rclade_logger: Rclade Logger
In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

rclade_logger

R Documentation

Rclade Logger

Description

A real-time logging system with flush support, timestamps, and log levels. Messages are printed immediately (not buffered) with formatted output.

Details

Thread safety: The logger uses a package-global environment and is not thread-safe. In concurrent contexts (e.g., multiple Shiny sessions or parallel Snakemake/Nextflow rule executions), multiple Rclade instances writing to the same log file will produce interleaved or corrupted log output.

Best practices for parallel execution:

Each process MUST use an independent log file (mandatory). Never point two concurrent Rclade processes at the same --log_file. Sharing one log file is only safe when the filelock package is installed (it provides an advisory lock on each write); otherwise concurrent writes will interleave/corrupt output.
Assign each Rclade instance a unique log file via --log_file (e.g., --log_file logs/task_\$SLURM_JOB_ID.log)
In Snakemake/Nextflow pipelines, use wildcards to generate per-rule or per-sample log paths
For Shiny deployments, disable file logging with enable_file_logging(FALSE) before launching the app
The console output (via message()) is process-local and does not suffer from interleaving issues

Limitation: The current design does not support a shared log file across concurrent Rclade processes. This is a known limitation tracked for a future release. For now, use per-instance log files as described above.