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Hi R-package-devel I'm developing an R package which uses `parallel::mclapply` and several other library dependencies which possibly rely upon OpenMP. Unfortunately, some functions explode the amount of memory used. I've noticed that if I set...

Thanks Dirk for the help! As a summary, based on the discussion here, it now compiles successfully on i386. https://github.com/kharchenkolab/N2R/pull/2 https://github.com/kharchenkolab/N2R/pull/3 Here is the rough outline of steps...

Hi there Creating an R package here which I plan to upload to CRAN. Upon checking the tarball created with `R CMD BUILD`, I try to use `R CMD CHECK` as follows: ``` R CMD CHECK my_package.tar.gz --as...

Hi BioConductor devel community (Apologies if these are obvious questions; I haven't quite grokked the answers from the documentation.) I'm someone who has submitted in the past to CRAN, but this is my first rodeo with Bioconductor. Please...

Thank you for the help! I'll try to fix in time. Best, Evan On Wed, Apr 19, 2023 at 7:56?AM Kern, Lori <Lori.Shepherd at roswellpark.org> wrote: > We encourage developers to fix any warnings but warnings...

@Keith > Unless I'm mistaken, neither are required to install binary packages. Can you check your *source* build setup; try: > curl -O https://cran.r-project.org/src/contrib/RcppArmadillo_0.8. 500.0.tar.gz > R CMD INSTALL RcppArmadillo...

Hello there I'm in the process uploading an R package to CRAN, which is a relatively simple interface to a C++ library: https://github.com/kharchenkolab/N2R The windows binaries just became available for RcppSpdLog, so I wanted to...

Hi Dirk and friends Thanks for the help. In my attempt to isolate the issue, I wonder if there's an issue with linking to RcppSpdlog. I tried compiling with "LinkingTo: Rcpp, RcppEigen, RcppSpdlog", and the error exists: https://win...

Hi Dirk I appreciate the help. > You have the hardest possibe deployment option here it requires temporary root to make a library a system library -- and R CMD ... does not have that. I think I was able to sidestep this...

Hi Lori Thank you so much for helping clarify this. I'm still learning the ropes. Ok, I could wait for the builds. So this is the development version of scde with fixes. https://bioconductor.org/packages/3.17/bioc...

Hi Wolfgang Thank you for the help; this is a very helpful suggestion: *> Check omp_set_num_threads() from the RhpcBLASctl package. I know from experience that it works for limiting the number of threads for BLAS inside a running...

Hi Jim *"""> if so removing and reinstalling XQuartz may fix the issue."""* You might be onto something here. I did this last week, and haven't had the issue since. I never did find out what's going on fwiw...

Hi all Thank you for the responses. @Keith > Looks like your PKG_LIBS arguments are ignored/overwritten on the Mac build; ?bambi.so? appears to be missing objects contained in -lbamdb, hence the load error. Yes, it's odd. @Dirk...

@Dirk > Could you possibly construct a smaller, self-contained example exhibiting the same problem? That may be more efficient than requiring volunteer helpers to install four other libraries. Apologies, this is on the to-do list. @Keith Thanks for trying...

Maybe my Mac OS needs updating...possibly something with XCode, but it's not clear how... --- mac OS Sierra 10.12.6 --- CRAN R 3.4.3 ---clang & gfortran $ clang --version Apple LLVM version 9.0.0 (clang-900.0...

I would add, I think clang and gfortran are working correctly, as these are required for `install.packages('RcppArmadillo')` to install properly. On Tue, May 1, 2018 at 3:06 AM, Evan Biederstedt <evan.biederstedt at gmail.com > wrote: > Maybe...

I agree with Henrik's assessment. *> However, then one of the direct or indirect dependenciesis updated and introduced non-fork-safe code, and Boom! - a "Boom!"that is often semi-random, some times rare, and hard to narrow down.* This...

Hi Simon Thank you for the detailed explanations; they're very clear and helpful thinking through how to debug this. I think I am still fundamentally confused why `export OMP_NUM_THREADS=1` would result in the (desirable) behavior of...

Dear list I have the following R package which is interacting with a C library via Rcpp and extern. At some point, the goal is to combine these....but I'm trying this with baby steps. R package with C...

Hi Simon I really appreciate the help, thanks for the message. I think uncontrolled forking could be the issue, though I don't see all cores used via `htop`; I just see the memory quickly surge. *> There are many things...