CRAN Package Check Results for Package rhierbaps

Last updated on 2019-10-13 10:47:06 CEST.

Check Details

Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'introduction.Rmd' using rmarkdown
    ggtree v1.99.1 For help: https://yulab-smu.github.io/treedata-book/
    
    If you use ggtree in published research, please cite the most appropriate paper(s):
    
    <1b>[36m-<1b>[39m 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
    <1b>[36m-<1b>[39m 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
    
    
    Loading required package: ape
    
    Attaching package: 'ape'
    
    The following object is masked from 'package:ggtree':
    
     rotate
    
    Loading required package: maps
    Warning in load_fasta(fasta.file.name) :
     Characters not in acgtnACGTN- will be treated as missing (-)...
    Warning in load_fasta(woodmouse) :
     Characters not in acgtnACGTN- will be treated as missing (-)...
    Read 1 item
    Quitting from lines 126-127 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    This function is defunct. Use treeio::tree_subset()
    --- failed re-building 'introduction.Rmd'
    
    SUMMARY: processing the following file failed:
     'introduction.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘introduction.Rmd’ using rmarkdown
    ggtree v1.99.1 For help: https://yulab-smu.github.io/treedata-book/
    
    If you use ggtree in published research, please cite the most appropriate paper(s):
    
    <1b>[36m-<1b>[39m 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
    <1b>[36m-<1b>[39m 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
    
    
    Loading required package: ape
    
    Attaching package: 'ape'
    
    The following object is masked from 'package:ggtree':
    
     rotate
    
    Loading required package: maps
    Warning in load_fasta(fasta.file.name) :
     Characters not in acgtnACGTN- will be treated as missing (-)...
    Warning in load_fasta(woodmouse) :
     Characters not in acgtnACGTN- will be treated as missing (-)...
    Read 1 item
    Quitting from lines 126-127 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    This function is defunct. Use treeio::tree_subset()
    --- failed re-building ‘introduction.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.1.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘ggtree’
Flavor: r-release-osx-x86_64

Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘introduction.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 40-46 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    there is no package called 'ggtree'
    --- failed re-building ‘introduction.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 40-46 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    package or namespace load failed for 'ggtree':
     object 'as_data_frame' is not exported by 'namespace:tidytree'
    Execution halted
Flavor: r-oldrel-osx-x86_64