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Dear Gavin,</div>
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This is the error that I got running xcrysden;</div>
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---------------</div>
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Error in startup script: Can not set ident to a window path name</div>
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Couldn't configure togl widget</div>
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while executing</div>
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------------------</div>
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just installed</div>
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tcl-togl</div>
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tcl-togl-devel</div>
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opengl</div>
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<br>
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Saludos</div>
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<br>
</div>
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Pablo</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De:</b> xcrysden-bounces@democritos.it <xcrysden-bounces@democritos.it> en nombre de delamora <delamora@unam.mx><br>
<b>Enviado:</b> lunes, 2 de septiembre de 2024 11:02 a. m.<br>
<b>Para:</b> XCrySDen mailing list <xcrysden@democritos.it><br>
<b>Asunto:</b> Re: [xcrysden] Running XCrySDen</font>
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Dear Gavin,</div>
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I try to install what is suggested in the xcrysden page;</div>
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----------------------------------------------------------</div>
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dnf install tk libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick openbabel libgfortran5</div>
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Última comprobación de caducidad de metadatos hecha hace 0:05:30, el lun 02 sep 2024 09:38:00.</div>
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El paquete tk-1:8.6.13-3.fc40.x86_64 ya está instalado.</div>
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No hay coincidencias para el argumento: libglu1-mesa</div>
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No hay coincidencias para el argumento: libtogl2</div>
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No hay coincidencias para el argumento: libfftw3-3</div>
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No hay coincidencias para el argumento: libxmu6</div>
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No hay coincidencias para el argumento: imagemagick</div>
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* Tal vez quiso decir: ImageMagick</div>
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No hay coincidencias para el argumento: libgfortran5</div>
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Error: No se pudo encontrar ningún resultado: libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick libgfortran5</div>
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-----------------------------------</div>
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There were no results for</div>
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libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick libgfortran5</div>
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but</div>
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ImageMagick</div>
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is already installed.</div>
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<br>
</div>
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Cheers</div>
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<br>
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Pablo</div>
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<b><br>
</b></div>
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Estimado Gavin,</div>
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<br>
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Running xcrysden, now it opens, but it gives this error;</div>
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<br>
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./ftnunit: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory</div>
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<br>
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I have intel fortran in</div>
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<br>
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pablo@fedora:/home/Programas/xcrysden-1.6.2-bin-shared$ locate libgfortran</div>
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/opt/intel/oneapi/intelpython/python3.9/pkgs/_openmp_mutex-4.5-1_gnu/info/recipe/parent/install-libgfortran.sh</div>
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/opt/intel/oneapi/intelpython/python3.9/pkgs/libgcc-ng-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh</div>
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/opt/intel/oneapi/intelpython/python3.9/pkgs/libgomp-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh</div>
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/opt/intel/oneapi/intelpython/python3.9/pkgs/libstdcxx-ng-9.3.0-hd4cf53a_17/info/recipe/parent/install-libgfortran.sh</div>
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/var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5</div>
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/var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5.0.0</div>
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<br>
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how to link intel fortran with xcrysden</div>
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<br>
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Pablo</div>
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<div dir="ltr" id="x_x_divRplyFwdMsg"><span style="font-family:Calibri,sans-serif; font-size:11pt; color:rgb(0,0,0)"><b>De:</b> xcrysden-bounces@democritos.it <xcrysden-bounces@democritos.it> en nombre de Gavin Abo <gabo13279@gmail.com><br>
<b>Enviado:</b> jueves, 29 de agosto de 2024 09:50 p. m.<br>
<b>Para:</b> xcrysden@democritos.it <xcrysden@democritos.it><br>
<b>Asunto:</b> Re: [xcrysden] Running XCrySDen</span>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">XCrySDen 1.6.2 works with Fedora 40 when libtk8.6.so from the operating system tk-devel package is used.</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">I've not tried libtk8.6.so from Intel's OneAPI. That library file likely was compiled with the Intel compiler. So, it might be that the file has different function declarations than that produced
by GCC. That might explain why you would need the libtk8.6.so from the operating system package that was compiled with GCC for being able to use xcrysden-1.6.2-linux_x86_64-shared.tar.gz.</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">Thus, if you wanted to use /opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so (instead of /lib64/libtk8.6.so), it is likely that you would need to compile XCrySDen using xcrysden-1.6.2.tar.gz
and you would need to modify Make.sys yourself to use the OneAPI compiler. Since that is probably a more difficult approach, I would recommend using the operating system version of libtk8.6.so instead.</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">For that, at [1], the webpage shows the Fedora 40 operating system tk-devel package. The tk-devel package when installed puts libtk.so (i.e., libtk8.6.so) also in the directory:</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">/usr/lib64/</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">With Fedora 40, when I checked that directory, the
<span style="color:rgb(0,0,255)">libtk8.6.so</span> was there:</p>
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</p>
<div style="direction:ltr">username@fedora:~$ ls -l /usr/lib64/libtk*<br>
-rwxr-xr-x. 1 root root 1343528 Jan 26 2024 /usr/lib64/<span style="color:rgb(0,0,255)">libtk8.6.so</span><br>
lrwxrwxrwx. 1 root root 11 Jan 26 2024 /usr/lib64/libtk.so -> libtk8.6.so<br>
-rwxr-xr-x. 1 root root 6640 Jan 26 2024 /usr/lib64/libtkstub8.6.a</div>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">When the tk-devel package has been successfully installed, the terminal should show the same or similar terminal display of:</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">username@fedora:~$ sudo yum install tk-devel<br>
[sudo] password for username:<br>
Last metadata expiration check: 0:27:44 ago on Thu 29 Aug 2024 09:16:34 PM MDT.<br>
Package tk-devel-1:8.6.13-3.fc40.x86_64 is already installed.<br>
Dependencies resolved.<br>
Nothing to do.<br>
Complete!</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">[1] <a href="https://packages.fedoraproject.org/pkgs/tk/tk-devel/fedora-40.html" id="OWAb4ef7ed3-d88d-274c-6042-ee53b7e52313" class="x_x_x_moz-txt-link-freetext x_OWAAutoLink" data-auth="NotApplicable" style="margin-top:0px; margin-bottom:0px">
https://packages.fedoraproject.org/pkgs/tk/tk-devel/fedora-40.html</a></p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">Kind Regards,</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">Gavin</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">XCrySDen user</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px"><br>
</p>
<div style="direction:ltr">On 8/29/2024 10:37 AM, delamora wrote:</div>
<blockquote>
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I found it;</div>
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----</div>
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# find / -name *libtk8.6*</div>
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/opt/intel/oneapi/intelpython/python3.9/pkgs/tk-8.6.10-hbc83047_0/lib/libtk8.6.so</div>
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/opt/intel/oneapi/intelpython/python3.9/envs/2022.0.2/lib/libtk8.6.so</div>
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/opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so</div>
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----</div>
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but xcrysden does not find it</div>
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<br>
</div>
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Pablo</div>
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<div dir="ltr" id="x_x_x_divRplyFwdMsg"><span style="font-family:Calibri,sans-serif; font-size:11pt; color:rgb(0,0,0)"><b>De:</b> <a href="mailto:xcrysden-bounces@democritos.it" id="OWA41da4d11-ace9-b434-8427-393a8671e0cb" class="x_x_x_moz-txt-link-abbreviated x_OWAAutoLink">xcrysden-bounces@democritos.it</a>
<a href="mailto:xcrysden-bounces@democritos.it" id="OWA9836dda1-fd5e-2993-daad-1ae0c89955cc" class="x_x_x_moz-txt-link-rfc2396E x_OWAAutoLink">
<xcrysden-bounces@democritos.it></a> en nombre de Gavin Abo <a href="mailto:gabo13279@gmail.com" id="OWA0fd65f4f-b1af-c043-9bab-0c1dcce65dcb" class="x_x_x_moz-txt-link-rfc2396E x_OWAAutoLink">
<gabo13279@gmail.com></a><br>
<b>Enviado:</b> miércoles, 28 de agosto de 2024 08:16 p. m.<br>
<b>Para:</b> <a href="mailto:xcrysden@democritos.it" id="OWA24ace44b-31eb-3d87-09c4-2ca5df52e388" class="x_x_x_moz-txt-link-abbreviated x_OWAAutoLink">xcrysden@democritos.it</a>
<a href="mailto:xcrysden@democritos.it" id="OWA2e3a19d6-89a2-a3a6-3e5c-255bb3b0c6d6" class="x_x_x_moz-txt-link-rfc2396E x_OWAAutoLink">
<xcrysden@democritos.it></a><br>
<b>Asunto:</b> Re: [xcrysden] Running XCrySDen</span>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">I see that you have the error "libtk8.6.so: cannot open shared object file: No such file or directory".</p>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">From the message, it looks like XCrySDen cannot find the libtk8.6.so file.</p>
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</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">That file should be in your /lib64 directory:</p>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">username@fedora:~$ ls -l /lib64/libtk8.6.so<br>
-rwxr-xr-x. 1 root root 1343528 Jan 26 2024 /lib64/libtk8.6.so</p>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">If it isn't, the package for it might not be installed.</p>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">In Fedora 40, it was likely installed by the command:</p>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">sudo yum install tk-devel</p>
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<p style="direction:ltr; margin-top:0px; margin-bottom:0px">Kind Regards,</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">Gavin</p>
<p style="direction:ltr; margin-top:0px; margin-bottom:0px">XCrySDen user</p>
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</p>
<div style="direction:ltr">On 8/28/2024 4:59 PM, delamora wrote:</div>
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I got the </div>
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xcrysden-1.6.2-bin-shared</div>
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then I ran</div>
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xcrysden</div>
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and I got</div>
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-------------</div>
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[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.</div>
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Code available from <a href="http://www.xcrysden.org/" id="OWA5b69d665-35f5-774c-5f0d-4c280bdeac49" class="x_x_x_x_moz-txt-link-freetext x_x_x_OWAAutoLink x_x_x_moz-txt-link-freetext" data-auth="NotApplicable">
http://www.xcrysden.org/</a>.</div>
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<br>
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XCRYSD[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.</div>
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Code available from <a href="http://www.xcrysden.org/" id="OWAaeb08975-bfa1-066b-bc92-102f39a01459" class="x_x_x_x_moz-txt-link-freetext x_x_x_OWAAutoLink x_x_x_moz-txt-link-freetext" data-auth="NotApplicable">
http://www.xcrysden.org/</a>.</div>
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<br>
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XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared</div>
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XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp</div>
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/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.6.so: cannot open shared object file: No such file or directoryEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared</div>
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XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp</div>
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<br>
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/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.6.so: cannot open shared object file: No such file or directory</div>
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------------------------------</div>
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In the xcrysden page it says;</div>
<li><br>
</li><li><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><b><i>Linux x86_64</i></b><i> binary packages (64bit):</i></span>
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Shared: <a href="http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz" id="OWAd7c9ee4c-8558-5400-aef8-02dc7d24f249" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">
xcrysden-1.6.2-linux_x86_64-shared.tar.gz</a><br>
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Requires: <tt>libtk8.6.so, libtcl8.6.so, libTogl.so.2, libGLU.so.1, libGL.so.1, libfftw3.so.3, libXmu.so.6, libX11.so.6, libgfortran.so.5, ..</tt></li></ul>
</ul>
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-------------------------</div>
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so I searched for these packages and I got</div>
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<br>
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dnf search libtk8.6.so libtcl8.6.so libTogl.so.2 libGLU.so.1 libGL.so.1 libfftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5</div>
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Última comprobación de caducidad de metadatos hecha hace 2:37:04, el mié 28 ago 2024 13:17:04.</div>
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No se encontraron coincidencias.</div>
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(=>there were no coincidences)</div>
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<br>
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Saludos</div>
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<br>
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Pablo</div>
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