dowser

B Cell Receptor Phylogenetics Toolkit

v2.4.1 · Mar 26, 2026 · AGPL-3

Description

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

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CRAN Check Status

2 ERROR

12 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	527.2s
r-devel-linux-x86_64-debian-gcc	OK	389.2s
r-devel-linux-x86_64-fedora-clang	OK	871.4s
r-devel-linux-x86_64-fedora-gcc	OK	902.7s
r-devel-macos-arm64	OK	138s
r-devel-windows-x86_64	OK	554s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	ERROR	12s
r-oldrel-windows-x86_64	ERROR	691s
r-patched-linux-x86_64	OK	524.5s
r-release-linux-x86_64	OK	519.4s
r-release-macos-arm64	OK	132s
r-release-macos-x86_64	OK	348s
r-release-windows-x86_64	OK	548s

Check details (2 non-OK)

ERROR r-oldrel-macos-x86_64

package dependencies

Package required but not available: ‘pwalign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

ERROR r-oldrel-windows-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building 'Building-Time-Trees-Vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `154991f5264cb97758da125dbea766fddec27d14.png'
 not found: using draft setting.

Error: processing vignette 'Building-Time-Trees-Vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/dowser.Rcheck/vign_test/dowser/vignettes/Building-Time-Trees-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Building-Time-Trees-Vignette.log for more info.
--- failed re-building 'Building-Time-Trees-Vignette.Rmd'

--- re-building 'Building-Trees-Vignette.Rmd' using rmarkdown
--- finished re-building 'Building-Trees-Vignette.Rmd'

--- re-building 'Discrete-Trait-Vignette.Rmd' using rmarkdown
--- finished re-building 'Discrete-Trait-Vignette.Rmd'

--- re-building 'Germlines-Vignette.Rmd' using rmarkdown
--- finished re-building 'Germlines-Vignette.Rmd'

--- re-building 'Measurable-Evolution.Rmd' using rmarkdown
--- finished re-building 'Measurable-Evolution.Rmd'

--- re-building 'NonB-Cell-Data.Rmd' using rmarkdown
--- finished re-building 'NonB-Cell-Data.Rmd'

--- re-building 'Plotting-Trees-Vignette.Rmd' using rmarkdown
--- finished re-building 'Plotting-Trees-Vignette.Rmd'

--- re-building 'Quickstart-Vignette.Rmd' using rmarkdown
--- finished re-building 'Quickstart-Vignette.Rmd'

--- re-building 'Resolve-Light-Chains-Vignette.Rmd' using rmarkdown
--- finished re-building 'Resolve-Light-Chains-Vignette.Rmd'

--- re-building 'Sequences-Vignette.Rmd' using rmarkdown
--- finished re-building 'Sequences-Vignette.Rmd'

SUMMARY: processing the following file failed:
  'Building-Time-Trees-Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted

Check History

ERROR 9 OK · 1 NOTE · 0 WARNING · 4 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>’

Found the following (possibly) invalid file URIs:
  URI: Resolve-Light-Chains-Vignette.md
    From: inst/doc/Building-Trees-Vignette.pdf
  URI: Plotting-Trees-Vignette.md
    From: inst/doc/Measurable-Evolution.pdf
  URI: Building-Trees-Vignette.md
    From: inst/doc/Resolve-Light-Chains-Vignette.pdf

ERROR r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>’

Found the following (possibly) invalid file URIs:
  URI: Resolve-Light-Chains-Vignette.md
    From: inst/doc/Building-Trees-Vignette.pdf
  URI: Plotting-Trees-Vignette.md
    From: inst/doc/Measurable-Evolution.pdf
  URI: Building-Trees-Vignette.md
    From: inst/doc/Resolve-Light-Chains-Vignette.pdf

ERROR r-devel-linux-x86_64-fedora-clang

whether package can be installed

Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/dowser.Rcheck/00install.out’ for details.

ERROR r-devel-linux-x86_64-fedora-gcc

whether package can be installed

Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/dowser.Rcheck/00install.out’ for details.

ERROR r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘pwalign’

Dependency Network

Version History

updated 2.4.1 ← 2.4.0 diff Mar 26, 2026

new 2.4.0 Mar 10, 2026

updated 2.4.0 ← 2.3 diff Oct 14, 2025

updated 2.3 ← 2.2.0 diff Oct 21, 2024

updated 2.2.0 ← 2.1.0 diff May 8, 2024

updated 2.1.0 ← 2.0.0 diff Dec 21, 2023

updated 2.0.0 ← 1.2.0 diff Sep 26, 2023

updated 1.2.0 ← 1.1.0 diff May 30, 2023

updated 1.1.0 ← 1.0.0 diff Oct 4, 2022

updated 1.0.0 ← 0.1.0 diff Apr 12, 2022

new 0.1.0 Jul 21, 2021