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Scientific formulae for the Homebrew package manager (macOS and Linux)

Ruby 100.00%

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sjackman linuxbrewtestbot gwang-jin randy3k zbeekman jonchang gaberoo jonkeane exoulster mtamai markcheno georgeezgm

homebrew-base's Issues

[email protected] compatibility

Please fill out the issue checklist below, and provide all of the requested information.

Please always follow these steps:

Confirmed this is a problem with brew installing one, specific formula 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 or https://github.com/Linuxbrew/brew/issues/new.
Ran brew update and retried your prior step?
Ran brew doctor, fixed all issues and retried your prior step?
Ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
If brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?

To help us debug your issue please explain:

What you were trying to do (and why)
rstudio-server installation broke on MacOS Catalina after brew upgrade upgraded openssl from version 1.0 to 1.1.
Why did this happen?
openssl 1.0 approached EOL at the end of 2019 and was consequently dropped from homebrew in favor of openssl 1.1.
See: Homebrew/homebrew-core#46876
What happened (include command output)
- Active instance of rstudio-server starts giving an error on login screen about incorrect username or password (on entering correct username an password).
- Running sudo rstudio-server restart gave error message complaining about missing library at /usr/local/opt/openssl/lib/libssl.1.0.0.dylib.
What you expected to happen
compatibility with openssl 1.1.
Step-by-step reproduction instructions (by running brew install commands)
Running following code will break current rstudio installation.

brew upgrade <openssl>
sudo rstudio-server start

Formula additions or changes

Solution for the problem:
Manually installing openssl 1.0.2t as identified to work here: aisingapore/TagUI#635

brew install https://github.com/tebelorg/Tump/releases/download/v1.0.0/openssl.rb

# Validate that openssl 1.0.2t is installed
ls -al /usr/local/Cellar/openssl*
# Start Rstudio again
sudo -k rstudio-server start

A more robust approach using homebrew's code base is:

brew install https://raw.githubusercontent.com/Homebrew/homebrew-core/8b9d6d688f483a0f33fcfc93d433de501b9c3513/Formula/openssl.rb

# or manually cloning the repo and installing
git clone https://github.com/Homebrew/homebrew-core.git
cd homebrew-core
git checkout 75b57384 Formula/openssl.rb
brew install Formula/openssl.rb

# Validate that it is installed
ls -al /usr/local/Cellar/openssl*

# Start Rstudio again
sudo -k rstudio-server start

brew install rstudio-server fails with Error 2

Please fill out the issue checklist below, and provide all of the requested information.

Please always follow these steps:

[Yes ] Confirmed this is a problem with brew installing one, specific formula 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 or https://github.com/Linuxbrew/brew/issues/new.
[ Yes] Ran brew update and retried your prior step?
[ Yes] Ran brew doctor, fixed all issues and retried your prior step?
[ Yes] Ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
https://gist.github.com/f7632a42310841b6359a24b145c04c58
[ N/A] If brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?

To help us debug your issue please explain:

What you were trying to do (and why)
brew install rstudio-server
What happened (include command output)

Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
No changes to formulae.

==> Installing rstudio-server from brewsci/base
==> Installing dependencies for brewsci/base/rstudio-server: ant, boost-rstudio-server, cmake, isl, mpfr, libmpc, gcc, openblas and r
==> Installing brewsci/base/rstudio-server dependency: ant
==> Downloading https://www.apache.org/dyn/closer.cgi?path=ant/binaries/apache-ant-1.10.5-bin.tar.xz
==> Downloading from http://us.mirrors.quenda.co/apache/ant/binaries/apache-ant-1.10.5-bin.tar.xz
######################################################################## 100.0%
==> Downloading https://www.apache.org/dyn/closer.cgi?path=ant/ivy/2.4.0/apache-ivy-2.4.0-bin.tar.gz
==> Downloading from http://www.trieuvan.com/apache/ant/ivy/2.4.0/apache-ivy-2.4.0-bin.tar.gz
######################################################################## 100.0%
==> Downloading https://www.apache.org/dyn/closer.cgi?path=commons/bcel/binaries/bcel-6.3.1-bin.tar.gz
==> Downloading from http://apache.claz.org/commons/bcel/binaries/bcel-6.3.1-bin.tar.gz
######################################################################## 100.0%
🍺  /usr/local/Cellar/ant/1.10.5: 1,653 files, 39.3MB, built in 14 seconds
==> Installing brewsci/base/rstudio-server dependency: boost-rstudio-server
==> Downloading https://downloads.sourceforge.net/project/boost/boost/1.63.0/boost_1_63_0.tar.bz2
==> Downloading from https://managedway.dl.sourceforge.net/project/boost/boost/1.63.0/boost_1_63_0.tar.bz2
######################################################################## 100.0%
==> ./bootstrap.sh --prefix=/usr/local/Cellar/boost-rstudio-server/1.63.0 --libdir=/usr/local/Cellar/boost-rstudio-server/1.63.0/lib --without-icu --without-libraries=python,mpi
==> ./b2 headers
==> ./b2 --prefix=/usr/local/Cellar/boost-rstudio-server/1.63.0 --libdir=/usr/local/Cellar/boost-rstudio-server/1.63.0/lib -d2 -j8 --layout=tagged --user-config=user-config.jam -sNO_LZMA=1 install
==> Caveats
boost-rstudio-server is keg-only, which means it was not symlinked into /usr/local,
because this is an alternate version of another formula.

For compilers to find boost-rstudio-server you may need to set:
  export LDFLAGS="-L/usr/local/opt/boost-rstudio-server/lib"
  export CPPFLAGS="-I/usr/local/opt/boost-rstudio-server/include"

==> Summary
🍺  /usr/local/Cellar/boost-rstudio-server/1.63.0: 12,493 files, 432MB, built in 9 minutes 9 seconds
==> Installing brewsci/base/rstudio-server dependency: cmake
==> Downloading https://homebrew.bintray.com/bottles/cmake-3.14.0.mojave.bottle.tar.gz
######################################################################## 100.0%
==> Pouring cmake-3.14.0.mojave.bottle.tar.gz
==> Caveats
Emacs Lisp files have been installed to:
  /usr/local/share/emacs/site-lisp/cmake
==> Summary
🍺  /usr/local/Cellar/cmake/3.14.0: 5,680 files, 53.2MB
==> Installing brewsci/base/rstudio-server dependency: isl
==> Downloading https://homebrew.bintray.com/bottles/isl-0.20.mojave.bottle.tar.gz
######################################################################## 100.0%
==> Pouring isl-0.20.mojave.bottle.tar.gz
🍺  /usr/local/Cellar/isl/0.20: 71 files, 3.9MB
==> Installing brewsci/base/rstudio-server dependency: mpfr
==> Downloading https://homebrew.bintray.com/bottles/mpfr-4.0.2.mojave.bottle.tar.gz
######################################################################## 100.0%
==> Pouring mpfr-4.0.2.mojave.bottle.tar.gz
🍺  /usr/local/Cellar/mpfr/4.0.2: 28 files, 4.7MB
==> Installing brewsci/base/rstudio-server dependency: libmpc
==> Downloading https://homebrew.bintray.com/bottles/libmpc-1.1.0.mojave.bottle.tar.gz
######################################################################## 100.0%
==> Pouring libmpc-1.1.0.mojave.bottle.tar.gz
🍺  /usr/local/Cellar/libmpc/1.1.0: 12 files, 354KB
==> Installing brewsci/base/rstudio-server dependency: gcc
==> Downloading https://homebrew.bintray.com/bottles/gcc-8.3.0.mojave.bottle.tar.gz
######################################################################## 100.0%
==> Pouring gcc-8.3.0.mojave.bottle.tar.gz
🍺  /usr/local/Cellar/gcc/8.3.0: 1,413 files, 288.6MB
==> Installing brewsci/base/rstudio-server dependency: openblas
==> Downloading https://homebrew.bintray.com/bottles/openblas-0.3.5.mojave.bottle.1.tar.gz
######################################################################## 100.0%
==> Pouring openblas-0.3.5.mojave.bottle.1.tar.gz
==> Caveats
openblas is keg-only, which means it was not symlinked into /usr/local,
because macOS provides BLAS and LAPACK in the Accelerate framework.

For compilers to find openblas you may need to set:
  export LDFLAGS="-L/usr/local/opt/openblas/lib"
  export CPPFLAGS="-I/usr/local/opt/openblas/include"

For pkg-config to find openblas you may need to set:
  export PKG_CONFIG_PATH="/usr/local/opt/openblas/lib/pkgconfig"

==> Summary
🍺  /usr/local/Cellar/openblas/0.3.5: 21 files, 120.7MB
==> Installing brewsci/base/rstudio-server dependency: r
==> Downloading https://homebrew.bintray.com/bottles/r-3.5.3.mojave.bottle.tar.gz
######################################################################## 100.0%
==> Pouring r-3.5.3.mojave.bottle.tar.gz
🍺  /usr/local/Cellar/r/3.5.3: 2,117 files, 55.8MB
==> Installing brewsci/base/rstudio-server
==> Downloading https://github.com/rstudio/rstudio/archive/v1.1.456.tar.gz
==> Downloading from https://codeload.github.com/rstudio/rstudio/tar.gz/v1.1.456
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/gin-1.5.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/gwt-2.7.0.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/junit-4.9b3.jar
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/selenium-java-2.37.0.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-2.37.0.jar
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/chromedriver-mac
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/mathjax-26.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/pandoc/1.19.2.1/macos/pandoc-1.19.2.1.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/pandoc/1.19.2.1/macos/pandoc-citeproc-0.10.4.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/libclang-3.5.zip
######################################################################## 100.0%
==> Downloading https://s3.amazonaws.com/rstudio-buildtools/libclang-builtin-headers.zip
######################################################################## 100.0%
==> cmake .. -DRSTUDIO_TARGET=Server -DCMAKE_BUILD_TYPE=Release -DRSTUDIO_USE_LIBCXX=Yes -DRSTUDIO_USE_SYSTEM_BOOST=Yes -DRSTUDIO_BOOST_VERSION='1.63.0' -DBoost_NO_SYSTEM_PATHS=On -DBoost_USE_STAT
==> make install
Last 15 lines from /Users/alansill/Library/Logs/Homebrew/rstudio-server/02.make:
[ 95%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/modules/tex/SessionViewPdf.cpp.o
[ 96%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/modules/vcs/SessionVCSCore.cpp.o
[ 96%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/modules/vcs/SessionVCSUtils.cpp.o
[ 96%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/modules/viewer/SessionViewer.cpp.o
[ 96%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/modules/viewer/ViewerHistory.cpp.o
[ 97%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/projects/SessionProjects.cpp.o
[ 97%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/projects/SessionProjectContext.cpp.o
[ 97%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/projects/SessionProjectFirstRun.cpp.o
[ 97%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/SessionAddins.cpp.o
[ 98%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/http/SessionPosixHttpConnectionListener.cpp.o
[ 98%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/modules/SessionCrypto.cpp.o
[ 98%] Building CXX object src/cpp/session/CMakeFiles/rsession.dir/SessionModuleContext.mm.o
[ 98%] Linking CXX executable rsession
[ 98%] Built target rsession
make: *** [all] Error 2

What you expected to happen

Not the "Error 2"

Step-by-step reproduction instructions (by running brew install commands)

As above

Formula additions or changes

None

To add or change formulae, please open a Pull Request.

Updates

Subscribe to this issue to receive updates about Brewsci/base.

rstudio-server "error 61" after reboot; rebuilding from source works

Confirmed this is a problem with brew installing one, specific formula 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 or https://github.com/Linuxbrew/brew/issues/new.
Ran brew update and retried your prior step?
Ran brew doctor, fixed all issues and retried your prior step?

I'm adding this more as a record in case anyone else hits it, but hopefully it might also be useful to maintainers.

After a recent reboot, rstudio-server stopped working. When visiting it in a browser, after logging in the error message "Unable to connect to service" appears. In the system logs (/var/log/system.log) output of the following form appears:

Oct 22 13:49:04 iMac rserver[1764]: ERROR system error 61 (Connection refused) [request-uri=/rpc/client_init]; OCCURRED AT: void rstudio::core::http::LocalStreamAsyncClient::handleConnect(const boost::system::error_code &) /tmp/rstudio-server-20190516-24750-15buw5s/rstudio-1.2.1335/src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp:119; LOGGED FROM: void rstudio::server::session_proxy::(anonymous namespace)::logIfNotConnectionTerminated(const rstudio::core::Error &, const http::Request &) /tmp/rstudio-server-20190516-24750-15buw5s/rstudio-1.2.1335/src/cpp/server/ServerSessionProxy.cpp:373

brew doctor shows no issues, and reinstalling rstudio-server from bottle also failed to resolve it. Running sudo rstudio-server verify-installation exits with 0, and sudo rstudio-server test-config also exits with 0. Rebooting multiple times had no effect, and turning off anti-virus also didn't resolve the issue.

The computer is running system version macOS 10.14.5 (18F132).

What ultimately resolved it was rebuilding this formula from source:

brew install boost-rstudio-server
brew cask install homebrew/cask-versions/adoptopenjdk8
brew install rstudio-server -s

I wonder if anyone else has hit this recently? I also noticed that the version of Xcode being used to build the bottle is 9.0, whereas the current version of Xcode is at least 11; might that be related?

Anyway, I hope this is useful to someone.

Cannot tap brewsci/base!

Cannot tap brewsci/base on my M1 Macbook Pro: fear, fire, foes, awake!

~ matthew$ brew tap brewsci/base
==> Tapping brewsci/base
Cloning into '/opt/homebrew/Library/Taps/brewsci/homebrew-base'...
remote: Enumerating objects: 177, done.
remote: Total 177 (delta 0), reused 0 (delta 0), pack-reused 177
Receiving objects: 100% (177/177), 39.66 KiB | 1.42 MiB/s, done.
Resolving deltas: 100% (76/76), done.
Error: Invalid formula: /opt/homebrew/Library/Taps/brewsci/homebrew-base/Formula/rstudio-server.rb
rstudio-server: Calling depends_on :java is disabled! Use "depends_on "openjdk@11", "depends_on "openjdk@8" or "depends_on "openjdk" instead.
Please report this issue to the brewsci/base tap (not Homebrew/brew or Homebrew/core), or even better, submit a PR to fix it:
  /opt/homebrew/Library/Taps/brewsci/homebrew-base/Formula/rstudio-server.rb:36

Error: Cannot tap brewsci/base: invalid syntax in tap!

rstudio-server

Hi,

The rstudio-server version 1.2 seems to be not compatible with new R versions! It says "R graphics engine version 14 is not supported by this version of RStudio". I can't go back and reinstall the old version of R via brew either. Is there any way the rstudio-server version can be updated?

Thanks so much,
SG

shiny-server node module version error

I'm getting this error when I try to run shiny-server with a completely fresh install of homebrew on an Intel Mac running MacOS Big Sur 11.3.1:

% shiny-server
node:internal/modules/cjs/loader:1168
return process.dlopen(module, path.toNamespacedPath(filename));
^

Error: The module '/usr/local/Cellar/shiny-server/1.5.13.944/shiny-server/build/Release/posix.node'
was compiled against a different Node.js version using
NODE_MODULE_VERSION 79. This version of Node.js requires
NODE_MODULE_VERSION 93. Please try re-compiling or re-installing
the module (for instance, using npm rebuild or npm install).
at Object.Module._extensions..node (node:internal/modules/cjs/loader:1168:18)
at Module.load (node:internal/modules/cjs/loader:989:32)
at Function.Module._load (node:internal/modules/cjs/loader:829:14)
at Module.require (node:internal/modules/cjs/loader:1013:19)
at require (node:internal/modules/cjs/helpers:93:18)
at Object. (/usr/local/Cellar/shiny-server/1.5.13.944/shiny-server/lib/core/fsutil.js:16:13)
at Module._compile (node:internal/modules/cjs/loader:1109:14)
at Object.Module._extensions..js (node:internal/modules/cjs/loader:1138:10)
at Module.load (node:internal/modules/cjs/loader:989:32)
at Function.Module._load (node:internal/modules/cjs/loader:829:14) {
code: 'ERR_DLOPEN_FAILED'
}

OSX Catalina rstudio-server does not access the file of users and passwords

Please fill out the issue checklist below, and provide all of the requested information.

After installing studio-server on osx Catalina 10.15.7 with the formula:
brew tap brewsci/base
brew install rstudio-server
And after reinstalling OpenSSL, and following th einstructions to solve all warnings, I start rstudio-server with sudo rstudio-server start, I go to the brower and start localhost:8787 and it works, but after introducir de user name and password it did not work.
Serveral year ago I installed the rstudio-server and I had the same problem but I solved it with copying a file: cp /etc/pam.d/sshd /etc/pam.d/rstudio
But now this solution does not work.
Any Idea?

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