Arch Linux User Repository

Okay, I tried rebuilding without LTO (twice for good measure). Here's the configuration summary, the only thing I changed in the pkgbuild was line 24 and removed the following: -flto=auto -fno-fat-lto-objects.

One thing I noticed was that in the config summary the -DNDEBUG flag was enabled, but I didn't do this, and apparently this is an issue according to count0's initial comment on this issue.

count0, just to make sure, is your build system fully up-to-date, and did you clear your pacman cache before doing your latest test build with the most recent pkgbuild file on the aur? I just want to make sure we can rule out everything that could by different and causing such an issue, as at this stage, I've done everything I can think of to isolate the issue and with no success, I'm guessing due to the fact that I am not an expert on C++.

If there is any other information I can provide, please let me know. According to npfeiler, apparently this issue is reproducible, though the fix he suggested didn't work for me (unless I failed to implement it properly).

================================================================================
                             CONFIGURATION SUMMARY
================================================================================
Using python version:   3.10.6
Python interpreter:     /usr/bin/python
Installation path:      /usr/lib/python3.10/site-packages/graph_tool

C++ compiler (CXX):     g++
C++ compiler version:   12.2.0

Prefix:                 /usr
Pkgconfigdir:           ${libdir}/pkgconfig

Python CPP flags:       -I/usr/lib/python3.10/site-packages/cairo/include -I/usr/include/python3.10
Python LD flags:        -L/usr/lib -lpython3.10
Boost CPP flags:        -pthread -I/usr/include
Boost LD flags:         -L/usr/lib64 -lboost_iostreams -lboost_python310 -lboost_regex -lboost_context -lboost_coroutine
Numpy CPP flags:        -I/usr/lib/python3.10/site-packages/numpy/core/include
Sparsehash CPP flags:
CGAL CPP flags:         -I/usr/include
CGAL LD flags:
Expat CPP flags:
Expat LD flags:          -lexpat
Cairomm CPP flags:      -I/usr/include/cairomm-1.0 -I/usr/lib/cairomm-1.0/include -I/usr/include/sigc++-2.0 -I/usr/lib/sigc++-2.0/include -I/usr/include/cairo -I/usr/include/lzo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-4 -pthread -I/usr/include/pixman-1
Cairomm LD flags:       -lcairomm-1.0 -lsigc-2.0 -lcairo
OpenMP compiler flags:  -fopenmp
OpenMP LD flags:
Extra CPPFLAGS:         -DNDEBUG
Extra CXXFLAGS:         -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS
Extra LDFLAGS:

Using OpenMP:           yes
Using sparsehash:       yes
Using cairo:            yes
================================================================================

Just a heads up; I fully updated arch, reinstalled graph tool and tried again, and I'm still getting the same error :/

Edit: Thanks npfeiler, I misread can as can't. I'll try disabling LTO and rebuilding, and I'll let you know what I get. Could you let me know what changes you made to the pkgbuild to disable it? Is it just -flto=false?

i can repro the issue

it doesn’t seem to happen with LTO disabled 🙈

I didn't change anything, I just rebuilt it after closing everything on my machine to free up enough RAM for LTO compilation.

In fact, here's a copy of the pkgbuild from my aur-helper cache, if that helps:

Also, just as a heads up, I fully deleted and reinstalled the package before rebuilding, but I can always try again after updating my whole system if you think it would help?

# Maintainer: Tiago de Paula Peixoto <tiago@skewed.de>

# Remove the --enable-openmp flag below if you do not want parallelization.

pkgname=python-graph-tool
pkgver=2.45
pkgrel=1
pkgdesc='A Python module for manipulation and statistical analysis of graphs'
arch=('i686' 'x86_64')
url='https://graph-tool.skewed.de'
license=(LGPL3)
depends=(boost-libs python expat python-scipy python-numpy cgal cairomm python-cairo python-zstandard python-gobject)
makedepends=(boost sparsehash autoconf-archive)
optdepends=('graphviz: graph layout'
'python-matplotlib: graph drawing')
provides=(python3-graph-tool)
conflicts=(python3-graph-tool)
replaces=(python3-graph-tool)
options=(!libtool)
source=("https://downloads.skewed.de/graph-tool/graph-tool-$pkgver.tar.bz2")
sha256sums=('f92da7accfda02b29791efe4f0b3ed93329f27232af4d3afc07c92421ec68668')
prepare() {
  cd "$srcdir/graph-tool-$pkgver"
  export CXXFLAGS="$CXXFLAGS -flto=auto -fno-fat-lto-objects"
  ./configure --enable-openmp --prefix=/usr --docdir="/usr/share/doc/$pkgname"
}

build() {
  cd "$srcdir/graph-tool-$pkgver"
  make -j 1  # most users will be surprised with the high memory usage required for parallel builds
}

check() {
  cd "$srcdir/graph-tool-$pkgver"
  make check
}

package() {
  cd "$srcdir/graph-tool-$pkgver"
  make DESTDIR="$pkgdir/" install
}

I cannot reproduce any of these errors, including the import issues — and it's entirely unclear how it could be throwing assertions in the first place without debugging being enabled during compilation, which is not by default.

Did you change anything in the PKGBUILD?

Thanks npfeiler, I got it built!

However, I'm now getting an error with the stochastic_blockmodel_dl function along the lines of the following:

/usr/include/c++/12.1.0/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.

This was from just following the documentation with the following input:

from graph_tool.all import *
g=graph_tool.collection.data["football"]
state = graph_tool.inference.minimize_blockmodel_dl(g)

If I don't run it with "graph_tool.inference", it says there is no attribute matching minimize_blockmodel_dl, though the documentation does not mention this, though I guess this is either an oversight, or an issue with needing to run import on the inference submodule. Regardless, that's not the issue.

Seems like another C++ problem? However, it built just fine with the current pkgbuild, so I'm not sure what's up.

I'll try closing everything before building; if that still fails, do I disable LTO in the pkgbuild?

I assume you run out of ram.
You could try to free some beforehand, or disable LTO.

Hi, I'm currently getting a build error of the following:

/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use <iterator> instead.' 10 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ CXXLD libgraph_tool_inference.la g++: fatal error: Killed signal terminated program lto1 compilation terminated. lto-wrapper: fatal error: g++ returned 1 exit status compilation terminated. /usr/bin/ld: error: lto-wrapper failed collect2: error: ld returned 1 exit status make[1]: [Makefile:3335: libgraph_tool_inference.la] Error 1 make[1]: Leaving directory '~/.cache/paru/clone/python-graph-tool/src/graph-tool-2.45' make: [Makefile:2051: all] Error 2 ==> ERROR: A failure occurred in build(). Aborting...

It occurred when building /src/graph/inference/graph_modularity.cc:18, apparently.

Anything I can do to help diagnose this?

@rommedahl Fixed, thanks!