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<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;font-family:"Arial",sans-serif">Hi Philippe,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;font-family:"Arial",sans-serif">It’s not an optimal workaround, but you can try using CFLAGS="-Wno-error=implicit-function-declaration" …<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;font-family:"Arial",sans-serif">Best, Luca<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black;mso-fareast-language:EN-GB">-<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black;mso-fareast-language:EN-GB">Luca Jovine, Ph.D.<br>
Professor of Structural Biology, Member of EMBO and the Nobel Assembly<br>
Karolinska Institutet<br>
Department of Biosciences and Nutrition<br>
Medicinaren 25 Neo<br>
Blickagången 16, SE-141 83 Huddinge, Sweden<br>
E-mail: luca.jovine@ki.se<br>
W3: http://jovinelab.org</span><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-left:36.0pt"><b><span lang="FR" style="font-size:12.0pt;color:black;mso-fareast-language:EN-GB">From:
</span></b><span lang="FR" style="font-size:12.0pt;color:black;mso-fareast-language:EN-GB"><phenixbb-bounces@phenix-online.org> on behalf of CUNIASSE Philippe <Philippe.CUNIASSE@cea.fr><br>
<b>Date: </b>Wednesday, 3 May 2023 at 15:09<br>
<b>To: </b>"phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br>
<b>Subject: </b>[phenixbb] Pb installing cryo_fit gromacs<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:12.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#212121;mso-fareast-language:EN-GB">You don't often get email from philippe.cuniasse@cea.fr.
<a href="https://aka.ms/LearnAboutSenderIdentification">Learn why this is important</a><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:14.0pt">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:14.0pt">I tried to install Cryo_fit on my labtop Macbook pro M1 running OSX 13.0.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:14.0pt">The installation of the Cryo_fit itself in Phenix went well.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:14.0pt">I then tried to install gromacs (</span><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">gromacs-4.5.5_cryo_fit) following the instructions found
on <a href="https://phenix-online.org/documentation/tutorials/cryo_fit_install.html#id1">
https://phenix-online.org/documentation/tutorials/cryo_fit_install.html#id1</a><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">But during the compilation, I encoutered the following error that stops the process.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="s1"><span lang="EN-US">cc</span></span><span class="apple-converted-space"><span lang="EN-US">
</span></span><span class="s1"><span lang="EN-US">-DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/Applications/phenix-1.20.1-4487/modules/cryo_fit/cryo_fit/share/top\"
</span></span><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="s1"><span lang="EN-US">-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -std=gnu99</span></span><span class="apple-converted-space"><span lang="EN-US">
</span></span><span class="s1"><span lang="EN-US">-I./include -MT md.o -MD -MP -MF .deps/md.Tpo -c -o md.o md.c</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="s1"><b><span lang="EN-US">md.c:414:9:
</span></b></span><span class="s2"><b><span lang="EN-US">error: </span></b></span><span class="s1"><b><span lang="EN-US">call to undeclared function 'please_cite'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]</span></b></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="apple-converted-space"><span lang="EN-US">
</span></span><span class="s1"><span lang="EN-US">please_cite(stderr,"Kim2019");</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p2" style="margin-left:36.0pt"><span class="apple-converted-space"><b><span lang="EN-US">
</span></b></span><span class="s1"><b><span lang="EN-US">^</span></b></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="s1"><b><span lang="EN-US">md.c:421:23:
</span></b></span><span class="s3"><b><span lang="EN-US">warning: </span></b></span><span class="s1"><b><span lang="EN-US">passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]</span></b></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="apple-converted-space"><span lang="EN-US">
</span></span><span class="s1"><span lang="EN-US">init_em_map(fplog,ftp2fn(efEMM, nfile, fnm), emmap, ir, state_global,cr);</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p2" style="margin-left:36.0pt"><span class="apple-converted-space"><b><span lang="EN-US">
</span></b></span><span class="s1"><b><span lang="EN-US">^~~~~~~~~~~~~~~~~~~~~~~~~</span></b></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="s1"><b><span lang="EN-US">../../include/cryoem.h:43:44: note:
</span></b></span><span class="s1"><span lang="EN-US">passing argument to parameter 'emfile' here</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="s1"><span lang="EN-US">extern void init_em_map(FILE *fplog, char *emfile,t_emmap *emmap, t_inputrec *ir, t_state *state, t_commrec *cr);</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p2" style="margin-left:36.0pt"><span class="apple-converted-space"><b><span lang="EN-US">
</span></b></span><span class="s1"><b><span lang="EN-US">^</span></b></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span class="s1"><span lang="EN-US">1 warning and 1 error generated.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">I did it under a bash shell,
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">Python version : 2.7.15<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;mso-fareast-language:EN-US">cc --version</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Verdana",sans-serif;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;mso-fareast-language:EN-US">Apple clang version 14.0.3 (clang-1403.0.22.14.1)</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Verdana",sans-serif;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;mso-fareast-language:EN-US">Target: arm64-apple-darwin22.1.0</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Verdana",sans-serif;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;mso-fareast-language:EN-US">Thread model: posix</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Verdana",sans-serif;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="p1" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;mso-fareast-language:EN-US">InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Verdana",sans-serif;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">Any suggestion to solve it ?
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">Thanks in advance for your help.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">Philippe.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:14.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span lang="FR" style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Philippe Cuniasse, PhD/HDR.</span><span lang="FR" style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Institut de Biologie Integrative de la cellule.</span><span lang="FR" style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">UMR 9198 CNRS-CEA-Univ Paris Sud</span><span lang="FR" style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Bat 144 CE-Saclay</span><span lang="FR" style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">91191 Gif-sur-Yvette Cedex</span><span lang="FR" style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-GB" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">France</span><span lang="FR" style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-GB" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Tel: (33) 1 69 08 56 35</span><span lang="FR" style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Web:</span><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:#0000F5;mso-fareast-language:FR"> <a href="http://biodev.cea.fr/rasmot3d/"><span style="color:purple">http://biodev.cea.fr/rasmot3d/</span></a></span><span lang="FR" style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span lang="FR" style="font-size:14.0pt"><o:p></o:p></span></p>
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<p class="p2"><span class="s1"><i>Sending email to Karolinska Institutet (KI) will result in KI processing your personal data.</i>
<a href="https://ki.se/en/staff/data-protection-policy"><span class="s2">You can read more about KI’s processing of personal data here</span></a>.<span class="Apple-converted-space"> </span></span></p>
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