Hello Martin,
Thanks for pointing that out. I reproduced it and it led me to a line of code with a comment against it: // FIXME getDefaultToolkit throws an exception in Headless mode which I added a year ago (blush). As you say, I don't think it creates a functional problem here, but we can tidy up the exception handling. Mit freundlichen Grüßen. Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carsta...@dundee.ac.uk<mailto:g.m.carsta...@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: jalview-dev-boun...@jalview.org <jalview-dev-boun...@jalview.org> on behalf of Martin Raden <mm...@informatik.uni-freiburg.de> Sent: 18 February 2018 17:05:00 To: jalview-dev@jalview.org Subject: [Jalview-dev] bioconda jalview : Headlessexception Hi all, with the recent bioconda jalview installation I get for a call like this jalview -nodisplay -open mRNA.fasta -feature mRNA_feature.txt -annotation mRNA_annotation.txt -svg mRNA.svg an output like that ######################### Java version: 1.8.0_121 amd64 Linux 2.6.32-696.18.7.el6.x86_64 Jalview Version: 2.10.3-1 (bioconda git-commit: []) CMD [-open mRNA.fasta] executed successfully! File format identified as Fasta Feb 18, 2018 5:55:40 PM jalview.util.MessageManager <clinit> INFO: Getting messages for lang: en_US java.awt.HeadlessException CMD [-annotations mRNA_annotation.txt] executed successfully! Written alignment in Fasta format to mRNA_feature.txt Creating SVG image: mRNA.svg ######################### I get the output I want but as far as I got the docu right, there shouldnt be any HeadlessException in -nodisplay mode.. right? Just to ping.. :) Thanks and best, Martin -- Dr. Martin Raden, nee Mann, Postdoc Bioinformatics - Prof. Dr. R. Backofen Department of Computer Science Albert-Ludwigs-University Freiburg Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany Tel: ++49-761-203-8254 (Monday-Wednesday) Fax: ++49-761-203-7462 http://www.bioinf.uni-freiburg.de/~mmann/ Forest Growth and Dendroecology Institute of Forest Sciences Albert-Ludwigs-University Freiburg Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany Tel: ++49-761-203-3733 (Thursday+Friday) Fax: ++49-761-203-3740 http://www.iww.uni-freiburg.de _______________________________________________ Jalview-dev mailing list Jalview-dev@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev The University of Dundee is a registered Scottish Charity, No: SC015096
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