGNview_1.14.0.tar.gz
StartedAt: 2023-10-18 21:28:09 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 21:37:13 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 544.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SBGNview.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SBGNview.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SBGNview_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SBGNview.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SBGNview/DESCRIPTION’ ... OK
* this is package ‘SBGNview’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... 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
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘SBGNview/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(disclaimer)

See section ‘Good practice’ in '?.onAttach'.

generate.cpd.mapping.table: no visible binding for global variable
  ‘cpd.simtypes’
generate.ko.mapping.list: no visible binding for global variable ‘korg’
loadMappingTable: no visible binding for global variable ‘korg’
mapping.ko.to.arbitrary.id.type: no visible binding for global variable
  ‘gene.idtype.list’
mapping.ko.to.arbitrary.id.type: no visible binding for global variable
  ‘korg’
mol.sum.multiple.mapping: no visible binding for global variable ‘IQR’
Undefined global functions or variables:
  IQR cpd.simtypes gene.idtype.list korg
Consider adding
  importFrom("stats", "IQR")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
SBGNview         17.000  0.597  31.554
sbgnNodes         8.781  0.286  15.889
print.SBGNview    6.577  0.187  11.983
downloadSbgnFile  6.086  0.147  10.882
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SBGNview.Rcheck/00check.log’
for details.



Installation output

SBGNview.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SBGNview
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘SBGNview’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (SBGNview)

Tests output

SBGNview.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
##############################################################################
SBGNview 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.

Users are required to formally cite the SBGNview paper and Pathview paper (not
just mention them) in publications or products. For details, do
'citation("SBGNview"); citation("Pathview")' within R.
##############################################################################
> 
> test_check("SBGNview")
trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/compound.name_metacyc.SBGN.RData'
Content type 'application/octet-stream' length 1795999 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/kegg_metacyc.SBGN.RData'
Content type 'application/octet-stream' length 171925 bytes (167 KB)
==================================================
downloaded 167 KB

trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/kegg_pathway.id.RData'
Content type 'application/octet-stream' length 195623 bytes (191 KB)
==================================================
downloaded 191 KB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 26.661   1.090  55.980 

Example timings

SBGNview.Rcheck/SBGNview-Ex.timings

nameusersystemelapsed
SBGNview17.000 0.59731.554
changeDataId0.0140.0040.031
changeIds0.8400.0261.552
downloadSbgnFile 6.086 0.14710.882
findPathways0.0510.0030.096
highlightArcs000
highlightNodes000
highlightPath000
loadMappingTable0.8010.0211.457
outputFile-set000
outputFile0.0000.0000.004
plus-.SBGNview0.0000.0010.001
print.SBGNview 6.577 0.18711.983
renderSbgn0.0010.0000.000
sbgn.gsets1.1410.0392.044
sbgnNodes 8.781 0.28615.889