https://git.openrobots.org/https://git.openrobots.org/favicon.ico?14752240372021-02-15T17:22:23ZOpenrobotsmatlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7352021-02-15T17:22:23ZAnthony Malletanthony.mallet@laas.fr
<ul></ul><blockquote>
<p>I have included the full configure.log file from<br />the robotpkg/supervision/matlab-genomix/work.#/configure.log<br />directory.</p>
</blockquote>
<p>It shows that there is a linking issue, but in order to know which<br />issue precisely, could you attach the "config.log" file found in the<br />build directory?</p>
<p>It should be found in the following directory:<br />robotpkg/supervision/matlab-genomix/work.#/matlab-genomix-1.8.4/config.log</p>
<blockquote>
<p>In the meantime I have got it to work on matlab 2020a, so this seems<br />to be an issue related to the matlab version. Hopefully this<br />information is useful and the bug can be squashed.</p>
</blockquote>
<p>OK, this looks a bit similar to an issue with matlab-2020b and gcc-7<br />on ubuntu-18.04. However, since you are running gcc-9 on ubuntu-20.04,<br />I need to see the config.log file to check what is the error exactly.</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7362021-02-16T09:46:15ZAnonymous
<ul><li><strong>File</strong> <a href="/attachments/155">config.log</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/155/config.log">config.log</a> added</li></ul><p>The config file was deleted and I am having trouble reproducing the error. Since I have got it working using matlab 2020a, it also installs when switching back to 2020b in the robotpkg.conf file. I have found that including simulation/mrsim-gazebo does cause issues and therefore produces this <a class="attachment" href="https://git.openrobots.org/attachments/157">config.log</a> file. I hope this can still be used!</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7372021-02-16T13:07:36ZAnthony Malletanthony.mallet@laas.fr
<ul></ul><p>Thanks.</p>
<p>However, this config.log file is useless here since it doesn't come<br />from the same package (and it has no error either, by the way).</p>
<p>If you have an issue with mrsim-gazebo, please open an issue there:<br /><a class="external" href="https://git.openrobots.org/projects/mrsim-gazebo/issues">https://git.openrobots.org/projects/mrsim-gazebo/issues</a></p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7382021-02-17T13:11:19ZAnonymous
<ul><li><strong>File</strong> <a href="/attachments/156">configure.log</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/156/configure.log">configure.log</a> added</li><li><strong>File</strong> <a href="/attachments/157">config.log</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/157/config.log">config.log</a> added</li><li><strong>File</strong> <a href="/attachments/158">robotpkg.conf</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/158/robotpkg.conf">robotpkg.conf</a> added</li></ul><p>Sorry for the confusion, I managed to reproduce the error by deinstalling matlab-genomix and attempting to reinstall using matlab 2020b in the robotpkg.conf file. I have included the relevant files, the error is listed below:</p>
<pre><code class="shell syntaxhl" data-language="shell"><span class="o">===></span> Configuring <span class="k">for </span>matlab-genomix-1.8.4
<span class="o">=></span> Modifying GNU configure scripts to avoid <span class="nt">--recheck</span>
<span class="o">=></span> Disabling fatal errors with C++ preprocessor <span class="k">in </span>GNU configure scripts
configure: error: please <span class="nb">set </span>MATLAB variable
An unexpected error occured. The last 10 log lines are shown below.
| checking <span class="k">for</span> /usr/bin/gcc option to accept ISO C89... <span class="o">(</span>cached<span class="o">)</span> none needed
| checking whether /usr/bin/gcc understands <span class="nt">-c</span> and <span class="nt">-o</span> together... <span class="o">(</span>cached<span class="o">)</span> <span class="nb">yes</span>
| checking dependency style of /usr/bin/gcc... <span class="o">(</span>cached<span class="o">)</span> gcc3
| checking <span class="k">for </span>ranlib... <span class="o">(</span>cached<span class="o">)</span> ranlib
| checking <span class="k">for </span>library containing getaddrinfo... none required
| checking mex.h usability... <span class="nb">yes</span>
| checking mex.h presence... <span class="nb">yes</span>
| checking <span class="k">for </span>mex.h... <span class="nb">yes</span>
| checking <span class="k">for </span>mxGetString <span class="k">in</span> <span class="nt">-lmx</span>... no
| configure: error: please <span class="nb">set </span>MATLAB variable
</code></pre>
<p>Hopefully this can be used to identify the problem, and matlab-genomix can be used with matlab 2020b</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7392021-02-17T15:10:08ZAnthony Malletanthony.mallet@laas.fr
<ul></ul>OK, so the same issue arises with matlab-2020b:
<ul>
<li>with gcc-7 and gcc-8 on ubuntu-18.04</li>
<li>with gcc-9 on ubuntu-20.04</li>
</ul>
<p>So far I have not found a precise explanation nor a workaround,<br />especially since I have access to matlab-2019b only. I initially<br />thought it was a version incompatibility but this would be weird that<br />matlab-2020b is incompatible with ubuntu-20.04.</p>
<p>I will still try to understand more precisely what is happening.</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7402021-02-17T16:30:33ZAnthony Malletanthony.mallet@laas.fr
<ul></ul><p>In order to understand better, could you please run this and report what it<br />says?</p>
<p><code>objdump -TC /home/max/matlab/2020b/sys/os/glnxa64/libstdc++.so.6 | grep thread_atexit</code></p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7412021-02-18T09:15:38ZAnonymous
<ul></ul><p>Here is the output:</p>
<pre><code class="shell syntaxhl" data-language="shell"><span class="nv">$ </span>objdump <span class="nt">-TC</span> /home/max/matlab/2020b/sys/os/glnxa64/libstdc++.so.6 | <span class="nb">grep </span>thread_atexit
0000000000000000 DF <span class="k">*</span>UND<span class="k">*</span> 0000000000000000 <corrupt> __cxa_thread_atexit_impl
000000000008ff30 g DF .text 0000000000000005 CXXABI_1.3.7 __cxa_thread_atexit
</code></pre> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7692021-04-21T10:22:33ZDavide Bicegod.bicego@utwente.nl
<ul><li><strong>File</strong> <a href="/attachments/159">DB-config.log</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/159/DB-config.log">DB-config.log</a> added</li><li><strong>Assignee</strong> set to <i>Anthony Mallet</i></li></ul><p>Dear Anthony,</p>
<p>I am experiencing the very same issue, running Matlab R2020b on Ubuntu 18.04.<br />Do you have any news regarding this?<br />I am attaching my "config.log" file ("DB-" as prefix) found in the build directory and copying the output of the objdump command in the following<br /><pre>
dbicego@prometheus:/usr/local/MATLAB/R2020b/sys/os/glnxa64$ objdump -TC libstdc++.so.6 | grep thread_atexit
0000000000000000 DF *UND* 0000000000000000 __cxa_thread_atexit_impl
000000000008ff30 g DF .text 0000000000000005 CXXABI_1.3.7 __cxa_thread_atexit
</pre></p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=7752021-04-26T12:14:33ZAnthony Malletanthony.mallet@laas.fr
<ul></ul><p>The problem is that the libstdc++ that comes with matlab-2020b seems a<br />bit weird and/or incompatible, as indicated by the "<corrupt>" tag<br />that is seen in the objdump output.</p>
<p>I have no workaround so far, and I don't have any matlab-2020b<br />installation to test either.</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=9232022-01-18T07:14:14ZJoudy Nader
<ul></ul><p>Hello all,</p>
<p>I was installing Matlab R2020b on Ubuntu 18.04 when I faced the same problem discussed in this issue.<br /><strong>PREFIX.matlab</strong> is set correctly in <em>robotkpg.conf</em>.</p>
<p>Any updates concerning this issues?</p>
<p>I did some more debugging and tried 2 things to see what happens:</p>
<p>1) when the error occurred, I went to <strong>supervision/matlab-genomix/work.${USER}/matlab-genomix/</strong> and commented the lines where we check for <em>libmx.so</em> in <strong>configure.ac</strong> since the library exists (logically speaking it's not correct to comment out, but just to give it a try), and ran <em>autoreconf</em> again and built <strong>matlab-genomix</strong> without any issue. And then <strong>make update-<pkgset-name></strong> worked well.</p>
<p>2) in <strong>supervision/matlab-genomix/Makefile</strong>, I tried to see what's inside <strong>PREFIX.matlab</strong> variable (which should be the same as in robotpkg.conf), but nothing was inside. Is that normal?</p>
<p>I don't know if this can help, but it might be a way to find a solution for the problem.</p>
<p>Thanks in advance.</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=9242022-01-18T11:18:39ZAnthony Malletanthony.mallet@laas.fr
<ul></ul><p>The test for libmx and libmex done by autoconf links a test<br />exectuable to check that the symbols are present.<br />However, it seems that with matlab-2020b, linking does not work if the<br />compiler is not a C++ compiler (by default, autoconf uses a C compiler<br />for the tests).</p>
<p>Since matlab-genomix does on purpose not use a C++ compiler (it's only<br />C, so that there is no ABI issues between matlab C++ version and the<br />system C++ version), it's a bit frustrating to have to require a C++<br />compiler for the test.</p>
<p>So I thing the easiest is to disable the autoconf test, and hardcode<br />the required library. Something like:</p>
<p><code>@ -40,11 +40,7 </code>@ LDFLAGS="$LDFLAGS -L$MATLAB/sys/os/$MATARCH -Wl,-rpath,$MATLAB/sys/os/$MATARCH" <br />AC_SUBST(MEXEXT)</p>
<p>AC_CHECK_HEADERS([mex.h], [], [AC_MSG_ERROR([please set MATLAB variable])])<br /><del>AC_CHECK_LIB([mx], [mxGetString],<br /></del> [], [AC_MSG_ERROR([please set MATLAB variable])])<br /><del>AC_CHECK_LIB([mex], [mexErrMsgIdAndTxt],<br /></del> [], [AC_MSG_ERROR([please set MATLAB variable])])<br />-<br />+LIBS="-lmx -lmex" </p>
<ol>
<li>output<br />AC_CONFIG_FILES([</li>
</ol>
<p>If this works for you, then I'll commit this.</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=9252022-01-18T11:30:23ZJoudy Nader
<ul></ul><p>Okay. I tested this change and it works.</p>
<p>The same problem then occurs in <strong>tk3-matlab-1.6</strong> in my case when I continue with <strong>make update-<pkgset-name></strong>.</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=9262022-01-18T12:27:10ZAnthony Malletanthony.mallet@laas.fr
<ul></ul><p>Yes, tk3-matlab is basically the same. I will commit and release the<br />same fix.</p>
<p>Thanks for helping with this issue!</p> matlab-genomix - Bug #297: make error in matlab-genomix for matlab 2020bhttps://git.openrobots.org/issues/297?journal_id=9272022-01-18T12:46:34ZAnthony Malletanthony.mallet@laas.fr
<ul><li><strong>Status</strong> changed from <i>New</i> to <i>Closed</i></li></ul><p>Applied in changeset <a class="changeset" title="Don't check for libmx and libmex in configure script The test for libmx and libmex done by autoc..." href="https://git.openrobots.org/projects/matlab-genomix/repository/matlab-genomix/revisions/c24aef0c3151a186c9d25556b984d228d5b55008">matlab-genomix|c24aef0c3151a186c9d25556b984d228d5b55008</a>.</p>