[Rcpp-devel] Troubleshooting dependency issues

[Dirk Eddelbuettel]

Hi Naeem,

On 14 July 2021 at 11:03, Naeem Khoshnevis wrote:
| Thank you so much for your response. Rcpp is excellent, and I am using it
| (with OpenMP), and it significantly improved the package (Thank you!). I
| have tried it on macOS and centos.

Ok, as stated, I do not work on or know macOS. Others may be of help, there
are tutorials (often by @coatless) which got a lot people going. Give that a
shot, ask here when you get stuck.

CentOS can be iffy. When I had to use in the past the setup in the distro was
so old that we went the "devtoolset" (IIRC) route: a semi- or fully official
newer compiler set a few versions ahead of what is in the distro. That should
include OpenMP.

| I was trying to set up a conda
| environment. There are many HPC clusters that are using old versions of R
| as well as rstudio. In the past, using conda env helped me to install an

HPC can indeed be tricky. Best to liaise with your local sysadmins. One
difficulty once you load the 'modules' (or however the scheme is called at
your end) you have to align it with R. Use 'R CMD config --all' to see what R
uses, you be able to tweak via your ~/.R/Makevars

| updated version of R., But I understand why you do not recommend it. I will
| prepare a reproducible example and will let you know. Thank you so much.

Sounds good. Hopefully we get that squared away in a few controlled steps.

Dirk

| Best regards,
| Naeem
| 
| On Wed, Jul 14, 2021 at 9:55 AM Dirk Eddelbuettel <edd at debian.org> wrote:
| 
| >
| > Hi Naeem,
| >
| > On 14 July 2021 at 09:41, Naeem Khoshnevis wrote:
| > | Hi,
| > |
| > | I hope this email finds you well.
| > | I wondered what the best approaches to troubleshooting C++ dependencies
| > | issues in general and specifically in R are; specifically, those packages
| > | which are using OpenMP and we want to install on macOS.
| >
| > Is this dependencies (plural) or a single core dependency (singular) on a
| > single OS (macOS) ?  Those are different issues. (And Rcpp has no incluence
| > over what Cupertino (macOS) or Auckland (macOS deployment for R does) -- we
| > have to play the card we are dealt, and that have always been "issues" and
| > some HOWTOs and duct tape.  On the margin, if this is your question, it may
| > also be one for r-sig-mac.
| >
| > Also, and to make this concrete: Do you have a minimally reproducible
| > issue?
| >
| > | So far, I am just googling the error and finding out what the problem is.
| > | However, it is hard to address issues and come up with long-term
| > solutions
| > | without internalizing the concepts.
| > | One example is creating a conda environment for each R package project
| > and
| > | installing llvm, clang, etc into each environment.
| >
| > As an R developer, I have a simple rule: Just say No to conda. Mixing and
| > matching between standard / core builds (using the recommended R toolchain)
| > and conda appears to mostly end in tears.
| >
| > | I talked to several software engineers; however, I could not find a
| > | convincing answer. I think I do not know what I do not know about this
| > | topic, which prevents me from asking good questions. I would be grateful
| > if
| > | you could let me know your thoughts about these questions.
| >
| > Again, a reproducible example would help.
| >
| > Rcpp is used by over 2300 packages on CRAN. Many use OpenMP. You can search
| > at GitHub within the mirroring 'cran' organisation to see what other
| > packages
| > do. Given that you can also see the outcome (the package 'status' pages at
| > CRAN) that is not a bad approach.
| >
| > Dirk
| >
| > | Where is a good place to start learning about this topic?
| > | Is a professional C++ developer necessarily good at troubleshooting
| > | problems with compilers and linkers? Or these are two different topics.
| > |
| > | Best regards,
| > | Naeem Khoshnevis
| > | _______________________________________________
| > | Rcpp-devel mailing list
| > | Rcpp-devel at lists.r-forge.r-project.org
| > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
| > --
| > https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
| >

-- 
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org