BIGr

Breeding Insight Genomics Functions for Polyploid and Diploid Species

v0.6.2 · Sep 18, 2025 · Apache License (>= 2)

Description

Functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data. 'BIGr' provides the ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs) from diversity arrays technology missing allele discovery count (DArT MADC) files, and manipulate genotype data for both diploid and polyploid species. It also serves as the core dependency for the 'BIGapp' 'Shiny' app, which provides a user-friendly interface for performing routine genotype analysis tasks such as dosage calling, filtering, principal component analysis (PCA), genome-wide association studies (GWAS), and genomic prediction. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, and the 'updog' output format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.

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CRAN Check Status

3 ERROR

11 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	284.1s
r-devel-linux-x86_64-debian-gcc	OK	198s
r-devel-linux-x86_64-fedora-clang	OK	430.6s
r-devel-linux-x86_64-fedora-gcc	OK	419.7s
r-devel-macos-arm64	OK	88s
r-devel-windows-x86_64	OK	346s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	ERROR	11s
r-oldrel-windows-x86_64	OK	465s
r-patched-linux-x86_64	OK	260.8s
r-release-linux-x86_64	OK	257.8s
r-release-macos-arm64	ERROR	89s
r-release-macos-x86_64	ERROR	271s
r-release-windows-x86_64	OK	346s

Check details (3 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-release-macos-arm64

tests

Running ‘testthat.R’ [10s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BIGr)
  > 
  > test_check("BIGr")
  The Ref_0001 sequence had to be added for: 0 tags
  The Alt_0002 sequence had to be added for: 1 tags
  Tags discarded due to lack of Ref_0001 sequence: 0 tags
  Tags discarded due to lack of Alt_0002 sequence: 0 tags
  Saving _problems/test-madc2vcf_all-25.R
  Saving _problems/test-madc2vcf_targets-78.R
  Scanning file to determine attributes.
  File attributes:
    meta lines: 14
    header_line: 15
    variant count: 499
    column count: 159
  
  Meta line 14 read in.
  All meta lines processed.
  gt matrix initialized.
  Character matrix gt created.
    Character matrix gt rows: 499
    Character matrix gt cols: 159
    skip: 0
    nrows: 499
    row_num: 0
  
  Processed variant: 499
  All variants processed
  Scanning file to determine attributes.
  File attributes:
    meta lines: 14
    header_line: 15
    variant
...[truncated]...
 fun, length(x), argfun)
   7.           └─parallel:::checkForRemoteErrors(val)
  ── Error ('test-madc2vcf_targets.R:75:3'): bottom strand markers have correct REF/ALT ──
  Error in `checkForRemoteErrors(val)`: one node produced an error: 'recursive' must be a length-1 vector
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-madc2vcf_targets.R:75:3
   2. │ └─base::withCallingHandlers(...)
   3. └─BIGr::madc2vcf_all(...)
   4.   └─BIGr:::loop_though_dartag_report(...)
   5.     └─parallel::parLapply(...)
   6.       ├─base::do.call(...)
   7.       └─parallel::clusterApply(...)
   8.         └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
   9.           └─parallel:::checkForRemoteErrors(val)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 88 ]
  Error:
  ! Test failures.
  Warning messages:
  1: closing unused connection 7 (<-localhost:11791) 
  2: closing unused connection 6 (<-localhost:11791) 
  3: closing unused connection 5 (<-localhost:11791) 
  Execution halted

ERROR r-release-macos-x86_64

tests

Running ‘testthat.R’ [17s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BIGr)
  > 
  > test_check("BIGr")
  The Ref_0001 sequence had to be added for: 0 tags
  The Alt_0002 sequence had to be added for: 1 tags
  Tags discarded due to lack of Ref_0001 sequence: 0 tags
  Tags discarded due to lack of Alt_0002 sequence: 0 tags
  Saving _problems/test-madc2vcf_all-25.R
  Saving _problems/test-madc2vcf_targets-78.R
  Scanning file to determine attributes.
  File attributes:
    meta lines: 14
    header_line: 15
    variant count: 499
    column count: 159
  
  Meta line 14 read in.
  All meta lines processed.
  gt matrix initialized.
  Character matrix gt created.
    Character matrix gt rows: 499
    Character matrix gt cols: 159
    skip: 0
    nrows: 499
    row_num: 0
  
  Processed variant: 499
  All variants processed
  Scanning file to determine attributes.
  File attributes:
    meta lines: 14
    header_line: 15
    variant
...[truncated]...
ottom strand markers have correct REF/ALT ──
  Error in `checkForRemoteErrors(val)`: one node produced an error: 'recursive' must be a length-1 vector
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-madc2vcf_targets.R:75:3
   2. │ └─base::withCallingHandlers(...)
   3. └─BIGr::madc2vcf_all(...)
   4.   └─BIGr:::loop_though_dartag_report(...)
   5.     └─parallel::parLapply(...)
   6.       ├─base::do.call(...)
   7.       └─parallel::clusterApply(...)
   8.         └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
   9.           └─parallel:::checkForRemoteErrors(val)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 88 ]
  Error:
  ! Test failures.
  Warning messages:
  1: In for (i in seq_len(n)) { :
    closing unused connection 6 (<-localhost:11944)
  2: In for (i in seq_len(n)) { :
    closing unused connection 5 (<-localhost:11944)
  3: In if (!is.null(partial)) .NotYetUsed("partial != NULL") :
    closing unused connection 5 (<-localhost:11944)
  Execution halted

Check History

ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 10, 2026

ERROR r-release-macos-arm64

tests

Running ‘testthat.R’ [10s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BIGr)
  > 
  > test_check("BIGr")
  The Ref_0001 sequence had to be added for: 0 tags
  The Alt_0002 sequence had to be 
...[truncated]...
 | SKIP 0 | PASS 88 ]
  Error:
  ! Test failures.
  Warning messages:
  1: closing unused connection 7 (<-localhost:11791) 
  2: closing unused connection 6 (<-localhost:11791) 
  3: closing unused connection 5 (<-localhost:11791) 
  Execution halted

ERROR r-release-macos-x86_64

tests

Running ‘testthat.R’ [17s/65s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BIGr)
  > 
  > test_check("BIGr")
  The Ref_0001 sequence had to be added for: 0 tags
  The Alt_0002 sequence had to be 
...[truncated]...
nection 6 (<-localhost:11963)
  2: In for (i in seq_len(n)) { :
    closing unused connection 5 (<-localhost:11963)
  3: In if (!is.null(partial)) .NotYetUsed("partial != NULL") :
    closing unused connection 5 (<-localhost:11963)
  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.

Dependency Network

Version History

new 0.6.2 Mar 10, 2026

updated 0.6.2 ← 0.5.5 diff Sep 17, 2025

new 0.5.5 May 18, 2025