Merge pull request #291 from SylvainLan/SylvainLan/issue290

OK thanks, @SylvainLan. Merging.

Author: dohmatob

README.rst

@@ -50,7 +50,7 @@ Installation
 ============
 To begin with, you may also want to install the pre-compiled version of SPM (in case you don't have matlab, etc.). Just run the following::
 
-     $ bash continuous_integration/install_spm.sh
+     $ . continuous_integration/install_spm12.sh
 
 First, install neurodebian-travis::
 
@@ -191,8 +191,14 @@ or if you have write privileges::
        
 Common problems and fixes
 =========================
-* libXp.so.6 missing (in ubuntu >= 15.10, for example)
-This is a known is http://askubuntu.com/questions/719839/libxp-so-6-missing-15-10. The idea is to install it manually from official sources https://launchpad.net/ubuntu/wily/+package/libxp6
+* libXp.so.6 missing (in ubuntu >= 15.10, for example). You'll need to install it manually by executing the following lines in a terminal (you'll need root)::
+
+       $ sudo add-apt-repository "deb http://securuty.ubuntu.com/ubuntu precise-security main"   
+       $ sudo apt update
+       $ sudo apt install lixp6
+       $ sudo add-apt-repository -r "deb http://securuty.ubuntu.com/ubuntu precise-security main"
+
+
 
 * whitespaces in the directory name for the variable 'scratch' triggers a bug in nipype and results in a crash (have not tested if this also occur for other path variables)
 

continuous_integration/install_spm12.sh

@@ -1,46 +1,71 @@
 #! /bin/bash
+# Time-stamp: <2018-02-14 11:26:59 cp983411>
+
+# Download and install SPM12 standalone (no Matlab license required)
+# see https://en.wikibooks.org/wiki/SPM/Standalone
+
 set -e
+# set -x  # echo on for debugging
 
-# set -x  # echo on
+#  Installation directory can be specified as first argument on the command line
+#  Warning: use a fully qualitifed path (from root) to correctly set up env variables
+
+if [ $# -eq 0 ]
+  then
+      SPM_ROOT_DIR=$HOME/opt/spm12   # default
+else
+      SPM_ROOT_DIR=$1
+fi
 
-SPM_ROOT_DIR=~/opt/spm12   #  Installation directory
+mkdir -p $SPM_ROOT_DIR
 
-SPM_SRC=spm12_r7219.zip  # this used to be spm12_r6914.zip, watch out it might get pulled down again!!!
+# Download
+SPM_SRC=spm12_r????.zip
 MCRINST=MCRInstaller.bin
 
-mkdir -p $SPM_ROOT_DIR && cd $SPM_ROOT_DIR
+wget -N -r -l1 --no-parent -nd  -P $SPM_ROOT_DIR -A.zip -R "index.html*" http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/
 
-if [ ! -d spm12 ]; then
-    if [ ! -f ${SPM_SRC} ]; then
-	wget http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/${SPM_SRC}
-    fi
-    unzip -q ${SPM_SRC}
-    chmod 755 spm12/run_spm12.sh
-fi
+wget -N -r -l1 --no-parent -nd  -P $SPM_ROOT_DIR -A.bin http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/glnxa64/
 
-if [ ! -d mcr ]; then
-    if [ ! -f MCRInstaller.bin ]; then
-	wget http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/glnxa64/${MCRINST}
-    fi
-    chmod 755 ${MCRINST}
-    ./${MCRINST} -P bean421.installLocation="mcr" -silent
-fi
 
+# Install
+cd $SPM_ROOT_DIR
+unzip -q -u ${SPM_SRC}
+chmod 755 spm12/run_spm12.sh
 
-if [ ! -f $SPM_ROOT_DIR/spm12.sh ]; then
-    cat <<EOF > $SPM_ROOT_DIR/spm12.sh
+if [ ! -d mcr ]; then
+   chmod 755 ${MCRINST}
+   ./${MCRINST} -P bean421.installLocation="mcr" -silent
+fi
+   
+# create start-up script
+cat <<EOF > spm12.sh
 #!/bin/bash
 SPM12_STANDALONE_HOME=$SPM_ROOT_DIR/spm12
 exec "\${SPM12_STANDALONE_HOME}/run_spm12.sh" "\${SPM12_STANDALONE_HOME}/../mcr/v713" \${1+"\$@"}
 EOF
 
-    chmod 755 $SPM_ROOT_DIR/spm12.sh
+chmod 755 spm12.sh
+
+if [ ! -f /usr/lib/x86_64-linux-gnu/libXp.so.6 ]; then
+    echo "WARNING!!!"
+    echo "/usr/lib/x86_64-linux-gnu/libXp.so.6 is missing"
+    echo 
+    echo To install it:
+    echo 'sudo add-apt-repository "deb http://securuty.ubuntu.com/ubuntu precise-security main"'
+    echo 'sudo apt update'
+    echo 'sudo apt install lixp6'
+    echo 'sudo add-apt-repository -r "deb http://securuty.ubuntu.com/ubuntu precise-security main"'
 fi
 
 # Create CTF
-$SPM_ROOT_DIR/spm12.sh quit
+${SPM_ROOT_DIR}/spm12.sh quit
 cmds="export SPM_DIR=$SPM_ROOT_DIR/spm12/; export SPM_MCR=$SPM_ROOT_DIR/spm12.sh"
 ${cmds}
-echo "You may want to add the following commands (the exports) to your ~/.bashrc file once and for all."
 echo
 echo ${cmds}
+echo "IMPORTANT: you should now execute the following line: "
+echo "echo ${cmds} >> $HOME/.bashrc"
+
+
+