Does Cytoscape have a silent/unattended uninstall command? - cytoscape

Im trying to build an automation script for my environment to install the newest version of cytoscape and uninstall its older version, Does cytoscape have a command line prompt to silently uninstall that older version?

Found my answer;
use the install4j -q option with the uninstaller to uninstall silently

Related

Error installing homebrew on MacOS 10.14 Beta Mojave

Im trying to install Homebrew on a fresh install of MacOS Mojave 10.14 beta.
Yet after running /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" (this is from https://brew.sh)
I am getting the error,
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
Failed during: /usr/bin/sudo /usr/bin/xcode-select --install
I have both the current command line tools from Xcode 9.4 and the beta command line tools for Xcode 10.0 beta.
Is there currently any workaround to allow me to install Homebrew?
I believe the problem is that the Command Line Tools for Xcode 10 do not install headers in /usr/include, but the install script checks there:
https://github.com/Homebrew/install/blob/bbf4a3a8b247c7dba159c3d557cc3853dd764171/install#L110
Thankfully, the code that tries to run xcode-select --install is bypassed if STDIN is not a TTY. Try adding a 0<&- after the install command to close STDIN and skip this command. I just tried it and it worked for me.
As an aside, Homebrew does not officially support 10.14 yet, and the maintainers do not want you to file issues about any problems you find. (Pull requests seem welcome, though.) Unfortunately this means that the Homebrew issue tracker is not a place to discuss problems and solutions.

Error installing Dart Development version on OS X with homebrew

Have installed several versions of Dart on OS X using homebrew.
brew tap dart-lang/dart
brew install dart
Today I did a 'brew upgrade' to Dart 1.11.3 stable, because I want to run cucumber/selenium/chromedriver tests in dartium. Dartium is still at version 39.* and chromedriver wants 40something.
note: windows users are able to run these tests in dartium :(
So, tried installing development version 1.12.0-dev.5.0 to see if dartium would also upgrade. No joy
brew install dart --devel
Warning: dart-lang/dart/dart-1.11.3 already installed
Do I really have to uninstall to install the development version?
Same thing happened to me too.
I solved it with uninstalling dart first:
brew uninstall --force dart
brew install dart --devel --with-dartium --with-content-shell

Error installing Ruby gem Jekyll [duplicate]

I'm having some trouble installing jekyll. Can't quite figure out how to patch the missing link. I think it's an update to Ruby, but RVM is having trouble installing alternate versions of ruby as well.
Heres the full post:
$ sudo gem install jekyll
ERROR: Error installing jekyll:
ERROR: Failed to build gem native extension.
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby extconf.rb
mkmf.rb can't find header files for ruby at /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/ruby.h
Gem files will remain installed in /Library/Ruby/Gems/1.8/gems/fast-stemmer-1.0.1 for inspection.
Results logged to /Library/Ruby/Gems/1.8/gems/fast-stemmer-1.0.1/ext/gem_make.out
Does this mean I need to update the version of ruby I'm using via rvm?
Ubuntu
sudo apt-get install ruby-dev
gem install jekyll
Your problem is that either you system doesn't know where make is located at or you don't have it installed. The easiest way to fix this (and probably other issues you'll run into trying to get a ruby system up and running) is to install xcode.
You can get it at http://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12 for lion. Or it came on a CD with your computer for earlier versions.
If you're using Lion, please see comments below for a link to how to install developer tools on Lion.
I had the same error on Ubuntu and this helped me sort it out.
You must have ruby-dev installed
apt-get install ruby-dev
If you installed XCode and command line tools are still missing go to Terminal and
xcode-select --install
it will prompt you to install these tools. After that just follow SrBlanco´s answer. That solved the problem for me.
Good luck.
Need to install "make".
I am using Ubuntu 12.10.
sudo apt-get install make
Should work on any Debian based distro.
Note: this problem also occurs on newer MacBook Pro models that come with Mavericks pre-installed. I updated another post with my own solution that didn't involve Xcode at all. My system had the Xcode developer tools installed when I got the machine.
ERROR: Error installing jekyll: ERROR: Failed to build gem native extension
Install Xcode as mentioned if you don't have it installed already (https://developer.apple.com/xcode/). Plus you need the command line tools.
Open Xcode. Go to Preferences > Downloads > Install Command Line Tools
Installing command line tools for Xcode solved the problem for me on my Mac
xcode-select --install.
sudo apt-get install ruby-dev
sudo gem install jekyll
hope this will help, it works with me.
I had this same exact error when trying to install Jekyll, and the following steps from this link helped me. Just in case anyone else comes across this!
http://davidensinger.com/2013/03/installing-jekyll/
I was facing the same issue in my Fedora 22 setup. I had ruby installed but didn't have ruby-devel. Installing ruby-devel fixed the issue for me.
dnf install -y ruby-devel
For older systems:
yum install -y ruby-devel
I followed this on Ubuntu/Linux Mint
sudo apt install build-essential
sudo apt install ruby-dev
sudo gem install jekyll
An addendum: You can install XCode now from the App Store on Mountain Lion. The process is transparent and pretty fast.
I had the same problems with you.
I use Mac OS X 10.9 develop preview version, and I had installed gcc and Xcode.
But my Xcode version is 4.6.
Then I install the Xcode 5.0
After that I type sudo gem install jekyll in the terminal again. Then it works.
Wish it could help someone.
Installing Xcode and going to perferencs > downloads > install commandline tools WORKS!
Same problem on Debian, I had forgot to run this command:
~/.rvm/scripts/rvm
All these answers did NOT work for me.
If you're looking for a solution on ubuntu 14.04, do this:
sudo apt-get install ruby1.9.1-dev zlib1g-dev nodejs
sudo gem install jekyll -v 2.5.3
Unfortunately, nodejs is required because of a bug in Jekyll that enforces existence of runtime JS engine even though it doesn't need one.
For Ubuntu, this helped in my case:
apt-get install libffi-dev
A general advice is to just follow what is displayed as the reason for the error and hopefully you'll be provided with a log file in which the first line suggests which package should be installed, in my case:
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/ffi-1.9.21/mkmf.log
MacOS
my solution to this problem
install xcode
type xcode-select --install in the command line
type sudo gem install jekyll in the command line
PS: It is the combination of the two answers in this question.
You are missing the ruby-dev file , just go ahead and run this command - sudo apt-get install ruby-dev
Hope this helps!!
I had the same issue on my macOS(10.14.2), the reason may be:
Apparently with OSX el Capitan, there is a new security function that prevents you from modifying system files called Rootless.
My solution is using rvm:
install ruby on Mac OS X with RVM
gem install jekyll
On windows I have this issue
I actually installed the version rubyinstaller-devkit-2.6.3-1-x64 of ruby
I have removed the ruby completely and Installed the rubyinstaller-devkit-2.5.5-1-x64
and issued the following commands on powershell
gem install bundler
gem install jekyll
and this time no errors where found
I had this issue and of all things, the error was occurring because I hadn't agreed to some updated terms of service in xcode. Running the following did the trick for me. Go figure.
sudo xcodebuild -license accept
For me, I had to upgrade homebrew and install rbenv to the latest ruby version. After that, I followed the instruction at jekyll website. My OS is Catalina 2019, I couldn't install Xcode, which is not compatible yet!
You have to set the path in your .bash_profile to make sure that it initializes the rbenv when you restart your terminal.
export PATH="$HOME/.rbenv/bin:$PATH"
eval "$(rbenv init -)"
then
$ rbenv version
2.2.3 (set by /Users/mislav/.rbenv/version)
$ rbenv shell
rbenv: no shell-specific version configured
hope that help!
Here is the (only?) reliable and simple way to install Jekyll on macOS
Install UTM
Install Ubuntu Server
Install Jekyll using Ubuntu instructions at https://jekyllrb.com/docs/installation/ubuntu/
Forward port 22 in the VM settings (22->localhost->22)
Use VS Code on the macOS host
Install Remote SSH
Connect to USER#localhost
Drag and drop the folder on Mac into VS Code (this transfers files to remote)
Enable port forwarding for 4000 (bottom bar on VS Code)
Work on your website
Right click on your website on the file explorer and click download
If you have not done these steps, you might be delighted by:
Ubuntu imports your public SSH key from GitHub
VS Code magically handles file transfer in and out
VS Code magically installs your VS Code extensions onto the remote server and allows file search on the remote host

PhantomJS version 1.4.0 version issue

I installed PhantomJS today and got this error trying to use it:
PhantomJS version 1.4.0
is too old. You must use at least version 1.7.0
(Capybara::Poltergeist::PhantomJSTooOld)
How can I install the newer version?
I can get the newer version (1.7) at: http://phantomjs.org/download.html
Once I've downloaded it though how do I actually install it?
Are you using Linux or OS X? You'll need to either build from source or install an updated PhantomJS package. You can also download the binaries and install over the system installed PhantomJS. Type "which phantomjs" and it should show the location of PhantomJS.
If you're using homebrew, just:
brew upgrade phantomjs
I had to solve this problem yesterday, it required me updating brew, telling brew to uninstall phantomJS, then updating xcode, then installing the latest xcode command utilities, then using brew to re-install phantomjs. Finally that got it to pull in the latest version. You might try this (mac):
brew update
brew uninstall phantomjs
brew doctor (follow the fixes it recommends if any... Mine was updating xcode)
brew install phantomjs
At that point it should grab the latest.
Good luck!

macOS, Rails: "Failed to build gem native extension"

I'm stuck trying to install rails on my mac. I have OS X 10.6.8 and I have confirmed that I have Ruby, version 1.8.7
I ran sudo gem update and sudo gem update --system to get the latest versions of the software.
However, when I run sudo gem install rails I get this error:
ERROR: Error installing rails:
ERROR: Failed to build gem native extension.
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby extconf.rb
mkmf.rb can't find header files for ruby at /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/ruby.h
Gem files will remain installed in /Library/Ruby/Gems/1.8/gems/json-1.6.3 for inspection.
Results logged to /Library/Ruby/Gems/1.8/gems/json-1.6.3/ext/json/ext/parser/gem_make.out
If you have XCode 4 or later you will need to open it and go to Preferences -> Downloads -> Components and install the Command Line tools as they aren't installed by default. Couldn't install Rails until this happened.
Im using osx 10.10. You can download from the command-line
xcode-select --install
Not sure what it needs to compile, but OSX can't compile any native ruby extensions at all unless the Apple developer tools are installed. On 10.7 Lion you can download it free from the app store, or Download it here for 10.6: http://developer.apple.com/xcode/index.php
It may also be on your OSX install discs, though probably much more out of date.
Did you install the OS X developer tools? You'll need to do this to be able to build native extensions
Just a follow up ...
it may be that you are on a mac and rails cannot find the right compiler for c headers.
just install xcode from apps store / homebrew or go to terminal ...
$ xcode-select --install
complete the installation and agree on the licensing etc, then ...
$ sudo gem install rails
There are two possible reasons for the fail:
PRIMARY REASON: Missing Xcode Command Line Tools
Verifying Xcode Command Line Tools Installation manually:
Check for presence of
"/usr/include/iconv.h" (if absent=>Missing or improperly installed Xcode CLT)
Installing Xcode CLT:
Try running xcode-select --install on terminal and follow the instructions. If it fails, open Xcode.app, select from menu "Xcode" - "Open Developer Tool" - "More Developer Tools" to open the developer site, download the installer for your OS version and run it.
SECONDARY REASON(if 1. fails): Version issues
Try upgrading the ruby version using rbenv.
Hope it helps!
Steps to sort out this issue:
Follow these steps unless error is fixed.
Open terminal and run commands:
sudo xcode-select --install
sudo xcodebuild -license accept
Make sure you have installed only one Xcode and it is the latest one. If more than one version is installed then keep only the latest one with name in applications like Xcode.app
Open Xcode->preferences->locations then check if any command line tools are selected; if not then select
Install Ruby by:
brew install ruby
Install CocoaPods by
sudo gem install cocoapods
Try to install Ruby via RVM. I solved in this way
How to install ruby on Ubuntu with rvm
The Command line tools didn't solve this issue for me.
I upgraded ruby installation through rbenv to 2.2.0, made that the global default ruby installation, and this issue was fixed.
Switch Ruby to Homebrew version:
$ brew install ruby
$ brew link --overwrite ruby
$ echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.bash_profile
$ echo 'export LDFLAGS="-L/usr/local/opt/ruby/lib"' >> ~/.bash_profile
$ echo 'export CPPFLAGS="-I/usr/local/opt/ruby/include"' >> ~/.bash_profile
Just had a similar issue. I can confirm that installing the command line tools fixes it.
https://stackoverflow.com/a/58226876/8070378
Solved after run:
sudo xcode-select --install
sudo xcodebuild -license accept
I had this problem on macOS Catalina 10.15.7, and it seems that Xcode 12.3's Ruby is a variant of 2.6, but my software needed 2.7.
I installed rvm and ran rvm install ruby-2.7, and now it works just fine 🎉

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