graph-tool issueshttps://git.skewed.de/count0/graph-tool/-/issues2017-07-26T11:47:49Zhttps://git.skewed.de/count0/graph-tool/-/issues/388Error installing on ubuntu 17.04/amd642017-07-26T11:47:49ZGleb ChipigaError installing on ubuntu 17.04/amd64Add to `/etc/apt/sources.list`
```
deb http://downloads.skewed.de/apt/zesty zesty universe
#deb-src http://downloads.skewed.de/apt/zesty zesty universe
```
Execute
```
sudo aptitude install -y python3-graph-tool
```
Got error:
...Add to `/etc/apt/sources.list`
```
deb http://downloads.skewed.de/apt/zesty zesty universe
#deb-src http://downloads.skewed.de/apt/zesty zesty universe
```
Execute
```
sudo aptitude install -y python3-graph-tool
```
Got error:
```
The following packages have unsatisfied dependencies:
...
python3-graph-tool : Depends: libcgal11v5 which is a virtual package and is not provided by any available package
```https://git.skewed.de/count0/graph-tool/-/issues/310Ubuntu 16.042017-10-06T14:40:04ZCogumelos MaravilhaUbuntu 16.04For when a version to use on 16.04?
Thanks in advance.For when a version to use on 16.04?
Thanks in advance.https://git.skewed.de/count0/graph-tool/-/issues/749Graph tool has unmet dependencies on Google Colab2023-02-17T08:53:14ZZake ChenGraph tool has unmet dependencies on Google ColabWhen trying to initialise graph tool on Google colab, it comes up with this error about broken packages.
```
The following packages have unmet dependencies:
python3-graph-tool : Depends: libboost-context1.65.1 but it is not installable...When trying to initialise graph tool on Google colab, it comes up with this error about broken packages.
```
The following packages have unmet dependencies:
python3-graph-tool : Depends: libboost-context1.65.1 but it is not installable
Depends: libboost-iostreams1.65.1 but it is not installable
Depends: libboost-python1.65.1 but it is not installable
Depends: libboost-regex1.65.1 but it is not installable
Recommends: libgv-python but it is not installable
Recommends: python-matplotlib but it is not installable
Recommends: python-cairo but it is not going to be installed
Recommends: python-gi-cairo but it is not going to be installed
Recommends: python-gi but it is not going to be installed
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:55
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:55
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:67
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:67
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:68
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:68
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:69
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:69
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:70
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:70
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:71
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:54 and /etc/apt/sources.list:71
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:56 and /etc/apt/sources.list:57
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:56 and /etc/apt/sources.list:57
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:56 and /etc/apt/sources.list:58
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:56 and /etc/apt/sources.list:58
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:63 and /etc/apt/sources.list:64
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:63 and /etc/apt/sources.list:64
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:63 and /etc/apt/sources.list:66
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:63 and /etc/apt/sources.list:66
E: Unable to correct problems, you have held broken packages.
```https://git.skewed.de/count0/graph-tool/-/issues/464python3-graph-tool not installable on Ubuntu 18.04 because incorrect dependen...2018-07-02T14:51:50ZClovis Gladstonepython3-graph-tool not installable on Ubuntu 18.04 because incorrect dependenciesI am unable to install graph-tool on Ubuntu 18.04. There's an issue with dependencies. Ubuntu 18.04 comes with libboost 1.65.1. Here's the output I get:
```
The following packages have unmet dependencies:
python3-graph-tool : Depends: ...I am unable to install graph-tool on Ubuntu 18.04. There's an issue with dependencies. Ubuntu 18.04 comes with libboost 1.65.1. Here's the output I get:
```
The following packages have unmet dependencies:
python3-graph-tool : Depends: libboost-graph1.65.0 but it is not installable
Depends: libboost-iostreams1.65.0 but it is not installable
Depends: libboost-python1.65.0 but it is not installable
Depends: libboost-system1.65.0 but it is not installable
Depends: libboost-thread1.65.0 but it is not installable
Depends: libboost-regex1.65.0 but it is not installable
Depends: libcgal12 but it is not installable
Recommends: python3-matplotlib but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
```https://git.skewed.de/count0/graph-tool/-/issues/159make's DESTDIR not set when using 'configure --prefix='2017-10-15T02:48:34ZTiago Peixotomake's DESTDIR not set when using 'configure --prefix='Hi,
I was trying to install graph-tool into a user specified directory (without cairo if that is important):
```text
./configure --prefix=$MYDIR --disable-cairo && make && make install
```
However ```make install``` fails while tryin...Hi,
I was trying to install graph-tool into a user specified directory (without cairo if that is important):
```text
./configure --prefix=$MYDIR --disable-cairo && make && make install
```
However ```make install``` fails while trying to install into the system default directory:
```text
Making install in src
make[1]: Entering directory `....../graph-tool-2.2.23/src'
Making install in graph
make[2]: Entering directory `....../graph-tool-2.2.23/src/graph'
Making install in centrality
make[3]: Entering directory `....../graph-tool-2.2.23/src/graph/centrality'
make[4]: Entering directory `....../graph-tool-2.2.23/src/graph/centrality'
make[4]: Nothing to be done for `install-exec-am'.
echo /bin/mkdir -p '/usr/lib/python2.7/site-packages/graph_tool/centrality'
/bin/mkdir: cannot create directory `/usr/lib/python2.7/site-packages': Permission denied
make[4]: *** [install-libgraph_tool_centralityLTLIBRARIES] Error 1
```
Resolved by manually specifying ```DESTDIR```:
```text
make DESTDIR=$MYDIR install
```
System:
```text
Linux 3.2.0-4-amd64 #1 SMP Debian 3.2.32-1 x86_64 GNU/Linux
GNU Make 3.81
automake (GNU automake) 1.11.6
gcc (Debian 4.7.2-4) 4.7.2
```https://git.skewed.de/count0/graph-tool/-/issues/741Assertion error running blockmodel inference after system update2023-02-19T19:35:51ZHerlander LimaAssertion error running blockmodel inference after system updateHello,
I am running graph-tool 2.45-1 installed from the AUR, with python 3.10.7.
After updating my system I get an error every time I ran functions for sbm inference.
Running the following script
```
from graph_tool.all import *
g = ...Hello,
I am running graph-tool 2.45-1 installed from the AUR, with python 3.10.7.
After updating my system I get an error every time I ran functions for sbm inference.
Running the following script
```
from graph_tool.all import *
g = collection.data["football"]
state = minimize_blockmodel_dl(g)
```
I get
```
/usr/include/c++/12.2.0/bits/stl_vector.h:1123: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = std::tuple<std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> > >; _Alloc = std::allocator<std::tuple<std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> > > >; reference = std::tuple<std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> > >&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
Aborted (core dumped)
```
The gdb backtrace for the script
```
Starting program: /usr/bin/python test.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib/libthread_db.so.1".
[Detaching after vfork from child process 324076]
[Detaching after vfork from child process 324077]
Error while mapping shared library sections:
`/usr/lib': not in executable format: file format not recognized
Program received signal SIGABRT, Aborted.
0x00007ffff78a149c in ?? () from /usr/lib/libc.so.6
#0 0x00007ffff78a149c in () at /usr/lib/libc.so.6
#1 0x00007ffff7851958 in raise () at /usr/lib/libc.so.6
#2 0x00007ffff783b53d in abort () at /usr/lib/libc.so.6
#3 0x00007fffd1cd2112 in std::__glibcxx_assert_fail(char const*, int, char const*, char const*)
(file=<optimized out>, line=<optimized out>, function=<optimized out>, condition=<optimized out>) at /usr/src/debug/gcc/libstdc++-v3/src/c++11/debug.cc:60
#4 0x00007fffc2dba710 in ()
at /usr/lib/python3.10/site-packages/graph_tool/inference/libgraph_tool_inference.so
#5 0x00007fffc3317f0e in ()
at /usr/lib/python3.10/site-packages/graph_tool/inference/libgraph_tool_inference.so
#6 0x00007fffc331a358 in ()
at /usr/lib/python3.10/site-packages/graph_tool/inference/libgraph_tool_inference.so
#7 0x00007fffc331dca0 in ()
at /usr/lib/python3.10/site-packages/graph_tool/inference/libgraph_tool_inference.so
#8 0x00007fffc32e64fc in do_multilevel_mcmc_sweep(boost::python::api::object, boost::python::api::object, pcg_detail::extended<(unsigned char)10, (unsigned char)16, pcg_detail::engine<unsigned long, unsigned __int128, pcg_detail::xsl_rr_mixin<unsigned long, unsigned __int128>, false, pcg_detail::specific_stream<unsigned __int128>, pcg_detail::default_multiplier<unsigned __int128> >, pcg_detail::engine<unsigned long, unsigned long, pcg_detail::rxs_m_xs_mixin<unsigned long, unsigned long>, true, pcg_detail::oneseq_stream<unsigned long>, pcg_detail::default_multiplier<unsigned long> >, true>&) ()
at /usr/lib/python3.10/site-packages/graph_tool/inference/libgraph_tool_inference.so
#9 0x00007fffc2eebb01 in ()
at /usr/lib/python3.10/site-packages/graph_tool/inference/libgraph_tool_inference.so
#10 0x00007fffd474cab2 in boost::python::objects::function::call(_object*, _object*) const () at /usr/lib/libboost_python310.so.1.80.0
#11 0x00007fffd474ce8d in () at /usr/lib/libboost_python310.so.1.80.0
#12 0x00007fffd474b263 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const () at /usr/lib/libboost_python310.so.1.80.0
#13 0x00007fffd282f948 in ()
at /usr/lib/python3.10/site-packages/graph_tool/libgraph_tool_core.so
#14 0x00007fffd282f918 in ()
at /usr/lib/python3.10/site-packages/graph_tool/libgraph_tool_core.so
#15 0x00007fffd282f8e8 in ()
at /usr/lib/python3.10/site-packages/graph_tool/libgraph_tool_core.so
#16 0x00007fffd4749dd1 in boost::python::handle_exception_impl(boost::function0<void>) () at /usr/lib/libboost_python310.so.1.80.0
#17 0x00007fffd4749ef7 in () at /usr/lib/libboost_python310.so.1.80.0
#18 0x00007ffff7b5024b in _PyObject_MakeTpCall ()
at /usr/lib/libpython3.10.so.1.0
#19 0x00007ffff7b4b58e in _PyEval_EvalFrameDefault ()
at /usr/lib/libpython3.10.so.1.0
#20 0x00007ffff7b56e29 in _PyFunction_Vectorcall ()
at /usr/lib/libpython3.10.so.1.0
#21 0x00007ffff7b465ba in _PyEval_EvalFrameDefault ()
at /usr/lib/libpython3.10.so.1.0
#22 0x00007ffff7b56e29 in _PyFunction_Vectorcall ()
at /usr/lib/libpython3.10.so.1.0
#23 0x00007ffff7b62c97 in PyObject_Call () at /usr/lib/libpython3.10.so.1.0
#24 0x00007ffff7b48c05 in _PyEval_EvalFrameDefault ()
at /usr/lib/libpython3.10.so.1.0
#25 0x00007ffff7b622b6 in () at /usr/lib/libpython3.10.so.1.0
#26 0x00007ffff7b62c97 in PyObject_Call () at /usr/lib/libpython3.10.so.1.0
#27 0x00007ffff7b48c05 in _PyEval_EvalFrameDefault ()
at /usr/lib/libpython3.10.so.1.0
#28 0x00007ffff7b56e29 in _PyFunction_Vectorcall ()
at /usr/lib/libpython3.10.so.1.0
#29 0x00007ffff7b46186 in _PyEval_EvalFrameDefault ()
at /usr/lib/libpython3.10.so.1.0
#30 0x00007ffff7b44dd0 in () at /usr/lib/libpython3.10.so.1.0
#31 0x00007ffff7bf3fb4 in PyEval_EvalCode () at /usr/lib/libpython3.10.so.1.0
#32 0x00007ffff7c039d3 in () at /usr/lib/libpython3.10.so.1.0
#33 0x00007ffff7bff36a in () at /usr/lib/libpython3.10.so.1.0
#34 0x00007ffff7aa273c in () at /usr/lib/libpython3.10.so.1.0
#35 0x00007ffff7aa23ed in _PyRun_SimpleFileObject ()
at /usr/lib/libpython3.10.so.1.0
#36 0x00007ffff7aa2da0 in _PyRun_AnyFileObject ()
at /usr/lib/libpython3.10.so.1.0
#37 0x00007ffff7c102ad in Py_RunMain () at /usr/lib/libpython3.10.so.1.0
#38 0x00007ffff7be547b in Py_BytesMain () at /usr/lib/libpython3.10.so.1.0
#39 0x00007ffff783c290 in () at /usr/lib/libc.so.6
#40 0x00007ffff783c34a in __libc_start_main () at /usr/lib/libc.so.6
#41 0x0000555555555045 in _start ()
```
Thanks in advance,
Herlanderhttps://git.skewed.de/count0/graph-tool/-/issues/724Importing graph_tool.all breaks argparse2021-11-30T12:53:25ZOleg PlatonovImporting graph_tool.all breaks argparseHi! I've come across this really weird behaviour: importing `graph_tool.all` leads to argparse ignoring some arguments.
Here is a simple example. I have a script `example.py` with the following code:
```python
import argparse
import gr...Hi! I've come across this really weird behaviour: importing `graph_tool.all` leads to argparse ignoring some arguments.
Here is a simple example. I have a script `example.py` with the following code:
```python
import argparse
import graph_tool.all as gt
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--name', type=str)
args = parser.parse_args()
print(args.name)
```
If I run it like this `python example.py --name test` it prints `None`. Removing the line `import graph_tool.all as gt` fixes the issue: running the script prints `test` as expected. Renaming the argument from `name` to something else also fixes the issue. I have no idea why this is happening.
OS: Ubuntu 18.04.5
Python version: 3.9.5https://git.skewed.de/count0/graph-tool/-/issues/657Missing Ubuntu focal distribution2020-05-07T23:38:24ZMatteo ZanellaMissing Ubuntu focal distributionA distribution for the new Ubuntu 20.04 LTS Focal Fossa is missingA distribution for the new Ubuntu 20.04 LTS Focal Fossa is missinghttps://git.skewed.de/count0/graph-tool/-/issues/651Choppy video of a mobile network2020-04-20T23:04:49ZLex FridmanChoppy video of a mobile networkI am creating a video of a mobile network (graph). For this case, they are following a simple mobility model: everyone moves right a small amount at every time step. Each image is written to file and loaded back in and written to video (...I am creating a video of a mobile network (graph). For this case, they are following a simple mobility model: everyone moves right a small amount at every time step. Each image is written to file and loaded back in and written to video (via OpenCV).
As far as I can tell the layout is turned off, but their movement is strangely choppy, plus their y-position changes a bit too. The resulting video of 1,000 steps is attached.
The drawing code for one frame is as follows:
```
gt.graph_draw(g,
g.vp.locs, # i thought this enforces node position & turns off layout
vertex_size = 10,
vertex_pen_width = 0.8, # default is 0.8
vertex_color = color['black'], # vertex stroke color
vertex_fill_color = color['red'],
edge_color = color['white'],
edge_pen_width = 0.8, # default is 1
vertex_anchor = 0,
bg_color = color['black'],
output_size = [iw, ih],
adjust_aspect = False,
output = img_out_path)
img = cm.imread(img_out_path) # this is my image reading function
```
[graph.mkv](/uploads/2dd18640876fbd8248c3b0bb639db48c/graph.mkv)
In addition, if I try to set `fit_view = False` to test if that fixes things I get the following error:
```
File "/usr/lib/python3/dist-packages/graph_tool/draw/cairo_draw.py", line 1146, in graph_draw
x, y, zoom = x, y, 1
UnboundLocalError: local variable 'x' referenced before assignment
```https://git.skewed.de/count0/graph-tool/-/issues/624Feature Request: Edge weights to SIRS models2020-04-01T20:08:30ZjamesruffleFeature Request: Edge weights to SIRS modelsDear Tiago / @count0 ,
Please could you include the ability to pass edge weights as edge property maps to the dynamic models, including SIS and SIRS models.
Furthermore, is it possible to pass multiple edge weights as multiple edge pro...Dear Tiago / @count0 ,
Please could you include the ability to pass edge weights as edge property maps to the dynamic models, including SIS and SIRS models.
Furthermore, is it possible to pass multiple edge weights as multiple edge property maps to these models? In a similar way that your stochastic block models can with state_args=dict(recs=...) ?
Thank you for your time,
Jameshttps://git.skewed.de/count0/graph-tool/-/issues/580Compilation fails "graph_sfdp.cc:55:68: error: call of overloaded ‘any_cast<g...2019-06-20T22:01:46ZMarkus OehmeCompilation fails "graph_sfdp.cc:55:68: error: call of overloaded ‘any_cast<group_map_t>(boost::python::extract<boost::any>)’ is ambiguous"- [x] Are you running the latest `graph-tool` version?
- [x] Do you observe the problem with the current git version?
- [x] Did you compile `graph-tool` manually?
- [x] If you answered yes above, did you use the exact same compiler to bu...- [x] Are you running the latest `graph-tool` version?
- [x] Do you observe the problem with the current git version?
- [x] Did you compile `graph-tool` manually?
- [x] If you answered yes above, did you use the exact same compiler to build `graph-tool`, `boost-python` and `Python`?
When building graph-tool with gcc-9.1.0 I encounter the following error:
```
graph_sfdp.cc:55:68: error: call of overloaded ‘any_cast<group_map_t>(boost::python::extract<boost::any>)’ is ambiguous
```
I'm using Gentoo ~amd64. The complete
[build log](/uploads/bf6610128225b087f5e3efe45895b866/graph-tool-9999_20190526-192119.log) as well as the corresponding [config.log](/uploads/958ef5d41c763fe825e19eec51030df0/config.log) are attached. That should cover all essential information, if not please let me know.https://git.skewed.de/count0/graph-tool/-/issues/576latest release doesn't compile with clang-8.02019-08-22T17:32:34ZMark Molllatest release doesn't compile with clang-8.0# Bug reports:
## Please follow the general troubleshooting steps first:
- [X] Are you running the latest `graph-tool` version?
- [ ] Do you observe the problem with the current git version?
- [X] Are you using Macports or Homebrew? If...# Bug reports:
## Please follow the general troubleshooting steps first:
- [X] Are you running the latest `graph-tool` version?
- [ ] Do you observe the problem with the current git version?
- [X] Are you using Macports or Homebrew? If yes, please submit an issue there instead: https://github.com/Homebrew/brew/issues and https://trac.macports.org/newticket
- [ ] Did you compile `graph-tool` manually?
- [ ] If you answered yes above, did you use the exact same compiler to build `graph-tool`, `boost-python` and `Python`?
Please replace this section with a brief summary of your issue.
## Do **not** forget to supply the following information:
- [X] **A _minimal_ and _self-contained_ example that shows the problem.**
- [X] Your operating system.
- [X] The Python version you are using.
- [ ] If you compiled graph-tool manually: Your compiler version, as well as the version of Boost being used.
- [ ] If you are reporting a compilation error, please provide the **entire** `./configure` output, as well as the **entire** contents of the `config.log` file and the **entire** compilation output.
I have locally added a clang8.0 variant to my py-graph-tool port in MacPorts. I get this error:
```
:info:build In file included from graph_closeness.cc:18:
:info:build In file included from ../../../src/graph/graph_filtering.hh:21:
:info:build In file included from ../../../src/graph/graph.hh:23:
:info:build In file included from /opt/local/include/boost/python/object.hpp:9:
:info:build In file included from /opt/local/include/boost/python/object_core.hpp:14:
:info:build In file included from /opt/local/include/boost/python/call.hpp:15:
:info:build In file included from /opt/local/include/boost/python/converter/arg_to_python.hpp:10:
:info:build In file included from /opt/local/include/boost/python/to_python_indirect.hpp:10:
:info:build In file included from /opt/local/include/boost/python/object/pointer_holder.hpp:14:
:info:build In file included from /opt/local/include/boost/python/instance_holder.hpp:11:
:info:build In file included from /opt/local/include/boost/python/type_id.hpp:14:
:info:build In file included from /opt/local/libexec/llvm-8.0/bin/../include/c++/v1/ostream:138:
:info:build In file included from /opt/local/libexec/llvm-8.0/bin/../include/c++/v1/ios:216:
:info:build In file included from /opt/local/libexec/llvm-8.0/bin/../include/c++/v1/__locale:15:
:info:build In file included from /opt/local/libexec/llvm-8.0/bin/../include/c++/v1/string:505:
:info:build In file included from /opt/local/libexec/llvm-8.0/bin/../include/c++/v1/string_view:176:
:info:build In file included from /opt/local/libexec/llvm-8.0/bin/../include/c++/v1/__string:57:
:info:build /opt/local/libexec/llvm-8.0/bin/../include/c++/v1/algorithm:2494:5: error: static_assert failed due to requirement '__is_forward_iterator<boost::adj_list<unsigned long>::edge_iterator>::value' "std::max_element requires a ForwardIterator"
:info:build static_assert(__is_forward_iterator<_ForwardIterator>::value,
:info:build ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:info:build ../../../src/graph/graph_adjacency.hh:452:26: note: in instantiation of function template specialization 'std::__1::max_element<boost::adj_list<unsigned long>::edge_iterator, (lambda at ../../../src/graph/graph_adjacency.hh:453:38)>' requested here
:info:build auto iter = std::max_element(erange.first, erange.second,
:info:build ^
:info:build ../../../src/graph/graph.hh:109:33: note: in instantiation of member function 'boost::adj_list<unsigned long>::shrink_to_fit' requested here
:info:build void shrink_to_fit() { _mg->shrink_to_fit(); }
:info:build ^
:info:build 2 warnings and 1 error generated.
```
I am using Boost 1.69, Python 3.7, Clang 8.0.
[main.log](/uploads/d4308e70d87ff25f1ed61c901232bbfd/main.log)
[config.log](/uploads/8135985a615b34b7f0e546d8badf416c/config.log)https://git.skewed.de/count0/graph-tool/-/issues/554Please support simultaneous custom Boost and CGAL2020-04-01T20:08:30ZJeff TrullPlease support simultaneous custom Boost and CGAL## Summary: CGAL check in configure does not consider custom Boost builds
- [X] Are you running the latest `graph-tool` version?
- [X] Do you observe the problem with the current git version?
- [ ] Are you using Macports or Homebrew? If...## Summary: CGAL check in configure does not consider custom Boost builds
- [X] Are you running the latest `graph-tool` version?
- [X] Do you observe the problem with the current git version?
- [ ] Are you using Macports or Homebrew? If yes, please submit an issue there instead: https://github.com/Homebrew/brew/issues and https://trac.macports.org/newticket
- [X] Did you compile `graph-tool` manually?
- [X] If you answered yes above, did you use the exact same compiler to build `graph-tool`, `boost-python` and `Python`?
*I didn't build Python but it was built with gcc 8.2.0 as well* (per `sys.version`)
The same program `configure` uses to determine if CGAL is properly installed does not pass along `BOOST_LDFLAGS` and in particular `-L/path/to/boost/lib`. As a result, if CGAL was built with a custom Boost version you can get link errors.
The following patch fixes the problem for me:
```
diff --git a/m4/ax_lib_cgal_core.m4 b/m4/ax_lib_cgal_core.m4
index 24d25aaa..bb193831 100644
--- a/m4/ax_lib_cgal_core.m4
+++ b/m4/ax_lib_cgal_core.m4
@@ -60,7 +60,7 @@ for ac_cgal_iterate in $ac_cgal_dirs ; do
CGAL_LDFLAGS="-L$ac_cgal_iterate/lib -lCGAL -lCGAL_Core -lgmp ${BOOST_THREAD_LIB}"
LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $CGAL_LDFLAGS"
+ LDFLAGS="$LDFLAGS $CGAL_LDFLAGS $BOOST_LDFLAGS"
```
I don't know if it's correct in general, though.
## Do **not** forget to supply the following information:
- [ ] **A _minimal_ and _self-contained_ example that shows the problem.**
- [X] Your operating system.
Ubuntu 18.10
- [X] The Python version you are using.
3.7.1
- [X] If you compiled graph-tool manually: Your compiler version, as well as the version of Boost being used.
gcc 8.2.0 and Boost 1.68.0
- [X] If you are reporting a compilation error, please provide the **entire** `./configure` output, as well as the **entire** contents of the `config.log` file and the **entire** compilation output.
Do not forget to add code snippets and error messages using [Markdown](/help/user/markdown.md), i.e.
```
./configure --with-boost=/media/jet/71c9e7fc-0208-49dd-89d0-6b357bdeec64/boost_1_68_0/installed -with-cgal=/media/jet/71c9e7fc-0208-49dd-89d0-6b357bdeec64/CGAL-4.13/installed
...
checking whether CGAL is available in /media/jet/71c9e7fc-0208-49dd-89d0-6b357bdeec64/CGAL-4.13/installed... no
configure: error: CGAL library not found.
```
configure output and config.log attached; there is no compilation output.[configure_output](/uploads/c92ca3c88f01f697bdcb6e04cf8c4eb6/configure_output)[config.log](/uploads/9694953f54dff3973c1a1ef22a4b4277/config.log)https://git.skewed.de/count0/graph-tool/-/issues/436Homebrew formula not maintained by anyone (Installation Instructions)2018-04-30T11:30:58ZVas SudanaguntaHomebrew formula not maintained by anyone (Installation Instructions)https://git.skewed.de/count0/graph-tool/wikis/installation-instructions
instructions for homebrew install currently are:
```
brew tap homebrew/science
brew install graph-tool
```
But the homebrew/science list was deprecated. It appear...https://git.skewed.de/count0/graph-tool/wikis/installation-instructions
instructions for homebrew install currently are:
```
brew tap homebrew/science
brew install graph-tool
```
But the homebrew/science list was deprecated. It appears the graph-tool formula was migrated to brewsci/science. But submitting an issue to them asking them to fix the tap results in this message:
> This tap is not maintained. Please consider opening a pull request to migrate this formula to Homebrew/core or a different tap within the [Brewsci organization](https://github.com/brewsci). Please open an issue if you are interested in creating and maintaining a new tap within the Brewsci organization.
>
> # Hosting Your Own Tap
>
> Anyone can host their own tap. See [Interesting Taps & Forks](https://docs.brew.sh/Interesting-Taps-and-Forks.html) and [How to Create and Maintain a Tap](https://docs.brew.sh/How-to-Create-and-Maintain-a-Tap.html)
https://git.skewed.de/count0/graph-tool/-/issues/378Request for feature: Ordering vertices on NSBM plot2017-10-31T16:36:00ZTimRequest for feature: Ordering vertices on NSBM plotorder the vertices on the rim of a NSBM plot such that the labels, say, as integers, of two neighboring vertices are as close as possible. For example, if I have 5 vertices, I'd like them to be ordered 0-1-2-3-4 on the NSBM plot.order the vertices on the rim of a NSBM plot such that the labels, say, as integers, of two neighboring vertices are as close as possible. For example, if I have 5 vertices, I'd like them to be ordered 0-1-2-3-4 on the NSBM plot.https://git.skewed.de/count0/graph-tool/-/issues/343Compiling graphtool on debian jessie with clang 3.52017-10-03T07:11:55ZrpiotaixCompiling graphtool on debian jessie with clang 3.5I'm trying to compile graphtool on debian Jessie for Python3.
Here are the commands used:
```bash
apt install git clang libboost-all-dev libexpat-dev python3-scipy libcgal-dev libsparsehash-dev python3-cairo-dev libcairomm-1.0-dev autom...I'm trying to compile graphtool on debian Jessie for Python3.
Here are the commands used:
```bash
apt install git clang libboost-all-dev libexpat-dev python3-scipy libcgal-dev libsparsehash-dev python3-cairo-dev libcairomm-1.0-dev automake
git clone https://git.skewed.de/count0/graph-tool.git
cd graph-tool
git checkout release-2.18
LANG=C LC_CTYPE=C ./autogen.sh
PYTHON=python3 CC=clang CXX=clang++ ./configure
make -j 4
```
Here is the output from the last 3 commands: [graphtool_compile_output.txt](/uploads/3649766b3cd6dcccde738936595ecb2f/graphtool_compile_output.txt)
Any idea on what happens? Maybe bump the required version of clang to over 3.5 instead of 3.4?https://git.skewed.de/count0/graph-tool/-/issues/325Error In state.copy with layered nested block model2017-09-20T15:01:22ZAlexander CrowellError In state.copy with layered nested block modelI'm having some trouble adapting the example on edge covariates with nested block models. The example code runs fine for my graph in the non-nested case and the initial minimization runs in the nested case:
```
>>> state = gt.minimi...I'm having some trouble adapting the example on edge covariates with nested block models. The example code runs fine for my graph in the non-nested case and the initial minimization runs in the nested case:
```
>>> state = gt.minimize_nested_blockmodel_dl(g2, deg_corr=False, layers=True, state_args=dict(ec=g2.ep.e_weight2, layers=False))
>>> state
<NestedBlockState object, with base \<LayeredBlockState object with 6 blocks, 164 edge covariates, for graph <Graph object, undirected, with 66 vertices and 2145 edges at 0x1114f8cd0>, at 0x12ae51a10>, and 2 levels of sizes [(66, 6), (6, 1)] at 0x129abcad0>
```
However the mcmc equilibration returns:
```
>>> gt.mcmc_equilibrate(state, wait=10000, nbreaks=4, mcmc_args=dict(niter=10),verbose=True)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/site-packages/graph_tool/inference/mcmc.py", line 120, in mcmc_equilibrate
delta, nmoves = state.mcmc_sweep(**mcmc_args)
File "/usr/local/lib/python2.7/site-packages/graph_tool/inference/nested_blockmodel.py", line 538, in mcmc_sweep
return self._h_sweep(lambda s, **a: s.mcmc_sweep(**a), c=c, **kwargs)
File "/usr/local/lib/python2.7/site-packages/graph_tool/inference/nested_blockmodel.py", line 462, in _h_sweep
get_entropy_args(eargs))
File "/usr/local/lib/python2.7/site-packages/graph_tool/inference/blockmodel.py", line 588, in _couple_state
self._state.couple_state(state._state, entropy_args)
AttributeError: 'graph_tool::Layers<graph_tool::BlockState<boost::U' object has no attribute 'couple_state'
```
I thought this may have to do with the `base_type = LayeredBlockState` parameter specified in the docs, however `minimize_nested_blockmodel_dl` doesn't accept it as a kwarg so I'm not sure if this is a bug or me just failing to understand how to properly specify that the nested block state should inherit from the layered block state. Thanks very much!Tiago PeixotoTiago Peixotohttps://git.skewed.de/count0/graph-tool/-/issues/291Error: renderer for pdf is unavailable (graphviz_draw)2017-10-06T14:40:05ZAndrewError: renderer for pdf is unavailable (graphviz_draw)See: http://graph-tool.skewed.narkive.com/BALintyF/graph-tool-can-t-find-graphviz-renderer
I'm in ubuntu 14.04. Originally I installed graphviz through the ubuntu repos with `apt-get` and `graphviz_draw` worked fine with pdf's. I remo...See: http://graph-tool.skewed.narkive.com/BALintyF/graph-tool-can-t-find-graphviz-renderer
I'm in ubuntu 14.04. Originally I installed graphviz through the ubuntu repos with `apt-get` and `graphviz_draw` worked fine with pdf's. I removed my installation of graphviz and built from source and I get the same error mentioned in the post. The fix works, although its in 'graphviz_draw.py' not '__init__.py'. Tiago PeixotoTiago Peixotohttps://git.skewed.de/count0/graph-tool/-/issues/266dyld: lazy symbol binding failed2017-10-06T14:40:05ZIandyld: lazy symbol binding failedThis is on OS X, possibly related to the boost 1.60 problems (https://github.com/Homebrew/homebrew-science/issues/3237). After reinstalling graph-tool dependencies and graph-tool from HEAD, I got the following runtime error message on a ...This is on OS X, possibly related to the boost 1.60 problems (https://github.com/Homebrew/homebrew-science/issues/3237). After reinstalling graph-tool dependencies and graph-tool from HEAD, I got the following runtime error message on a call to `pyplot.savefig` after using `graph_tool.draw.graph_draw` with mplfig:
```
dyld: lazy symbol binding failed: Symbol not found: __ZN10graph_tool6detail15action_dispatchIN5boost6lambda14lambda_functorINS3_19lambda_functor_baseINS3_12other_actionINS3_17assignment_actionEEENS2_6tuples5tupleINS4_INS3_8identityIRmEEEENS4_INS5_INS3_6actionILi2ENS3_15function_actionILi2EmEEEENSA_IKNS_15HardNumVerticesEKNS4_INS3_11placeholderILi1EEEEENS9_9null_typeESP_SP_SP_SP_SP_SP_SP_EEEEEESP_SP_SP_SP_SP_SP_SP_SP_EEEEEEN4mpl_5bool_ILb0EEEJNS0_15all_graph_viewsEEEC1ERKS10_
Referenced from: /usr/local/lib/python3.5/site-packages/graph_tool/libgraph_tool_core.so
Expected in: flat namespace
dyld: Symbol not found: __ZN10graph_tool6detail15action_dispatchIN5boost6lambda14lambda_functorINS3_19lambda_functor_baseINS3_12other_actionINS3_17assignment_actionEEENS2_6tuples5tupleINS4_INS3_8identityIRmEEEENS4_INS5_INS3_6actionILi2ENS3_15function_actionILi2EmEEEENSA_IKNS_15HardNumVerticesEKNS4_INS3_11placeholderILi1EEEEENS9_9null_typeESP_SP_SP_SP_SP_SP_SP_EEEEEESP_SP_SP_SP_SP_SP_SP_SP_EEEEEEN4mpl_5bool_ILb0EEEJNS0_15all_graph_viewsEEEC1ERKS10_
Referenced from: /usr/local/lib/python3.5/site-packages/graph_tool/libgraph_tool_core.so
Expected in: flat namespace
```
The only warning I got during compilation with Homebrew was:
```
Warning: homebrew/science/graph-tool dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
🍺 /usr/local/Cellar/graph-tool/HEAD: 250 files, 202M, built in 27 minutes 28 seconds
```
But I'm pretty sure I've seen that before.https://git.skewed.de/count0/graph-tool/-/issues/239Cairo-Error when attempting ARF layout of graph2017-10-06T14:40:07ZTianCairo-Error when attempting ARF layout of graphHello,
I am currently facing a problem similar to the one reported a few months ago (Crash when generating arf_layout for a directed twitter network). Plotting other layouts such as SFDP or radial work fine, but when attempting the AR...Hello,
I am currently facing a problem similar to the one reported a few months ago (Crash when generating arf_layout for a directed twitter network). Plotting other layouts such as SFDP or radial work fine, but when attempting the ARF layout on some graphs, I am receiving the error shown below. I am not too sure when this error occurs, because the ARF layout does work for some graphs. I have attached one example which is not working for me.
Error message:
```python
Traceback (most recent call last):
File "graph_layout.py", line 17, in <module>
graph_draw(g, pos=arf_layout(g, max_iter=0), output="graph-arf.png")
File "/home/tl393/anaconda/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.py", line 1015, in graph_draw
cr.translate(offset[0], offset[1])
cairo.Error: invalid matrix (not invertible)
```
Files:
[graph.xml](https://git.skewed.de/count0/graph-tool/uploads/08212ab01149f9af66dcb13bc006abf9/graph.xml)
[graph_layout.py](https://git.skewed.de/count0/graph-tool/uploads/946791a76965d9e6bf16e051e5c1ab08/graph_layout.py)
Tiago PeixotoTiago Peixoto