Dev main by smasongarrison · Pull Request #141 · R-Computing-Lab/BGmisc

smasongarrison · 2026-03-25T19:56:18Z

Fix non-ASCII character warning in R/buildComponent.R (em dash — replaced with \u2014 Unicode escape)

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…kpoint (#139) * Initial plan * Fix vapply missing FUN.VALUE argument in .loadOrComputeParList Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com> Agent-Logs-Url: https://github.com/R-Computing-Lab/BGmisc/sessions/93bb6734-9e37-4cd1-b415-9d67049126ca --------- Co-Authored-By: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-Authored-By: smasongarrison <6001608+smasongarrison@users.noreply.github.com>

Copilot

Pull request overview

This PR enhances BGmisc’s pedigree-to-relatedness matrix pipeline by extending ped2com() with chunked transpose support, improved checkpoint/resume behavior, and optional ID subsetting, alongside CI/release automation and associated documentation/test updates.

Changes:

Extended ped2com() with transpose_method = "chunked", chunk_size, keep_ids, force_symmetric, and improved checkpoint/resume logic (including RAM/tcrossprod checkpoint fixes).
Added/expanded test coverage for chunked tcrossprod, checkpoint resumability, and keep_ids behavior.
Added GitHub Actions workflows (multi-OS R CMD check, branch/main checks, releases) plus Codecov/pkgdown/config/metadata updates.

Reviewed changes

Copilot reviewed 26 out of 29 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
`R/buildComponent.R`	Core implementation updates for chunked transpose, keep-id subsetting, checkpointing/resume, and transpose helper changes.
`R/buildComponentWrappers.R`	Moves `ped2com` wrappers into a dedicated file and updates wrapper signatures.
`tests/testthat/test-convertPedigree.R`	Updates checkpoint file list to include `tcrossprod_ids`.
`tests/testthat/test-buildComponent.R`	Adds tests for `ram_checkpoint` resume and `keep_ids` subsetting behavior.
`tests/testthat/test-buildComponent_chunks.R`	New tests covering chunked tcrossprod correctness and per-chunk checkpoint/resume behavior.
`man/ped2com.Rd`	Documents new `ped2com()` arguments/options (generated from roxygen).
`man/dot-computeTranspose.Rd`	Documents updated `.computeTranspose()` interface (generated from roxygen).
`man/ped2add.Rd`	Updates wrapper documentation for new args (generated).
`man/ped2mit.Rd`	Updates wrapper documentation for new args (generated).
`man/ped2cn.Rd`	Updates wrapper documentation for new args (generated).
`man/ped2gen.Rd`	Updates wrapper documentation for new args (generated).
`man/ped2ce.Rd`	Updates `ped2ce()` usage to include `personID` (generated).
`.github/workflows/check_on_different_r_os.yml`	Adds multi-OS/R-version R CMD check workflow.
`.github/workflows/check_on_main.yml`	Adds main-branch checklist-based package check workflow.
`.github/workflows/check_on_branch.yml`	Adds non-main branch checklist-based package check workflow.
`.github/workflows/release.yml`	Adds GitHub release automation on tag pushes / workflow completion.
`codecov.yml`	Adds Codecov configuration (one of two configs added).
`codecov.yaml`	Adds an additional Codecov configuration file (overlaps with `codecov.yml`).
`_pkgdown.yml`	Updates pkgdown site URL/template settings.
`DESCRIPTION`	Reflows/updates package description and dependency ordering.
`NEWS.md`	Adds a “Development version” section summarizing recent changes.
`.Rbuildignore`	Expands ignored build artifacts/config files (CI/docs/dev files).
`.gitignore`	Expands ignored artifacts (R outputs, docs build outputs, local tooling).
`data-raw/optimizing_transpose.R`	Adds benchmarking script for transpose methods.
`data-raw/ped2com_benchmark_summary.csv`	Updates benchmark summary output.
`data-raw/ped2com_benchmark_results.csv`	Updates benchmark results output.
`data-raw/ped2com_benchmark_design_com.csv`	Adds benchmark design table output.
`data-raw/ped2com_benchmark_start_time.txt`	Updates benchmark run start timestamp.
`data-raw/ped2com_benchmark_end_time.txt`	Updates benchmark run end timestamp.

Comments suppressed due to low confidence (1)

.github/workflows/check_on_main.yml:20

The workflow uses inbo/actions/check_pkg@main, which is a moving branch and can change without notice (affecting reproducibility and supply-chain safety). Prefer pinning to a tagged release or a commit SHA.

    steps:
      - uses: inbo/actions/check_pkg@main

R/buildComponent.R

tests/testthat/test-buildComponent_chunks.R

tests/testthat/test-buildComponent.R

DESCRIPTION

R/buildComponentWrappers.R

tests/testthat/test-buildComponent_chunks.R

tests/testthat/test-buildComponent.R

R/buildComponent.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

smasongarrison · 2026-03-25T21:57:57Z

can you fix this? @copilot ❯ checking code files for non-ASCII characters ... WARNING
Found the following file with non-ASCII characters:
R/buildComponent.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function 'tools::showNonASCIIfile' can help in finding non-ASCII
characters in files.

…014 escape Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com> Agent-Logs-Url: https://github.com/R-Computing-Lab/BGmisc/sessions/1f51ade1-dbed-4745-9e6b-e3b18880f36c

Copilot · 2026-03-25T21:59:13Z

can you fix this? @copilot ❯ checking code files for non-ASCII characters ... WARNING
Found the following file with non-ASCII characters:
R/buildComponent.R
...

Fixed in d596f0f. Replaced the em dash (—) on line 395 of R/buildComponent.R with its Unicode escape sequence \u2014, which is the portable R way to include non-ASCII characters in code files.

…into dev_main

Update tests/testthat/test-buildComponent_chunks.R Update tests/testthat/test-buildComponent_chunks.R Co-Authored-By: Copilot <175728472+Copilot@users.noreply.github.com>

smasongarrison · 2026-03-26T13:21:21Z

The big change is that we can now create a subsetted pedigree for the additive genetic matrix.

…into dev_main

smasongarrison · 2026-03-27T03:01:04Z

R/buildComponent.R

-  if (mz_method %in% c("merging") && mz_twins == TRUE && !is.null(mz_row_pairs) && length(mz_row_pairs) > 0 &&
-        config$component %in% c("additive")) {
+  if (config$mz_method %in% c("merging") && config$mz_twins == TRUE && !is.null(mz_row_pairs) && length(mz_row_pairs) > 0 &&
+    config$component %in% c("additive")) {


Suggested change

config$component %in% c("additive")) {

config$component %in% c("additive")) {

smasongarrison · 2026-03-27T03:01:49Z

R/buildComponent.R

+    mtSum <- 0
+    count <- 0
+  } else if (config$resume == TRUE && file.exists(checkpoint_files$r_checkpoint) &&
+    file.exists(checkpoint_files$gen_checkpoint) &&


Suggested change

file.exists(checkpoint_files$gen_checkpoint) &&

file.exists(checkpoint_files$gen_checkpoint) &&

Copilot AI and others added 19 commits March 24, 2026 12:17

split to move wrappers to own file

ffe4b0e

Update buildComponent.R

6926bff

chunked?

ec23c11

check that ids match

fc934ec

smarter wrapper

dc093c7

docs

ef13bde

Update buildComponent.R

956ef18

Update test-buildComponent.R

e0d881f

tests

f9b0096

resume chunks

8f4276b

Add force_symmetric option and docs

91c3952

moving chunk tests

ae7c681

yamls

4b2b8ce

clean up

aaf973f

Update _pkgdown.yml

0f6d318

Update test-buildComponent.R

8fab0c8

fixed chunks

bca15c5

smarter

4da01af

Copilot AI review requested due to automatic review settings March 25, 2026 19:56

Copilot started reviewing on behalf of smasongarrison March 25, 2026 19:56 View session

Copilot AI reviewed Mar 25, 2026

View reviewed changes

Update buildComponent.R

b0b5457

smasongarrison force-pushed the dev_main branch from 05de8e9 to b0b5457 Compare March 25, 2026 21:19

smasongarrison and others added 2 commits March 25, 2026 17:36

docs

94cabd3

Update DESCRIPTION

a272140

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot started work on behalf of smasongarrison March 25, 2026 21:58 View session

Fix non-ASCII character in buildComponent.R: replace em dash with \u2…

d596f0f

…014 escape Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com> Agent-Logs-Url: https://github.com/R-Computing-Lab/BGmisc/sessions/1f51ade1-dbed-4745-9e6b-e3b18880f36c

tests

3a2b8e2

Copilot finished work on behalf of smasongarrison March 25, 2026 21:59

smasongarrison and others added 2 commits March 25, 2026 17:59

Merge branch 'dev_main' of https://github.com/R-Computing-Lab/BGmisc …

a397295

…into dev_main

Apply suggestions from code review

607f609

Update tests/testthat/test-buildComponent_chunks.R Update tests/testthat/test-buildComponent_chunks.R Co-Authored-By: Copilot <175728472+Copilot@users.noreply.github.com>

smasongarrison force-pushed the dev_main branch from a62f43f to 607f609 Compare March 26, 2026 01:18

whitespace

9ad9f7e

smasongarrison force-pushed the dev_main branch from 8de68e3 to 9ad9f7e Compare March 26, 2026 03:57

smasongarrison assigned Xuanyu-Lyu and mhunter1 Mar 26, 2026

smasongarrison added 7 commits March 26, 2026 10:24

clean up yamls

a462396

all keep_ids to be used on all matrices

2562330

Add ignores

17ddb4d

Update test-buildComponent.R

effa5cf

TRUE, not T

e29f0a2

TRUE, not T

c2b938a

Merge branch 'dev_main' of https://github.com/R-Computing-Lab/BGmisc …

1081da0

…into dev_main

smasongarrison commented Mar 27, 2026

View reviewed changes

smasongarrison merged commit 053eace into main Mar 27, 2026
14 of 15 checks passed

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Dev main#141

Dev main#141
smasongarrison merged 34 commits intomainfrom
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smasongarrison commented Mar 25, 2026 •

edited by Copilot AI

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	config$component %in% c("additive")) {
	config$component %in% c("additive")) {

	file.exists(checkpoint_files$gen_checkpoint) &&
	file.exists(checkpoint_files$gen_checkpoint) &&

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smasongarrison commented Mar 25, 2026 •

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