Conversion to dgCMatrix Causes Segmentation Fault

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#129 opened on Sep 10, 2026 11 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 4/5
Estimated time: 3-5 days
Newbie friendliness: 38/100

Issue type: Bug
Clarity: Needs clarification
Activity status: Active
Tech stack: r
Domain: data

Research direction

No source file or test is named. Start by reproducing the conversion from a DelayedMatrix to dgCMatrix using the reported dimensions, then trace the conversion entry point and capture the relevant R and package versions. Done means the conversion no longer segfaults for this case and a regression test covers it.

Written by the indexing model from the issue text.

Description

dim(database)
    109578 2389155
class(counts(database))
    "DelayedMatrix"

After about four hours.

assay(database, "counts") <- as(assay(database, "counts"), "dgCMatrix")
     *** caught segfault ***
    address 0x7fc394337000, cause 'invalid permissions'

Dominant language: R
Stars: 29
Forks: 12
PR merge metrics: No merged PRs in 30d

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