* using log directory 'd:/Rcompile/CRANpkg/local/3.5/ggmsa.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'ggmsa/DESCRIPTION' ... OK * this is package 'ggmsa' version '0.0.2' * 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 'ggmsa' 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 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 ... [14s] 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 ... [11s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [32s] WARNING Error in re-building vignettes: ... Warning: attributes are not identical across measure variables; they will be dropped Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning: attributes are not identical across measure variables; they will be dropped Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning: attributes are not identical across measure variables; they will be dropped Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning: attributes are not identical across measure variables; they will be dropped Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning: attributes are not identical across measure variables; they will be dropped Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type, : All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2. Warning: attributes are not identical across measure variables; they will be dropped 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: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, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XVector 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 v1.14.6 For help: https://guangchuangyu.github.io/software/ggtree If you use ggtree in published research, please cite the most appropriate paper(s): - 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 - 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, accepted. doi: 10.1093/molbev/msy194 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: `data_frame()` is deprecated as of tibble 1.1.0. Please use `tibble()` instead. This warning is displayed once every 8 hours. Call `lifecycle::last_warnings()` to see where this warning was generated. Warning: attributes are not identical across measure variables; they will be dropped Quitting from lines 128-140 (ggmsa.Rmd) Error: processing vignette 'ggmsa.Rmd' failed with diagnostics: could not find function "geom_facet" Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING