Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the Path2PPI package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1347/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Path2PPI 1.22.0 (landing page) Oliver Philipp
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Path2PPI |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Path2PPI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Path2PPI_1.22.0.tar.gz |
StartedAt: 2021-10-14 22:08:10 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:09:28 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 78.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Path2PPI.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Path2PPI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Path2PPI_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Path2PPI.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Path2PPI/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Path2PPI’ version ‘1.22.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 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 ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed predictPPI 9.866 0.044 9.92 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/Path2PPI.Rcheck/00check.log’ for details.
Path2PPI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Path2PPI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > 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 -- Thu Oct 14 22:09:13 2021 *********************************************** 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 4.118 0.152 4.258
Path2PPI.Rcheck/Path2PPI-Ex.timings
name | user | system | elapsed | |
Path2PPI | 0.001 | 0.001 | 0.002 | |
addReference | 1.090 | 0.043 | 1.134 | |
ai | 0.242 | 0.003 | 0.245 | |
getHybridNetwork | 3.947 | 0.040 | 3.992 | |
getPPI | 3.949 | 0.023 | 3.975 | |
homologyScore | 0.000 | 0.000 | 0.001 | |
plot.Path2PPI | 3.952 | 0.026 | 3.982 | |
predictPPI | 9.866 | 0.044 | 9.920 | |
removeReference | 0.726 | 0.013 | 0.739 | |
showInteraction | 3.208 | 0.032 | 3.242 | |
showReferences | 0.566 | 0.010 | 0.576 | |