[R-SIG-Mac] R 3.0.1 build from sources: Wrong library paths

[Simon Urbanek]

On Sep 12, 2013, at 5:50 AM, Simon Zehnder wrote:

> I compiled R and made a check-all without errors (only for the PDF manuals - but this is ok). Then I used
> 
> sudo make install 
> 
> to install it to the R.framework. Now, when I want to use R on the shell no command can be found, as the installation has not installed the binaries in /usr/bin. If I try to change my PATH variable and add /Library/Frameworks/R.framework/Ressources/bin it does not change a thing, I still get the error: -bash: R: command not found. The only thing to make it work is to go into the folder /Libraries/Frameworks/R.framework/Ressources/bin/ and start it via ./R.
> 

What the CRAN installer does is essentially

sudo ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/bin/R

Obviously, changing the PATH works as well  - make sure you check the value of PATH in the session you're running (bash uses a cached lookup, but recent versions should have no trouble re-trying after PATH changes) -- assuming running
/Libraries/Frameworks/R.framework/Ressources/bin/R
works. If it doesn't then maybe check the version symlinks.

Re you earlier post - FSF builds of gcc don't support ObjC with Apple runtime, so you have to use Apple's clang (as you did). In my tests few months ago gcc 4.7/4.8 was too unreliable - it was miscompiling R so things were breaking randomly at run-time. If your build seems reliable, please share with use the exact version and settings.

Thanks,
Simon


> I remember no such behaviour for prior builds of R. It seems Mac has changed something since my last compilation of R sources. 
> 
> Can anyone help?
> 
> Best
> 
> Simon
> 
> On Sep 12, 2013, at 10:49 AM, Simon Zehnder <szehnder at uni-bonn.de> wrote:
> 
>> I did some progress on my problem: 
>> 
>> Using LDFLAGS and CPPFLAGS on the shell instead of in the config.site file changes the directories and make can find all the libraries. 
>> 
>> The next thing that came up, was the Mac-specific Cocoa issue. When I compile R sources with OBJC="gcc -arch x86_64" I get the following outputs: 
>> 
>> config.log: https://gist.github.com/anonymous/6534550
>> 
>> make.log: https://gist.github.com/anonymous/6534560
>> 
>> with errors starting in line 883 of the make.log. So it seems the gcc cannot handle the .m files properly. 
>> 
>> Then I used OBJC="clang" and I get the following output:
>> 
>> config.log: https://gist.github.com/anonymous/6534614
>> 
>> make.log: https://gist.github.com/anonymous/6534606
>> 
>> Here I get (see line 879 in the make.log) some weird warning. I know these are only warnings, they do not influence the way R works later on, but I am interested why gcc cannot handle the Cocoa files at all and clang has these warnings.
>> 
>> 
>> Best
>> 
>> Simon
>> 
>> 
>> On Sep 11, 2013, at 11:08 PM, Simon Zehnder <szehnder at uni-bonn.de> wrote:
>> 
>>> Dear R-Users and R-Devels,
>>> 
>>> I made a brand new install of Mac OS X Mountain Lion 10.8.4 on a new hard drive and want to build R from sources. As I use OpenMP 3.1 in my C++ extensions I used MacPorts to get the gcc48 compiler collection. Installation run without a hassle and I set the mp-gcc48 active. 
>>> 
>>> I downloaded the R-3.0.1 tar.gz and extracted it. Then I changed the config.site to the following:
>>> 
>>> https://gist.github.com/anonymous/6529767
>>> 
>>> Furthermore I had to change my PATH variable in the .profile as it included /usr/local/bin:/usr/local/sbin and I have not such a folder in my /usr. 
>>> 
>>> Now when I run configure I get the following config.log
>>> 
>>> https://gist.github.com/anonymous/6529743
>>> 
>>> with the warning:  "ld: warning: directory not found for option '-L/usr/local/lib' "on line 217. This warning becomes an error if running the make command. I still see the C linker using -L/usr/local/lib which does not exist. I changed the LDFLAGS in the config.site to -L/opt/local/lib but Rs configure script seems to be very resistant to my new proposal. 
>>> 
>>> I need some help. How should I proceed? Which FLAGS can change the directory the make script searches for libraries? What configure options should be used with R-3.0.1 on OS X 10.8.4 using gcc-4.8.1?    
>>> 
>>> 
>>> Best
>>> 
>>> Simon
>>> 
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>> 
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