CRAN Package Check Results for Package nosoi

Last updated on 2020-02-15 01:01:32 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 6.61 322.46 329.07 WARN
r-devel-linux-x86_64-debian-gcc 1.0.0 5.85 456.20 462.05 WARN
r-devel-linux-x86_64-fedora-clang 1.0.0 324.11 WARN
r-devel-linux-x86_64-fedora-gcc 1.0.0 269.27 WARN
r-devel-windows-ix86+x86_64 1.0.0 13.00 195.00 208.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.0 20.00 224.00 244.00 OK
r-patched-linux-x86_64 1.0.0 6.44 385.82 392.26 WARN
r-patched-solaris-x86 1.0.0 199.20 WARN
r-release-linux-x86_64 1.0.0 6.12 365.79 371.91 WARN
r-release-windows-ix86+x86_64 1.0.0 11.00 169.00 180.00 OK
r-release-osx-x86_64 1.0.0 NOTE
r-oldrel-windows-ix86+x86_64 1.0.0 8.00 157.00 165.00 OK
r-oldrel-osx-x86_64 1.0.0 WARN

Check Details

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'continuous.Rmd' using rmarkdown
    Loading required package: sp
    Loading required package: viridisLite
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:raster':
    
     intersect, select, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building 'continuous.Rmd'
    
    --- re-building 'discrete.Rmd' using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 44-65 (discrete.Rmd)
    Error: processing vignette 'discrete.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building 'discrete.Rmd'
    
    --- re-building 'none.Rmd' using rmarkdown
    --- finished re-building 'none.Rmd'
    
    --- re-building 'nosoi.Rmd' using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 42-68 (nosoi.Rmd)
    Error: processing vignette 'nosoi.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building 'nosoi.Rmd'
    
    --- re-building 'output.Rmd' using rmarkdown
    Loading required package: data.table
    Starting the simulation
    Initializing ... running ...
    Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
    Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
    Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
    Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
    done.
    The simulation has run for 46 units of time and a total of 204 hosts have been infected.
    `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
    ggtree v2.1.1 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
    
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building 'output.Rmd'
    
    SUMMARY: processing the following files failed:
     'discrete.Rmd' 'nosoi.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.0
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘utils’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘continuous.Rmd’ using rmarkdown
    Loading required package: sp
    Loading required package: viridisLite
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:raster':
    
     intersect, select, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘continuous.Rmd’
    
    --- re-building ‘discrete.Rmd’ using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 44-65 (discrete.Rmd)
    Error: processing vignette 'discrete.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building ‘discrete.Rmd’
    
    --- re-building ‘none.Rmd’ using rmarkdown
    --- finished re-building ‘none.Rmd’
    
    --- re-building ‘nosoi.Rmd’ using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 42-68 (nosoi.Rmd)
    Error: processing vignette 'nosoi.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building ‘nosoi.Rmd’
    
    --- re-building ‘output.Rmd’ using rmarkdown
    Loading required package: data.table
    Starting the simulation
    Initializing ... running ...
    Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
    Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
    Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
    Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
    done.
    The simulation has run for 46 units of time and a total of 204 hosts have been infected.
    `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
    ggtree v2.1.1 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
    
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘output.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘discrete.Rmd’ ‘nosoi.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘continuous.Rmd’ using rmarkdown
    Loading required package: sp
    Loading required package: viridisLite
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:raster':
    
     intersect, select, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘continuous.Rmd’
    
    --- re-building ‘discrete.Rmd’ using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 44-65 (discrete.Rmd)
    Error: processing vignette 'discrete.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building ‘discrete.Rmd’
    
    --- re-building ‘none.Rmd’ using rmarkdown
    --- finished re-building ‘none.Rmd’
    
    --- re-building ‘nosoi.Rmd’ using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 42-68 (nosoi.Rmd)
    Error: processing vignette 'nosoi.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building ‘nosoi.Rmd’
    
    --- re-building ‘output.Rmd’ using rmarkdown
    Loading required package: data.table
    Starting the simulation
    Initializing ... running ...
    Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
    Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
    Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
    Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
    done.
    The simulation has run for 46 units of time and a total of 204 hosts have been infected.
    `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
    ggtree v2.0.1 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
    
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘output.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘discrete.Rmd’ ‘nosoi.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘gifski’
Flavor: r-patched-solaris-x86

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘continuous.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.
    Loading required package: sp
    Loading required package: viridisLite
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:raster':
    
     intersect, select, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘continuous.Rmd’
    
    --- re-building ‘discrete.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.
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 44-65 (discrete.Rmd)
    Error: processing vignette 'discrete.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building ‘discrete.Rmd’
    
    --- re-building ‘none.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.
    --- finished re-building ‘none.Rmd’
    
    --- re-building ‘nosoi.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.
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Quitting from lines 42-68 (nosoi.Rmd)
    Error: processing vignette 'nosoi.Rmd' failed with diagnostics:
    $ operator is invalid for atomic vectors
    --- failed re-building ‘nosoi.Rmd’
    
    --- re-building ‘output.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.
    Loading required package: data.table
    Starting the simulation
    Initializing ... running ...
    Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
    Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
    Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
    Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
    done.
    The simulation has run for 46 units of time and a total of 204 hosts have been infected.
    `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
    ggtree v2.0.1 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
    
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building ‘output.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘discrete.Rmd’ ‘nosoi.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
     betweenness, bonpow, closeness, components, degree, dyad.census,
     evcent, hierarchy, is.connected, neighborhood, triad.census
    
    Warning: Removed 3 rows containing missing values (geom_text).
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    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.
    Starting the simulation
    Initializing ... running ...
    Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
    Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
    Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
    Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
    done.
    The simulation has run for 46 units of time and a total of 204 hosts have been infected.
    `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
    Quitting from lines 351-360 (output.Rmd)
    Error: processing vignette 'output.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