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