OE Webex 5Feb08
Jump to navigation
Jump to search
02/05/2008 09:42:08 AM from David OS to All Participants: :( 02/05/2008 09:42:15 AM from Nomi Harris to All Participants: That was the first time WebEx died on me! 02/05/2008 09:42:20 AM from Nomi Harris to All Participants: I guess I've been lucky so far! 02/05/2008 09:42:22 AM from Jen Deegan to All Participants: no problem :-) 02/05/2008 09:42:33 AM from Nomi Harris to All Participants: Anyway, Jen, did you stick the regulates into your ontology by hand? 02/05/2008 09:43:12 AM from Nomi Harris to All Participants: Hello? 02/05/2008 09:43:40 AM from Jen Deegan to All Participants: the first time I did, but this time I chose it from the list 02/05/2008 09:43:40 AM from midori to All Participants: OK, changed to built-in icons and they're all still showing up. 02/05/2008 09:43:57 AM from Jen Deegan to All Participants: what term are you looking at? 02/05/2008 09:44:09 AM from Nomi Harris to All Participants: Are you two co-located, Jen and midori? 02/05/2008 09:44:14 AM from midori to All Participants: yes 02/05/2008 09:44:24 AM from midori to All Participants: (I'm looking at some metabolism terms ...) 02/05/2008 09:44:26 AM from Nomi Harris to All Participants: So maybe you can work together and figure out why it's not showing up for Jen? 02/05/2008 09:45:12 AM from Jen Deegan to All Participants: we're workign on it 02/05/2008 09:45:20 AM from Nomi Harris to All Participants: Ok. 02/05/2008 09:45:27 AM from Nomi Harris to All Participants: I've been trying to figure out the sub-selection bug. 02/05/2008 09:45:45 AM from midori to All Participants: argh. that one's gly. 02/05/2008 09:45:52 AM from midori to All Participants: ... ugly (like my typing) 02/05/2008 09:46:06 AM from Nomi Harris to All Participants: I'm confused about what's happening. For some reason, when it considers its candidates for what's currently the subselection, it doesn't always consider everything that's selected. 02/05/2008 09:46:12 AM from Nomi Harris to All Participants: Sometimes it leaves out some of the items. 02/05/2008 09:46:20 AM from Nomi Harris to All Participants: But I'm not sure why that's happening. 02/05/2008 09:46:24 AM from Nomi Harris to All Participants: I will continue investigating. 02/05/2008 09:46:42 AM from Nomi Harris to All Participants: Meanwhile, I'm also trying to track down memory leaks in OE2 that may be causing it to run out of memory sometimes. 02/05/2008 09:46:49 AM from Nomi Harris to All Participants: Have you guys had it run out of memory? 02/05/2008 09:47:00 AM from Erika to All Participants: sometimes 02/05/2008 09:47:16 AM from Nomi Harris to All Participants: I added a memory-checking thread that should warn you if you're almost out of memory. 02/05/2008 09:47:18 AM from Jen Deegan to All Participants: I have trouble with it running slowly 02/05/2008 09:47:21 AM from Nomi Harris to All Participants: Of course at that point it may already be too late to save. 02/05/2008 09:47:31 AM from Nomi Harris to All Participants: The running slowly could be a symptom of running out of memory. 02/05/2008 09:47:36 AM from midori to All Participants: I haven't seen the low-memory warning in beta29 yet, but I've certainly had symptoms consistent with out-of-memory in several betas 02/05/2008 09:47:39 AM from David OS to All Participants: Only if runining on my puny latop. OK on a mac with 2G ram. 02/05/2008 09:48:15 AM from Nomi Harris to All Participants: There's also evidence that there are components that are doing stuff even when they're not showing, which could be contributing to the slowness. 02/05/2008 09:48:41 AM from Erika to All Participants: It happend to me when I load three ontology at the same time.OE run out of memory 02/05/2008 09:49:04 AM from Nomi Harris to All Participants: You're looking at all three together, not sequentially? 02/05/2008 09:49:25 AM from Erika to All Participants: mmm! unfortunately three together 02/05/2008 09:49:47 AM from Nomi Harris to All Participants: Hmm. I'm not sure that fixing memory leaks will help that much, since you have them all in memory at the same time. 02/05/2008 09:50:27 AM from Nomi Harris to All Participants: What happens with memory leaks is that when you load a new ontology, OE may still have dangling references to the old one, so it doesn't reclaim that memory, and after a while you run out. 02/05/2008 09:50:46 AM from Nomi Harris to All Participants: This used to happen in Apollo before Mark Gibson fixed the memory leaks. 02/05/2008 09:51:09 AM from Erika to All Participants: oh, I understand!...an other case was when I selected too many terms to be showed in DAG viewer 02/05/2008 09:51:21 AM from Nomi Harris to All Participants: The DAG viewer seems to be problematic in various ways. 02/05/2008 09:51:47 AM from Nomi Harris to All Participants: I haven't tried loading multiple ontologies at the same time--how do you even do that? 02/05/2008 09:51:56 AM from Erika to All Participants: Load terms 02/05/2008 09:52:06 AM from Erika to All Participants: and then select more than one file 02/05/2008 09:52:18 AM from Erika to All Participants: I usually work with CheBI and GO 02/05/2008 09:52:26 AM from Erika to All Participants: or Plant ontology and GO 02/05/2008 09:52:33 AM from Nomi Harris to All Participants: I'll have to try that. 02/05/2008 09:52:35 AM from David OS to All Participants: Ahhh - Chebi's pretty huge. 02/05/2008 09:52:41 AM from Erika to All Participants: yes! 02/05/2008 09:53:45 AM from midori to All Participants: Meanwhile, we've solved the icon problem -- Jen and I had different files loaded! 02/05/2008 09:54:01 AM from Nomi Harris to All Participants: Different ontology files? 02/05/2008 09:54:17 AM from midori to All Participants: long story ... 02/05/2008 09:54:27 AM from Nomi Harris to All Participants: Ok, glad you got it straightened out. 02/05/2008 09:54:49 AM from Nomi Harris to All Participants: So the top priority bugs are still slowness/memory problems and sub-selection, right? 02/05/2008 09:54:55 AM from Jen Deegan to All Participants: I have an icon question 02/05/2008 09:54:57 AM from Nomi Harris to All Participants: Any other ones on that must-fix-before-public-release list? 02/05/2008 09:55:02 AM from Nomi Harris to All Participants: Yes, Jen, what's your icon question? 02/05/2008 09:55:09 AM from Jen Deegan to All Participants: do you know how the icon size is set? 02/05/2008 09:55:15 AM from Jen Deegan to All Participants: is it be the sidth or height or what? 02/05/2008 09:55:23 AM from Jen Deegan to All Participants: width, that was 02/05/2008 09:55:33 AM from Nomi Harris to All Participants: Hmm, I don't know. I can check later and let you know. Why? 02/05/2008 09:56:03 AM from Jen Deegan to All Participants: some of mine are different sizes from other and the is_a and part_of ones look neater because they are square and the same size with a nice background 02/05/2008 09:56:07 AM from midori to All Participants: Oughta fix, #1: sub-selection (but you knew that) 02/05/2008 09:56:27 AM from Jen Deegan to All Participants: would be better if R ones were also square with nice background 02/05/2008 09:56:28 AM from midori to All Participants: Oughta fix, #2: right-click editing bug has reappeared; new SF item today 02/05/2008 09:56:44 AM from Nomi Harris to All Participants: Reappeared! It went away for a while? 02/05/2008 09:56:57 AM from Nomi Harris to All Participants: I can't imagine what I've changed that would have affected that. 02/05/2008 09:57:50 AM from midori to All Participants: yup. and I can't think of anything either ... would it be worthwhile for me to go back and figure out which betas do and don't have it working? 02/05/2008 09:58:10 AM from Nomi Harris to All Participants: If that's easy for you to do, that would be useful info. 02/05/2008 09:58:34 AM from midori to All Participants: A bit tedious, but not difficult, so if it'll help, ok. 02/05/2008 09:58:59 AM from Nomi Harris to All Participants: Tell you what, I'll try to do it myself, assuming I can recreate the bug in the current version. 02/05/2008 09:59:09 AM from Nomi Harris to All Participants: If I can't, I'll let you know. 02/05/2008 09:59:23 AM from Nomi Harris to All Participants: I'm still mystified about why I have to click twice to see the selected thing in the Text Editor and you don't. 02/05/2008 09:59:23 AM from midori to All Participants: ok 02/05/2008 09:59:29 AM from midori to All Participants: me too 02/05/2008 10:00:10 AM from Nomi Harris to All Participants: I hope I can fix sub-selection. The whole selection process is pretty complicated. 02/05/2008 10:00:14 AM from midori to All Participants: I've tried Mac installer and platform-independent; Mac OS X 10.4.11; PowerPC ... 02/05/2008 10:00:44 AM from Nomi Harris to All Participants: I wish I could look over your shoulder. Any trips to California in your near future? 02/05/2008 10:01:04 AM from midori to All Participants: nope ... 02/05/2008 10:01:19 AM from midori to All Participants: would webex app sharing help at all? 02/05/2008 10:01:25 AM from Nomi Harris to All Participants: Hey, that's a good idea! 02/05/2008 10:01:41 AM from Nomi Harris to All Participants: Maybe when we're done with the official meeting, midori can hang around and we can try it? 02/05/2008 10:02:13 AM from midori to All Participants: OK; I can be here for about another half hour from now. 02/05/2008 10:02:29 AM from Nomi Harris to All Participants: Are we pretty much done now? 02/05/2008 10:02:32 AM from Nomi Harris to All Participants: Any other issues? 02/05/2008 10:02:43 AM from Jen Deegan to All Participants: hi 02/05/2008 10:02:48 AM from midori to All Participants: I've done a tiny bit of documentation today ... 02/05/2008 10:02:53 AM from Jen Deegan to All Participants: I have just tried making an icon that is the same width as height 02/05/2008 10:03:06 AM from Jen Deegan to All Participants: and it gets the left hand side chopped odff in oboedit 02/05/2008 10:03:09 AM from Jen Deegan to All Participants: off 02/05/2008 10:03:18 AM from Jen Deegan to All Participants: isn't that a bit weird 02/05/2008 10:03:27 AM from Wasila to All Participants: (have to run to a meeting -- will attend next week - bye!) 02/05/2008 10:03:45 AM from Nomi Harris to All Participants: (Bye, Wasila) I don't know how it constrains the icons. Send me that one and I will investigate. 02/05/2008 10:03:48 AM from David OS to All Participants: Bye Wasila 02/05/2008 10:05:29 AM from Jen Deegan to All Participants: thanks, will do 02/05/2008 10:05:48 AM from Nomi Harris to All Participants: Ok, bye everyone except midori? 02/05/2008 10:06:04 AM from Erika to All Participants: Thanks Nomi. Bye everybody! 02/05/2008 10:06:08 AM from Nomi Harris to All Participants: See you all next Tues. 02/05/2008 10:06:32 AM from Jen Deegan to All Participants: cheerio :-) 02/05/2008 10:06:48 AM from David OS to All Participants: OK. See you next week. Back to editing next week so may have more to report. D 02/05/2008 10:07:12 AM from Nomi Harris to All Participants: Could you see that? 02/05/2008 10:07:25 AM from Nomi Harris to All Participants: Oh, did Karen just join? Hi, Karen! 02/05/2008 10:07:52 AM from midori to All Participants: yes, I saw your OBO-Edit. Should I look for something specific? 02/05/2008 10:08:00 AM from midori to All Participants: (& hi Karen) 02/05/2008 10:08:09 AM from Nomi Harris to All Participants: Could you see me select a relation and click on it? 02/05/2008 10:08:26 AM from Nomi Harris to All Participants: The first one I clicked, nothing showed up in the Text Editor. The second one did. 02/05/2008 10:08:32 AM from Nomi Harris to All Participants: Should I do it again? 02/05/2008 10:08:51 AM from midori to All Participants: yes please! things can go by pretty fast when sharing ... 02/05/2008 10:08:56 AM from Nomi Harris to All Participants: Ok! 02/05/2008 10:09:12 AM from Karen Christie to All Participants: Sorry I missed the meeting, had a doctor's appt, thought I'd check if it was still going, but I see that most people have logged out, so I'm assuming it's over 02/05/2008 10:09:40 AM from Nomi Harris to All Participants: Yes, it's basically over--I'm working with midori to try to figure out why we see different behavior in the Text Editor 02/05/2008 10:09:45 AM from Nomi Harris to All Participants: Did you see it that time? 02/05/2008 10:09:47 AM from midori to All Participants: It's just me and Nomi trying to figure out why she has a bug and I don't. 02/05/2008 10:10:16 AM from Karen Christie to All Participants: OK, till next week., bye 02/05/2008 10:10:20 AM from midori to All Participants: Yes, got it. That's definitely not happening to me. 02/05/2008 10:10:24 AM from Nomi Harris to All Participants: So weird! 02/05/2008 10:10:24 AM from midori to All Participants: bye Karen 02/05/2008 10:10:37 AM from Nomi Harris to All Participants: I wonder if we have some difference in our preferences/config? 02/05/2008 10:10:48 AM from midori to All Participants: I could show you mine .. but it's probably pretty easy to imagine. 02/05/2008 10:10:55 AM from Nomi Harris to All Participants: You saw what I meant, right? I'm not dreaming? 02/05/2008 10:10:58 AM from midori to All Participants: (my obo-edit behavior, that is) 02/05/2008 10:11:11 AM from Nomi Harris to All Participants: Right, I assume yours works the way it should--you choose a term, it shows up in the Text Editor. 02/05/2008 10:11:23 AM from midori to All Participants: I did see it -- I'm convinced it's happening to you. And yep, mine's working. 02/05/2008 10:11:39 AM from Nomi Harris to All Participants: So weird. 02/05/2008 10:11:43 AM from midori to All Participants: Soooo ... what's different?? 02/05/2008 10:11:48 AM from Nomi Harris to All Participants: Can you zip up your .oboeditbeta and send it to me? 02/05/2008 10:11:56 AM from midori to All Participants: sure 02/05/2008 10:12:02 AM from Nomi Harris to All Participants: Note that I had not loaded an ontology yet. But I see the same behavior if I do. 02/05/2008 10:12:14 AM from Nomi Harris to All Participants: It also ignores my first selection when I switch between a class and a relation. 02/05/2008 10:12:37 AM from Nomi Harris to All Participants: I would be happy if this is *not* in fact a bug and I just have something configured strangely! 02/05/2008 10:12:45 AM from Nomi Harris to All Participants: The sub-selection bug is bad enough! 02/05/2008 10:12:50 AM from midori to All Participants: LIkewise, mine works with or without a file loaded. 02/05/2008 10:13:15 AM from Nomi Harris to All Participants: Ok, send me your .oboeditbeta zip file. I can't think what else to try. 02/05/2008 10:13:45 AM from Nomi Harris to All Participants: Bye? 02/05/2008 10:14:21 AM from midori to All Participants: ok, bye 02/05/2008 10:14:28 AM from Nomi Harris to All Participants: See you later.