I've been (Teams) chatting with Mateusz as after I recommended using the snap install of Eclipse on linux, he's spotted that you can't put the j2s jar into the dropins dir because snap installs it ro (in fact, MW says it mounts it ro). I gave him the recipe of command line args that the gradle build uses to add an external dropins dir and he reports that that does the trick. I've also tested that a snap installed eclipse works well with the gradle jalviewjs build itself (as an alternative to a ~buildtools installation). As it's RO it can't get messed up.
This info should definitely go in the building.md for JalviewJS, which I will keep in mind. I wonder about having a one line script in utils/jalviewjs too just as a helper script (as a workaround for system installed eclipse, or anyone who doesn't want to put a plugin directly into the dropins folder).
In which case I should probably make an issue to a) remind me and b) put the information somewhere.
Curious...example.org, example.com, example.net seem to have disappeared off DNS servers. example.edu is still there. I used example.org in HelpLinksChecker to test for internet connectivity.
@benzoid is it possible to add Gradle tasks to run this class and also MessageBundleChecker? Can't run directly from Eclipse since /utils is not a source folder.
@benzoid is it possible to add Gradle tasks to run this class and also MessageBundleChecker? Can't run directly from Eclipse since /utils is not a source folder.
...ran HelpLinksChecker (hacked source path) and found this curiosity: help/index.html has a link to http://www-test.jalview.org/about/documentation which is now an invalid path (domain is there). I propose to remove the "-test" (added Nov 2012).
That is, the link from http://www.jalview.org/help.html to '.../about/documentation' is broken.
If I click through from a JIRA issue to view commit diffs, they don't display.
Unable to get content for src/jalview/api/JalviewApp.java@7eea865f7a04c9dde807f907155f0e6e4c86f7b9
Error while communicating with VCS:
While executing: "git cat-file blob 0548c85fb1ca4de1eb4cc5d2f68da67b17cb28ef" in [/opt/homes/crucible/fisheye_data/var/cache/jalview/clone]
git could not be started
Cannot run program "git" (in directory "/opt/homes/crucible/fisheye_data/var/cache/jalview/clone"): error=2, No such file or directory
error=2, No such file or directory
Unable to get content for src/jalview/api/JalviewApp.java@7eea865f7a04c9dde807f907155f0e6e4c86f7b9
Error while communicating with VCS:
While executing: "git cat-file blob 0548c85fb1ca4de1eb4cc5d2f68da67b17cb28ef" in [/opt/homes/crucible/fisheye_data/var/cache/jalview/clone]
git could not be started
Cannot run program "git" (in directory "/opt/homes/crucible/fisheye_data/var/cache/jalview/clone"): error=2, No such file or directory
error=2, No such file or directory
3 replies
there's also 3.30-4pm but I think I need to have a break from continuous meetings today.
yes - agree with that. If there are 'defects' still flagged then the person who raised them could take a look - particularly if you are closing the review without having resolved them, but for the most part code reviews are just to make sure others have taken a look at the code you committed to spot crazies and to see what new things you've brought in.
@foreveremain When Preferences.java looks to see if USE_PROXY is true, if it isn't then it looks like Preferences.ok_actionPerformed actively removes values from the system properties http.proxyHost and http.proxyPort. These might have been passed in by user or getdown. What do we want to do here? Obviously if it's already set and saved in .jalview_properties then they will be used, but if they get set by a launching agent, disable? warn?
My suggestion is USE_PROXY should be false to allow external setting, and an info could go in the Java console if the properties are already set.
My suggestion is USE_PROXY should be false to allow external setting, and an info could go in the Java console if the properties are already set.
2 replies
Hmm, but in the case of a user turning it off then they need to be unset...
My last build (just now) failed https://builds.jalview.org/browse/JB-GDB191-JOB1-3/log
Not quite sure why but
_XSERVTransSocketUNIXCreateListener: ...SocketCreateListener() failed
20-Jul-2020 09:18:59 _XSERVTransMakeAllCOTSServerListeners: server already running
20-Jul-2020 09:18:59 (EE)
20-Jul-2020 09:18:59 Fatal server error:
20-Jul-2020 09:18:59 (EE) Cannot establish any listening sockets - Make sure an X server isn't already running(EE)
Not quite sure why but
_XSERVTransSocketUNIXCreateListener: ...SocketCreateListener() failed
20-Jul-2020 09:18:59 _XSERVTransMakeAllCOTSServerListeners: server already running
20-Jul-2020 09:18:59 (EE)
20-Jul-2020 09:18:59 Fatal server error:
20-Jul-2020 09:18:59 (EE) Cannot establish any listening sockets - Make sure an X server isn't already running(EE)
1 reply
Actually compile and test seems to have run ok. Error return code from Clover after this? :
/usr/bin/xvfb-run: line 186: kill: (499) - No such process
/usr/bin/xvfb-run: line 186: kill: (499) - No such process
The branch name is right but not right :( It stems from me having merged a lot of branches I'd been working on together to avoid clashes when merged onto the release branch.
i.e. it is a merge of all those issues, but JAL-3633 (the last of them) is open again.
foreveremain @foreveremain waves
@foreveremain @gmungoc Whilst testing JAL-3509 I've found that drag and dropping an alignment file onto an alignment window stopped working in releases/Release_2_11_1_Branch which I have tracked down to commit db9f5c502 which was merging in my JAL-3609 and JAL-3608 branches (the behaviour changed to opening a new alignment window rather than appending the sequences into the existing alignment window). JAL-3609 and JAL-3608 were HiDPI (linux) and LaF changes, I don't think anything in jalview.gui changed, so I can't immediately think what has caused the problem -- any ideas where I should be looking?
8 replies
@/all
Hi folks, I'm Adhitya, a visualization-user interfaces-data analyst guy. I really wanted to apply for the research engineer position, but it turns out that I just landed another job. Anyway, I would still like to contribute and learn more. I am generally free on the evenings/nights and weekends. So let me know if there any low-hanging fruits! :)
6 replies