graph_triangulation.cc:55:61: fatal error: CGAL/Periodic_3_Delaunay_triangulation_traits_3.h: No such file or directory

graph-tool
#1

Running `make` on the github version of graph-tool returns an error stating
(it runs for a while first):

graph_triangulation.cc:55:61: fatal error:
CGAL/Periodic_3_Delaunay_triangulation_traits_3.h: No such file or directory
compilation terminated.
make[4]: *** [graph_triangulation.lo] Error 1
make[4]: Leaving directory `/home/pmj27/git/graph-tool/src/graph/generation'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/pmj27/git/graph-tool/src/graph'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/pmj27/git/graph-tool/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/pmj27/git/graph-tool'
make: *** [all] Error 2

Does anybody know what this is caused by?

Best,

Philipp

#2

It is impossible to tell without you giving the usual necessary information:
CGAL version, output of config.log, etc.

#3

running dpkg -s libcgal-dev returns:
Package: libcgal-dev
Status: install ok config.log
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026812/config.log&gt;
installed
Priority: optional
Section: libdevel
Installed-Size: 26244
Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com>
Architecture: amd64
Source: cgal
Version: 4.2-5ubuntu1
Depends: libcgal10 (= 4.2-5ubuntu1), libboost-dev, libboost-thread-dev,
libboost
-system-dev, libboost-program-options-dev, libgmp10-dev, libmpfr-dev,
zlib1g-dev

I didn't realise config.log played a role for make. It is now attached. It
shows a few errors at the beginning but, to me, looked like it happily ran
to completion. Am I missing something in there?
config.log
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026812/config.log&gt;

#4

I should maybe add that on this system I was already running a version of
graph-tool compiled from source (2.14dev, I think) which I wanted to update.

#5

Is there anybody who knows what the cause of this error migh be? I am
slightly struggling in making sense of the error messages. Any help would be
much appreciated!

#6

I have decided to delete the files I had and do it from scratch again.

To start with I am running git clone
gitlab(a)git.skewed.de:count0/graph-tool.git

I am then executing autogen.sh. This returns the following:

libtoolize: putting auxiliary files in `.'.
libtoolize: linking file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: linking file `m4/libtool.m4'
libtoolize: linking file `m4/ltoptions.m4'
libtoolize: linking file `m4/ltsugar.m4'
libtoolize: linking file `m4/ltversion.m4'
libtoolize: linking file `m4/lt~obsolete.m4'
libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
configure.ac:22: installing './compile'
configure.ac:18: installing './config.guess'
configure.ac:18: installing './config.sub'
configure.ac:20: installing './install-sh'
configure.ac:20: installing './missing'
src/graph/Makefile.am: installing './depcomp'
src/graph_tool/Makefile.am:3: installing './py-compile'
configure.ac:39: error: possibly undefined macro: PKG_INSTALLDIR
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.

I can then run the configure file that it has generated but is this an error
that I would need to fix first?

If I run configure it seems to happily run to the end. The only on-screen
message that sticks out at me as being odd is:
./configure: line 16350: PKG_INSTALLDIR: command not found

If I read the config.log (attached config.log
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026818/config.log&gt;
) though I find a number of error messages largely revolving around
ac_nonexistent.h, such as:
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>

and:

conftest.c:54:26: fatal error: minix/config.h: No such file or directory
#include <minix/config.h>

Does anybody know what I need to do about these? Any help would be greatly
appreciated!

Best wishes,

Philipp

#7

I have decided to delete the files I had and do it from scratch again.

To start with I am running git clone
gitlab(a)git.skewed.de:count0/graph-tool.git

I am then executing autogen.sh. This returns the following:

libtoolize: putting auxiliary files in `.'.
libtoolize: linking file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: linking file `m4/libtool.m4'
libtoolize: linking file `m4/ltoptions.m4'
libtoolize: linking file `m4/ltsugar.m4'
libtoolize: linking file `m4/ltversion.m4'
libtoolize: linking file `m4/lt~obsolete.m4'
libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
configure.ac:22: installing './compile'
configure.ac:18: installing './config.guess'
configure.ac:18: installing './config.sub'
configure.ac:20: installing './install-sh'
configure.ac:20: installing './missing'
src/graph/Makefile.am: installing './depcomp'
src/graph_tool/Makefile.am:3: installing './py-compile'
configure.ac:39: error: possibly undefined macro: PKG_INSTALLDIR
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.

I can then run the configure file that it has generated but is this an error
that I would need to fix first?

You need to install pkg-config.

If I run configure it seems to happily run to the end. The only on-screen
message that sticks out at me as being odd is:
./configure: line 16350: PKG_INSTALLDIR: command not found

If I read the config.log (attached config.log
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026818/config.log&gt;
) though I find a number of error messages largely revolving around
ac_nonexistent.h, such as:
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>

and:

conftest.c:54:26: fatal error: minix/config.h: No such file or directory
#include <minix/config.h>

Does anybody know what I need to do about these? Any help would be greatly
appreciated!

These are not errors, they are a normal part of the configure tests.

Best,
Tiago

#8

Tiago Peixoto wrote

I have decided to delete the files I had and do it from scratch again.

To start with I am running git clone

gitlab(a).skewed

:count0/graph-tool.git

I am then executing autogen.sh. This returns the following:

libtoolize: putting auxiliary files in `.'.
libtoolize: linking file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: linking file `m4/libtool.m4'
libtoolize: linking file `m4/ltoptions.m4'
libtoolize: linking file `m4/ltsugar.m4'
libtoolize: linking file `m4/ltversion.m4'
libtoolize: linking file `m4/lt~obsolete.m4'
libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
configure.ac:22: installing './compile'
configure.ac:18: installing './config.guess'
configure.ac:18: installing './config.sub'
configure.ac:20: installing './install-sh'
configure.ac:20: installing './missing'
src/graph/Makefile.am: installing './depcomp'
src/graph_tool/Makefile.am:3: installing './py-compile'
configure.ac:39: error: possibly undefined macro: PKG_INSTALLDIR
      If this token and others are legitimate, please use
m4_pattern_allow.
      See the Autoconf documentation.

I can then run the configure file that it has generated but is this an
error
that I would need to fix first?

You need to install pkg-config.

It seems to already be installed. Running sudo apt-get install pkg-config
tells me that the latest version is already installed. Running dpkg -l
pkg-config returns:

dpkg -l pkg-config
Desired=Unknown/Install/Remove/Purge/Hold

Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend

/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)

/ Name Version

Architecture Description

#9

Well, in that case I have no clue.

#10

Posting on Stackoverflow
(http://stackoverflow.com/questions/40427879/graph-tool-autoconf-configure-ac39-error-possibly-undefined-macro-pkg-inst/40429414#40429414
) I got the answer that there might be an issue with the pkg-config version
on Ubuntu 14.04. Somebody else reported a similiar problem
(http://redmine.audacious-media-player.org/issues/248) where it looks like
it may have been "solved" by commenting out the line containing
PKG_INSTALLDIR. Would something like that be possible here too as a
work-around?

#11

You tell me!

#12

Happy to give it a shot though have absolutely no clue what I am doing here.
I will simply comment out line 39 in configure.ac and see what happens.

What does the line do? In your opinion, will it cause problems somewhere
else down the line that won't be aparent during compilation? (i.e. if it
could lead to incorrect results when using graph_tool I'd rather not mess
with it.)

#13

Alas, that did not solve the problem.

The error messages about
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
  #include <ac_nonexistent.h>

and

conftest.c:54:26: fatal error: minix/config.h: No such file or directory
  #include <minix/config.h>

in config.log persist but autogen.sh runs without any errors. Running make
still eventually throws the error "graph_triangulation.cc:55:61: fatal
error: CGAL/Periodic_3_Delaunay_triangulation_traits_3.h: No such file or
directory"

#14

Alas, that did not solve the problem.

The error messages about
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
  #include <ac_nonexistent.h>

and

conftest.c:54:26: fatal error: minix/config.h: No such file or directory
  #include <minix/config.h>

in config.log persist but autogen.sh runs without any errors.

As I already explained, these are not errors.

Running make
still eventually throws the error "graph_triangulation.cc:55:61: fatal
error: CGAL/Periodic_3_Delaunay_triangulation_traits_3.h: No such file or
directory"

This is completely unrelated to any of this. It probably just means that
your cgal version is too old.

Some modifications were made recently in graph-tool to allow compilation
with newer cgal that possibly have broken compatibility with older versions.
I will investigate.

#15

Dear all

I add the same problem on Fedora 20, with CGAL 4.3.
In order to solve the problem remove CGAL 4.3 and install 4.9 version,
then graph-tool compiles

regards
Claudio

#16

Hi Claudio,

Alas, Ubunutu 14.04 only has CGAL4.2 in Launchpad so that probably won't
work without compiling CGAL from scratch I would guess.

Best wishes,

Philipp