Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 862/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggtreeSpace 1.2.0 (landing page) Guangchuang Yu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the ggtreeSpace package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggtreeSpace.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: ggtreeSpace |
Version: 1.2.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtreeSpace.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggtreeSpace_1.2.0.tar.gz |
StartedAt: 2024-12-20 02:05:21 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:07:08 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 107.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ggtreeSpace.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggtreeSpace.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggtreeSpace_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ggtreeSpace.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ggtreeSpace/DESCRIPTION' ... OK * this is package 'ggtreeSpace' version '1.2.0' * 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 whether package 'ggtreeSpace' 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 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 intern_call: no visible binding for global variable 'dat' Undefined global functions or variables: dat * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'geom_treespace.Rd': geom_treespace Code: function(tr, trait, mapping = NULL, ...) Docs: function(tr, data, mapping = NULL, ...) Argument names in code not in docs: trait Argument names in docs not in code: data Mismatches in argument names: Position: 2 Code: trait Docs: data Codoc mismatches from Rd file 'ggtreespace.Rd': ggtreespace Code: function(tr, trait, mapping = NULL, ...) Docs: function(tr, data, mapping = NULL, ...) Argument names in code not in docs: trait Argument names in docs not in code: data Mismatches in argument names: Position: 2 Code: trait Docs: data Codoc mismatches from Rd file 'make_ts_data.Rd': make_ts_data Code: function(tr, trait) Docs: function(tr, data) Argument names in code not in docs: trait Argument names in docs not in code: data Mismatches in argument names: Position: 2 Code: trait Docs: data * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/ggtreeSpace.Rcheck/00check.log' for details.
ggtreeSpace.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ggtreeSpace ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ggtreeSpace' ... ** using staged installation ** R ** 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 (ggtreeSpace)
ggtreeSpace.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(ggtreeSpace) > > test_check("ggtreeSpace") ggtree v3.14.0 Learn more at https://yulab-smu.top/contribution-tree-data/ Please cite: 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 Loading required package: ape Attaching package: 'ape' The following object is masked from 'package:ggtree': rotate Loading required package: maps Attaching package: 'dplyr' The following object is masked from 'package:ape': where The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Joining with `by = join_by(node)` [ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 4.73 0.50 5.17
ggtreeSpace.Rcheck/ggtreeSpace-Ex.timings
name | user | system | elapsed | |
geom_treespace | 0.22 | 0.01 | 0.23 | |
geom_tsheatmap | 1.37 | 0.02 | 4.15 | |
ggtreespace | 0.40 | 0.03 | 0.44 | |
make_ts_data | 0.15 | 0.00 | 0.16 | |
phylospm | 4.24 | 0.14 | 4.37 | |
theme_treespace | 0.34 | 0.03 | 0.38 | |
theme_treespace2 | 0.33 | 0.02 | 0.34 | |