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This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 1864/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SBGNview 1.18.0  (landing page)
Weijun Luo
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/SBGNview
git_branch: RELEASE_3_19
git_last_commit: d75f5f1
git_last_commit_date: 2024-04-30 11:15:39 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for SBGNview on palomino3

To the developers/maintainers of the SBGNview package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SBGNview.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.18.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SBGNview.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SBGNview_1.18.0.tar.gz
StartedAt: 2024-06-27 05:45:28 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 05:51:24 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 355.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SBGNview.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SBGNview.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SBGNview_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SBGNview.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SBGNview/DESCRIPTION' ... OK
* this is package 'SBGNview' version '1.18.0'
* 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 code 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 whether 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         17.02   1.11   41.12
sbgnNodes         8.85   0.32    9.20
print.SBGNview    6.13   0.27    6.44
downloadSbgnFile  5.67   0.08    5.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/SBGNview.Rcheck/00check.log'
for details.


Installation output

SBGNview.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SBGNview
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  30.04    2.32   31.62 

Example timings

SBGNview.Rcheck/SBGNview-Ex.timings

nameusersystemelapsed
SBGNview17.02 1.1141.12
changeDataId0.030.000.04
changeIds0.770.030.80
downloadSbgnFile5.670.085.75
findPathways0.080.010.09
highlightArcs000
highlightNodes000
highlightPath000
loadMappingTable0.650.050.70
outputFile-set000
outputFile000
plus-.SBGNview000
print.SBGNview6.130.276.44
renderSbgn000
sbgn.gsets1.620.111.77
sbgnNodes8.850.329.20