Ubuntu – TypeError: ‘NoneType’ object is not iterable


I am trying to install a toolbox for analyzing spinal cord MRI images. install dependencies are: python 2.7, FSL and git. I have installed them.
I launch the installer:


but errors occur, Here is what is happening after I wrote my password:

>>Edit .bashrc...
  Deleting previous SCT entries in .bashrc
>> awk '!/SCT_DIR|SPINALCORDTOOLBOX|ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS/' ~/.bashrc > .bashrc_temp && > ~/.bashrc && cat .bashrc_temp >> ~/.bashrc && rm .bashrc_temp
awk '!/SCT_DIR|SPINALCORDTOOLBOX|ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS/' ~/.bashrc > .bashrc_temp && > ~/.bashrc && cat .bashrc_temp >> ~/.bashrc && rm .bashrc_temp
  Deleting previous SCT entries in .bash_profile
>> awk '!/SCT_DIR|SPINALCORDTOOLBOX|ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS/' ~/.bash_profile > .bash_profile_temp && > ~/.bash_profile && cat .bash_profile_temp >> ~/.bash_profile && rm .bash_profile_temp
awk '!/SCT_DIR|SPINALCORDTOOLBOX|ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS/' ~/.bash_profile > .bash_profile_temp && > ~/.bash_profile && cat .bash_profile_temp >> ~/.bash_profile && rm .bash_profile_temp

.bashrc seems to be called in .bash_profile

>> . ~/.bashrc
. ~/.bashrc
/bin/sh: 13: /home/shokufeh/.bashrc: shopt: not found
/bin/sh: 21: /home/shokufeh/.bashrc: shopt: not found
/bin/sh: 105: /home/shokufeh/.bashrc: shopt: not found
/bin/sh: 28: /etc/bash_completion: [[: not found
/bin/sh: 34: /etc/bash_completion: [[: not found
/bin/sh: 51: /etc/bash_completion: Bad substitution
Traceback (most recent call last):
  File "./installer.py", line 883, in <module>
  File "./installer.py", line 741, in __init__
    status, output = runProcess(cmd) # runProcess does not seems to work on Travis when sourcing .bashrc
TypeError: 'NoneType' object is not iterable

the content of my .bashrc:

~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
[ -z "$PS1" ] && return

# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options

# append to the history file, don't overwrite it
shopt -s histappend

# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar

# make less more friendly for non-text input files, see lesspipe(1)
[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "$debian_chroot" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color) color_prompt=yes;;

# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt

if [ -n "$force_color_prompt" ]; then
    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
    # We have color support; assume it's compliant with Ecma-48
    # (ISO/IEC-6429). (Lack of such support is extremely rare, and such
    # a case would tend to support setf rather than setaf.)

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
unset color_prompt force_color_prompt

# If this is an xterm set the title to user@host:dir
case "$TERM" in
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"

# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
    alias ls='ls --color=auto'
    #alias dir='dir --color=auto'
    #alias vdir='vdir --color=auto'

    alias grep='grep --color=auto'
    alias fgrep='fgrep --color=auto'
    alias egrep='egrep --color=auto'

# some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'

# Add an "alert" alias for long running commands.  Use like so:
#   sleep 10; alert
alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'

# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
    . ~/.bash_aliases

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if [ -f /etc/bash_completion ] && ! shopt -oq posix; then
    . /etc/bash_completion

# . /usr/share/fsl/5.0/etc/fslconf/fsl.sh
. /etc/fsl/5.0/fsl.sh

# added by Miniconda 3.10.1 installer
export PATH="/home/shokufeh/miniconda/bin:$PATH"

# SPINALCORDTOOLBOX (added on 2015-05-06)
export PATH=${PATH}:$SCT_DIR/bin
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=4shokufeh@shokufeh-

I do not know how to fix it.

Best Answer

  • The issue appears to be that the Python installer attempts to verify its changes to the .bashrc/.bash_profile files by spawning a shell and sourcing them. To do that, it uses the Python subprocess.Popen with shell=True, which defaults to using /bin/sh. On Ubuntu systems, /bin/sh is the dash shell rather than the bash shell (see DashAsBinSh), which doesn't support much of the syntax in the .bashrc file.

    I can think of a couple of fixes:

    1. Open the installer.py file in a text editor and tell the runProcess function to use bash by changing

      def runProcess(cmd, verbose=1):
          if verbose:
              print cmd
          process = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
      def runProcess(cmd, verbose=1):
          if verbose:
              print cmd
          process = subprocess.Popen(cmd, shell=True, executable='/bin/bash', stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)

    2. Temporarily symlink sh to bash before you run the installer

      sudo ln -sf bash /bin/sh

      You can revert it when you're done with

      sudo ln -sf dash /bin/sh
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