[R-SIG-Mac] gfortran: command not found

Simon Urbanek @|mon@urb@nek @end|ng |rom R-project@org
Fri Jul 7 01:07:18 CEST 2023 


> On 7/07/2023, at 10:15 AM, Spencer Graves <spencer.graves using prodsyse.com> wrote:
> 
> Hi, Simon:
> 
> 
> 	  Thanks for this.  I have more questions:
> 
> 
> On 7/6/23 4:52 PM, Simon Urbanek wrote:
>> In the shell:
>> PATH=/opt/gfortran/bin:$PATH R CMD INSTALL ...
> 
> 
> 	  Please excuse my ignorance, but I don't understand this.  I previously tried "PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH", recommended on a page associated with support.apple.com, as mentioned below.  That did not seem to work for me.
> 

That one sets the specified fixed path and then exports it. Setting a fixed PATH by hand is typically a bad idea since it removes all existing entries - and the one you listed didn't even have gfortran on it. Exporting is another alternative if you want to set the PATH for all subsequent commands.

The line I sent just prepends the /opt/gfortran/bin to the PATH for the one R CMD command, but doesn't affect anything else. I would recommend reading a basic tutorial on unix shell if you really want to know more (actually a good idea if you ever want to use the Terminal and not kill your machine).


> 	  How is this different?  What did I do wrong before that this would fix?  [Or feel free to ignore this question:  My immediate problem seems to be fixed, and I'm not eager to do more experimentation with this now ;-]
> 
>> in R if using install.packages()
>> Sys.setenv(PATH=paste0("/opt/gfortran/bin:", Sys.getenv("PATH")))
> 
> 
> 	  If I set this in RStudio, will it affect what I do in "Terminal" on my Mac and vice versa?
> 

No, it is only valid for the current R session (and I don't know about RStudio - it's not R so sometimes R rules don't apply), that's why I said it's for the case where you run install.packages() in the R session.


Note that another alternative is to simply symlink gfortran to your /usr/local/bin since that is on the PATH on macOS by default, i.e., you only need to run this in the Terminal once (requires admin access):

sudo ln -sfn /opt/gfortran/bin/gfortran /usr/local/bin/gfortran

Cheers,
Simon




> 
> 	  This looks like a potentially similar thing to do from what I did. Is the effect of this different?  If so, how? [Again, please feel free to ignore this question.  I'm not eager to practice my "do-it-myself lobotomy" skills ;-]
> 
> 
> 	  Thanks,
> 	  Spencer Graves>
>>> On Jul 7, 2023, at 5:58 AM, Spencer Graves <spencer.graves using prodsyse.com> wrote:
>>> 
>>> 1.  I need to apologize to Simon:  I failed to see his reply to the original post.  Then I found the instructions and installed gfortran-12.2-universal.pkg, as indicated there, but it still didn't work.
>>> 
>>> 
>>> 2.  I'm not finding clear instructions on how to update the path on macOS 11.7.8, which is the latest version available for my 2014 MacBook Pro with a 2.8 GHz Quad-Core Intel Core i7.  I found several pages with differing instructions.  I found one in "support.apple.com" that recommended something that didn't work.[2]
>>> 
>>> 
>>> 	  Further suggestions?
>>> 	
>>> 
>>> 	  Thanks again very much.
>>> 	  Spencer Graves
>>> 
>>> 
>>> [2] "support.apple.com" recommended "PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH", then "env".  I did "env" to get the current path, than appended ":/opt/gfortran/bin" to that and executed the revised "PATH=...:/opt/gfortran/bin export PATH".  However, when I checked with "env" again, the change was not displayed.  I rebooted with the same result.
>>> 
>>> 
>>> https://support.apple.com/guide/terminal/use-environment-variables-apd382cc5fa-4f58-4449-b20a-41c53c006f8f/mac
>>> 
>>> 
>>> On 7/6/23 11:01 AM, Simon Urbanek wrote:
>>>> AFACT he didn't say so, there was no response, just double-posting of the same question after is was answered.
>>>> The installer says:
>>>> The resulting compiler will live in /opt/gfortran and can be called with
>>>> /opt/gfortran/bin/gfortran
>>>> so it's advisable to have /opt/gfortran/bin on the PATH.
>>>> (Side note: the arm64 build of R uses the full path, but some people have been objecting to that since they wanted to use other compilers for the legacy Intel builds, but as I suspected that causes other issues, so I'll change that for the next release).
>>>> Cheers,
>>>> Simon
>>>>> On Jul 6, 2023, at 11:45 PM, Peter Dalgaard <pdalgd using gmail.com <mailto:pdalgd using gmail.com>> wrote:
>>>>> 
>>>>> AFAICT, Spencer followed the implied instructions and it still didn't work.
>>>>> 
>>>>> There may also be a PATH issue when upgrading to 4.3.x, /usr/local -> /opt/R/<arch> Does gfortran 12.2 install to /opt/R/.../bin ?
>>>>> 
>>>>> -pd
>>>>> 
>>>>>> On 6 Jul 2023, at 07:42 , Simon Urbanek <simon.urbanek using r-project.org <mailto:simon.urbanek using r-project.org>> wrote:
>>>>>> 
>>>>>> Already answered to you and on R-pkg-devel [9 mins after you posted there - now more than 5h ago...]:
>>>>>> 
>>>>>> To quote from the page you downloaded R from:
>>>>>> 
>>>>>> This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to compile R packages which contain Fortran code, you may need to download the corresponding GNU Fortran compiler from https://mac.R-project.org/tools <https://mac.R-project.org/tools> <https://mac.r-project.org/tools <https://mac.r-project.org/tools>>.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Jul 6, 2023, at 5:16 PM, Spencer Graves <spencer.graves using prodsyse.com <mailto:spencer.graves using prodsyse.com>> wrote:
>>>>>>> 
>>>>>>> Hello, All:
>>>>>>> 
>>>>>>> 
>>>>>>>  "R CMD check KFAS" under macOS 11.7.8 (the latest version that will run on my aging Mac) complains "gfortran: command not found".
>>>>>>> 
>>>>>>> 
>>>>>>>  I just upgraded to R 4.3.1 and installed "gfortran-12.2-universal.pkg" per "https://cran.r-project.org/bin/macosx/tools/ <https://cran.r-project.org/bin/macosx/tools/>".  I expected this to solve the problem.  It didn't.
>>>>>>> 
>>>>>>> 
>>>>>>>  Suggestions?
>>>>>>>  Thanks,
>>>>>>>  Spencer Graves
>>>>>>> 
>>>>>>> 
>>>>>>> p.s.  This is my fork of KFAS, available at "https://github.com/sbgraves237/KFAS <https://github.com/sbgraves237/KFAS>".  "sessionInfo()" appears below.
>>>>>>> 
>>>>>>> 
>>>>>>> ##########
>>>>>>> 
>>>>>>> 
>>>>>>> sessionInfo()
>>>>>>> R version 4.3.1 (2023-06-16)
>>>>>>> Platform: x86_64-apple-darwin20 (64-bit)
>>>>>>> Running under: macOS Big Sur 11.7.8
>>>>>>> 
>>>>>>> Matrix products: default
>>>>>>> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>>>>>>> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
>>>>>>> 
>>>>>>> locale:
>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>> 
>>>>>>> time zone: America/Chicago
>>>>>>> tzcode source: internal
>>>>>>> 
>>>>>>> attached base packages:
>>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>> 
>>>>>>> loaded via a namespace (and not attached):
>>>>>>> [1] compiler_4.3.1  R6_2.5.1        magrittr_2.0.3  cli_3.6.1
>>>>>>> [5] tools_4.3.1     glue_1.6.2      rstudioapi_0.14 roxygen2_7.2.3
>>>>>>> [9] xml2_1.3.4      vctrs_0.6.2     stringi_1.7.12  knitr_1.42
>>>>>>> [13] xfun_0.39       stringr_1.5.0   lifecycle_1.0.3 rlang_1.1.1
>>>>>>> [17] purrr_1.0.1
>>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
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>>>>>>> 
>>>>>> 
>>>>>> 
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>>>>>> 
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>>>>> 
>>>>> -- 
>>>>> Peter Dalgaard, Professor,
>>>>> Center for Statistics, Copenhagen Business School
>>>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>>>> Phone: (+45)38153501
>>>>> Office: A 4.23
>>>>> Email: pd.mes using cbs.dk <mailto:pd.mes using cbs.dk>  Priv: PDalgd using gmail.com <mailto:PDalgd using gmail.com>
>>>>> 
>>> 
>

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