Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:26 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (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

CHECK results for treeio on palomino3


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.

raw results

Package 2048/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treeio 1.20.2  (landing page)
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)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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


Installation output

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)

Tests output

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};",
	"data":[
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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
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  {
    "edge_num": 23,
    "subs": "T211C / T279C / G1134A / T1149C / C1179T / G1695T",
    "AA_subs": "",
    "t": 0.008,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0094,
    "N_x_dN": 0,
    "S_x_dS": 6
  },
  {
    "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": "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 

Example timings

treeio.Rcheck/treeio-Ex.timings

nameusersystemelapsed
Nnode.treedata000
beast-parser0.260.030.33
drop.tip-methods0.180.000.19
getNodeNum000
read.astral0.050.000.05
read.codeml0.440.010.95
read.codeml_mlc0.120.000.12
read.hyphy0.080.000.08
read.hyphy.seq0.020.000.02
read.jplace0.090.000.11
read.mcmctree0.130.000.13
read.nhx0.060.000.06
read.paml_rst0.340.010.67
read.phylip0.050.000.05
read.phyloxml0.750.020.76
read.r8s000
read.raxml0.030.000.04
read.treeqza0.090.110.25
rename_taxa000
tree_subset000
write.beast0.020.000.02
write.beast.newick0.020.000.01