* using log directory ‘/Users/ripley/R/packages/tests-devel/ggmsa.Rcheck’ * using R Under development (unstable) (2021-08-13 r80752) * using platform: aarch64-apple-darwin20.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘ggmsa/DESCRIPTION’ ... OK * this is package ‘ggmsa’ version ‘1.0.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘ggtreeExtra’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ggmsa’ can be installed ... [13s/16s] 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 loading without being on the library search path ... OK * checking use of S3 registration ... 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 ... [18s/34s] 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 R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [12s/24s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [26s/63s] WARNING Error(s) in re-building vignettes: --- re-building ‘ggmsa.Rmd’ using rmarkdown Coordinate system already present. Adding new coordinate system, which will replace the existing one. Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: kableExtra Attaching package: 'kableExtra' The following object is masked from 'package:dplyr': group_rows Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'ape' The following object is masked from 'package:Biostrings': complement ggtree v3.0.3 For help: https://yulab-smu.top/treedata-book/ If you use ggtree in published research, please cite the most appropriate paper(s): 1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96 2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194 3. 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 Attaching package: 'ggtree' The following object is masked from 'package:ape': rotate The following object is masked from 'package:Biostrings': collapse The following object is masked from 'package:IRanges': collapse The following object is masked from 'package:S4Vectors': expand Warning: Unknown or uninitialised column: `name`. Warning: Unknown or uninitialised column: `name`. Loading required package: gggenes Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Coordinate system already present. Adding new coordinate system, which will replace the existing one. Quitting from lines 210-224 (ggmsa.Rmd) Error: processing vignette 'ggmsa.Rmd' failed with diagnostics: there is no package called 'ggtreeExtra' --- failed re-building ‘ggmsa.Rmd’ SUMMARY: processing the following file failed: ‘ggmsa.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/Users/ripley/R/packages/tests-devel/ggmsa.Rcheck/00check.log’ for details. 243.59 real 109.58 user 34.83 sys