[Rcpp-devel] Troubleshooting dependency issues

[Naeem Khoshnevis]

Dear Dirk and Simon,

Thank you so much for letting me know. Yes, I understand it is off-topic.

Best regards,
Naeem

On Thu, Jul 15, 2021 at 5:46 PM Simon Urbanek <simon.urbanek at r-project.org>
wrote:

> Naeem,
>
> sorry, no, I can't help you then, the instructions only apply to standard
> macOS and won't help in your case. Also your issues seem to be stemming
> from the modified conda environment you're using so you're entirely on your
> own.
>
> Cheers,
> Simon
>
>
>
> > On 16/07/2021, at 8:44 AM, Naeem Khoshnevis <khoshnevis.naeem at gmail.com>
> wrote:
> >
> >
> > Thanks, Simon and Dirk,
> >
> > I can install the packages normally on macOS. However, I want to install
> it in a conda environment. Thanks for sharing the link. I really appreciate
> it.
> >
> > Here is a reproducible example, in case you have time to try.
> >
> > On macOS:
> >
> > Step 1: create a conda environment and install R
> >
> > conda create -n r-environment r-essentials r-base
> >
> > Step 2: activate the environment
> >
> > conda activate r-environment
> >
> > Step 3: Install rstudio
> >
> > conda install -c r rstudio
> >
> > Step 4: Install some required packages
> >
> > conda install -c r r-devtools
> > conda install -c r r-wcorr
> > conda install -c r r-ranger
> > conda install -c conda-forge r-rcpparmadillo
> > conda install -c r r-testthat
> > conda install -c conda-forge r-superlearner
> > conda install -c conda-forge r-polycor
> > conda install -c conda-forge r-logger
> >
> > Step 6:
> > According to this page, download dependencies:
> > https://mac.r-project.org/openmp/
> >
> > And copied them into the environment include and lib directory.
> >
> >
> > Step 7:
> > According to this page, I exported variables in step 6.
> >
> https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#set-env-vars
> >
> > #!/bin/sh
> >
> > export PKG_CPPFLAGS='-Xclang -fopenmp'
> > export PKG_LIBS='-lomp'
> >
> > Step 8:
> > Reactivated the conda environment
> >
> > Step 9:
> > run: rstudio
> >
> > Step 10:
> > inside rstudio
> > library(devtools)
> > install_github("fasrc/CausalGPS")
> >
> > I get the following error:
> >
> > Downloading GitHub repo fasrc/CausalGPS at master
> > Error: Could not find tools necessary to compile a package
> >
> > I think something is wrong with Step 7. Because apparently, I lost the
> path to Xcode. Without Step 7, I get the following error:
> >
> > In file included from ColorSpace.cpp:1:
> > In file included from ./ColorSpace.h:4:
> > In file included from env/bin/../include/c++/v1/typeinfo:60:
> > In file included from env/bin/../include/c++/v1/exception:81:
> > In file included from env/bin/../include/c++/v1/cstdlib:85:
> > In file included from env/bin/../include/c++/v1/stdlib.h:100:
> > env/bin/../include/c++/v1/math.h:773:12: error: no member named 'labs'
> in the global namespace; did you mean 'abs'?
> >   return ::labs(__x);
> >          ~~^
> > ~/env/bin/../include/c++/v1/math.h:772:39: note: 'abs' declared here
> > inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
> >                                       ^
> > ~/env/bin/../include/c++/v1/math.h:777:12: error: no member named
> 'llabs' in the global namespace
> >   return ::llabs(__x);
> >          ~~^
> > ~/env/bin/../include/c++/v1/math.h:785:12: error: no member named
> 'fabsf' in the global namespace
> >   return ::fabsf(__lcpp_x);
> >          ~~^
> > ~/env/bin/../include/c++/v1/math.h:789:12: error: no member named 'fabs'
> in the global namespace; did you mean 'abs'?
> >   return ::fabs(__lcpp_x);
> >          ~~^
> > ~/env/bin/../include/c++/v1/math.h:772:39: note: 'abs' declared here
> > inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
> >                                       ^
> > ~/env/bin/../include/c++/v1/math.h:794:12: error: no member named
> 'fabsl' in the global namespace
> >   return ::fabsl(__lcpp_x);
> >          ~~^
> >
> > Best regards,
> > Naeem
> >
> > On Thu, Jul 15, 2021 at 3:25 AM Simon Urbanek <
> simon.urbanek at r-project.org> wrote:
> > Naeem,
> >
> > I'm not sure which issues are you talking about specifically. If your
> package is well written, the instructions at
> https://mac.r-project.org/openmp/ should be sufficient with regular CRAN
> installation of R and standard tools.
> >
> > Cheers,
> > Simon
> >
> >
> >
> > > On Jul 15, 2021, at 02:41, Naeem Khoshnevis <
> khoshnevis.naeem at gmail.com> 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.
> > > 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.
> > > 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.
> > >
> > > 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
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20210715/8aef128e/attachment.html>