Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-11 11:07:23 -0400 (Thu, 11 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4165
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

CHECK results for SBGNview on palomino4


To the developers/maintainers of the SBGNview package:
- Please 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 How and When does the builder pull? When will my changes propagate? 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 1738/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SBGNview 1.11.0  (landing page)
Weijun Luo
Snapshot Date: 2022-08-10 14:00:02 -0400 (Wed, 10 Aug 2022)
git_url: https://git.bioconductor.org/packages/SBGNview
git_branch: master
git_last_commit: 84fd2b1
git_last_commit_date: 2022-04-26 11:57:04 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SBGNview
Version: 1.11.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SBGNview_1.11.0.tar.gz
StartedAt: 2022-08-11 05:37:32 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 05:41:44 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 251.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SBGNview.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SBGNview_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SBGNview.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SBGNview/DESCRIPTION' ... OK
* this is package 'SBGNview' version '1.11.0'
* 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
* 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 ... 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       16.05   0.61   18.28
sbgnNodes       6.25   0.18    6.49
print.SBGNview  4.97   0.18    5.16
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/SBGNview.Rcheck/00check.log'
for details.



Installation output

SBGNview.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/SBGNview_1.11.0.tar.gz && rm -rf SBGNview.buildbin-libdir && mkdir SBGNview.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SBGNview.buildbin-libdir SBGNview_1.11.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL SBGNview_1.11.0.zip && rm SBGNview_1.11.0.tar.gz SBGNview_1.11.0.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
 27 1660k   27  464k    0     0  3091k      0 --:--:-- --:--:-- --:--:-- 3097k
100 1660k  100 1660k    0     0  4528k      0 --:--:-- --:--:-- --:--:-- 4524k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'SBGNview' as SBGNview_1.11.0.zip
* DONE (SBGNview)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'SBGNview' successfully unpacked and MD5 sums checked

Tests output

SBGNview.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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
##############################################################################
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 
  24.45    1.09   26.15 

Example timings

SBGNview.Rcheck/SBGNview-Ex.timings

nameusersystemelapsed
SBGNview16.05 0.6118.28
changeDataId0.010.000.03
changeIds0.570.020.59
downloadSbgnFile4.550.114.66
findPathways0.050.010.06
highlightArcs000
highlightNodes000
highlightPath000
loadMappingTable0.560.000.56
outputFile-set000
outputFile000
plus-.SBGNview000
print.SBGNview4.970.185.16
renderSbgn000
sbgn.gsets1.030.211.26
sbgnNodes6.250.186.49