481. A little bit of samba on the command line

I have a bit of a problem with samba currently.

My problem is that my computers are sitting behind a router (on a 192.168.2.0/24 subnet) and the computers that I want to access sit on the university network, to which the router is connected. The address range is, say, 131.172.x.x.

In other words, I (think I) want to use samba across two subnets.

I've opened up ports 13-139,445 to tcp and udp on both the router and in iptables on my desktop.

My problem:
1. I can't see the network shares of the other computers using
   a) nautilus (Network/Windows Network)
   b) nmblookup
   c) sambascanner

2. I can't connect to network shares using their netbios names. For example, I'd like to connect to e.g. smb://avance400/data, but I have to use the IP address instead. For some curious reason not even that works using nautilus.

Workaround:
So here's not a solution, but a workaround.

I can connect to other computers from the command line as long as I know the IP address, and here's how

smbclient //131.172.123.30/data -U myuni/me

If you actually want to mount the share, which is password protected, and you do, then do

sudo mount -t cifs -o user=me //131.172.123.30/data /media/smbmounts/

where /media/smbmounts belong to you (e.g. sudo mkdir /media/smbmounts && sudo chown $USER /media/smbmounts).

And that's more or less it.

Some additional information:
If you don't get prompted for the password, and get

mount: block device //131.172.123.30/data is write-protected, mounting read-only
mount: cannot mount block device //131.172.123.30/data read-only

but supplying the password as part of the command line works, then you are missing cifs-utils, so install them.

Note that mount.cifs can handle credentials from a special file, e.g. like this , which you chmod to 600. My chief issue with that is that ~/.bash_history has exactly the same permissions (u+rw, go-rwx) and so I don't see how it's that's any safer than exposing everything by supplying your password as part of the mount command. Both should be avoided if possible.

On the other hand you could argue that since the password is transmitted over the network in cleartext you're inviting trouble either way...

480. MS data, part II. Plotting and comparing with predicted isotopic enveloped

NOTE: I've heard rumours about problems with Matt Monroe's calculator on Windows 7 Home, and on Windows 8. I've heard reports of it working on Windows 7 Professional. Given that wsearch also has issues,  this may be linked to VB.

This post is, like this one, is written with two particular students in mind.

MS here stands for Mass Spectrometry.

I'll be presuming that you have exported your data as a csv file as shown in http://verahill.blogspot.com.au/2013/07/474-exporting-data-from-wsearch32-and.html

Our scenario:
So you've exported your data as e.g. data.csv, and you have assigned a signal in your spectrum to a species, and you'd now like to plot the predicted and observed isotopic envelopes in a way that will help you compare them.

The signal we have identified is at 211.90 m/z and we think it belongs to [Ga(CH₃OH)₂(OH)(NO₃)]⁺.

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The Linux way:
You'll need: sed, gawk, gnuplot, pyisocalc or Matt Monroe's Molecular Weight calculator

1. Generating the isotopic envelope:

A. Using pyisocalc:
Set the charge to 1 and output the data to 1.dat, with a gaussian broadening factor of 0.3:

isocalc -f 'Ga(CH3OH)2(OH)(NO3)' -c 1 -o 1.dat -g 0.3

B. Using Matt Monroe's molecular weight calculator
Go to Tools/Isotopic Distribution Modelling

In the spectrum window, go to Edit, Copy Data Points, and paste into e.g. a Gedit window. Save as 1.dat

2. Formatting the data.csv for gnuplot (can skip for spreadsheet programs):
In a single line we remove the first eight lines, replace all commans (,) with tabs, only keep the m/z and relative isotopic abundance columns (2 an 4) and save the output to data.dat

tail -n +8 data.csv |sed 's/\,/\t/g'|gawk '{print $2,$4}' > data.dat

3. Plotting:

A. Using gnuplot:
Create a file called 1.gplt which contains the gnuplot commands:

set term postscript eps enhanced color
set output '1.eps'
set xrange [206:220]
plot '1.dat' u ($1-0.05):($2*0.092) w lines ti 'Calculated' lc -1 lw 2,\
 'data.dat' u 1:2 w lines ti 'Observed' lc 1 lw 2

($1-0.05) means we're offsetting the calculated data by 0.05 m/z. ($2*0.092) means that we're scaling the calculated data intensity to match that of the observed. lc sets line colour and lw sets the width


If you want the output as png instead of eps, just change the first two lines to

set term png size 1000,667
set output '1.png'

Using pyisocalc

Using Matthew Monroe's calculator

B. Using QtiPlot
Qtiplot is in the debian repos and is 'origin'-like (as in Microcal Origin).

You'll need to rescaled your calculated data first, which is a major drawback:

cat 1.dat|gawk '{print $1-0.05,$2*0.095}'> 1_scaled.dat

Start QtiPlot and select Open. Make sure you select 'all files' as the file type. Open 1_scaled.dat.

Next, make sure that the spreadsheet is active, and go to File, Import, Import Ascii

Change the type of column 3

Select all columns and go to Plot, Line. Change the axes (double click on the axes and set the new ranges), set the top and right axes no to show, edit the titles etc.

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The Windows way: 
You'll probably need: excel or open/libreoffice, origin, pyisocalc or Matt Monroe's Molecular Weight calculator

Doing this on windows is a PITA compared to Linux, and I don't have the time to go through it. If you do have Origin, it should be straightforward to translate the instructions above into an MS Win-like environment.

Any scaling will have to be done in Excel or a similar spreadsheet program. Not difficult, but it'll add a few extra steps.

479. Compiling Wine 1.6 on Debian (using a chroot)

Update:
I noticed

configure: libOSMesa 32-bit development files not found (or too old), OpenGL rendering in bitmaps won't be supported.

popping up at the end of ./configure. I've added a fix for it based on http://forum.winehq.org/viewtopic.php?f=2&t=17713

Original post:
Here's a generic way of building Wine 1.6 which is now stable. And yes, it's the instructions for 1.5.28-1.6-rcX recycled.

See here for information about 3D acceleration using libGL/U with Wine: http://verahill.blogspot.com.au/2013/05/429-briefly-wine-libglliubglu-blender.html

Getting started:
If you set up a e.g. chroot to build 1.5.28 you don't need to set up a new chroot to build 1.6. In that case, skip the set-up step below and instead re-enter your existing chroot like this:

sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32
su sandbox

cd ~/tmp

And skip to 'Building wine'.

Otherwise do this:
Setting up the Chroot

sudo apt-get install debootstrap
mkdir $HOME/tmp/architectures/wine32 -p
cd $HOME/tmp/architectures
sudo debootstrap --arch i386 wheezy $HOME/tmp/architectures/wine32 http://ftp.au.debian.org/debian/
sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32

You're now in the chroot:

apt-get update
apt-get install locales sudo vim
echo 'export LC_ALL="C"'>>/etc/bash.bashrc
echo 'export LANG="C"'>>/etc/bash.bashrc
echo '127.0.0.1 localhost beryllium' >> /etc/hosts
source /etc/bash.bashrc
adduser sandbox
usermod -g sudo sandbox
echo 'Defaults !tty_tickets' >> /etc/sudoers
su sandbox
cd ~/

Replace 'beryllium' with the name your host system (it's just to suppress error messages)

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Building Wine
While still in the chroot, continue (the i386 is ok; don't worry about it -- you don't actually need it):

sudo apt-get install libx11-dev:i386 libfreetype6-dev:i386 libxcursor-dev:i386 libxi-dev:i386 libxxf86vm-dev:i386 libxrandr-dev:i386 libxinerama-dev:i386 libxcomposite-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libdbus-1-dev:i386 libgnutls-dev:i386 libncurses-dev:i386 libsane-dev:i386 libv4l-dev:i386 libgphoto2-2-dev:i386 liblcms-dev:i386 libgstreamer-plugins-base0.10-dev:i386 libcapi20-dev:i386 libcups2-dev:i386 libfontconfig-dev:i386 libgsm1-dev:i386 libtiff-dev:i386 libpng-dev:i386 libjpeg-dev:i386 libmpg123-dev:i386 libopenal-dev:i386 libldap-dev:i386 libxrender-dev:i386 libxml2-dev:i386 libxslt-dev:i386 libhal-dev:i386 gettext:i386 prelink:i386 bzip2:i386 bison:i386 flex:i386 oss4-dev:i386 checkinstall:i386 ocl-icd-libopencl1:i386 opencl-headers:i386 libasound2-dev:i386 build-essential

mkdir ~/tmp
cd ~/tmp
wget http://prdownloads.sourceforge.net/wine/wine-1.6.tar.bz2

tar xvf wine-1.6.tar.bz2
cd wine-1.6/

Optional:
To avoid getting the

configure: libOSMesa 32-bit development files not found (or too old), OpenGL rendering in bitmaps won't be supported.

message, do the following:
1. Edit configure

 9450 LIBS="-lOSMesa -lGLU -lGL $X_LIBS $X_PRE_LIBS $XLIB -lm $X_EXTRA_LIBS $LIBS"

2. Also change

 9473     *) ac_cv_lib_soname_OSMesa=libOSMesa.so

Does it change anything? I don't know. But it removes the error message which is triggered by missing symbols so I think it does since the symbols are found in GLU/GL.
End optional.

Then do

./configure
time make -j3
sudo checkinstall --install=no

checkinstall 1.6.2, Copyright 2009 Felipe Eduardo Sanchez Diaz Duran
           This software is released under the GNU GPL.


The package documentation directory ./doc-pak does not exist. 
Should I create a default set of package docs?  [y]: 

Preparing package documentation...OK

Please write a description for the package.
End your description with an empty line or EOF.
>> wine 1.6
>> 

*****************************************
**** Debian package creation selected ***
*****************************************

This package will be built according to these values: 

0 -  Maintainer: [ root@beryllium ]
1 -  Summary: [ wine 1.6]
2 -  Name:    [ wine ]
3 -  Version: [ 1.6]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ i386 ]
8 -  Source location: [ wine-1.6 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ wine ]
12 - Conflicts: [  ]
13 - Replaces: [  ]

Checkinstall takes a little while (In particular this step: 'Copying files to the temporary directory...').

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Installing Wine

Exit the chroot

sandbox@beryllium:~/tmp/wine-1.6$ exit
exit
root@beryllium:/# exit
exit
me@beryllium:~/tmp/architectures$ 

On your host system
 Enable multiarch* and install ia32-libs, since you've built a proper 32 bit binary:

sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install ia32-libs

*At some point I think ia32-libs may be replaced by proper multiarch packages, but maybe not. So we're kind of doing both here.

 Copy the .deb package and install it

sudo cp wine32/home/sandbox/tmp/wine-1.6/wine_1.6-1_i386.deb .
sudo chown $USER wine_1.6-1_i386.deb
sudo dpkg -i wine_1.6-1_i386.deb

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