From f078d5a70ee3fbb42fb1f81a2f50062ad709f464 Mon Sep 17 00:00:00 2001 From: Sarah Huang Date: Wed, 20 May 2026 13:21:11 -0700 Subject: [PATCH] Fix CI dependency resolution: add Remotes for ccflowR + presto R-CMD-check and lint have failed on main at the "Setup R dependencies" step since the package was set up: DESCRIPTION declares `ccflowR` and `presto` under Suggests, but `Remotes:` only covered nichenetr and multinichenetr, so pak could not locate these GitHub-only packages ("Could not solve package dependencies: Can't find package called ccflowR, presto") and aborted before any checking ran. Add the two missing remotes, matching the pins already used by inst/bootstrap.R and the install docs: - immunogenomics/presto (public) - settylab/ccflowR@6056c0fe1d1cecfc68aa059bacfbe6bd16725231 (audited SHA) Note: settylab/ccflowR is a PRIVATE repository. CI's default GITHUB_TOKEN cannot read other private repos, so dependency setup will still fail to clone ccflowR until the workflow is given a PAT secret with read access to settylab/ccflowR (see PR description). presto resolves with the default token. Co-Authored-By: Claude Opus 4.7 (1M context) --- DESCRIPTION | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 56e3503..0befc23 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -40,7 +40,9 @@ Suggests: testthat (>= 3.0.0) Remotes: saeyslab/nichenetr, - saeyslab/multinichenetr + saeyslab/multinichenetr, + immunogenomics/presto, + settylab/ccflowR@6056c0fe1d1cecfc68aa059bacfbe6bd16725231 Config/testthat/edition: 3 URL: https://github.com/settylab/ContextNet BugReports: https://github.com/settylab/ContextNet/issues