Conda Build R Package Fails at C Compiler Issue on Macos Mojave

Failing to conda build R package

Try the following:

conda install conda-build
conda skeleton cran --recursive treatSens
conda build r-treatsens
conda install -c local r-treatsens

The recursive option should account for the dependencies you need.

Unable to install various R packages probably after upgrading to Mac OS Catalina

> mkdir -p ~/opt/src
> cd ~/opt/src
> curl -O http://mirror.us-midwest-1.nexcess.net/gnu/gsl/gsl-2.6.tar.gz
> tar zxf gsl-2.6.tar.gz
> cd gsl-2.6
> ./configure --prefix=$HOME/opt/usr/local
> make
> make install

> export CFLAGS="-I$HOME/opt/usr/local/include"
> export LDFLAGS="-L$HOME/opt/usr/local/lib -lgsl -lgslcblas" 
> R 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
...
...
> install.packages("gsl")
...
...
...
There is a binary version available but the source version is later:
      binary source needs_compilation
gsl 1.9-10.3  2.1-6              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
...
...
> install.packages("copula")
> library(copula)
>

Update

It looks like in your case situation is little bit messy. Your gcc is resolved as x86_64-apple-darwin13.4.0-clang.

Try compiling this code

/* confdefs.h */
#define PACKAGE_NAME "gsl"
#define PACKAGE_TARNAME "gsl"
#define PACKAGE_VERSION "2.6"
#define PACKAGE_STRING "gsl 2.6"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define PACKAGE "gsl"
#define VERSION "2.6"
#define RELEASED /**/
/* end confdefs.h.  */

int
main ()
{
  ;
  return 0;
}

following way

> clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs main.c

using tools from XCode installation

Then, try o set C compiler like this.

export CC="/usr/bin/clang"

before configuring GSL.

MacOS configure: error: cannot run C compiled programs

It's really easy to miss the answer from melpomene in the small comments to this question so let me post this here for everyone to see. This error usually means you're missing compiler tools (headers actually) that have been removed from Xcode.

You can find them in /Library/Developer/CommandLineTools/Packages/ since their name might be different depending on your version of macOS in the future.

Assuming you're running macOS Mojave (10.14), you need to run:

open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

And an macOS-style package installer will start, asking you for your adminstrator password. This is an official Apple package and although it might be weird to install something out of a random directory, you can trust it. You don't have to take my word for it though. Apple buried this change in the Xcode 10 release notes and you can find their explanation here: https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes#3035623

I'll reproduce this here in case this link ever goes away or gets changed:

The Command Line Tools package installs the macOS system headers inside the macOS SDK. Software that compiles with the installed tools will search for headers within the macOS SDK provided by either Xcode at:

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk

or the Command Line Tools at:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

depending on which is selected using xcode-select.

The command line tools will search the SDK for system headers by default. However, some software may fail to build correctly against the SDK and require macOS headers to be installed in the base system under /usr/include. If you are the maintainer of such software, we encourage you to update your project to work with the SDK or file a bug report for issues that are preventing you from doing so. As a workaround, an extra package is provided which will install the headers to the base system. In a future release, this package will no longer be provided. You can find this package at:

/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

> To make sure that you're using the intended version of the command line tools, run xcode-select -s or xcode select -s /Library/Developer/CommandLineTools after installing.

rjava and java issue with r on mac os mojave issue

Jumping between Mac OS versions, Java versions and rJava releases might be a struggle.

Take a look here for quite comprehensive list of steps you might need to take:

http://www.owsiak.org/r-3-4-rjava-macos-and-even-more-mess/

It might be you need to recompile rJava from sources to get it working in your environment.

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