Homebrew-core: brew install r doesn't create r.framework and files in /usr/local/cellar/r/3.4.1/bin

[luispuerto]

Please always follow these steps:

• [x] Confirmed this is a problem with brew installing one, specific formula (not cask) and not every time you run brew? If it's a general brew problem please file this issue at https://github.com/Homebrew/brew/issues/new. If it's a brew cask problem please file this issue at https://github.com/Homebrew/caskroom/homebrew-cask/new
• [x] Ran brew update and retried your prior step?
• [x] Ran brew doctor, fixed all issues and retried your prior step?
• [x] Ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
• [x] If brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?

HOMEBREW_VERSION: 1.2.4-76-g27cd396
ORIGIN: https://github.com/Homebrew/brew
HEAD: 27cd396d2e59ebf3e65a34e31ea5dc4a238643a1
Last commit: 2 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: de22bd54af88996a84b55fbd82dbca97f31d0c79
Core tap last commit: 10 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local/Homebrew
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: octa-core 64-bit sandybridge
Homebrew Ruby: 2.0.0-p648
Clang: 8.0 build 800
Git: 2.13.3 => /usr/local/bin/git
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.8.0_131, 1.8.0_121
macOS: 10.11.6-x86_64
Xcode: 8.2.1
CLT: 8.2.0.0.1.1480973914
X11: 2.7.11 => /opt/X11

Gist https://gist.github.com/luisspuerto/78b00826297457b7901f398bdc9f3823

I've been trying to install r with openblas today and I haven't been able (brew install r --with-openblas)

Although the output is satisfactory

brew reinstall r --with-openblas                                                       
==> Reinstalling r --with-openblas
==> Using the sandbox
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading https://cran.rstudio.com/src/base/R-3/R-3.4.1.tar.gz
Already downloaded: /Users/lpuerto/Library/Caches/Homebrew/r-3.4.1.tar.gz
==> ./configure --prefix=/usr/local/Cellar/r/3.4.1 --enable-memory-profiling --without-cairo --without-x --with-aqua --w
==> make
==> make install
==> make
==> make install

The result is not.

When I'm going to use R in rStudio I get this message.

When I check that location this is what I get:

There isn't a libR.dylib in that location and there is also missing other files in there. I've also noted that r.framework isn't there.

I don't know that I'm doing wrong. R was working until now, but for a problem in package compilation from source I decided to reinstall it just to give it a shot. I don't know if I deleted something I shouldn't when I uninstall. I just run the commands

sudo rm -rf /Library/Frameworks/R.framework /Applications/R.app \
   /usr/bin/R /usr/bin/Rscript

And also brew uninstall r

I did that way because although I have a homebrew r installation I wasn't sure that everything was gone from a previous installation from binaries from CRAN.

When I installed R from homebrew I more or less follow this guide: https://www.karambelkar.info/2017/01/setup-osx-for-r/

If I install R using the binaries from CRAN everything works. At least rStudio starts.

Any thought?

Thanks!

[ilovezfs]

Please test https://github.com/Homebrew/homebrew-core/pull/15711 if you can.

[luispuerto]

@ilovezfs can you tell me how can I test that new formula?

Sorry I'm quite new.

[ilovezfs]

brew pull 15711
brew uninstall r
brew install --build-from-source r

[luispuerto]

now it seems that works...

But I don't understand why is install in /usr/local/Cellar/r/3.4.1_1 instead of /usr/local/Cellar/r/3.4.1

Any solution to this?

[ilovezfs]

Thanks for testing it!

But I don't understand why is install in /usr/local/Cellar/r/3.4.1_1 instead of /usr/local/Cellar/r/3.4.1

That is due to the revision 1

If you need a persistent location use

/usr/local/opt/r

which is a symlink to the current version in the Cellar.

[luispuerto]

ahh!

No I don't need a persisten location, in general... I was just wondering why the different name.

is going to change the name at some point to /usr/local/Cellar/r/3.4.1?
I ask because it isn't the first time I see the folder 3.4.1_1

thanks!

[ilovezfs]

is going to change the name at some point to /usr/local/Cellar/r/3.4.1?
I ask because it isn't the first time I see the folder 3.4.1_1

it'll be 3.4.1, 3.4.1_1, 3.4.1_2, 3.4.1_3, etc. until 3.4.2 is released by upstream

[luispuerto]

ok thanks!

[slhck]

@ilovezfs

If you need a persistent location use

/usr/local/opt/r

How do I use this, preferably, with R on macOS? I mean, which file should be edited to set that path?

[MikeMcQuaid]

@luisspuerto Can you also try:

brew pull 15723
brew uninstall --force r
brew install --build-from-source r

that's a different approach we're trying that hopefully should fix your issue.

[MikeMcQuaid]

@luisspuerto Actually, before you do that run git -C $(brew --repo homebrew/core) reset --hard origin/master to undo the previous patch.

[MikeMcQuaid]

Fixed by https://github.com/Homebrew/homebrew-core/pull/15723.

[luispuerto]

@MikeMcQuaid I guess it's already late, but yeah, everything works fine now.

Thanks!

[MikeMcQuaid]

@luisspuerto I'm glad and thanks for letting me know. Sorry for the inconvenience!

[tkosaka1976]

This problem still remaining in 3.4.1_1.
Probably, R.framework was not installed in /usr/local/Cellar/r/3.4.1_1
I also tried as told by @MikeMcQuaid.

I'm using:
Homebrew 1.2.4-96-ge0560ff
Homebrew/homebrew-core (git revision fa5b7; last commit 2017-07-21)

[MikeMcQuaid]

@tkosaka1976 Can you elaborate on what you need the framework specifically for?

[tkosaka1976]

I'm using rsruby gem in ruby.
I see. I understand.
I'll change the code for install it.

[MikeMcQuaid]

@tkosaka1976 Thanks! If that doesn't work, please let us know. We're trying to get by without a framework option but if it's needed by many places we would be tempted to re-add it.

[tkosaka1976]

I forget to tell this.
Other problem also happen in R REPL.
Error will come when I call package installed.

Ex.
> library("edgeR")
要求されたパッケージ limma をロード中です
エラー: package or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...):
共有ライブラリ '/usr/local/lib/R/3.4/site-library/edgeR/libs/edgeR.so' を読み込めません:
dlopen(/usr/local/lib/R/3.4/site-library/edgeR/libs/edgeR.so, 6): Library not loaded: ``/usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
Referenced from: /usr/local/lib/R/3.4/site-library/edgeR/libs/edgeR.so
Reason: image not found

Probably proper library location cannot found.
Could you tell me how to solve this?

[MikeMcQuaid]

@tkosaka1976 brew install gfortran should fix that for you.

[tkosaka1976]

I already installed gcc.
"GNU Fortran is now provided as part of GCC, and can be installed with:"
However, the problem have been continued.
I'm not sure reason why.

Do you need another information to know my situation?

[tkosaka1976]

I'm using GCC 7.1.0

[MikeMcQuaid]

@tksohishi Try to run brew reinstall gcc r

[tkosaka1976]

Reinstall of gcc and r worked well.
Thanks!

[tkosaka1976]

I have a question.
The R Framework dir have already removed.
How do we specify the R_Home?
I tried as "export R_HOME=/usr/local/Cellar/r/3.4.1_1" but did not work well.
I'm also using rsruby gem.
Please let me know how to install it.

[tkosaka1976]

Anyway, I hope to know the alternative way for R.framework setup for brew installed R.
Previously, I do make a symlink to installed in /usr/local/Cellar/r/VERSION/ and copied it in /Library/Frameworks/

[MikeMcQuaid]

@tkosaka1976 Sorry for the delay. R_HOME should be set to /usr/local/opt/r/lib/R. What else do you need the Framework for? Thanks!

[tkosaka1976]

Probably, I'm not sure about Framework for use.
I hope to use rsruby, which bridge R into ruby.
Do you know how to install?
I usually do like this.

sudo ln -s $"r forlder from homebrew"/R.framework /Library/Frameworks/R.framework
gem install rsruby -- --with-R-include=/Library/Frameworks/R.framework/Headers --with-R-lib=/Library/Frameworks/R.framework/Libraries

[MikeMcQuaid]

@tkosaka1976 I'd imagine gem install rsruby -- --with-R-include=/usr/local/opt/r/lib/R/include --with-R-lib=/usr/local/opt/r/lib/R/include would be it if it can't detect the paths automatically.

[tkosaka1976]

@MikeMcQuaid Thank you for your kind help. Now, all things go well!

[MikeMcQuaid]

@tkosaka1976 Great, thanks again for your kind words!

[krackers]

@MikeMcQuaid R.framework is needed for the r-gui app which has the framework path hardcoded

[MikeMcQuaid]

@krackers That's not the case, I've tested the R GUI application and it works without the framework with the latest version of the r formula.