> On Jul 7, 2023, at 6:54 PM, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote:
>
> An alternative is not to have gfortran on the path and use a personal
> Makevars file, as documented at
> https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS-packages .
>
> Reasons to do it that way include
>
> a) GCC builds have included other compilers including gcc in the same
> directory as gfortran, and I have been caught in the past by badly-written
> software looking for gcc as a C compiler and finding that one rather than
> Apple's gcc which is a wrapper for clang. (The current gfortran distribution
> only includes x86_64-apple-darwin20.0-gcc and similar.)
>
> b) If the gfortran you have installed differs from that used to build R, you
> may need to set FLIBS, and this has happened as different CRAN distributions
> have been built with different versions of gfortran.
>
> When I do want gfortran on the path, for example to build other software, I
> do symlink it to somewhere on my path.
>
> I would prefer if Simon continues to give the full path as FC in
> etc/Makeconf: anyone who wants a different compiler can use a personal
> Makevars. (Continues at least for arm64, and I would prefer consistency.)
>
I agree - it wasn't entirely intentional (it's really historical), but then
there was request for a PATH-less gfortran settings. After this discussion I
agree that it's not a good idea since the instructions on CRAN should be fully
self-sufficient *and* we want to avoid other incompatible Fortran compilers. (I
have trouble reaching the x86_64 build machine from home right now, so I'll
change it on Monday).
Thanks,
Simon
>
> On 07/07/2023 00:07, Simon Urbanek wrote:
>>> On 7/07/2023, at 10:15 AM, Spencer Graves <spencer.gra...@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.gra...@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 <pda...@gmail.com
>>>>>>> <mailto:pda...@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.urba...@r-project.org
>>>>>>>> <mailto:simon.urba...@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.gra...@prodsyse.com <mailto:spencer.gra...@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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org>
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [[alternative HTML version deleted]]
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org>
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>
>>>>>>> --
>>>>>>> Peter Dalgaard, Professor,
>>>>>>> Center for Statistics, Copenhagen Business School
>>>>>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>>>>>> Phone: (+45)38153501
>>>>>>> Office: A 4.23
>>>>>>> Email: pd....@cbs.dk <mailto:pd....@cbs.dk> Priv: pda...@gmail.com
>>>>>>> <mailto:pda...@gmail.com>
>>>>>>>
>>>>>
>>>
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>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
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