I'm trying to make some Networkx Graphviz graphs.
After running: pos = nx.graphviz_layout(G, prog = 'sfdp'). An error occured, saying:
Error: remove_overlap: Graphviz not built with triangulation library
After some Google research I found that GTS is the problem. Bug report stated:
The Graphviz package is built --without-gts. This is bad news for sfdp, which complains “Error: remove_overlap: Graphviz not built with triangulation library” and fails to produce the beautiful output it creates when compiled --with-gts
Looking at comments ( on bug report ), someone said that the upstream sources for Graphviz are kept at link but I couldn't find new versions to download.
On package list I have the latest one (2.36 for trusty).
Anyone else having problems with sfdp?
Any help will be greatly appreciated!
For the ubuntu users, this is how I got grapvhiz to work on 16.04,compiling graphviz-2.40.1 from source:
In a first step , GTS needs to be installed , as graphviz looks for the gts.pc file.
Running
apt-file search gts.pc
Informs me I have to install 'libgts-dev' :
sudo apt install libgts-dev
next make pkg-config aware of the files:
pkg-config --libs gts
pkg-config --cflags gts
run configure to link in the gts library:
./configure --with-gts --prefix ~
make
make install
SFDP no longer throws the error 'Error: remove_overlap: Graphviz not built with triangulation library'
The command line codes for the pkg config I modified from this answer.
I know the question is for Ubuntu, but in case someone is having the same problem on macOS using homebrew the following worked for me:
brew reinstall graphviz --with-gts
I might have it working for Ubuntu 14.04, YMMV
Download the following graphviz packages directly from https://packages.debian.org/search?keywords=graphviz
graphviz_2.38.0-13_amd64.deb
libcgraph6_2.38.0-13_amd64.deb
libgvc6_2.38.0-13_amd64.deb
libgvpr2_2.38.0-13_amd64.deb
libltdl7_2.4.6-0.1_amd64.deb
python-pygraphviz_1.3.1-1_amd64.deb
I used version 2.38.0-13 from the stretch(testing) group.
You will need to remove the 32bit libltdl7 if present:
sudo apt-get remove libltdl7:i386
Install the packages directly with
sudo dpkg -i graphviz_2.38.0-13_amd64.deb
sudo dpkg -i libcgraph6_2.38.0-13_amd64.deb libgvc6_2.38.0-13_amd64.deb libgvpr2_2.38.0-13_amd64.deb libltdl7_2.4.6-0.1_amd64.deb
You can expect dependency errors. I cleared them with:
sudo apt-get install -f
And then re-install
sudo dpkg -i graphviz_2.38.0-13_amd64.deb
sudo dpkg -i python-pygraphviz_1.3.1-1_amd64.deb
The error no longer appeares though I would be hard pushed to say the graphs are any better.
Related
I cannot figure this out for the life of me.
When I pip install django-tenant-schemas it tries to install the dependency psycopg2 which requires the Python headers and gcc. I have all this installed and still keep getting this error!
./psycopg/psycopg.h:35:10: fatal error: libpq-fe.h: No such file or directory
So to install libpq-fe-h I need to sudo apt-get install libpq-dev..
..which returns..
libpq-dev is already the newest version (10.10-0ubuntu0.18.04.1).
Then when I sudo find / libpq-fe.h it doesn't seem to be in my OS.
I am lost at this point. If anyone can help I would highly appreciate it.
For some reason, the file is missing on the system.
As you're using apt-get, the system is dpkg based, presumably Debian or it's derivative. You can try the Ubuntu's package search to get which package contains a file with name ending in libpq-fe.h.
I found the package is libpq-dev and file's absolute path is /usr/include/postgresql/libpq-fe.h.
FWIW, on a dpkg based system, you can check which package gives a file if you know the file's absolute path:
% dpkg -S /usr/include/postgresql/libpq-fe.h
libpq-dev: /usr/include/postgresql/libpq-fe.h
Also, unlike find, locate keeps a cache of found files (mlocate.db) that is created everyday via cron; so if the file happens to be removed after the last run, you can run locate libfq-fe.h to get the absolute path to the file without needing to check the Ubuntu package search online.
So the package is libpq-dev. Now, reinstalling it will get everything to the default state i.e. all relevant files will be copied to the right places. As it is only a library package, no user/system level configurations will be overridden (and dpkg will prompt you for action for any package that does that).
To reinstall the package:
sudo apt-get install --reinstall libpq-dev
For me, I realized it was trying to use the deprecated setup.py so I installed wheel (pip install wheel) and that sorted it all out.
Well after installing these libraries
sudo dnf install python-virtualenv openssl-devel gcc libffi-devel libxslt-devel issue was not gone.
I used mlocate to find where libpq-fe.h file is located. On my system (Fedora 32) it was located at /usr/pgsql-10/include/libpq-fe.h
yum install mlocate
sudo updateb
locate libpq-fe.h
After all added this line to ~/.bash_profile
nano ~/.bash_profile
export PATH=/usr/pgsql-10/bin/:$PATH
Works fine, I can easily install psycopg2 without any trouble.
You need to create a LD_LIBRARY_PATH that indicates the path of your library /user/pgsql-11/lib
Source: The 3rd point of build prerequisites at https://www.psycopg.org/docs/install.html#build-prerequisites
I am trying to install octave from the "Its Pointless" repository mentioned in the termux wiki. The repository is added successfully as far as I can tell. However, when I try the command pkg install octave I get the error "octave Depends openblas" "octave Depends arpack-ng" "Unable to correct problems, you have held broken packages"
I have run dpkg --get-selections | grep held but it doesn't return anything.
When I try to run pkg install openblas it gives the error "openblas Depends libgcc but it is not installable"
When I try to run pkg install libgcc it gives the error "package libgcc is not available but is referred to by another package, this may mean the package is missing, has been obsoleted, or is only available from another source. However, the following packages replace it: ndk-sysroot"
After searching some more I did pkg install clang but I still get the same errors. ndk-sysroot has been installed during installation of clang.
I have done apt-get autoclean, apt-get autoremove and apt-get purge but that did not do anything.
What can I do to fix this problem and install octave on my phone?
The problem got solved by itself.
I tried pkg install octave again and got a response saying "The repository https://termux.net stable Release is no longer signed."
So I ran the command bash setup-pointless-repo.sh again.
And that was it! pkg install octave is now working.
I have R 3.4.1.1 on my computer (Linux).
I want to install R version 2.14.1 since the package Rmosek does not work in newer version.
I have downloaded the R-2.14.2.tar.gz from Cran.
My problem is that I do not understand the INSTALL instructions,
It says to unpack the R sources and go to the top directory and issue the following commands:
./configure
make
I wrote the following in a terminal:
tar -zxvf R-2.14.2.tar.gz
cd Downloads
cd R-2.14.2
./configure
It is run but finally gives the error:
configure: error: --with-x=yes (default) and X11 headers/libs are not available
make
and it gives the error:
make: *** No targets specified and no makefile found. Stop.
The file explains that If my make is not called `make', set the environment variable MAKE to
its name, and use that name throughout these instructions. I really do not know how I should do it since I am new in Linux.
Is there any other instruction with more explanation? I would be very thankful in advance for your help or guidances.
Regards,
Shima.
This is answered in detail in the R installation and administration guide,
http://cran.r-project.org/doc/manuals/R-admin.html#Essential-programs-and-libraries
Unless you do not want to view graphs on-screen (or use a Mac) you
need ‘X11’ installed, including its headers and client libraries. For
recent Fedora distributions it means (at least) RPMs ‘libX11’,
‘libX11-devel’, ‘libXt’ and ‘libXt-devel’. On Debian we recommend the
meta-package ‘xorg-dev’. If you really do not want these you will need
to explicitly configure R without X11, using --with-x=no.
More specifically, for Ubuntu, this means:
sudo apt-get install xorg-dev
and then proceed with compiling and installing R.
If you have to compile R in your system and install you should have libx11-dev package installed in Ubunut.Can you check whether this package is installed or not.
Otherwise you can configure the source with this option as a work around solution only in the case if you are not going to use any GUI functionality in R.
./configure --with-x=no
You need to install these libraries:
sudo apt-get install -y libx11-dev \
xorg-dev \
libcurl4-openssl-dev
Then run:
./configure
make
And then it should work.
Good luck!
recently i tried to install oracle on my linux with apt (I never used yum before) using fast manual:
http://www.oracle.com/technetwork/articles/servers-storage-admin/ginnydbinstallonlinux-488779.html
And after command:
sudo yum install oracle-rdbms-server-11gR2-preinstall
I got error:
Failed: ca-certificates.noarch 0:2010.63-3.el6_1.5 chkconfig.x86_64 0:1.3.49.3-2.el6 file-libs.x86_64 0:5.04-15.el6 filesystem.x86_64 0:2.4.30-3.el6
initscripts.x86_64 0:9.03.38-1.0.1.el6_4.2
Complete!
And something gone wrong because command like: ps, top are crashing
login#Ass-K55VJ:/etc/yum/repos.d$ ps -e
ps: relocation error: ps: symbol procps_number_version, version _3_2_5 not defined in file libproc-3.2.8.so with link time reference
login#Ass-K55VJ:/etc/yum/repos.d$ top
Segmentation fault (core dumped)
then I tryied to uninstall oracle and dependencies but after command:
sudo yum remove oracle-rdbms-server-11gR2-preinstall
There was a problem importing one of the Python modules
required to run yum. The error leading to this problem was:
No module named yum
Please install a package which provides this module, or
verify that the module is installed correctly.
It's possible that the above module doesn't match the
current version of Python, which is:
2.6.6 (r266:84292, Jul 10 2013, 06:42:56) [GCC 4.4.7 20120313 (Red Hat 4.4.7-3)]
If you cannot solve this problem yourself, please go to the yum faq at: http://wiki.linux.duke.edu/YumFaq
So it seems like yum install in my system new libraries but didn't link it correctly? I dont know what do in this moment because it seems like armagedon on my ubuntu...
Does this mean you're on ubuntu and tried to install rpm packages using yum? The manual you used is for Oracle Linux 6, why would you try that on ubuntu?
rpm packages are not compatible with debian based systems like ubuntu, which use deb packages. So you've probably screwed your system big time, overwriting important system libraries with incompatible ones.
If apt-get is still working, then you can try to reinstall (apt-get --reinstall install) the equivalent libraries to the ones mentioned in the install manual you linked to - naming isn't always the same for rpm and deb packages. dpkg -l should help you see which the correct installed libraries are. I'd start with the C libraries (libc) etc.
But if apt-get is screwed also, then you'd need to download the packages manually from an ubuntu mirror and install them using dpkg, but I think a reinstall (or restore from backup if you have one) would be the best option.
I downloaded the Haskell-platform source from here: http://www.haskell.org/platform/linux.html, installed ghc, and did /.configure. However when I do sudo make, I get the following error:
Preprocessing library HUnit-1.2.4.2...
Test/HUnit/Base.hs:1:1:
Could not find module `Prelude'
Perhaps you haven't installed the profiling libraries for package `base'?
Use -v to see a list of the files searched for.
Error:
Building the HUnit-1.2.4.2 package failed
make: *** [build.stamp] Error 2
Does anyone knows how to fix this?
I'm trying to install on Ubuntu 12.04.1 LTS
Instead of trying to install from the sources, simply install the Ubuntu packages, which will be much simpler, with:
$ sudo apt-get install haskell-platform
If you need a local version of the documentation and the profiling libraries, install the additional packages with:
$ sudo apt-get install haskell-platform-doc haskell-platform-prof
Daniel Fisher's comment led me to the solution. You have to install all the profiling libraries for each of the ghc packages you have installed.
Just write
sudo apt-get install ghc*-prof
That's how it worked for me