- Pharo-dev - lists.pharo.org

Re: [Pharo-dev] pharo 3.0 image

by kilon alios

you better post a screenshot and the precise specs of your system. Pharo works fine here. Have you tried PharoLauncher ? On Sun, Dec 29, 2013 at 1:34 PM, Johan Brichau <johan(a)inceptive.be> wrote: > Thereâs a debug log I attach to this page. > According to the log, itâs in non-interactive modeâ¦ but Iâm launching it > from the Mac Finder... > > I tried both stable and latest vm > > A download with the zeroconf scripts will work but if I try to put the vm > and the image at those places I intend to work with, it breaks. > Mind that it does work with the 30526 image > > > > > On 29 Dec 2013, at 12:23, Johan Brichau <johan(a)inceptive.be> wrote: > > > What is the latest âworkingâ pharo 3 image? > > > > Every recent build I try to download opens with a blank screen and I > cannot do anything. > > The latest build I downloaded some time ago was 30526 and that one opens > fineâ¦ > > > > Ideas? > > > > Johan > > >

Dec. 29, 2013

Re: [Pharo-dev] Class-side hierarchy to show meta-classes?

by HernÃ¡n Morales Durand

Hi Ben, What you may like is to browse multiple parallel hierarchies. This is done in TaxoNote: http://www.nomencurator.org/InfoVis2003/questions.html AFAIK it was never done in any Smalltalk flavor. Cheers, HernÃ¡n 2013/12/27 <btc(a)openinworld.com> > Working on case 12498 [1] has evolved to the idea of the class-side > hierarchy showing meta-classes per attached snapshot. I'd like some > community feedback on the idea. Note the metaclasses are bolded similar to > how bold indicates class-side methods. > > Thanks Nicolai for your help so far. > cheers -ben > > [1] https://pharo.fogbugz.com/f/cases/12498/ >

Dec. 29, 2013

Re: [Pharo-dev] pharo 3.0 image

by Sven Van Caekenberghe

It seems the search for the .sources fails. On 29 Dec 2013, at 12:34, Johan Brichau <johan(a)inceptive.be> wrote: > Thereâs a debug log I attach to this page. > According to the log, itâs in non-interactive modeâ¦ but Iâm launching it from the Mac Finder... > > I tried both stable and latest vm > > A download with the zeroconf scripts will work but if I try to put the vm and the image at those places I intend to work with, it breaks. > Mind that it does work with the 30526 image > > > <PharoDebug.log> > On 29 Dec 2013, at 12:23, Johan Brichau <johan(a)inceptive.be> wrote: > >> What is the latest âworkingâ pharo 3 image? >> >> Every recent build I try to download opens with a blank screen and I cannot do anything. >> The latest build I downloaded some time ago was 30526 and that one opens fineâ¦ >> >> Ideas? >> >> Johan >

Dec. 29, 2013

Re: [Pharo-dev] pharo 3.0 image

by Johan Brichau

Thereâs a debug log I attach to this page. According to the log, itâs in non-interactive modeâ¦ but Iâm launching it from the Mac Finder... I tried both stable and latest vm A download with the zeroconf scripts will work but if I try to put the vm and the image at those places I intend to work with, it breaks. Mind that it does work with the 30526 image On 29 Dec 2013, at 12:23, Johan Brichau <johan(a)inceptive.be> wrote: > What is the latest âworkingâ pharo 3 image? > > Every recent build I try to download opens with a blank screen and I cannot do anything. > The latest build I downloaded some time ago was 30526 and that one opens fineâ¦ > > Ideas? > > Johan

Dec. 29, 2013

Re: [Pharo-dev] pharo 3.0 image

by HernÃ¡n Morales Durand

Try this: wget -O- get.pharo.org/30+vm | bash Pharo3.0 Latest update: #30664 2013/12/29 Johan Brichau <johan(a)inceptive.be> > What is the latest âworkingâ pharo 3 image? > > Every recent build I try to download opens with a blank screen and I > cannot do anything. > The latest build I downloaded some time ago was 30526 and that one opens > fineâ¦ > > Ideas? > > Johan >

Dec. 29, 2013

Tagging #catalogContactInfo?

by HernÃ¡n Morales Durand

Hi Stef, Is there any format for defining #catalogContactInfo contents? For example ^ '[[Author:Walter White]] [[e-mail: blabla(a)bla.com]] [[website: http://www.www.www]]' Cheers, HernÃ¡n

Dec. 29, 2013

pharo 3.0 image

by Johan Brichau

What is the latest âworkingâ pharo 3 image? Every recent build I try to download opens with a blank screen and I cannot do anything. The latest build I downloaded some time ago was 30526 and that one opens fineâ¦ Ideas? Johan

Dec. 29, 2013

Re: [Pharo-dev] A small patch for Zinc (related to XMLParser)

by Sven Van Caekenberghe

Hi Monty, On 29 Dec 2013, at 07:47, monty <monty.os(a)engineer.com> wrote: > Hi Sven. your ZnMimeType>>isBinary method is wrongly treating application/xml-dtd and other XML application subtypes like xml-external-parsed-entity as binary instead of text. To be consistent, if you're going to treat one applicaiton/xml type as text, you should treat them all that way. I attached a patch that fixes it by treating "-" as a subtype separator too. More info: http://www.ietf.org/rfc/rfc3023.txt Excellent extension, I integrated it in Zinc upstream, bleedingEdge === Name: Zinc-Resource-Meta-Core-SvenVanCaekenberghe.30 Author: SvenVanCaekenberghe Time: 29 December 2013, 12:05:01.614278 pm UUID: 18ce8118-2e25-43f1-8524-0d6b817be8cb Ancestors: Zinc-Resource-Meta-Core-SvenVanCaekenberghe.29 Extend ZnMimeType>>#isBinary to recognize application/xml-dtd (and more from http://www.ietf.org/rfc/rfc3023.txt) as non-binary by using both + and - as subtype separators when looking for xml (thanks monty); Extend ZnMimeTypeTests>>testIsBinary to cover the new functionality === Name: Zinc-Resource-Meta-Tests-SvenVanCaekenberghe.18 Author: SvenVanCaekenberghe Time: 29 December 2013, 12:05:30.83878 pm UUID: 4c2e4a78-c496-41b7-9f5c-cd90b982a9d6 Ancestors: Zinc-Resource-Meta-Tests-SvenVanCaekenberghe.17 Extend ZnMimeType>>#isBinary to recognize application/xml-dtd (and more from http://www.ietf.org/rfc/rfc3023.txt) as non-binary by using both + and - as subtype separators when looking for xml (thanks monty); Extend ZnMimeTypeTests>>testIsBinary to cover the new functionality === > Also, my lack of commit messages is because if I'm just making some small changes to private classes/methods or refactoring, I don't see the point in detailing it for users who don't (and shouldn't) care. They should just focus on the public API (which I haven't changed much). Hmm, I think that for both the community and for yourself in half a year it is important to write commit messages like the one I wrote above. It does not have to go into much detail, something like ârefactored the DOM parser for entitiesâ is enough - it will help hunting for regressions and other problems. The writeup of your changes that was in the email is already very helpful. BTW, thanks for working on XML parser, it is an important tool. > <ZnMimeType-isBinary.st> Thanks again for the patch ! Regards, Sven -- Sven Van Caekenberghe Proudly supporting Pharo http://pharo.org http://association.pharo.org http://consortium.pharo.org

Dec. 29, 2013

Re: [Pharo-dev] Error in loading libreries

by StÃ©phane Ducasse

you should pay attention that you added the right kind of repository. Because repository kinds (ss, ss3, smalltalkhub) check that they got the right format. Stef > Hi, > > every time I try to load a package from Monticello, I receive the message: > > ERROR: MCHttpRepository expected. > > Can anybody tell me why and suggest me a workeround? > > Many thanks and seasonâs greetings > > Lorenzo > >

Dec. 28, 2013

Re: [Pharo-dev] Relation tower is coming for Roassal

by HernÃ¡n Morales Durand

Hi Tudor. This is clearer now. Let me rewrite my concern so you can have a better understanding. I have been reviewing the Roassal code and resulted very clear to me how to get a visualization by scripting. But I am afraid that you would get better feedback from scientists using MATLAB, R and similar software every day. Most of them, I presume, didn't hear about Smalltalk or Moose. Having a more directed bridge to attract them would pay off. See for example what people is doing behind the University of Florida http://www2.research.att.com/~yifanhu/gallery/indexAll.html (first hit for "visualizing big matrices" in Google). They're using MATLAB, Rutherford/Boeing and MatrixMarket formats http://www.cise.ufl.edu/research/sparse/matrices/ Please don't get me wrong, I am not asking you or anyone to implement such layer. I am saying it would be nice to have more Smalltalkers to build these missing pieces. What can we do about it? BTW I've just found another inspirational picture for the relation tower: http://biopython.org/DIST/docs/tutorial/images/tRNA_chrom.png Cheers, HernÃ¡n 2013/12/27 Tudor Girba <tudor(a)tudorgirba.com> > Hi, > > I think there is a little confusion here. > > I meant to say that Roassal allows you to map your whatever objects onto a > visualization. How you do this mapping is completely up to you. If you have > a million objects, you will have to do some preprocessing yourself. That is > all. There really is no magic involved. I just like to use "transformation" > as a term in order to point out that visualization is no different than any > other object manipulation. > > Did I address your concern? > > Cheers, > Doru > > > > > On Thu, Dec 26, 2013 at 9:48 PM, HernÃ¡n Morales Durand < > hernan.morales(a)gmail.com> wrote: > >> Hi Tudor, >> Thanks for the clarification. >> Can you comment or point a link for the mechanism to transform my data >> for Roassal? Because if you want to visualize big data like population or >> association studies input is sometimes millions of rows. Of course I am not >> asking you to write my parsers :) >> >> Cheers, >> >> HernÃ¡n >> >> >> >> >> 2013/12/26 Tudor Girba <tudor(a)tudorgirba.com> >> >>> Hi HernÃ¡n, >>> >>> The input should be independent from the visualization engine. Roassal >>> offers you a way of transforming your objects into a visualization and it >>> should not be responsible for the input formats. >>> >>> Cheers, >>> Doru >>> >>> >>> On Thu, Dec 26, 2013 at 9:28 PM, HernÃ¡n Morales Durand < >>> hernan.morales(a)gmail.com> wrote: >>> >>>> Hi Alexandre and Ricardo, >>>> >>>> I am glad to see your advances in Roassal visualization! >>>> I wonder which input formats do you plan to support? >>>> >>>> Your relation tower can be used to visualize the crossover percentages >>>> between haplotype blocks. For example, here are some Haplotypes drawings >>>> from Haploview (http://en.wikipedia.org/wiki/Haploview) which may >>>> interest you: >>>> >>>> >>>> http://www.jnsbm.org/viewimage.asp?img=JNatScBiolMed_2012_3_2_139_101887_f1… >>>> from this paper >>>> http://www.jnsbm.org/temp/JNatScBiolMed32139-5367486_145434.pdf >>>> >>>> http://www.mailund.dk/wp-content/uploads/2010/04/haplotypes.png >>>> >>>> http://www.mailund.dk/wp-content/uploads/2010/04/journal.pone_.0010207.g005… >>>> >>>> I can send you the exported haplotypes from a study if you are >>>> interested. It contains 131 blocks which is somewhat big to attach to this >>>> list. The only problem I see is that a parser is needed to parse the >>>> Haplotype text output file, although the format should not be difficult to >>>> parse. >>>> >>>> Cheers, >>>> >>>> HernÃ¡n >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 2013/12/17 Alexandre Bergel <alexandre.bergel(a)me.com> >>>> >>>>> Hi! >>>>> >>>>> A new builder for Roassal is comingâ¦ The goal of Relation tower is to >>>>> easily visualize relations between group of elements. We had the >>>>> inspiration from the following website http://peoplemov.in/#! >>>>> >>>>> Here are some screenshots: >>>>> >>>>> https://www.facebook.com/media/set/?set=a.559114290841839.1073741837.340543… >>>>> >>>>> If you like these screenshots, then you know where the like button is >>>>> :-) >>>>> >>>>> We will have this visualization on the web, thanks to our smooth and >>>>> nice Pharo2Amber migration process. >>>>> >>>>> Any idea on how to extend/apply Relation tower? Any set of data you >>>>> want us to play with? Your data? >>>>> Feedback are very welcome! >>>>> >>>>> Cheers, >>>>> Ricardo & Alexandre >>>>> >>>>> -- >>>>> _,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;: >>>>> Alexandre Bergel http://www.bergel.eu >>>>> ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;. >>>>> >>>>> >>>>> >>>> >>> >>> >>> -- >>> www.tudorgirba.com >>> >>> "Every thing has its own flow" >>> >> >> > > > -- > www.tudorgirba.com > > "Every thing has its own flow" >

Dec. 28, 2013