<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br>Hi Stef & Graham, <br><br>did you manage to solve this issue ? I'm running in the same trouble here with e62 and e63 checkouts.<br><br>Jan <br><br>On Jun 24, 2011, at 7:23 AM, <a href="mailto:mailsvl@fastmail.fm">mailsvl@fastmail.fm</a> wrote:<br><br><blockquote type="cite">Hi everyone,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">We have a script based on ensembl api v60 (where it works without<br></blockquote><blockquote type="cite">errors) and it almost runs flawless with v62 as well except for one<br></blockquote><blockquote type="cite">error:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Can't call method "display_term" on an undefined value at<br></blockquote><blockquote type="cite">/data/common_modules/ensembl62/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeatureOverlap.pm<br></blockquote><blockquote type="cite">line 530.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If I remove this call/line everything runs fine:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">$consequence = $transcript_variation->display_consequence if defined<br></blockquote><blockquote type="cite">$transcript_variation->display_consequence;<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">...but then I'm left without the consequences so thats not really an<br></blockquote><blockquote type="cite">option ;) Anyone knows what change from v60 to v62 makes this method now<br></blockquote><blockquote type="cite">run into problems?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks!<br></blockquote><blockquote type="cite">Stef<br></blockquote><blockquote type="cite">__________________<br></blockquote><blockquote type="cite"><a href="http://www.fastmail.fm/">http://www.fastmail.fm</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br></blockquote><blockquote type="cite">List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br></blockquote><blockquote type="cite">Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote><br><div><div>On Jun 24, 2011, at 8:31 AM, Graham Ritchie wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Stef,<br><br>This part of the variation API changed quite a lot under the hood for v62, and we did try to maintain the same interface, but you may have found somewhere where the interface has changed. If you could send me a copy of the script, or even just a minimal script that exhibits the same bug, I will be able to try to establish the problem much more quickly.<br><br>Cheers,<br><br>Graham<br><br><br>On 24 Jun 2011, at 15:23, <a href="mailto:mailsvl@fastmail.fm">mailsvl@fastmail.fm</a> wrote:<br><br><blockquote type="cite">Hi everyone,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">We have a script based on ensembl api v60 (where it works without<br></blockquote><blockquote type="cite">errors) and it almost runs flawless with v62 as well except for one<br></blockquote><blockquote type="cite">error:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Can't call method "display_term" on an undefined value at<br></blockquote><blockquote type="cite">/data/common_modules/ensembl62/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeatureOverlap.pm<br></blockquote><blockquote type="cite">line 530.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If I remove this call/line everything runs fine:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">$consequence = $transcript_variation->display_consequence if defined<br></blockquote><blockquote type="cite">$transcript_variation->display_consequence;<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">...but then I'm left without the consequences so thats not really an<br></blockquote><blockquote type="cite">option ;) Anyone knows what change from v60 to v62 makes this method now<br></blockquote><blockquote type="cite">run into problems?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks!<br></blockquote><blockquote type="cite">Stef<br></blockquote><blockquote type="cite">__________________<br></blockquote><blockquote type="cite"><a href="http://www.fastmail.fm">http://www.fastmail.fm</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br></blockquote><blockquote type="cite">List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br></blockquote><blockquote type="cite">Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote><br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></div></blockquote></div><br></body></html>