The license this software is released under is unclear as there is no license file nor discussion in the README. The DESCRIPTION state GPL-3 but a LICENSE file would clarify things.

Issue

Hi, I'm running reverse dependency checks on the future package, and I noticed that I caused the CPU load to explode on a 96-core machine that I shared with several other users.

I tracked it down to your ppcseq package that uses ncores = detect_cores() by default, where:

Suggestion

FWIW, over on CRAN, they ask you to test with a maximum of two cores, e.g. max(2L, parallel::detectCores()). On Bioconductor, I think they target 4 cores, e.g. BiocParallel respects environment variables BBS_HOME and BIOCPARALLEL_WORKER_NUMBER, and the former is set to 4 on their test machines. So, you could make your detect_cores() agile to those. If so, then people like I, but also sysadms, could set those environment variables to make your package run nicer on machines where there are other users running at the same time.

(Disclaimer: I'm the author). Alternatively, you could just replace parallel::detectCores() with parallelly::availableCores(). That functions respects above environment variables and much more, including nproc (as you've prototyped but commented out), and HPC scheduler allocations. It's designed to make your package play nice by respecting various kind of system and env var settings, cf. https://parallelly.futureverse.org/#availablecores-vs-paralleldetectcores.

Thanks.

I found some typos in the README:

You can identify anrtefactual calls from your differential transcribt anundance analysis, due to outliers.

There is no indication in the README as to what this package does, a brief intro section stating the intented purpose would be very helpful.

The readme currently instructs users to run:

fileConn<-file("~/.R/Makevars")
writeLines(c( "CXX14FLAGS += -O3","CXX14FLAGS += -DSTAN_THREADS", "CXX14FLAGS += -pthread"), fileConn)
close(fileConn)

This blasts away any config a user may already have configured at ~/.R/Makevars and is accompanied with no warnings. Users should be strongly warned that this will happen.

Moreover, the whole instruction could be avoided by detecting platforms and available compiler features in configure. Users would then not have to do anything special to configure the build environment.

FYI, future::multiprocess has been deprecated since October 2020, and defunct since March 2023. It will soon be removed from future. When that happens, your package will break (see below). Could you please fix this? It's probably not used by your package anyway, since it's already defunct. Thank you.

* installing *source* package ‘ppcseq’ ...
** using staged installation
** libs


g++ -std=gnu++17 -I"/software/c4/cbi/software/R-4.2.2-gcc10/lib64/R/include" -DNDEBUG -I"../inst/include" -I"/c4/home/henrik/repositories/future/revdep/library/ppcseq/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/c4/home/henrik/repositories/future/revdep/library/ppcseq/BH/include' -I'/c4/home/henrik/repositories/future/revdep/library/ppcseq/Rcpp/include' -I'/c4/home/henrik/repositories/future/revdep/library/ppcseq/RcppEigen/include' -I'/c4/home/henrik/repositories/future/revdep/library/ppcseq/rstan/include' -I'/c4/home/henrik/repositories/future/revdep/library/ppcseq/StanHeaders/include' -I/usr/local/include   -I'/c4/home/henrik/repositories/future/revdep/library/ppcseq/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /c4/home/henrik/repositories/future/revdep/library/ppcseq/RcppEigen/include/Eigen/Core:397,
                 from /c4/home/henrik/repositories/future/revdep/library/ppcseq/RcppEigen/include/Eigen/Dense:1,
                 from /c4/home/henrik/repositories/future/revdep/library/ppcseq/RcppEigen/include/RcppEigenForward.h:30,
                 from /c4/home/henrik/repositories/future/revdep/library/ppcseq/RcppEigen/include/RcppEigen.h:25,
...
installing to /c4/home/henrik/repositories/future/revdep/checks/ppcseq/new/ppcseq.Rcheck/00LOCK-ppcseq/00new/ppcseq/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘multiprocess’ is not exported by 'namespace:future'
Execution halted
ERROR: lazy loading failed for package ‘ppcseq’
* removing ‘/c4/home/henrik/repositories/future/revdep/checks/ppcseq/new/ppcseq.Rcheck/ppcseq’

UPDATE: +2 hours later: I pasted the wrong installation output before. Corrected above.