[Rcpp-devel] Troubleshooting dependency issues

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

https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel