Fix missing FUN.VALUE in vapply call when resuming ped2com checkpoint

[Copilot]

When calling ped2com() with resume = TRUE, the .loadOrComputeParList function crashes because vapply is called without the required FUN.VALUE argument.

Change

R/buildComponent.R — add logical(1) as the FUN.VALUE template to vapply:

# Before
computed_indices <- which(!vapply(parList, is.null))

# After
computed_indices <- which(!vapply(parList, is.null, logical(1)))

This code path is only hit on resume (loading a saved parList checkpoint), which is why normal runs succeed while resumed runs fail.

Original prompt

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This section details on the original issue you should resolve

<issue_title>[Bug] can you help with Error in vapply(parList, is.null) : argument "FUN.VALUE" is missing, with no default</issue_title>
<issue_description> biggestPed <- BGmisc::ped2com(df_ped,
component = "additive",
verbose=run_verbose,gc=TRUE,
saveable = TRUE, resume=F,
save_rate_gen=3,
save_rate_parlist=25000000,
update_rate = 200,
sparse = TRUE,
adjacency_method="direct",
max.gen = max.gen,
save_path=paste0(outcome_name,'slimmed',slim_tree,'_add/'),
isChild_method="partialparent"
)

Family Size = 4020067
Building parent adjacency matrix...
Computing parent-child adjacency matrix...

Constructed sparse matrix
Initializing adjacency matrix...
Completed first degree relatives (adjacency)
Preparing checkpointing...
Creating save path...
Standardizing column names...
Family Size = 4020067
Building parent adjacency matrix...
Computing parent-child adjacency matrix...
Final checkpoint saved for adjacency matrix.
Constructed sparse matrix
Initializing adjacency matrix...
Completed first degree relatives (adjacency)
Computing isChild matrix...
About to do RAM path tracing
Completed 0 degree relatives
Completed 1 degree relatives
Completed 2 degree relatives
Completed 3 degree relatives
Completed 4 degree relatives
Completed 5 degree relatives
Completed 6 degree relatives
Completed 7 degree relatives
Completed 8 degree relatives
Completed 9 degree relatives
Completed 10 degree relatives
Completed 11 degree relatives
Completed 12 degree relatives
Completed 13 degree relatives
Completed 14 degree relatives
Completed RAM path tracing
Doing I-A inverse times diagonal multiplication
Doing tcrossprod
Error in .local(x, y = y, ...) :
CHOLMOD error 'out of memory' at file 'Utility/t_cholmod_realloc.c', line 80

biggestPed <- BGmisc::ped2com(df_ped,

•                             component = "additive", 
  

•                             verbose=run_verbose,gc=TRUE,
  

•                             saveable = TRUE, resume=T,
  

•                             save_rate_gen=3,
  

•                             save_rate_parlist=25000000,
  

•                             update_rate = 200,
  

•                             sparse = TRUE,
  

•                             adjacency_method="direct",
  

•                             max.gen = max.gen,
  

•                             save_path=paste0(outcome_name,'_slimmed_',slim_tree,'_add/'),
  

•                             isChild_method="partialparent"
  

• )
  Preparing checkpointing...

Standardizing column names...
Family Size = 4020067
Resuming: Loading parent-child adjacency data...

Error in vapply(parList, is.null) :
argument "FUN.VALUE" is missing, with no default</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes [Bug] can you help with Error in vapply(parList, is.null) : argument "FUN.VALUE" is missing, with no default #138

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[codecov]

Codecov Report

❌ Patch coverage is 0% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 84.47%. Comparing base (8a7ce30) to head (7178c20).
⚠️ Report is 2 commits behind head on dev_main.

Files with missing lines	Patch %	Lines
R/buildComponent.R	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##           dev_main     #139   +/-   ##
=========================================
  Coverage     84.47%   84.47%           
=========================================
  Files            30       30           
  Lines          4973     4973           
=========================================
  Hits           4201     4201           
  Misses          772      772           

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