bkmrhat
A parallel-chain helper for bkmr that has settled into pure upkeep.
Comparison · Infra & APIs
pathfindR vs profoc
A side-by-side editorial comparison of pathfindR and profoc — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:rcppr-package
pathfindR vs profoc: at a glance
What is pathfindR?
pathfindR dropped Java from its subnetwork search and rebuilt it in C++
pathfindR runs active-subnetwork-oriented pathway enrichment on gene expression results. Version 3.0.0 re-implemented the greedy, simulated-annealing and genetic search algorithms in R and C++ through Rcpp, removing the Java dependency the package had carried since its early releases, and renamed three exported functions in the process. The two patches since have been consolidation: 3.0.1 fixed signed integer overflow in the new C++ hash function flagged by gcc-UBSAN and clang-UBSAN on CRAN, and 3.0.2 repaired tests after a companion data package changed a dataset structure.
What is profoc?
A forecast combination package that spun its profiler out into its own project
profoc combines probabilistic forecasts online, using the Bernstein online aggregation family with B-spline smoothing over quantiles and time. The recent releases are infrastructure rather than method: 1.3.4 removed a using namespace arma directive for CRAN compliance and closed a timer edge case, 1.3.3 adjusted the integration with rcpptimer against its now-stable 1.2.0 API. The last release to change what users can do was 1.3.0, which exposed the conline C++ class to R and exported init_experts_list(), make_basis_mats(), make_hat_mats() and post_process_model() so the engine can be driven directly.
pathfindR vs profoc: editorial side-by-side
pathfindR
0.0INFRA · APIS
pathfindR dropped Java from its subnetwork search and rebuilt it in C++
◆ Current state
pathfindR runs active-subnetwork-oriented pathway enrichment on gene expression results. Version 3.0.0 re-implemented the greedy, simulated-annealing and genetic search algorithms in R and C++ through Rcpp, removing the Java dependency the package had carried since its early releases, and renamed three exported functions in the process. The two patches since have been consolidation: 3.0.1 fixed signed integer overflow in the new C++ hash function flagged by gcc-UBSAN and clang-UBSAN on CRAN, and 3.0.2 repaired tests after a companion data package changed a dataset structure.
◆ Where it's heading
The dependency surface has been shrinking for two years and Java was the last heavy one. 2.4.0 removed magick, KEGGgraph and KEGGREST by moving KEGG visualization onto ggkegg; 2.7.0 pushed org.Hs.eg.db from Imports to Suggests under CRAN policy, with functions degrading to defaults when it is absent; 3.0.0 finished the job on the search engine itself. The corresponding cost is now visible in 3.0.1: owning the algorithms in C++ means owning their undefined-behaviour reports too.
◆ Prediction
Expect the near-term releases to keep hardening the Rcpp search code against sanitizer findings and to verify GA parity with the legacy JAR, since 3.0.0 claimed numerically identical results only for the greedy and simulated-annealing methods.
profoc
0.0INFRA · APIS
A forecast combination package that spun its profiler out into its own project
◆ Current state
profoc combines probabilistic forecasts online, using the Bernstein online aggregation family with B-spline smoothing over quantiles and time. The recent releases are infrastructure rather than method: 1.3.4 removed a using namespace arma directive for CRAN compliance and closed a timer edge case, 1.3.3 adjusted the integration with rcpptimer against its now-stable 1.2.0 API. The last release to change what users can do was 1.3.0, which exposed the conline C++ class to R and exported init_experts_list(), make_basis_mats(), make_hat_mats() and post_process_model() so the engine can be driven directly.
◆ Where it's heading
The direction is toward a reusable C++ core with thin language bindings. The timing code that lived inside profoc was extracted into the standalone rcpptimer package in 1.3.2, deliberately so other R packages and Python projects could use it through cpptimer and cppytimer, and the clock header was reworked in 1.3.1 to maximise the code shared between the R and Python versions. Method work sits earlier in the history - periodic splines and penalties in 1.2.0, the penalty() function in 1.1.0 - while the recent cadence, a single release in the last sixteen months, points at a package the maintainer considers finished.
◆ Prediction
The repeated references to future Python use suggest the next significant work happens outside this package, in the shared C++ components, rather than in profoc's R surface.
Alternatives to pathfindR and profoc
Other Infra & APIs products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either pathfindR or profoc.
driveR
A cancer driver prioritization package that ships rarely and mostly to stay installable
metR
A meteorology ggplot2 extension where the netCDF reader became the main event
IsoriX
An isotope geolocation package still recovering from the r-spatial retirement
fdacluster
Functional data clustering grew from one algorithm into a comparable suite
adjustedCurves
A survival curve package spending release after release correcting its own estimates
See all pathfindR alternatives → · See all profoc alternatives →
Recent activity from pathfindR and profoc
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agopathfindRTest fixes after a companion data package changed a dataset
- 1mo agopathfindRUndefined-behaviour fixes harden the new C++ search engine
- 1mo agopathfindRActive subnetwork search re-implemented in C++, Java dependency removed ⚡
- 6mo agoprofocCRAN compliance fix removing a namespace directive
- 7mo agopathfindRHuman annotation database moves from Imports to Suggests
- 7mo agopathfindRGraceful handling for gene-set URL failures
- 1y agopathfindRKappa matrix fix for the igraph update
- 1y agoprofocTimer integration updated to the stable rcpptimer API
- 2y agoprofocTiming code extracted into the standalone rcpptimer package
- 2y agoprofocInteger overflow fix and Welford timing statistics
- 2y agoprofocThe conline C++ class opens up to R users
- 2y agoprofocQuantile crossing flagged and tidy methods added
Frequently asked questions
What is the difference between pathfindR and profoc?
Both compete on the same themes — rcpp, r-package — within Infra & APIs. pathfindR and profoc are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is pathfindR better than profoc?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. pathfindR and profoc are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Infra & APIs products to evaluate alongside.
What are the best alternatives to pathfindR?
Top pathfindR alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "pathfindR alternatives" section above for the current picks, or visit /alternatives/pathfindr for the full list with editorial commentary on each.
What are the best alternatives to profoc?
Top profoc alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "profoc alternatives" section above for the current picks, or visit /alternatives/profoc for the full list with editorial commentary on each.