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)

---

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...').

---

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

---

478. Briefly: proftpd on debian

I need to transfer raw mass spec files off of the computer controlling our waters zmd, and it seems like I may be the only one in the department wishing to do so.

Since the computer is running Windows NT 4 and doesn't support USB drives out of the box, and I'm a bit worried about installing new software (e.g. old versions of filezilla via oldapps) on a computer on which a lot of people rely, I have two options:

* use SMB i.e. a windows share
or
* use ftp

I'm having all sorts of trouble getting my samba to work well at work -- my computers are sitting on a 192.168.2.0/24 LAN behind a router connected to the corporate network which has proper IP addresses (i.e. not using a reserved private network address space). I haven't managed to get my computer behind the router to 'see' the other computers and their shares at work beyond my router . I can, however, connect directly to the computers using e.g. smbclient -- they just won't show up in e.g. nautilus under windows network or using nmblookup. At any rate, connection directly to the target computer prompts me for a password and it seems that there are no open, accessible shares on that computer, only password protected ones.

Win NT has a DOS ftp client, so I finally decided to set up a quick and dirty ftp server on my workstation in my office so that I could transfer a couple of data files to figure out my other issue -- whether I have any piece of software that can actually open the masslynx .raw files. Turns out that neither wsearch32 nor openchrom can, so the exercise has been somewhat futile, although it has to be said that I'd like to be in charge of any raw data that leads to publications, and so I should be able to manage the storage of it myself.

Note: ftp is an inherently unsafe method since it doesn't use encryption. Use a separate user for this with no privileges, change the password of that user regularly, and close port 21 whenever you aren't using it in order to not advertise that you are running an ftp server. Use ssh/sftp if at all possible.

Anyway, setting up an ftp server was easy.

This method follows this post, http://ubuntuforums.org/showthread.php?t=79588, almost verbatim.

First install proftpd

sudo apt-get install proftpd

Edit /etc/shells:

# /etc/shells: valid login shells
/bin/csh
/bin/sh
#/usr/bin/es
#/usr/bin/ksh
#/bin/ksh
#/usr/bin/rc
#/usr/bin/esh
/bin/dash
/bin/bash
/bin/rbash
#/usr/bin/screen
#/bin/tcsh
#/usr/bin/tcsh
#/bin/ksh93
/bin/false

sudo adduser ftpuser

su ftpuser
cd ~
mkdir download
mkdir upload
exit

Edit /etc/proftpd/proftpd.conf. In addition to what was already there, I added

UserAliasOnly                   on
UserAlias spinebill ftpuser
ExtendedLog                     /var/log/ftp.log
TransferLog                     /var/log/xferlog
SystemLog                       /var/log/syslog.log
AllowStoreRestart               on  

<Directory /home/ftpuser>
Umask 022 022 
AllowOverwrite off 
        <Limit MKD STOR DELE XMKD RNRF RNTO RMD XRMD>
        DenyAll
        </Limit>
</Directory>

<Directory /home/ftpuser/download/*>
Umask 022 022 
AllowOverwrite off 
        <Limit MKD STOR DELE XMKD RNEF RNTO RMD XRMD>
        DenyAll
        </Limit>
</Directory>

<Directory /home/ftpuser/upload/>
Umask 022 022 
AllowOverwrite on
        <Limit READ RMD DELE>
        DenyAll
        </Limit>

        <Limit STOR CWD MKD>
        AllowAll
        </Limit>
</Directory>

Include /etc/proftpd/conf.d/

su ftpuser
chsh -s /bin/false
exit

Check the syntax:

sudo proftpd -td5

Test:

ftp `hostname`

Connected to beryllium.
220 ProFTPD 1.3.4a Server (Debian) [192.168.1.1]
Name (beryllium:me): spinebill
331 Password required for spinebill
Password:
230 User spinebill logged in
Remote system type is UNIX.
Using binary mode to transfer files.
ftp>

I have since tested this from the Win NT 4 computer and everything is working well. I had to familiarise myself with the windows ftp client first: http://www.nsftools.com/tips/MSFTP.htm

477. OpenChrom - Dempster

I don't want to get into writing software reviews, but given how much OpenChrom, an open source program for mass spectrometry which can open a range of proprietary formats, has evolved since I tried the release code-named Syringe (http://verahill.blogspot.com.au/2012/09/using-openchrom-to-open-aglient-d-esi.html) in September 2012, I think a brief update may be in order.

Essentially, OpenChrom now seems a lot easier and more natural to use.

The installation is the same as before (I've copied the old post below):

---

1. Install Java v1.7 (need > 1.6)
You can either use openjdk 7 or (Oracle) Java. See here for a general guide to installing Oracle/Sun Java.

As for openjdk, you can easily install it:
sudo apt-get install openjdk-7-jdk

(the openjdk-7-jre package is enough if you don't want the full developer's kit)

Anyway.

Make sure that you've selected the right version:

 sudo update-alternatives --config java
There are 7 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
  1            /usr/bin/gij-4.4                                 1044      manual mode
  2            /usr/bin/gij-4.6                                 1046      manual mode
  3            /usr/bin/gij-4.7                                 1047      manual mode
  4            /usr/lib/jvm/j2re1.6-oracle/bin/java             314       manual mode
  5            /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/java        315       manual mode
  6            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
 *7            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode

---

2. Get openchrom

cd ~/tmp

wget http://aarnet.dl.sourceforge.net/project/openchrom/REL-0.8.0-PREV/openchrom_linux.gtk.x86_64_0.8.0-PREV.zip

unzip openchrom_linux.gtk.x86_64_0.6.0.zip

cd linux.gtk.x86_64/OpenChrom/

sudo mkdir /opt/openchrom

sudo chown $USER /opt/openchrom 

cp * -R /opt/openchrom

chmod +x /opt/openchrom/openchrom

Stick

alias openchrom='/opt/openchrom/openchrom'

in your ~/.bashrc and source it.

---

A few notes:
You can now start OpenChrom by running

openchrom

from the command line.

You can install plug-ins, e.g. to open Agilent files, by going to Plugins/OpenChrom Marketplace. Plugins will typically run for 30 days, but can be unlocked for perpetuity by adding a serial key, which is free. Add license keys by first registering on the openchrom website, going to http://www.openchrom.net/main/content/plugins.php, and clicking on the plugin you want a serial key for. You can then enter that key by going e.g. Window/Preferences/Converter in the OpenChrom software.

Everyone has their own idea of what a good piece of mass spec software should look like, and I suspect that OpenChrom caters to them all. Layouts are called Perspectives here. On the flip side, if you accidentally use a perspective that doesn't suit you, you may be incredibly frustrated until you figure out what's going on.

I like wsearch32, so my preferred view is to go to Window/Perspective Switcher -> Chromatogram MS (exact).

Opening spectra is much easier than before: now simply go to File/Open Chromatogram (MSD) and click on the file (or directory structure in the case of e.g. Agilent .D directories) and open:

Anyway, openchrom is getting better, is easier to use, and is still the only open source program that I know which can handle such an array of proprietary formats. Also, it can export data in both .csv and .xls formats, but you will need to install plugins for that, which is luckily very simple.