<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>We haven't planned to update pathway-tools to v 14.0 now, but I upgrade the sorghumcyc on pathway-tools v 14.0 locally and have no problem so far. I have put the upgraded version sorghumcyc_v1_0_ptool_v14.tgz on our ftp site <a href="ftp://ftp.gramene.org/pub/gramene/pathways/sorghumcyc/">ftp://ftp.gramene.org/pub/gramene/pathways/sorghumcyc/</a>. Let me know if you still have a problem.</div><div><br></div><div><br></div><div>Liya</div><div><br><div><div>On Jun 27, 2010, at 3:12 PM, Sidibe bocs Stephanie wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div bgcolor="#ffffff" text="#000000"> Dear curators,<br> <br> As explained below, we have problems upgrading from your SorghumCyc database obtained with the PathwayTools version 12.5 into our PathwayTools version 14.0. <br> The ptools-support don't support the old pathway tools versions and suggested to contact you to obtained an upgraded version of your work. <br> Do you have the same problem? Could you please update SorghumCyc for Pathway Tools version 14.0 ? <br> <br> Thank you very much for your help, best regards,<br> <br> Le 24/06/2010 21:43, Markus Krummenacker a écrit : <blockquote cite="mid:19491.46429.770308.382970@Chili.AI.SRI.COM" type="cite"> <pre wrap="">Sidibe bocs Stephanie writes:
> Dear all,
>
> We downloaded BioCyc / Pathway Tools Bundle Version 14.0.
> For a first try, we want to browse and compare of already computed plant
> data from our Web server connected to our database server.
> So we also downloaded riceCyc, AraCyc, PoplarCyc, PlantCyc
> <a class="moz-txt-link-freetext" href="http://www.plantcyc.org:1555/ARA/server.html">http://www.plantcyc.org:1555/ARA/server.html</a>?
> <a class="moz-txt-link-freetext" href="http://www.gramene.org/pathway/">http://www.gramene.org/pathway/</a>
>
> Apparently there is a problem of version compatibility and the update
> process does not work (see details below).
> Should we work with the 12.5 Biocyc version ? if yes, where can we
> download it ?
Hi,
Due to limited resources, we generally can't support such an old
Pathway Tools version, and it is no longer made available for download.
But it is true that the upgrade of various plant-related PGDBs from
12.5 to 14.0 caused several problems. If I understand the situation,
PlantCyc and AraCyc have been successfully upgraded by now. I don't
know when those new versions are made available for download.
I suggest that you contact the staff at PlantCyc directly, and ask
them how you could obtain the upgraded versions that work with Pathway
Tools 14.0 . This will save you a lot of problems.
</pre> </blockquote> <br> --------------------------------------------------------------------------------------------------<br> I have problems with three biocyc databases : aracyc, plantcyc and sorghumcyc. <br> When I use pathwaytools in Web mode with this commande line<br> $ ./pathway-tools -www <br> <br> This dialogue window open : <br> The following PGDB(s) were built with, or last upgraded to Pathway Tools version 12.5, and may be incompatible with the current Pathway Tools version 14.0. Do you wish to upgrade now ? <br> If you choose to upgrade now, you will need to specify a new version number for each PGDB. <br> If you choose not to upgrade, Pathway Tools will exit. <br> Arabidopsis thaliana col (ARA) <br> PlantCyc (PLANT) <br> Sorghum biolor BTx623 (SORGHUM) <br> <br> I click on Upgrade Now, the window for changing the version number for each PGDB opens and when I click on OK , this window close and I have this error message : <br> <br> 244931920 bytes have been tenured, next gc will be global. <br> See the documentation for variable EXCL:<b class="moz-txt-star"><span class="moz-txt-tag">*</span>GLOBAL-GC-BEHAVIOR<span class="moz-txt-tag">*</span></b> for more information. <br> Error: Invalid frame name RNA(N) in KB ARABASE: <br> Frame name "RNA(N)" contains the illegal character "(" <br> Error: KB ARABASE contains one or more frames whose names <br> (unique identifiers) are syntactically invalid <br> (contain illegal characters or exceed the allowed length). <br> [condition type: INVALID-FRAME-NAME] <br> <br> Restart actions (select using :continue): <br> 0: Abort entirely from this (lisp) process. <br> <br> [changing package from "COMMON-LISP-USER" to "ECOCYC"] <br> [Current process: Initial Lisp Listener] <br> <pre class="moz-signature" cols="72">--
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<a class="moz-txt-link-freetext" href="http://umr-dap.cirad.fr/">http://umr-dap.cirad.fr/</a></pre> </div> <span><stephanie_sidibe-bocs.vcf></span>_______________________________________________<br>Gramene mailing list<br><a href="mailto:Gramene@brie4.cshl.edu">Gramene@brie4.cshl.edu</a><br><a href="http://mail.gramene.org/mailman/listinfo/gramene">http://mail.gramene.org/mailman/listinfo/gramene</a><br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>--</div><div><div>Liya Ren</div><div><a href="mailto:ren@cshl.edu">ren@cshl.edu</a></div><div><br></div><div><a href="http://www.gramene.org">www.gramene.org</a></div><div>Ware Lab</div><div>Cold Spring Harbor Laboratory</div></div></div></span></div></span> </div><br></div></body></html>