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<p class="MsoNormal"><span style="font-size:14.0pt">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><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"><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"><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"><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"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="p1"><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"><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"><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"><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"><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"><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"><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"><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"><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"><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"><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"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><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"><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"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="p1"><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"><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"><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"><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"><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"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><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"><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"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black">Philippe.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Philippe Cuniasse, PhD/HDR.</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Institut de Biologie Integrative de la cellule.</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">UMR 9198 CNRS-CEA-Univ Paris Sud</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Bat 144 CE-Saclay</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">91191 Gif-sur-Yvette Cedex</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">France</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><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 style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Fax: (33) 1 69 08 47 12</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Email: </span><span style="font-size:9.0pt;font-family:Courier;color:#0000FE;mso-fareast-language:FR"><a href="mailto:philippe.cuniasse@cea.fr"><span style="color:purple">philippe.cuniasse@cea.fr</span></a></span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Web:</span><span 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 style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:FR"><img border="0" id="Image_x0020_3" src="cid:image001.png@01D97DD0.4AFE9C50" alt="signature_1537351220"></span></i></b><span style="font-size:12.0pt;font-family:"Comic Sans MS";color:black;mso-fareast-language:FR"><img border="0" id="Image_x0020_2" src="cid:image002.png@01D97DD0.4AFE9C50" alt="signature_732259530"><img border="0" id="Image_x0020_1" src="cid:image003.png@01D97DD0.4AFE9C50" alt="signature_3011392973"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span style="font-size:14.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif;color:black"></span><span lang="EN-US" style="font-size:14.0pt"><o:p></o:p></span></p>
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