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Configuration Problems and Solutions

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Michael Jackson edited this page May 9, 2017 · 85 revisions

Despite our best efforts to ensure that workshop attendees configure their computers ahead of time, installation and configuration issues pop up frequently during workshops. This page collates common configuration problems encountered by instructors and presents their solutions.

Please feel free to edit this page to add new problems and solutions to the appropriate sections as you encounter them. The only requirement is that you should only add a problem once you have identified and confirmed a solution that at least worked for the cases that you encountered personally. If you encounter a problem that you don't know how to solve, please raise it in an issue in the repo so that the community can find a resolution.

Bash

Windows (Git Bash)

  • None of the bash commands seem to work, although the student opened "Git Bash" and the command window is open

    • Ensure that the student has run the program mysys and not git-cmd - the latter will not open the bash emulator environment.

  • User has created/saved files and doesn't know where they are

    • Have users run cd after opening Git Bash and before doing anything else - this will place users in a home directory with Desktop as a subdirectory. cd then cd Desktop will place users on their Desktop.

  • Copy/paste doesn't work

    • Right click the title bar and select Properties. In the Options tab, make sure QuickEdit Mode is checked. When QuickEdit mode is enabled, you can select text using the mouse cursor and right-click to copy it. To paste text, right-click when no text is selected.

  • User would like to use nano

    • in git bash, run the following commands:

      curl -L -O http://www.nano-editor.org/dist/v2.2/NT/nano-2.2.6.zip
unzip nano-2.2.6.zip -d nano-2.2.6
echo "alias nano='winpty `pwd`/nano-2.2.6/nano'" >~/.bashrc

    Then quit and restart git bash.

Python

All

  • Command ipython notebook fails with an error like ipython not found.

    • It's very likely that Canopy or Anaconda did not properly append the path to its Python installation to the system path. (On Canopy, this easily occurs if students do not open GUI after installation or if they accidentally select "No" when asked if they want to make Canopy the default Python environment.) The fix is to add the right directory to the path. On a Mac using Canopy, for example, the command to do this is:

      export PATH=/Users/<username>/Library/Enthought/Canopy_64bit/User/bin:$PATH

  • Imports of scientific Python packages fails from a command line interpreter or script (i.e., python myfile.py) even though user installed Canopy or Anaconda.

    • Use which python to make sure the Python being run is actually Anaconda or Canopy's; if not, ensure that path to Canopy or Anaconda's Python is before the system's Python in the path.
    • Ask if the user wants their path restored after the workshop and, if so, ensure this is done.

  • The IPython notebook appears to be running but no output is shown after cells are run.

  • The IPython kernel dies soon after starting in old OSX using Safari (see this issue)

    • Make Chrome or Firefox the default browser
    • Try ipython notebook again from the terminal.

  • The ggplot package does not get installed by conda (see this issue)

    • Try pip install -U ggplot (pip should be provided by anaconda).

    • If that fails, try:

      conda create -n py34 python=3.4 anaconda
source activate py34
conda install -c conda-forge ggplot

Windows (Anaconda)

  • Anaconda apps aren't running (i.e. IPython).

    • Make sure Git Bash is running as administrator. To fix permanently, one has to change the settings. When searching for the program, right click on Git Bash, and select 'Properties'. On the 'Compatibility' tab, check the box titled 'Run as Administrator'.

  • New users can't easily open an IPython notebook in an arbitrary directory.

    • The start menu shortcut created by Anaconda starts a notebook server in %USERPROFILE%\Documents\IPython Notebooks by default.
    • New users, who may be unfamiliar with the command prompt, might have trouble opening a notebook in any other directory.
    • A simple batch file with the single-line command ipython notebook will start a notebook server in any directory from which it is run.
    • To make a batch file script that opens an IPython notebook in whatever directory it's run:
      1. Create a simple text file on the desktop using Right Click->New->Text Document.
      2. Re-name it "Start IPython Notebook Here.bat". (Don't forget to change the extension!)
      3. Open it with Notepad using Right Click->Edit.
      4. Add the text "ipython notebook" to the file: it should look just like you would type it in a command prompt.
      5. Save and close.
    • Now when a user double clicks on the .bat file, a notebook server will spawn in that directory.
    • The user can move or copy the .bat file wherever they want their IPython notebook's working directory to be.
    • Instructors can distribute a copy of the file in the same folder as any example notebooks, so the users can just double-click-and-go in the correct directory without ever seeing a command-line prompt.

  • matplotlib import error when non-ASCII characters are present in the user's current working directory or user name

    • See matplotlib issue 3516
    • If attendee has permission on their computer, then re-install Anaconda in another location without non-ASCII characters in the directory path e.g. C:\Local\

  • Chrome reports the installation file as malicious.

    • According to the vendor, requires verification by Chrome, which is pending,
    • It is okay to ignore this warning, and the next "do you really want to harm your computer?"
    • See issue swcarpentry/workshop-template#146

  • Wrong Python version runs, despite Anaconda appearing to install right version, or numpy or matplotlib won't import, despite Anaconda having them installed, or nosetests script fails with error Failed to import module nose.

    • Check with the student: do they have ArcGIS installed on the machine, and have they opened it since installing Anaconda.
    • If yes, ArcGIS has stomped all over the Python environment variables.
    • A short term solution is to
      1. Create an environment (conda create -n swc python=3)
      2. Switch to environment (activate swc). When Anaconda does this, it overwrites the Python environment variables.
      3. (First time only) Update packages in environment (conda install numpy matplotlib nose)
      4. When done, go back to default (deactivate swc). This will restore the environment variables.
    • If asked, it seems to be possible to install Anaconda so it plays nicely with ArcGIS, but is not straightforward.

Mac(Anaconda)

R

All

  • When trying to install a package from RStudio, an error returns saying it is not available.

The issue is that when trying to install a package (specifically dplyr) from RStudio, install.packages("dplyr") returns an error saying that the package is not available for this version of R.

This was happening on a brand new installation of R and RStudio from the links in the workshop page.

The problem seems to be that there was an older version of R installed in the computer and RStudio was picking this one up by default, instead of the newer. (You can check this with sessionInfo()). All the machines involved were running Windows, but other OS may be have show the same behavior.

Forcing RStudio to run the newer version of R fixed the problem. This post explains how to switch between R versions on RStudio and different operating systems.

Git

All

  • When pushing to GitHub, the username or password is rejected although student knows that they are correct.
    • Some students have needed to use their full email address, rather than their username, in the username field.
    • (Although this makes little sense) Try hitting backspace many times in the password field to "clear out old password info". This might be a Git Bash issue, but is unconfirmed.

Windows (Git Bash)

  • The user is prompted to enter email address on first commit.

    • Appears to be a bug in Git 1.8.4, as the user is prompted even if the email address is set in her global configuration. This should only occur on first commit.

  • git push to a GitHub repo fails with the error could not read Username for https:...: No such device or address.

    • This is a bug in Git Bash 1.8.5 - have users install 1.8.4.
    • If Git Bash 1.8.5 has been installed, using SSH instead of HTTPS for the push is a workaround, but takes several minutes to set up. First generate and set up the SSH key. After generating the SSH key and setting up GitHub to use it, change the origin from the Git repository directory using commands like these (with the appropriate user name and repository name):

  • git push to BitBucket using [email protected]:USER/REPOSITORY gives Permission denied (publickey). fatal: Could not read from remote repository.

    • This can happen if a user has set up BitBucket to use SSH keys but the SSH keys are not present on the machine they are using for the workshop (e.g. they have the SSH keys on their desktop but not their laptop).
    • A workaround is to use https://bitbucket.org/USER/REPOSITORY and they will be prompted for their username and password.

  • Configuring the git editor to a Windows program like Notepad++.exe is not intuitive. If the path to the program is not in the PATH, changing the system environment variable may require a restart. Additionally, the editor program may open with the previous session and tabs, causing the commit to abort. The following setup works for Notepad++ (adjust for the correct install path for 32-bit / 64-bit executable):

    git config --global core.editor "'C:/Program Files/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"

  • nano is not installed.

    • Ensure that the Software Carpentry installer has run. Try re-executing the installer.

  • nano has been installed but calling nano returns command not found

    • Find nano.exe on your computer
    • Edit `.bash_profile and add
export PATH=/c/path_to_nano.exe_directory:$PATH

  • calling nano from the shell doesn't work and returns 'Redirection is not supported'

    • Reinstall Git Bash, and during the install process, be sure to Select "Use Windows' default console window" (which is not the default option)

  • The Git Bash window does not open to full screen.

    • One has to change the settings. When searching for the program, right click on Git Bash, and select 'Properties'. On the 'Layout' tab, change the size to roughly 237x69.

Windows (Rstudio):

  • The Git tab does not appear in Rstudio.
    • You need to tell Rstudio where to find your git executable. Assuming you are using Git Bash:
      • Go to Tools->Global options.
      • Select Git/SVN.
      • Under Git executable select Browse.
      • Navigate to and select following file: C:/Program Files (x64)/git/bin/git.
    • Restart Rstudio. See also this screenshot.

Mac

  • Running the git command fails with an error like Illegal operation.

  • Running git on Mac OS X 10.8.5 produced an error message reporting "lazy symbol binding failed".

    • Most online advice involved installing XCode with the command line tools, which is a 1.6 GByte download...
    • Note that as April 2015, XCode for Mac OS X 10.8.5 is no longer available from the App Store, so you'll need to get an older version from the Apple Developer website. For that you'll need a Developer account with Apple (so probably an instructor should do download this in advance and keep it in a USB stick).
    • The Snow Leopard images from the git-osx-installer project work too, and don't require an XCode download.

  • Trying to clone a repository from github fails with an error like error: SSL certificate problem, verify that the CA cert is OK

    • A temporary fix that should allow the learner to progress with the lesson is to run

      export GIT_SSL_NO_VERIFY=true`

    • This setting change will not persist after rebooting the machine. The error is probably caused by expired SSL certificates and should be fixed by updating the OS.

    • If an OS update is not possible, you can also try installing the tigerbrew port of git, like so:

      ruby -e "$(curl -fsSkL raw.github.com/mistydemeo/tigerbrew/go/install)"
export PATH=/usr/local/sbin:/usr/local/bin:$PATH
brew install git
hash -r
git clone ...

Linux

  • The recommend configuration for gedit doesn't work.

    • Check gedit's version with gedit --version and update it to 3.x.

  • Permission denied (public key) on pushing to Github.

    • This has several causes and thus several solutions: GitHub has a list. In a nutshell:
      • Don't use sudo (and check whether the permissions for SSH keys are correct).
      • Connection problems or weird routing problems: ssh -vT [email protected] should print github.com and port 22.
      • Connect only as user git .
      • Check whether ssh-add -l prints a key, if not, create one.
      • Check whether ssh-keygen -lf ~/.ssh/id_rsa.pub prints several keys, and check which one GitHub uses in the account settings.
      • You can always troubleshoot more using ssh -vT [email protected].

  • Error 403 returned on a git push to GitHub.

  • A git push results in a dialog requiring a password to unlock the private key: "Enter password to unlock the private key. An application wants access to the private key xxxxx".

SQL (sqlite3)

Mac

  • Issue with sqlite3 and no readline support on the macs. That is, up arrow will not return the last command typed. This can be fixed, but requires installing sqlite3 from source: sqlite3 shipts without readline support.

Make

Windows (Git Bash)

This problem arose on Git Bash git version 1.9.4.msysgit.1 and make GNU Make 3.81 on Windows 7 SP 1.

Using a wildcard in an action can throw an exception e.g.

all :
        touch sample1.txt
        touch sample2.txt

clean : 
        rm -f *.txt

$ make all
touch sample1.txt
touch sample2.txt
$ make clean
c:\Users\mjj\.swc\lib\make\bin\make.exe: Interrupt/Exception caught (code = 0xc0
0000fd, addr = 0x4227d3)

One fix is to use Make's $(wildcard ...) function e.g.

clean : 
        rm -f $(wildcard sample*.txt)

$ make clean
rm -f sample1.txt sample2.txt

Another solution is to add the following at the start of the Makefile:

SHELL=C:/Windows/System32/cmd.exe

However, the former is preferable as it uses Make's own functions and does not lead to an unportable Makefile.

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