I'm a beginner at Debian, and GNU/linux in general and I was following a tutorial to create a cross compiler, when I stumbled upon the message
/usr/bin/fakeroot: line 178: /debian/rules/: No such file or directory
when running the following command
TARGET="alpha-dec-osf4" fakeroot debian/rules binary-cross
or even
fakeroot /debian/rules/ clean
I'm trying to find a manual or guide to learn about debian/rules, but I even have problems finding something for beginners.
Does anybody know what I'm doing wrong? I'm using Debian GNU/Linux 7.5 (wheezy)
Thank you very much in advance
EDIT: I tried these commands to compile a binutils 2.17, in order to make a cross compiler that would output Alpha OSF/1 binaries on x86 systems. I downloaded binutils from the GNU webpage, so perhaps this was my main mistake, as #Sigi explained that it should be a debian package.
You must not use /debian/rules, but instead debian/rules (note the missing slash at the beginning). If you start a path to a file with a slash (/), the system will start the search in the root directory of your filesystem (this is the top-most directory on any Unix system). On the other hand, if your path does not begin with a slash, the search will always be relative to your current directory. The latter is what applies to invoking debian/rules.
The command is supposed to be executed inside an extracted Debian source package. Check if ls debian/rules will list a file, otherwise you are in the wrong directory.
Regarding a guide for beginners or anything: Debian package building, let alone the creating or modification of Debian packages is decidedly not a beginner's topic. You should first get a solid foundational knowledge in Linux administration before getting your hands dirty in that area.
Related
My main goal is that I want to understand how parameters works in ./configure. So, I decided to install ncurses and vim in $HOME/local/, so, as to not affect my system.
while configuring vim, I looked into --with-local-dir and includedir. I want to know what is the difference between them.
When I looked into vim-git-INSTALL-script, it said:
Unix: LOCAL HEADERS AND LIBRARIES NOT IN /usr/local
Sometimes it is necessary to search different path than /usr/local for locally
installed headers (/usr/local/include) and libraries (/usr/local/lib).
To search /stranger/include and /stranger/lib for locally installed
headers and libraries, use:
./configure --with-local-dir=/stranger
I thought that was the purpose of includedir. I would appreciate if someone can tell me where I went wrong. Thank you!
Conventionally (and per documentation), includedir is used for the directory where the current program would install header files. That's not the same as the places where the configure script might have to tell the compiler to find the header files needed to compile the program.
I want to recompile a Ubuntu package to use it on Debian
https://launchpad.net/ubuntu/+source/hollywood
how can I do that please ? I'm a beginner
You need the original tar-ball for the package, and the "debian" tarball which contains the scripts and patches needed to build the package. Finding those on Ubuntu's website is really the hard part.
Given those, you could use dpkg-buildpackage (on a system comparable to your target, of course), which expects the latter untar'd in the current directory, along with the original tar-ball.
(I build my own packages with a script which stages things into this arrangement; Debian packagers use a different scheme).
Consider these 4 pieces of software:
COBRA 2.05
LibSBML 5.10
MATLAB R2013a (Also known as 8.1, 64-bit; MATLAB no longer supports 32-bit Linux anyway)
A 64-bit Linux OS (such as Ubuntu 14.04 or the latest Mint but not restricted to them)
Intro
The COBRA toolbox is an optimization suite that runs on top of MATLAB aimed at the development of MATLAB code for metabolic network modelling. Such a "network" is a system of equations that can have a very large number of equations and variables (such as thousands). Therefore, routines to read and write those large models according to some format specification are a must-have, and COBRA uses the standard SBML for that.
Problem
Unlike the Windows versions, the Linux binary packages do not integrate well out-of-the-box: to begin with, the pre-compiled Linux binary of libSBML (open-source) available for download does not come with MATLAB support. If one tries to use the pre-compiled libSBML, COBRA won't find the "MATLAB bindings" and therefore won't be able to, for example, read and write SBML XML files from the disk in a m-script.
The question
What needs to be done to make COBRA 2.05 running on top of MATLAB R2013a under Linux (Ubuntu 14.04 or the latest Mint, but this is not likely distro-specific) able to read and write SBML XML files? In other words, what needs to be done system-wide to make COBRA pass its own testSBML test?
This is how I got it working and what I could learn from all the hassle regarding how my Linux box works. I hope I am not forgetting/missing/mistaking anything.
1. MATLAB
1.1. Install MATLAB
Install it in its default location (you will need root access for this), don't be stubborn like I tried to be. Why:
1.1.1. Integration
It is very likely you will want to install some other software that uses the MATLAB framework at some point, and in the real world software doesn't always find other software even if you know how to tell it where to look for.
1.1.2. Make your life easier
Even though it seems like a good idea to install a big software in a place where you have lots of available space and that you can use in multiple machines (specially in Linux, which doesn't have that abomination called Registry, and has symbolic links), that would only perhaps be a good idea - apart from item 1.1.1 - if that place is a partition with a Linux filesystem, since at some point, some executable/script will need execution permission, and mounting the entire partition with execution permission for all its files is rather unsafe. Therefore, do not put MATLAB in an NTFS partition of an external HD; perhaps creating a Linux partition in the external HD just for Linux-specific stuff could work for this matter, but how much hassle is that?
1.2. Setup MATLAB so people and other software can launch it
Even though I have seen somewhere that the MATLAB installer eventually shows an option to create symbolic links in the system path for convenience, it didn't in my case. But that is OK, since I would have to replace the symbolic link /usr/local/bin/matlab by the following shell-script (same path, same filename) anyway:
#!/bin/sh
export LD_LIBRARY_PATH=/usr/local/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
exec /usr/local/MATLAB/R2013a/bin/matlab $*
OBS: That LD_LIBRARY_PATH is needed for MATLAB to find SBML bindings later and to be able to use them. Also, if you install some third-party solver such as TOMLAB, you will most likely need to add some more paths in this little launcher script.
OBS 2: In my case, the installation script didn't automatically create any launchers or shortcuts, but I have found an iconless and extension-less Matlab 8.01 file and a matlab icon as a png file, and that first file was a template .desktop file that I could edit to fit my needs and put in /usr/share/applications so the Unity Dash would find it. The contents of this Matlab.desktop file are:
[Desktop Entry]
Type=Application
Icon=/usr/local/MATLAB/R2013a/Matlab.png
Name=Matlab 8.01
Comment="Start Matlab 8.01"
Exec=/usr/local/MATLAB/R2013a/bin/matlab -desktop
Categories=Development;
Name=Matlab 8.01
GenericName=Matlab 8.01
Comment="Start Matlab 8.01"
2. libSBML
2.1. Install libSBML
libSBML is provided by a deb package specific for Ubuntu (and for CentOS), and also versions for several flavours of Windows and MacOSX (their home page: http://sbml.org/Software/libSBML). Guess which is the only platform whose binaries weren't compiled with MATLAB support? Linux, of course. That means you will need to compile from source (and that the deb package is therefore useless to you). To compile:
2.1.1. Install dependencies
The dependency libxml2-dev (from software manager or from a terminal):
sudo apt-get install libxml2-dev
2.1.2. Save yourself some time in the future
Usually, one would do configure, make and then make install. But this is not recommended for the same reason as installing anything that doesn't come in a pretty little package: you will loose control of which files went where, and will need to keep the source-code to be able to run make uninstall if you need to uninstall it later. So, install checkinstall and use it to replace the step make install, since checkinstall creates a package for your system that can be later uninstalled or reinstalled just as any regular packaged software (from software manager or from a terminal):
sudo apt-get install checkinstall
2.1.3. Configure the compiling-process
Get LibSBML source code and extract it to some folder. From a terminal, navigate to that folder and configure the compilation:
./configure --with-matlab
OBS: with the with-matlab flag, the configure script will fail it it cannot find an executable whose filename is matlab. If it fails, it outputs that the matlab file could not be found, but the test it performs is actually both for the existence of the file and whether it is executable. So, if the file is in an NTFS partition, configure will fail even if it finds the file, but will tell you the file couldn't be found. You can enforce it to look for the executable in /path/to/matlab/root by passing (it will look for a bin folder inside that path, and for the executable inside that bin folder):
./configure --with-matlab=/path/to/matlab/root
OBS: This will install libSBML in the default location: /usr/local/lib. Again, it is a good idea to just let it install in its default location, but if you need to change it, you can pass the path with the flag: --prefix=/your/installation/path
OBS 2: You might ask why libSBML needs to find and execute matlab to be compiled with support for it: it needs to fire up MATLAB later to build MEX-files (compiled MATLAB code), so I would speculate you wouldn't be able to install libSBML after all if your MATLAB has no compiler to generate MEX-files.
2.1.4. Build and install libSBML
make
checkinstall
VERY IMPORTANT OBS:
I) checkinstall asks for confirmation of the metadata of the package it is about to create. In my case, the string for the version field came by default as "Source" (without the quotes), which caused checkinstall to fail because dpkg (the system tool that actually builds the deb file) failed complaining the version number must start with, well, a number. So, save yourself some time and make sure the string in the version field starts with a number (i.e. "5.10", without the quotes obviously)
II) checkinstall asks if you want to exclude from the future package files that the make install command would put in your home folder and says it is a good idea to exclude them. LibSBML has a test.xml file that it needs to be in the $HOME folder later, or else it won't let you integrate with MATLAB. And even though it tells you a test.xml is missing, it doesn't tell you where that file should be or if that file was something that came with the library. I only noticed it because checkinstall had found a $HOME/test.xml reference earlier (that I excluded from the package, of course) and I had found that odd. So, save yourself some time and exclude $HOME/test.xml from the package generated by checkinstall, and then search for test.xml inside the source-code folder and copy it to $HOME as soon as libSBML finishes being installed by checkinstall.
2.2. Integrate libSBML to MATLAB
Fire up MATLAB, navigate to where the SBML MATLAB-bindings were installed in step 2.1.5 (in my case: /usr/local/lib) and run the file installSBML.m that should be there.
2.2.1. Shared libraries problems
In my case, I had an error due to an old unresolved issue: libstdc++.so.6 not having a reference to GLIBCXX_3.4.15. Turns out that MATLAB was trying to use a libstdc++.so.6.0.13 (libstdc++.so.6 was a symbolic link pointing to this file) that came with it in /usr/local/MATLAB/R2013a/sys/os/glnxa64, which indeed didn't have that reference (one could verify that by issuing:
strings /usr/local/MATLAB/R2013a/sys/os/glnxa64/libstdc++.so.6.0.13 | grep GLIBC
). My system has a libstdc++.so.6.0.19 located in /usr/lib/x86_64-linux-gnu that has that reference, so I enforced MATLAB to use 6.0.19 one by setting the LD_LIBRARY_PATH properly (refer to step 1.2) and also by renaming the libstdc++.so.6 that came with MATLAB to something else so it would not find it and would keep looking until it found my system's. A friend of mine running Linux Mint didn't need to rename anything: for him, setting the LD_LIBRARY_PATH was enough.
2.2.2. Other problems
installSBML.m will fail if it doesn't find that $HOME/test.xml file mentioned in step 2.1.5, regardless of whether the library actually works. It assumes that if it could not test itself using a file that it assumes to be in $HOME, the user shouldn't have the option to install it anyway.
3. COBRA / SBML toolbox
3.1. Setup COBRA
In MATLAB, navigate to <YOUR_COBRA_ROOT_FOLDER_HERE>/external/toolboxes/SBMLToolbox-4.1.0/toolbox and run the file install.m there. You should have all set so it finds the MATLAB-bindings you set up in step 2.2.
3.2. MATLAB setpaths problems
I had to manually edit the file /usr/local/MATLAB/R2013a/toolbox/local/pathdef.m as root to include the folder /usr/local/lib (where libSBML and its MATLAB-bindings are) to make that setting persistent. Every time I restarted MATLAB, its setpath had gone back to the default, no matter if I started MATLAB as root when setting its setpath via the MATLAB GUI.
3.3. Test
Now you have hopefully connected all the dots. Try it: in MATLAB, navigate to <YOUR_COBRA_ROOT_FOLDER_HERE> and issue:
initCobraToolbox
testAll
If you haven't got any third-party solvers installed and configured, it should pass 14 of the 19 tests, including the SBML test (testSBML). Now you can load SBML files into MATLAB and play with them.
I also needed to add a symbolic link from /usr/local/lib/libsbml.so.5 to the MATLAB sys folder by:
sudo ln -s /usr/local/lib/libsbml.so.5 /usr/local/MATLAB/R2014a/sys/os/glnxa64/
This finally made the installation possible.
I installed using Cmake. To do this it is necessary to find the FindMatlab.cmake in the source package and insert the MATLAB path manually!
.............
elseif(EXISTS "/Applications/MATLAB_R2008a.app/")
set(MATLAB_ROOT_PATH "/Applications/MATLAB_R2008a.app/")
endif()
else()
if (EXISTS "/usr/local/MATLAB/R2014a/")
set(MATLAB_ROOT_PATH "/usr/local/MATLAB/R2014a/")
endif()
endif()
..........
FYI, to resolve the shared library issue at point 2.2.1 I needed to install the package matlab-support (in Ubuntu repositories)
I asked IT to install Mono on CentOS using the following commands:
$yum install bison gettext glib2 freetype fontconfig libpng libpng-devel libX11 libX11-devel glib2-devel libgdi* libexif glibc-devel urw-fonts java unzip gcc gcc-c++ automake autoconf libtool make bzip2 wget
$cd /usr/local/src
$wget http://download.mono-project.com/sources/mono/mono-3.2.5.tar.bz2
$tar jxf mono-3.2.5.tar.bz2
$cd mono-3.2.5
$./configure --prefix=/opt/mono
$make && make install
However, when I run mono myapp.exe I get
-bash: mono: command not found
I know nothing about Linux - I feel like I'm in Japan. Assuming Linux has a path variable or something like it, maybe mono isn't in the path?
I can't even find an executable called mono in /usr/local/src, just a mono folder. Mind you I can't work out how to even search for a file so I might not be looking properly.
How can I tell whether its installed correctly? Maybe its just not available to the non-admin account I use?
I'm lost. Help!
If mono is properly installed, you should not get a message like -bash: mono: command not found. If something is installed then it most typically is in the $PATH.
On my system the executable is located on /usr/bin/mono (as most things are) but things may be different on a RPM-based system.
Your ./configure, however, got the prefix /opt/mono, so probably your executable also is located under that special path. (And thus mono isn't properly installed.) Why did you install it there? Anyway. If this is the fact, then you can execute it using sth like
/opt/mono/bin/mono foo.exe
to find the executable below your prefix path you could use
find /opt/mono -name mono
to see all directory entries which are named exactly mono. One of those should be your executable.
If your programm is properly installed you will usually find it's executable using "which"
which programm
like:
which firefox
/usr/bin/firefox
There are many guides and tutorials out there that recommend installing in /opt/mono in order to not conflict with the mono supplied by official distribution packages (which would be installed in /usr).
However what most of those guides miss is that /opt/mono is a non-standard prefix that will not be taken in account by the system when trying to find the executables (the system looks at the $PATH environment variable).
There are 2 possible solutions to this:
Instead of using the prefix /opt/mono use /usr/local (which is actually what ./configure or ./autogen.sh uses by default if you don't supply any prefix!). This prefix is normally included in the $PATH environment variable of most distributions.
Use your custom mono installation from a Parallel Environment. This is a bit more complicated to set up, but it's specially recommended for people who want to install two versions of mono in parallel (i.e. a very modern version, and a more stable version supplied by the official distribution packages), and have good control of when they can use one or another.
The reason that many internet tutorials recommend /opt/mono instead of /usr/local is actually because most of them are based on the wiki page (referenced above) that explains how to set up a Mono Parallel Environment, but they of course don't include the other steps to properly set up such an environment (they just borrowed the bit about how to call configure).
I'm trying to build a Win32 DLL from an audio-DSP related Linux library (http://breakfastquay.com/rubberband/). There are makefiles and config scripts for Linux, but no help for Windows. The author provides a Win32 binary of a sample app using the library, and I see a number of "#ifdef MSVC" and "#ifdef WIN32" scattered around, so I don't think I'm starting completely from scratch but I'm stuck nevertheless.
As my programming knowledge in either platform is rather limited, I'd appreciate any help.
First of all, what is the right way to get started here? Visual Studio? Cygwin? Initially I started off creating a Win32 DLL project in Visual Studio, adding the source files, thinking about adding a .def file, etc, but at some point I felt like this was going nowhere.
As for Cygwin, this was the first time using it, and I don't even know if this is the sort of thing that Cygwin is designed for. Is it?
On Cygwin, I ran ./configure and got stuck at something like this:
"checking for SRC... configure: error: Package requirements (samplerate) were not met: No package 'samplerate' found"
After looking through the log, it appears that pkg-config is looking for samplerate.pc. How do I handle packages in Windows? libsamplerate is just an open source library, and I have source and a DLL for this. But I'm not sure how to use them to satisfy the dependency requirements for librubberband (which is what I'm trying to build)
I'm completely lost at this point and if anyone can give me a nudge in the right direction... and, is there an easier way to do this?
Many thanks in advance.
If you're still stuck on this I can throw a little light.
You may have to build everything from sources (or have the libraries installed in your environment). You're using Cygwin, I would recommend MinGW and MSYS too, but sometimes it's just not possible to use this combination to build the program or library.
So if using Cygwin, first ensure that you have a proper environment installed. This is that you have the correct development headers installed.
Then download libsndfile. Extract the sources to a directory and from the Cygwin bash shell navigate to that directory. There perform:
./configure
make
make install prefix=/cygdrive/c/cygwin
Notice that I use a prefix, that prefix should point to the directory Cygwin is installed in order to correctly install the libraries (the same happens to MinGW and MSYS, the prefix should point to the MinGW installation directory). Maybe using the usr directory in the prefix works too, I've never tried it.
Now download FFTW, as it will be needed for libsamplerate and rubberband. Same procedure as with libsndfile: extract, configure, make & make install using the prefix. Now copy the header files of FFTW (in the example they'd be in /cygdrive/c/cygwin/include) to the include directory in the usr directory (in the example /cygdrive/c/cygwin/usr/include).
Next SRC (libsamplerate), same procedure.
Then the Vamp plugin SDK. In order to compile the it you may need to edit the file src\vamp-hostsdk\PluginLoader.cpp, deleting RTLD_LOCAL from a dlopen() call (it's safe, it's already the default behaviour).
Also, you may need to install it by hand (in my experiences it didn't like the prefix). Or set the environmental variable PKG_CONFIG_PATH pointing to the paths of pkgconfig, e.g.:
set PKG_CONFIG_PATH=/cygdrive/c/cygwin/lib/pkgconfig:/usr/local/lib/pkgconfig
Now, create a file called ladspa.h in the include directory with the contents of the LADSPA header
Finally, configure and build rubberband, it should find everything it needs.
To build in MSYS using MinGW follow the same procedure, using the according prefix. Using Visual Studio is another alternative, but you may need to use some of the pre-built libraries (for example for libsndfile) as building Linux libraries natively in Windows may be complicated or even impossible (without hacking the source code) in VS.
Anyway, the autor of rubberband provides binaries; I think you should consider use them instead of going through all of this.
Linux to w32 is mostly a tricky thing.
For each of your dependencies, download the source and:
./configure
make
sudo make install
Also, I recommend you to use MinGW + msys in place of CygWin (as the latter produces executables that depend on its libraries). However in your situtation, use the VS approach -- 't will save you a lot of time.