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PACVr

Plastome Assembly Coverage Visualization

v1.1.4 · Mar 30, 2026 · BSD 3-clause License + file LICENSE
CRAN GitHub Mirror

Description

Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2020) <doi:10.1186/s12859-020-3475-0>.

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

tests

Running ‘testthat.R’ [104s/127s]
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(PACVr)
  > 
  > test_check("PACVr")
  Saving _problems/test-PACVr-9.R
  Warning: stack imbalance in '<-', 123 then 125
  Warning: stack imbalance in '{', 119 then 121
  Warning: stack imbalance in '{', 112 then 114
  Warning: stack imbalance in '<-', 105 then 107
  Warning: stack imbalance in 'withVisible', 99 then 101
  Warning: stack imbalance in '<-', 88 then 90
  Warning: stack imbalance in '{', 84 then 86
  Saving _problems/test-readingOps-50.R
  Saving _problems/test-readingOps-50.R
  [ FA
...[truncated]...
ount)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  ── Error ('test-readingOps.R:50:5'): successful parsing of `MG936619/MG936619.gb` ──
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
       ▆
    1. └─PACVr:::PACVr.read.gb(gbkFileFull) at test-readingOps.R:50:5
    2.   └─PACVr:::read.gbWithHandling(gbkRaw)
    3.     └─base::tryCatch(...)
    4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    6.           └─value[[3L]](cond)
    7.             └─PACVr:::read.gbOnFix(gbkRaw, count)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  
  [ FAIL 3 | WARN 3 | SKIP 0 | PASS 27 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘testthat.R’ [70s/85s]
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(PACVr)
  > 
  > test_check("PACVr")
  Saving _problems/test-PACVr-9.R
  Warning: stack imbalance in '<-', 123 then 125
  Warning: stack imbalance in '{', 119 then 121
  Warning: stack imbalance in '{', 112 then 114
  Warning: stack imbalance in '<-', 105 then 107
  Warning: stack imbalance in 'withVisible', 99 then 101
  Warning: stack imbalance in '<-', 88 then 90
  Warning: stack imbalance in '{', 84 then 86
  Saving _problems/test-readingOps-50.R
  Saving _problems/test-readingOps-50.R
  [ FAIL
...[truncated]...
ount)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  ── Error ('test-readingOps.R:50:5'): successful parsing of `MG936619/MG936619.gb` ──
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
       ▆
    1. └─PACVr:::PACVr.read.gb(gbkFileFull) at test-readingOps.R:50:5
    2.   └─PACVr:::read.gbWithHandling(gbkRaw)
    3.     └─base::tryCatch(...)
    4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    6.           └─value[[3L]](cond)
    7.             └─PACVr:::read.gbOnFix(gbkRaw, count)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  
  [ FAIL 3 | WARN 3 | SKIP 0 | PASS 27 ]
  Error:
  ! Test failures.
  Execution halted
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-patched-linux-x86_64

tests

Running ‘testthat.R’ [100s/124s]
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(PACVr)
  > 
  > test_check("PACVr")
  Saving _problems/test-PACVr-9.R
  Warning: stack imbalance in '<-', 123 then 125
  Warning: stack imbalance in '{', 119 then 121
  Warning: stack imbalance in '{', 112 then 114
  Warning: stack imbalance in '<-', 105 then 107
  Warning: stack imbalance in 'withVisible', 99 then 101
  Warning: stack imbalance in '<-', 88 then 90
  Warning: stack imbalance in '{', 84 then 86
  Saving _problems/test-readingOps-50.R
  Saving _problems/test-readingOps-50.R
  [ FA
...[truncated]...
ount)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  ── Error ('test-readingOps.R:50:5'): successful parsing of `MG936619/MG936619.gb` ──
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
       ▆
    1. └─PACVr:::PACVr.read.gb(gbkFileFull) at test-readingOps.R:50:5
    2.   └─PACVr:::read.gbWithHandling(gbkRaw)
    3.     └─base::tryCatch(...)
    4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    6.           └─value[[3L]](cond)
    7.             └─PACVr:::read.gbOnFix(gbkRaw, count)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  
  [ FAIL 3 | WARN 3 | SKIP 0 | PASS 27 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-release-linux-x86_64

tests

Running ‘testthat.R’ [101s/127s]
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(PACVr)
  > 
  > test_check("PACVr")
  Saving _problems/test-PACVr-9.R
  Warning: stack imbalance in '<-', 123 then 125
  Warning: stack imbalance in '{', 119 then 121
  Warning: stack imbalance in '{', 112 then 114
  Warning: stack imbalance in '<-', 105 then 107
  Warning: stack imbalance in 'withVisible', 99 then 101
  Warning: stack imbalance in '<-', 88 then 90
  Warning: stack imbalance in '{', 84 then 86
  Saving _problems/test-readingOps-50.R
  Saving _problems/test-readingOps-50.R
  [ FA
...[truncated]...
ount)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  ── Error ('test-readingOps.R:50:5'): successful parsing of `MG936619/MG936619.gb` ──
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
       ▆
    1. └─PACVr:::PACVr.read.gb(gbkFileFull) at test-readingOps.R:50:5
    2.   └─PACVr:::read.gbWithHandling(gbkRaw)
    3.     └─base::tryCatch(...)
    4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    6.           └─value[[3L]](cond)
    7.             └─PACVr:::read.gbOnFix(gbkRaw, count)
    8.               └─PACVr:::fixGbkChar(gbkRaw)
    9.                 └─base::writeLines(gbkCharFixed, gbkFileFixed)
   10.                   └─base::file(con, "w")
  
  [ FAIL 3 | WARN 3 | SKIP 0 | PASS 27 ]
  Error:
  ! Test failures.
  Execution halted

Check History

ERROR 10 OK · 0 NOTE · 3 WARNING · 1 ERROR · 0 FAILURE Mar 31, 2026
WARNING r-devel-linux-x86_64-debian-clang

dependencies in R code

Missing or unexported objects:
  ‘Biostrings::compareStrings’
  ‘Biostrings::nucleotideSubstitutionMatrix’
  ‘Biostrings::pairwiseAlignment’
WARNING r-devel-linux-x86_64-debian-gcc

dependencies in R code

Missing or unexported objects:
  ‘Biostrings::compareStrings’
  ‘Biostrings::nucleotideSubstitutionMatrix’
  ‘Biostrings::pairwiseAlignment’
WARNING r-devel-windows-x86_64

dependencies in R code

Missing or unexported objects:
  'Biostrings::compareStrings'
  'Biostrings::nucleotideSubstitutionMatrix'
  'Biostrings::pairwiseAlignment'
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.
WARNING 11 OK · 0 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
WARNING r-devel-linux-x86_64-debian-gcc

dependencies in R code

Missing or unexported objects:
  ‘Biostrings::compareStrings’
  ‘Biostrings::nucleotideSubstitutionMatrix’
  ‘Biostrings::pairwiseAlignment’
WARNING r-devel-linux-x86_64-fedora-clang

dependencies in R code

Missing or unexported objects:
  ‘Biostrings::compareStrings’
  ‘Biostrings::nucleotideSubstitutionMatrix’
  ‘Biostrings::pairwiseAlignment’
WARNING r-devel-linux-x86_64-fedora-gcc

dependencies in R code

Missing or unexported objects:
  ‘Biostrings::compareStrings’
  ‘Biostrings::nucleotideSubstitutionMatrix’
  ‘Biostrings::pairwiseAlignment’

Dependency Network

Dependencies Reverse dependencies Biostrings dplyr GenomicAlignments GenomicRanges IRanges logger read.gb RCircos (>= 1.2.0) tidyr pwalign R6 PACVr

Version History

updated 1.1.4 ← 1.0.11 diff Mar 30, 2026
new 1.0.11 Mar 10, 2026
updated 1.0.11 ← 1.0.8 diff Apr 9, 2024
updated 1.0.8 ← 1.0.7 diff Feb 27, 2024
updated 1.0.7 ← 1.0.6 diff Feb 4, 2024
updated 1.0.6 ← 1.0.5 diff Jan 8, 2024
updated 1.0.5 ← 0.9.4 diff Dec 7, 2023
updated 0.9.4 ← 0.9.2 diff Nov 21, 2020
updated 0.9.2 ← 0.9.1 diff Feb 20, 2020
updated 0.9.1 ← 0.8.2 diff Feb 8, 2020
updated 0.8.2 ← 0.8.1 diff Sep 12, 2019
new 0.8.1 Jul 25, 2019