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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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r-devel-linux-x86_64-debian-clang ERROR
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 (17 non-OK)
ERROR r-devel-linux-x86_64-debian-clang

package dependencies

Packages required but not available: 'rtracklayer', 'ggbio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
OK r-devel-linux-x86_64-debian-gcc

*


            

            

              

                OK
                r-devel-linux-x86_64-fedora-clang
              

              
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                OK
                r-devel-linux-x86_64-fedora-gcc
              

              
*

              

            

            

              

                OK
                r-devel-macos-arm64
              

              
*

              

            

            

              

                OK
                r-devel-windows-x86_64
              

              
*

              

            

            

              

                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’ [7s/7s]
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/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 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' [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 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

            

            

              

                OK
                r-patched-linux-x86_64
              

              
*

              

            

            

              

                OK
                r-release-linux-x86_64
              

              
*

              

            

            

              

                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.

            

            

              

                OK
                r-release-windows-x86_64
              

              
*

              

            

          

        

      



      

      
      

        
Check History

        

          

            
              ERROR
              
                8 OK ·                 0 NOTE ·                 0 WARNING ·                 6 ERROR ·                 0 FAILURE              
              Mar 9, 2026
            
            

              

                

                  ERROR
                  r-devel-linux-x86_64-debian-clang
                

                
package dependencies

                
Packages required but not available: 'rtracklayer', 'ggbio'

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

              

              

                

                  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’ [7s/7s]
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(Po

              

              

                

                  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 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(

              

              

                

                  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 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(PopP

              

            

          

        

      


      

      
      

        
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 9, 2026