Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:41 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 2174/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
treeio 1.31.0 (landing page) Guangchuang Yu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the treeio package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/treeio.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: treeio |
Version: 1.31.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:treeio.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings treeio_1.31.0.tar.gz |
StartedAt: 2024-12-23 03:04:02 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 03:05:05 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 62.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: treeio.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:treeio.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings treeio_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/treeio.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘treeio/DESCRIPTION’ ... OK * this is package ‘treeio’ version ‘1.31.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘treeio’ 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
treeio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL treeio ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘treeio’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (treeio)
treeio.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(treeio) treeio v1.31.0 Learn more at https://yulab-smu.top/contribution-tree-data/ Please cite: LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. doi: 10.1093/molbev/msz240 > > test_check("treeio") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 129 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 129 ] > > proc.time() user system elapsed 5.885 0.236 6.110
treeio.Rcheck/treeio-Ex.timings
name | user | system | elapsed | |
beast-parser | 0.186 | 0.003 | 0.190 | |
find.hclust | 0.062 | 0.001 | 0.063 | |
getNodeNum | 0.007 | 0.000 | 0.008 | |
read.astral | 0.035 | 0.000 | 0.035 | |
read.codeml | 0.270 | 0.006 | 0.278 | |
read.codeml_mlc | 0.071 | 0.001 | 0.072 | |
read.hyphy | 0.035 | 0.001 | 0.037 | |
read.hyphy.seq | 0.015 | 0.000 | 0.016 | |
read.jplace | 0.053 | 0.000 | 0.054 | |
read.mcmctree | 0.057 | 0.000 | 0.057 | |
read.nextstrain.json | 0.553 | 0.019 | 0.572 | |
read.nhx | 0.064 | 0.001 | 0.067 | |
read.paml_rst | 0.183 | 0.005 | 0.188 | |
read.phylip | 0.039 | 0.002 | 0.042 | |
read.phyloxml | 0.368 | 0.001 | 0.370 | |
read.r8s | 0.007 | 0.000 | 0.008 | |
read.raxml | 0.027 | 0.000 | 0.028 | |
read.treeqza | 0.049 | 0.008 | 0.058 | |
rename_taxa | 0.001 | 0.000 | 0.001 | |
spt-methods | 0.037 | 0.001 | 0.038 | |
write.beast | 0.009 | 0.001 | 0.011 | |
write.beast.newick | 0.015 | 0.000 | 0.015 | |
write.jplace | 0.131 | 0.000 | 0.131 | |