Guangchuang Yu
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/treeio |
| git_branch: RELEASE_3_15 |
| git_last_commit: ed457d6 |
| git_last_commit_date: 2022-08-13 05:52:50 -0400 (Sat, 13 Aug 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:26 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
To the developers/maintainers of the treeio package: - Please 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 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. |
| Package 2048/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| treeio 1.20.2 (landing page) Guangchuang Yu
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: treeio |
| Version: 1.20.2 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:treeio.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings treeio_1.20.2.tar.gz |
| StartedAt: 2022-10-19 04:56:37 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 04:58:28 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 110.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: treeio.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:treeio.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings treeio_1.20.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/treeio.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 'treeio/DESCRIPTION' ... OK * this is package 'treeio' version '1.20.2' * 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 '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 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 ... 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 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: OK
treeio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL treeio ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 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(treeio)
treeio v1.20.2 For help: https://yulab-smu.top/treedata-book/
If you use the ggtree package suite in published research, please cite
the appropriate paper(s):
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
Guangchuang Yu. Using ggtree to visualize data on tree-like structures.
Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
ggtree: an R package for visualization and annotation of phylogenetic
trees with their covariates and other associated data. Methods in
Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
>
> test_check("treeio")
{
"tree": "(K:0.081785{11},N:0.062341{14},(D:0.082021{4},(L:0.005508{12},(J:0.013996{10},(G:0.045746{7},((C:0.02773{3},(E:0.031104{5},O:0.048389{15})23:0.008328{23})22:0.015959{22},(H:0.021007{8},(I:0.014739{9},(B:0.031643{2},(A:0.01034{1},(F:0.006649{6},M:0.009195{13})28:0.028303{28})27:0.008072{27})26:0.0035{26})25:0.020359{25})24:0.000555{24})21:0.023675{21})20:0.045745{20})19:0.014684{19})18:0.059308{18})17:0.231628{17})16{16};",
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"t": 0.003,
"N": 1514.9,
"S": 633.1,
"dN_vs_dS": 1.5591,
"dN": 0.0013,
"dS": 0.0008,
"N_x_dN": 2,
"S_x_dS": 0.5
},
{
"edge_num": 27,
"subs": "C1168T / G1180A / A1242G / T1249C / T1257C",
"AA_subs": "D394N",
"t": 0.008,
"N": 1514.9,
"S": 633.1,
"dN_vs_dS": 0.0863,
"dN": 0.0007,
"dS": 0.0076,
"N_x_dN": 1,
"S_x_dS": 4.8
},
{
"edge_num": 28,
"subs": "A21G / T186A / T211C / G294A / T299C / A348T / C438T / C444T / C582T / A744G / C771T / A785G / G786A / C1374T / C1467T / A1500G / A1869G / G1878A / C2043T",
"AA_subs": "V100A / K262R",
"t": 0.028,
"N": 1514.9,
"S": 633.1,
"dN_vs_dS": 0.0453,
"dN": 0.0013,
"dS": 0.0289,
"N_x_dN": 2,
"S_x_dS": 18.3
}
],
"metadata": {"info": "R-package treeio", "data": "Wed Oct 19 04:57:56 2022"}
}
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 139 ]
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 139 ]
>
> proc.time()
user system elapsed
12.54 0.73 18.17
treeio.Rcheck/treeio-Ex.timings
| name | user | system | elapsed | |
| Nnode.treedata | 0 | 0 | 0 | |
| beast-parser | 0.26 | 0.03 | 0.33 | |
| drop.tip-methods | 0.18 | 0.00 | 0.19 | |
| getNodeNum | 0 | 0 | 0 | |
| read.astral | 0.05 | 0.00 | 0.05 | |
| read.codeml | 0.44 | 0.01 | 0.95 | |
| read.codeml_mlc | 0.12 | 0.00 | 0.12 | |
| read.hyphy | 0.08 | 0.00 | 0.08 | |
| read.hyphy.seq | 0.02 | 0.00 | 0.02 | |
| read.jplace | 0.09 | 0.00 | 0.11 | |
| read.mcmctree | 0.13 | 0.00 | 0.13 | |
| read.nhx | 0.06 | 0.00 | 0.06 | |
| read.paml_rst | 0.34 | 0.01 | 0.67 | |
| read.phylip | 0.05 | 0.00 | 0.05 | |
| read.phyloxml | 0.75 | 0.02 | 0.76 | |
| read.r8s | 0 | 0 | 0 | |
| read.raxml | 0.03 | 0.00 | 0.04 | |
| read.treeqza | 0.09 | 0.11 | 0.25 | |
| rename_taxa | 0 | 0 | 0 | |
| tree_subset | 0 | 0 | 0 | |
| write.beast | 0.02 | 0.00 | 0.02 | |
| write.beast.newick | 0.02 | 0.00 | 0.01 | |