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PopPsiSeqR

Process and Visualize Evolve & Resequence Experiments

v1.0.2 · Jan 12, 2026 · MIT + file LICENSE
CRAN GitHub Mirror

Description

Handle data from evolve and resequence experiments. Measured allele frequencies (e.g., from variants called from high-throughput sequencing data) are compared using an update of the PsiSeq algorithm (Earley, Eric and Corbin Jones (2011) <doi:10.1534/genetics.111.129445>). Functions for saving and loading important files are also included, as well as functions for basic data visualization.

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CRAN Check Status

5 ERROR
9 OK
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r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc OK
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 OK
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 ERROR
r-oldrel-macos-x86_64 ERROR
r-oldrel-windows-x86_64 ERROR
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
r-release-macos-arm64 ERROR
r-release-macos-x86_64 ERROR
r-release-windows-x86_64 OK
Check details (8 non-OK)
ERROR r-oldrel-macos-arm64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘PopPsiSeq_and_Helpers.Rmd’ using rmarkdown

Quitting from PopPsiSeq_and_Helpers.Rmd:120-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     x
  1. +-ggplot2::autoplot(...)
  2. \-ggbio::autoplot(...)
  3.   \-ggbio (local) .local(object, ...)
  4.     +-BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
  5.     +-base::do.call(ggplot, c(list(data = object), list(aes.res)))
  6.     +-ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
  7.     \-ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
  8.       \-ggbio::GGbio(gg, data = data)
  9.         +-BiocGenerics::do.call(...)
 10.         +-base::do.call(...)
 11.         \-methods (local) `<fn>`(...)
 12.           +-methods::initialize(value, ...)
 13.           \-methods::initialize(value, ...)
 14.             \-methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building ‘PopPsiSeq_and_Helpers.Rmd’

SUMMARY: processing the following file failed:
  ‘PopPsiSeq_and_Helpers.Rmd’

Error: Vignette re-building failed.
Execution halted
ERROR r-oldrel-macos-arm64

tests

Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PopPsiSeqR)
  > 
  > test_check("PopPsiSeqR")
  Saving _problems/test-plot-26.R
  Saving _problems/test-plot-27.R
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
  Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
  Actually got a <simpleError> with message:
    invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
  ── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
  Error in `eval(code, test_env)`: object 'mock.plot' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-macos-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘PopPsiSeq_and_Helpers.Rmd’ using rmarkdown

Quitting from PopPsiSeq_and_Helpers.Rmd:120-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     x
  1. +-ggplot2::autoplot(...)
  2. \-ggbio::autoplot(...)
  3.   \-ggbio (local) .local(object, ...)
  4.     +-BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
  5.     +-base::do.call(ggplot, c(list(data = object), list(aes.res)))
  6.     +-ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
  7.     \-ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
  8.       \-ggbio::GGbio(gg, data = data)
  9.         +-BiocGenerics::do.call(...)
 10.         +-base::do.call(...)
 11.         \-methods (local) `<fn>`(...)
 12.           +-methods::initialize(value, ...)
 13.           \-methods::initialize(value, ...)
 14.             \-methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building ‘PopPsiSeq_and_Helpers.Rmd’

SUMMARY: processing the following file failed:
  ‘PopPsiSeq_and_Helpers.Rmd’

Error: Vignette re-building failed.
Execution halted
ERROR r-oldrel-macos-x86_64

tests

Running ‘testthat.R’ [17s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PopPsiSeqR)
  > 
  > test_check("PopPsiSeqR")
  Saving _problems/test-plot-26.R
  Saving _problems/test-plot-27.R
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
  Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
  Actually got a <simpleError> with message:
    invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
  ── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
  Error in `eval(code, test_env)`: object 'mock.plot' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-windows-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building 'PopPsiSeq_and_Helpers.Rmd' using rmarkdown

Quitting from PopPsiSeq_and_Helpers.Rmd:120-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     x
  1. +-ggplot2::autoplot(...)
  2. \-ggbio::autoplot(...)
  3.   \-ggbio (local) .local(object, ...)
  4.     +-BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
  5.     +-base::do.call(ggplot, c(list(data = object), list(aes.res)))
  6.     +-ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
  7.     \-ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
  8.       \-ggbio::GGbio(gg, data = data)
  9.         +-BiocGenerics::do.call(...)
 10.         +-base::do.call(...)
 11.         \-methods (local) `<fn>`(...)
 12.           +-methods::initialize(value, ...)
 13.           \-methods::initialize(value, ...)
 14.             \-methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building 'PopPsiSeq_and_Helpers.Rmd'

SUMMARY: processing the following file failed:
  'PopPsiSeq_and_Helpers.Rmd'

Error: Vignette re-building failed.
Execution halted
ERROR r-oldrel-windows-x86_64

tests

Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PopPsiSeqR)
  > 
  > test_check("PopPsiSeqR")
  Saving _problems/test-plot-26.R
  Saving _problems/test-plot-27.R
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
  Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
  Actually got a <simpleError> with message:
    invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
  ── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
  Error in `eval(code, test_env)`: object 'mock.plot' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-release-macos-arm64

package dependencies

Package required but not available: ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ERROR r-release-macos-x86_64

package dependencies

Package required but not available: ‘ggbio’

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

Check History

ERROR 9 OK · 0 NOTE · 0 WARNING · 5 ERROR · 0 FAILURE Mar 10, 2026
ERROR r-release-macos-arm64

package dependencies

Package required but not available: ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ERROR r-release-macos-x86_64

package dependencies

Package required but not available: ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ERROR r-oldrel-macos-arm64

tests

Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional te
...[truncated]...
ng::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-macos-x86_64

tests

Running ‘testthat.R’ [17s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional 
...[truncated]...
ng::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-windows-x86_64

tests

Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test
...[truncated]...
ng::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted

Dependency Network

Dependencies Reverse dependencies rtracklayer GenomicRanges ggplot2 dplyr S4Vectors magrittr ggbio withr patchwork tidyr rlang devtools PopPsiSeqR

Version History

new 1.0.2 Mar 10, 2026
updated 1.0.2 ← 1.0.0 diff Jan 11, 2026
new 1.0.0 Aug 19, 2025