Package: jalview Version: 2.11.5.0+dfsg-2 Severity: normal X-Debbugs-Cc: [email protected]
Dear Maintainer, F2 is supposed to toggle Cursor mode in Jalview. When I start Jalview and open an alignment, pressing F2 does nothing and the program stays in Normal mode. Nor does editing an alignment work: pressing up/down arrow with a sequence selected does not move it up or down, pressing space does not insert a gap, etc. However, if I just click around enough, the program starts working normally: going to Tools -> Preferences -> Web Services and deleting a service URL makes editing an alignment and switching to Cursor mode work. So does opening and closing another view of the alignment. Here is the info that Jalview prints when started from the command line: Jalview non-release Version: TEST Jalview non-release Installation: unknown Channel: default Build Date: unknown Preferences file: unknown Log file: unknown Java version: 25.0.4-ea Java home: /usr/lib/jvm/java-25-openjdk-amd64 Java launch class: jalview.bin.Jalview Java platform: Linux 7.1.3+deb14-amd64 (amd64) Java LAF: Metal (javax.swing.plaf.metal.MetalLookAndFeel) Java Virtual Machine PID: 10070 Using default properties file '/home/stepan/.jalview_nonrelease_properties' Jalview non-release version: 2.11.5.0+dfsg-2 (deb) Setting log level to INFO Setting log level to INFO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (107ms) INFO - Getting messages for lang: en_US Linux platform only! You may have the following warning next: "WARNING: An illegal reflective access operation has occurred" This is expected and cannot be avoided, sorry about that. INFO - JALVIEW: CREATED DESKTOP WARN - Error when running commands WARN - When trying to access questionnaire URL https://www.jalview.org/cgi-bin/questionnaire.pl java.io.IOException: Server returned HTTP response code: 500 for URL: https://www.jalview.org/cgi-bin/questionnaire.pl?checkresponse=1 at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1696) ~[?:?] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1302) ~[?:?] at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:223) ~[?:?] at jalview.util.HttpUtils.openStream(HttpUtils.java:286) ~[jalview-2.11.5.0.jar:2.11.5.0] at jalview.util.HttpUtils.openStream(HttpUtils.java:268) ~[jalview-2.11.5.0.jar:2.11.5.0] at jalview.gui.UserQuestionnaireCheck.checkresponse(UserQuestionnaireCheck.java:65) ~[jalview-2.11.5.0.jar:2.11.5.0] at jalview.gui.UserQuestionnaireCheck.run(UserQuestionnaireCheck.java:108) ~[jalview-2.11.5.0.jar:2.11.5.0] at java.lang.Thread.run(Thread.java:1474) ~[?:?] Warning - overwriting a sequenceSetId for a viewport! INFO - ALL CLOSED INFO - Desktop exiting. LAUNCHER - JVM exited with value 0 -- System Information: Debian Release: forky/sid APT prefers testing APT policy: (900, 'testing'), (800, 'unstable') Architecture: amd64 (x86_64) Kernel: Linux 7.1.3+deb14-amd64 (SMP w/8 CPU threads; PREEMPT) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages jalview depends on: ii debconf [debconf-2.0] 1.5.92 ii default-jre 2:1.25-77 ii groovy 2.4.21-10 ii javahelp2 2.0.05.ds1-10 ii libandroid-json-org-java 20121204-20090211-7 ii libapache-mime4j-java 0.8.13-1 ii libaxis-java 1.4-29 ii libbiojava6-java 6.1.0+dfsg-6 ii libcommons-discovery-java 0.5-4 ii libcommons-math3-java 3.6.1-4 ii libhtsjdk-java 5.0.0+dfsg-1 ii libhttpclient-java 4.5.14-1 ii libhttpcore-java 4.4.16-1 ii libhttpmime-java 4.5.14-1 ii libintervalstorej-java 1.2+dfsg-5 ii libjaba-client-java 2.2.0-2 ii libjaxb-api-java 2.3.1-1 ii libjaxb-java 2.3.0.1-11 ii libjaxrs-api-java 2.1.2-2 ii libjaxws-java 2.3.0.2-2 ii libjersey1-client-java 1.19.3-8 ii libjersey1-core-java 1.19.3-8 ii libjetty9-java 9.4.58-2 ii libjfreesvg-java 5.0.7-1 ii libjmol-java 16.3.55+dfsg-1 ii libjson-simple-java 2.3.0-2 ii libjsoup-java 1.15.3-1 ii libjswingreader-java 0.3-4 ii liblog4j1.2-java 1.2.17-11 ii liblog4j2-java 2.19.0-2 ii libmiglayout-java 11.4.2+ds-2 ii libslf4j-java 1.7.32-2 ii libvamsas-client-java 0.2+dfsg-2 ii varna 3-93+ds-7 jalview recommends no packages. Versions of packages jalview suggests: ii clustalw 2.1+lgpl-7 ii kalign 1:3.5.1-1+b1 ii t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -- debconf information: jalview/identifiersservice: true jalview/jws2services: true jalview/news: true jalview/questionnaire: true jalview/htmltemplates: true __ This is the maintainer address of Debian's Java team <https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-java-maintainers>. Please use [email protected] for discussions and questions.
