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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Thanks. Just done that. Hopefully it’ll work this time.
<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>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Hao<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" style="margin-left:.5in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">"Shepherd, Lori" <Lori.Shepherd@RoswellPark.org><br>
<b>Date: </b>Wednesday, January 10, 2024 at 8:30 PM<br>
<b>To: </b>"Wu, Hao" <hao.wu@emory.edu>, Andreas Tille <andreas@an3as.eu>, Harry Feng <hxf155@case.edu><br>
<b>Cc: </b>"1058613@bugs.debian.org" <1058613@bugs.debian.org>, Debian R <debian-r@lists.debian.org>, Bioconductor Package Maintainer <maintainer@bioconductor.org><br>
<b>Subject: </b>Re: [External] Re: Source archive of DSS missing<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Two points: <o:p></o:p></span></p>
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<![if !supportLists]><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">You need a valid version bump for it to propagate on Bioconductor systems. so it devel you would need to push a bump to 1.51.1<o:p></o:p></span></p>
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<![if !supportLists]><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"> There are always two active branches in Bioconductor. devel and the current release found currently on branch RELEASE_3_18. You would have to push to
RELEASE_3_18 branch in order fo the change to be active in release. (with a valid version bump of 1.50.1)<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Hope this helps!
</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Cheers,
</span><o:p></o:p></p>
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<p style="margin-left:.5in;background:white"><span style="font-size:12.0pt;color:black">Lori Shepherd - Kern</span><o:p></o:p></p>
<p style="margin-left:.5in;background:white"><span style="font-size:12.0pt;color:black">Bioconductor Core Team</span><o:p></o:p></p>
<p style="margin-left:.5in;background:white"><span style="font-size:12.0pt;color:black">Roswell Park Comprehensive Cancer Center</span><o:p></o:p></p>
<p style="margin-left:.5in;background:white"><span style="font-size:12.0pt;color:black">Department of Biostatistics & Bioinformatics</span><o:p></o:p></p>
<p style="margin-left:.5in;background:white"><span style="font-size:12.0pt;color:black">Elm & Carlton Streets</span><o:p></o:p></p>
<p style="margin-left:.5in;background:white"><span style="font-size:12.0pt;color:black">Buffalo, New York 14263</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><b><span style="color:black">From:</span></b><span style="color:black"> Wu, Hao <hao.wu@emory.edu><br>
<b>Sent:</b> Tuesday, January 9, 2024 5:29 PM<br>
<b>To:</b> Kern, Lori <Lori.Shepherd@RoswellPark.org>; Andreas Tille <andreas@an3as.eu>; Hao Feng <hxf155@case.edu><br>
<b>Cc:</b> 1058613@bugs.debian.org <1058613@bugs.debian.org>; Debian R <debian-r@lists.debian.org>; Bioconductor Package Maintainer <maintainer@bioconductor.org><br>
<b>Subject:</b> Re: [External] Re: Source archive of DSS missing</span> <o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">I thought I have fixed this. Just checked, at least from my end I have added edgeR to suggests, and have pushed the change. What else can I do?
</span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">@Lori, if the change is not there, could you please help me to make this change? DSS is pretty widely used and I certainly don’t want it to be deprecated.
Thank you so much.</span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Regards,</span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Hao</span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">"Shepherd, Lori" <Lori.Shepherd@RoswellPark.org><br>
<b>Date: </b>Tuesday, January 9, 2024 at 11:51 PM<br>
<b>To: </b>Andreas Tille <andreas@an3as.eu>, "Wu, Hao" <hao.wu@emory.edu>, Harry Feng <hxf155@case.edu><br>
<b>Cc: </b>"1058613@bugs.debian.org" <1058613@bugs.debian.org>, Debian R <debian-r@lists.debian.org>, Bioconductor Package Maintainer <maintainer@bioconductor.org><br>
<b>Subject: </b>[External] Re: Source archive of DSS missing</span><o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"> <o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"> </span><o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">DSS is unavailable because it has yet to build this release. The DSS maintainers have been notified multiple times but have yet to fix
the package; DSS is currently at risk of deprecation if it is not fixed. </span><o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><a href="https://secure-web.cisco.com/10v_7NJ8sPgXorW2rpTNuQ9cK8B04xcbNiWYaEpjmbsc71G0WySa4wDrOpxI0DHBSnGbKriM05uWWGln-Yr1FI79EQyZnT9klBdkr6DcuA2wt0-8mALjxcZ2jk2M5D27fqNvA3Y-oBp-qnzOEanGJxDCujwi9u6to15e3KOHYFVjaa7IsAkHnvI30UnDIeZkbvyEVmTqQstL6EDmo8BfZhKeJYWlpFZEo6mfyhpLp7Ptw4_VwLc2hGZTXjbFw4gYNMwVHym_goTU4xM8_JlK1PxmbbpwaOGWVLswtLQw_38GaUGLKUcgtpcpFlVF-xeTh/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FDSS%2F">https://bioconductor.org/checkResults/release/bioc-LATEST/DSS/</a></span><o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"> <o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Per the build report the solution is very simple. DSS needs to add the needed dependency edgeR to the list of Suggests package in the DESCRIPTION
and push a valid version bump. </span><o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"> </span><o:p></o:p></p>
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<p style="margin-left:1.0in;background:white"><span style="font-size:12.0pt;color:black">Lori Shepherd - Kern</span><o:p></o:p></p>
<p style="margin-left:1.0in;background:white"><span style="font-size:12.0pt;color:black">Bioconductor Core Team</span><o:p></o:p></p>
<p style="margin-left:1.0in;background:white"><span style="font-size:12.0pt;color:black">Roswell Park Comprehensive Cancer Center</span><o:p></o:p></p>
<p style="margin-left:1.0in;background:white"><span style="font-size:12.0pt;color:black">Department of Biostatistics & Bioinformatics</span><o:p></o:p></p>
<p style="margin-left:1.0in;background:white"><span style="font-size:12.0pt;color:black">Elm & Carlton Streets</span><o:p></o:p></p>
<p style="margin-left:1.0in;background:white"><span style="font-size:12.0pt;color:black">Buffalo, New York 14263</span><o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"><b><span style="color:black">From:</span></b><span style="color:black"> Andreas Tille <andreas@an3as.eu><br>
<b>Sent:</b> Tuesday, January 9, 2024 10:32 AM<br>
<b>To:</b> Hao Wu <hao.wu@emory.edu>; Hao Feng <hxf155@case.edu><br>
<b>Cc:</b> 1058613@bugs.debian.org <1058613@bugs.debian.org>; Debian R <debian-r@lists.debian.org>; Bioconductor Package Maintainer <maintainer@bioconductor.org><br>
<b>Subject:</b> Re: Source archive of DSS missing</span> <o:p></o:p></p>
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<p class="xmsonormal" style="margin-left:1.0in"> <o:p></o:p></p>
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<p class="xmsonormal" style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
Hi again,<br>
<br>
putting Bioconductor Package Maintainer in CC since I can not yet find<br>
the source archive of DSS 2.50.0 neither at<br>
<br>
<a href="https://secure-web.cisco.com/1IXs1DXRx2Y9dsRzzvLX84yK4Ym9eNeMVhLE8Z1rSs1XEmkvc9TlBtwJTB7DOPYrI0g0KgeG9hBwAaYvDvLqRK1ebqhCu939zH8_Ck55gAkqlcowiWK7FEtyGnoy96fpqFd5u8Kq4cTsmPqXSGOGVe3Ee8qt1XYN4fraNRyxTAewqnC9SkVz0R1nQdaUPBhbBNAJo5E-R9em72gaphy1VOuwNul219-EPQug_O_SL0CFbt7Twf2Xgmt2U8Y0Zml2cIDGiSRYkPfiQxbJMohb-19idtd9WZ813UCm9Twqayf_KuxiqzTKEcPRDqbpKVcTT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDSS.html">
https://secure-web.cisco.com/1IXs1DXRx2Y9dsRzzvLX84yK4Ym9eNeMVhLE8Z1rSs1XEmkvc9TlBtwJTB7DOPYrI0g0KgeG9hBwAaYvDvLqRK1ebqhCu939zH8_Ck55gAkqlcowiWK7FEtyGnoy96fpqFd5u8Kq4cTsmPqXSGOGVe3Ee8qt1XYN4fraNRyxTAewqnC9SkVz0R1nQdaUPBhbBNAJo5E-R9em72gaphy1VOuwNul219-EPQug_O_SL0CFbt7Twf2Xgmt2U8Y0Zml2cIDGiSRYkPfiQxbJMohb-19idtd9WZ813UCm9Twqayf_KuxiqzTKEcPRDqbpKVcTT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDSS.html</a><br>
<br>
We need the source code to update the Debian package.<br>
<br>
Kind regards<br>
Andreas.<br>
<br>
Am Tue, Dec 12, 2023 at 03:09:29PM +0100 schrieb Andreas Tille:<br>
> Hi,<br>
> <br>
> could someone please have a look at the source download?<br>
> <br>
> Thank you<br>
> Andreas.<br>
> <br>
> Am Fri, Dec 08, 2023 at 04:04:27PM +0100 schrieb Andreas Tille:<br>
> > Hi,<br>
> > <br>
> > when looking at<br>
> > <br>
> > <a href="https://secure-web.cisco.com/1IXs1DXRx2Y9dsRzzvLX84yK4Ym9eNeMVhLE8Z1rSs1XEmkvc9TlBtwJTB7DOPYrI0g0KgeG9hBwAaYvDvLqRK1ebqhCu939zH8_Ck55gAkqlcowiWK7FEtyGnoy96fpqFd5u8Kq4cTsmPqXSGOGVe3Ee8qt1XYN4fraNRyxTAewqnC9SkVz0R1nQdaUPBhbBNAJo5E-R9em72gaphy1VOuwNul219-EPQug_O_SL0CFbt7Twf2Xgmt2U8Y0Zml2cIDGiSRYkPfiQxbJMohb-19idtd9WZ813UCm9Twqayf_KuxiqzTKEcPRDqbpKVcTT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDSS.html">
https://secure-web.cisco.com/1IXs1DXRx2Y9dsRzzvLX84yK4Ym9eNeMVhLE8Z1rSs1XEmkvc9TlBtwJTB7DOPYrI0g0KgeG9hBwAaYvDvLqRK1ebqhCu939zH8_Ck55gAkqlcowiWK7FEtyGnoy96fpqFd5u8Kq4cTsmPqXSGOGVe3Ee8qt1XYN4fraNRyxTAewqnC9SkVz0R1nQdaUPBhbBNAJo5E-R9em72gaphy1VOuwNul219-EPQug_O_SL0CFbt7Twf2Xgmt2U8Y0Zml2cIDGiSRYkPfiQxbJMohb-19idtd9WZ813UCm9Twqayf_KuxiqzTKEcPRDqbpKVcTT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDSS.html</a><br>
> > <br>
> > and following the link "Source Archive" at bottom of the page linking<br>
> > to<br>
> > <a href="https://secure-web.cisco.com/15BklqjFB-NkLwrDhwI3-Chm5lIsfsZx3HGG4qR9PglFPGp8MDxMcMhd53rhclhE1eG5z0mpDqljZ8aI2luxCjYaJRC5FmDMfUoyjm_D_a1Y8WRQ3aLjtPntuNWsRSuvmnS-UMkwWWHSzG6ngdm5sMDHLC_xudenk0l3XKkHs8-NVh47VDo-25g67Oham6vEDGZhTAbePruF86hxZG2Gi_Gp8ozOtWHVxTIhkx0AbGXQUCcnK-VqaVSr0Hccm4ihUo-Nd4x3ZeSe7uwT0gJcnU-3IJPz4S7eH0bawwmQLxYdOuJPQUXaev51clpMOkXyT/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.18%2Fbioc%2Fsrc%2Fcontrib%2FArchive%2FDSS%2F">
https://secure-web.cisco.com/15BklqjFB-NkLwrDhwI3-Chm5lIsfsZx3HGG4qR9PglFPGp8MDxMcMhd53rhclhE1eG5z0mpDqljZ8aI2luxCjYaJRC5FmDMfUoyjm_D_a1Y8WRQ3aLjtPntuNWsRSuvmnS-UMkwWWHSzG6ngdm5sMDHLC_xudenk0l3XKkHs8-NVh47VDo-25g67Oham6vEDGZhTAbePruF86hxZG2Gi_Gp8ozOtWHVxTIhkx0AbGXQUCcnK-VqaVSr0Hccm4ihUo-Nd4x3ZeSe7uwT0gJcnU-3IJPz4S7eH0bawwmQLxYdOuJPQUXaev51clpMOkXyT/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.18%2Fbioc%2Fsrc%2Fcontrib%2FArchive%2FDSS%2F</a><br>
> > <br>
> > I can only see<br>
> > <br>
> > Page Not Found<br>
> > The page you were looking for was not found. <br>
> > <br>
> > I'm trying to upgrade the Debian package of DSS to its latest version<br>
> > and would need the source tarball which can be usually downloaded from<br>
> > the "Source Archive" link.<br>
> > <br>
> > Kind regards<br>
> > Andreas.<br>
> > <br>
> > -- <br>
> > <a href="http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de">
http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de</a><br>
> <br>
> -- <br>
> <a href="http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de">
http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de</a><br>
> <br>
> <br>
<br>
-- <br>
<a href="http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de">http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de</a><o:p></o:p></p>
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