Guangchuang Yu
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/treeio |
| git_branch: devel |
| git_last_commit: 2105d01 |
| git_last_commit_date: 2023-10-24 10:54:47 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:13 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 2175/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| treeio 1.27.0 (landing page) Guangchuang Yu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 1.27.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:treeio.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings treeio_1.27.0.tar.gz |
| StartedAt: 2024-03-28 03:32:38 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:33:43 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 64.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: treeio.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:treeio.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings treeio_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/treeio.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘treeio/DESCRIPTION’ ... OK
* this is package ‘treeio’ version ‘1.27.0’
* 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-3.19-bioc/R/bin/R CMD INSTALL treeio ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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) (2024-03-18 r86148) -- "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 v1.27.0 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
S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
visualization of richly annotated phylogenetic data. Molecular Biology
and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166
Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan
Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data
object for visualization of a phylogenetic tree and annotation data.
iMeta 2022, 1(4):e56. doi:10.1002/imt2.56
>
> 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};",
"data":[
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"AA_subs": "K603R",
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"S": 633.1,
"dN_vs_dS": 0.0646,
"dN": 0.0007,
"dS": 0.0101,
"N_x_dN": 1,
"S_x_dS": 6.4
},
{
"edge_num": 2,
"subs": "C222T / G555A / C732A / C828T / G939T / T999C / A1047G / G1083A / C1263T / G1329A / A1341G / A1344T / T1405C / T1440C / C1752T / A1827G / C1911T / C1941T / G2013A / T2022C / C2043T",
"AA_subs": "",
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},
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{
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},
{
"edge_num": 8,
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"AA_subs": "I38V / E258D / T570I",
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},
{
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{
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},
{
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"subs": "G96A / T279C / C282T / G297A / C303T / C318A / C333T / C336T / A417G / G420A / A477G / T486C / C513A / G525A / C762T / A777T / G840A / T861C / C864T / C888T / A912G / C945T / C993T / A1053G / G1159A / T1188C / A1194G / G1197A / A1219G / C1233T / T1249C / G1294A / G1308A / A1326G / G1407A / G1470A / G1482A / T1512C / T1581C / T1623C / C1641T / C1665T / G1722A / A1761G / T1800C / A1827G / G1887A / A1920G / C1921T / A1929G / C2143T",
"AA_subs": "V387I / I407V / V432I",
"t": 0.082,
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},
{
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},
{
"edge_num": 14,
"subs": "A126G / A171G / T207C / G243A / T321A / A342G / G369A / C405T / C483T / G504A / A537G / C804T / G810A / G909A / G1098A / G1101A / A1131G / G1137A / T1227C / A1290G / G1329A / A1518G / A1521G / C1545T / C1603T / A1608G / T1626C / T1629C / C1647A / G1671A / C1719T / G1779A / A1881G / G1971A / G2028T / A2037G / C2043T",
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{
"edge_num": 15,
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"AA_subs": "N96H / N115S / N321I / S364G",
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},
{
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},
{
"edge_num": 21,
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},
{
"edge_num": 22,
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},
{
"edge_num": 23,
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"AA_subs": "",
"t": 0.008,
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},
{
"edge_num": 24,
"subs": "",
"AA_subs": "",
"t": 0.001,
"N": 1514.9,
"S": 633.1,
"dN_vs_dS": 0.0001,
"dN": 0,
"dS": 0.0006,
"N_x_dN": 0,
"S_x_dS": 0.4
},
{
"edge_num": 25,
"subs": "G96A / T162C / T214C / G303A / T318C / A366G / C390T / G498A / A1146G / G1425A / C1461T / G1677A / A1902G / A1959G",
"AA_subs": "",
"t": 0.02,
"N": 1514.9,
"S": 633.1,
"dN_vs_dS": 0.0001,
"dN": 0,
"dS": 0.023,
"N_x_dN": 0,
"S_x_dS": 14.6
},
{
"edge_num": 26,
"subs": "G785A / A1067G / C1548T",
"AA_subs": "R262K / K356R",
"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": "Thu Mar 28 03:33:33 2024"}
}
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 108 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 108 ]
>
> proc.time()
user system elapsed
6.784 0.250 7.026
treeio.Rcheck/treeio-Ex.timings
| name | user | system | elapsed | |
| beast-parser | 0.193 | 0.008 | 0.202 | |
| find.hclust | 0.066 | 0.004 | 0.070 | |
| getNodeNum | 0.001 | 0.000 | 0.001 | |
| read.astral | 0.034 | 0.000 | 0.034 | |
| read.codeml | 0.326 | 0.004 | 0.331 | |
| read.codeml_mlc | 0.082 | 0.000 | 0.082 | |
| read.hyphy | 0.041 | 0.000 | 0.041 | |
| read.hyphy.seq | 0.017 | 0.000 | 0.017 | |
| read.jplace | 0.073 | 0.008 | 0.080 | |
| read.mcmctree | 0.058 | 0.000 | 0.059 | |
| read.nextstrain.json | 0.541 | 0.004 | 0.546 | |
| read.nhx | 0.043 | 0.000 | 0.044 | |
| read.paml_rst | 0.213 | 0.004 | 0.217 | |
| read.phylip | 0.046 | 0.000 | 0.046 | |
| read.phyloxml | 0.377 | 0.004 | 0.382 | |
| read.r8s | 0.008 | 0.000 | 0.008 | |
| read.raxml | 0.038 | 0.000 | 0.038 | |
| read.treeqza | 0.053 | 0.004 | 0.058 | |
| rename_taxa | 0.002 | 0.000 | 0.001 | |
| spt-methods | 0.048 | 0.003 | 0.052 | |
| write.beast | 0.013 | 0.000 | 0.013 | |
| write.beast.newick | 0.010 | 0.000 | 0.009 | |