Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1845/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SBGNview 1.20.0 (landing page) Weijun Luo
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: SBGNview |
Version: 1.20.0 |
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_1.20.0.tar.gz |
StartedAt: 2024-11-09 12:19:26 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 12:25:00 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 334.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SBGNview.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SBGNview.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SBGNview/DESCRIPTION’ ... OK * this is package ‘SBGNview’ version ‘1.20.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 6.441 0.105 6.555 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/SBGNview.Rcheck/00check.log’ for details.
SBGNview.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SBGNview ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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)
SBGNview.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 11.118 0.245 11.919
SBGNview.Rcheck/SBGNview-Ex.timings
name | user | system | elapsed | |
SBGNview | 6.441 | 0.105 | 6.555 | |
changeDataId | 0.006 | 0.002 | 0.007 | |
changeIds | 0.329 | 0.012 | 0.341 | |
downloadSbgnFile | 3.132 | 0.049 | 3.181 | |
findPathways | 0.021 | 0.001 | 0.022 | |
highlightArcs | 0 | 0 | 0 | |
highlightNodes | 0 | 0 | 0 | |
highlightPath | 0 | 0 | 0 | |
loadMappingTable | 0.286 | 0.002 | 0.289 | |
outputFile-set | 0 | 0 | 0 | |
outputFile | 0 | 0 | 0 | |
plus-.SBGNview | 0 | 0 | 0 | |
print.SBGNview | 3.214 | 0.019 | 3.233 | |
renderSbgn | 0 | 0 | 0 | |
sbgn.gsets | 0.662 | 0.047 | 0.711 | |
sbgnNodes | 4.398 | 0.100 | 4.501 | |