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 |
---|---|---|---|---|
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 1506/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Path2PPI 1.36.0 (landing page) Oliver Philipp
| 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 Path2PPI package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Path2PPI.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: Path2PPI |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Path2PPI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Path2PPI_1.36.0.tar.gz |
StartedAt: 2024-11-09 09:23:50 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 09:27:51 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 241.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Path2PPI.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Path2PPI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Path2PPI_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Path2PPI.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 ‘Path2PPI/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Path2PPI’ version ‘1.36.0’ * 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 ‘Path2PPI’ 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. * 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 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 ... NOTE .getInteractions,.ReferenceSpecies: no visible global function definition for ‘combn’ addReference,Path2PPI: no visible global function definition for ‘read.table’ initialize,.ReferenceSpecies: no visible global function definition for ‘read.table’ plot.Path2PPI,Path2PPI: no visible global function definition for ‘rgb’ plot.Path2PPI,Path2PPI: no visible global function definition for ‘rainbow’ plot.Path2PPI,Path2PPI: no visible global function definition for ‘par’ plot.Path2PPI,Path2PPI: no visible global function definition for ‘adjustcolor’ plot.Path2PPI,Path2PPI: no visible global function definition for ‘legend’ Undefined global functions or variables: adjustcolor combn legend par rainbow read.table rgb Consider adding importFrom("grDevices", "adjustcolor", "rainbow", "rgb") importFrom("graphics", "legend", "par") importFrom("utils", "combn", "read.table") 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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/Path2PPI.Rcheck/00check.log’ for details.
Path2PPI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Path2PPI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘Path2PPI’ ... ** 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 (Path2PPI)
Path2PPI.Rcheck/tests/runTests.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. > BiocGenerics:::testPackage("Path2PPI") Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Search for all relevant interactions: 0%--25%--50%--75%--100% Remove irrelevant homologs. Search for all relevant interactions: 0%--25%--50%--75%--100% Remove irrelevant homologs. Begin with Homo sapiens 6 interactions processed. These lead to 0 interactions in target species. ------------------------------- Begin with Saccharomyces cerevisiae (S288c) 15 interactions processed. These lead to 8 interactions in target species. ------------------------------- Combine results to one single PPI. A total of 8 putative interactions were predicted in target species. RUNIT TEST PROTOCOL -- Sat Nov 9 09:27:48 2024 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : Path2PPI RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 0.948 0.033 0.978
Path2PPI.Rcheck/Path2PPI-Ex.timings
name | user | system | elapsed | |
Path2PPI | 0 | 0 | 0 | |
addReference | 0.236 | 0.008 | 0.244 | |
ai | 0.055 | 0.001 | 0.055 | |
getHybridNetwork | 0.639 | 0.007 | 0.646 | |
getPPI | 0.611 | 0.012 | 0.623 | |
homologyScore | 0 | 0 | 0 | |
plot.Path2PPI | 0.641 | 0.007 | 0.648 | |
predictPPI | 1.494 | 0.014 | 1.508 | |
removeReference | 0.167 | 0.005 | 0.172 | |
showInteraction | 0.629 | 0.009 | 0.637 | |
showReferences | 0.172 | 0.003 | 0.176 | |