Thanks for your input, Steve, I was able to clone the source code from the github using a git client (SmartGit 2.02). As a note to others who may be attempting to do the same, it took a really long time, probably about an hour, to clone all the files, just let it keep running.
Cheers, Matthew > Message: 1 > Date: Thu, 6 Jan 2011 16:56:42 -0600 > From: "Steve Darnell" <[email protected]> > Subject: Re: [Biojava-l] how to access biojava source control on svn > To: "Sj Pookpan" <[email protected]> > Cc: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > In the past, I have had problems using the Subclipse plug-in in Eclipse to > checkout BioJava from the svn service at github on both Windows and Mac. > This is how I worked around it... > > http://lists.open-bio.org/pipermail/biojava-dev/2010-August/004356.html > > The Subclipse svn plug-in from Tigris would fail during checkout with an > exception stating "RA layer request failed svn: REPORT of '[...]' 200 > OK" for both Windows 7 and OSX 10.6. For Windows, there are reports of > the Windows indexing service, antivirus scanners, or the Subclipse > JavaHL adapter causing svn problems. Resolving these issues did not > help. > > In the end, I used a git client on Windows to clone the biojava project > from github and then imported it into Eclipse as an existing Maven > project with the m2eclipse plug-in. > > -- > > I did not revisit my search for an integrated Eclipse solution. Now, I > mainly use the jars made by the maven auto-build system. > > ~Steve > > -----Original Message----- > From: [email protected] [mailto: > [email protected]] On Behalf Of Andreas Prlic > Sent: Wednesday, January 05, 2011 10:27 PM > To: Sj Pookpan > Cc: [email protected] > Subject: Re: [Biojava-l] how to access biojava source control on svn > > try > > svn co http://svn.github.com/biojava/biojava.git ./biojava > > > A > > On Wed, Jan 5, 2011 at 8:21 PM, Sj Pookpan <[email protected]> wrote: > > Thank you for your answer > > ??? I try the account mention on > > 'http://www.biojava.org/wiki/CVS_to_SVN_Migration' > > > > - Anonymous SVN access or > > - Developer SVN access (ssh account required) or > > - BioJava SNAPSHOT builds (anonymous, Maven required) > > > > on eclipse SVN connection user interface, the application always ask for > > 'password' to access 'svn', how do I get it pass? > > > > How ever, I already subscibe my mail to biojava mailing list (yesterday > > 05/01/2011) and waiting for mail confirmation, but until now nothing send > to > > me what the next action for me. > > > > Regards, > > > > SJP. > > > > On 1/6/2011 12:20 AM, Marco Valtas wrote: > > > > You might check the Github mirror too, code.open-bio.org seem offline > > sometimes. > > > > Cheers Marco. > > > > Sent from my iPhone > > > > On 05/01/2011, at 13:46, Andreas Prlic <[email protected]> wrote: > > > > Hi Sj, > > > > Better to post such questions to the public lists, otherwise they > > might get lost... > > > > SVN access instructions are available from > > http://www.biojava.org/wiki/CVS_to_SVN_Migration > > > > Andreas > > > > > > > > > > 2011/1/5 Sj Pookpan <[email protected]>: > > > > Dear biojava master > > > > I'm java developer and new to biojava, I want to know that how can get > > access to biojava source code from SVN (by eclipse SVN). Do I need to > > register to biojava to get user account and password (I try to find on > > biojava site but no where to register). Would you please give me the way > to > > startup this. > > > > SJP. > > > > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > ------------------------------ > > Message: 2 > Date: Thu, 6 Jan 2011 16:09:29 -0800 > From: Hara Dilley <[email protected]> > Subject: [Biojava-l] biojava3 getting the features from > alignedsequence > To: "[email protected]" <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I would like to align a set of sequences against a scaffold and get the > list of the modifications for each aligned sequence. > I am using biojava3 > I have tried to create a profile thinking that I can get the > AlignedSequences from it but that it appears to be null. > Here is part of my code: > > Profile<ProteinSequence, AminoAcidCompound> profile = > Alignments.getMultipleSequenceAlignment(lst); > Profile.getAlignedSequence(0); > > Can someone please point to an example for this or to the classes I have to > use. > Thank you, > Hara > > > > > ------------------------------ > > Message: 3 > Date: Thu, 6 Jan 2011 16:45:13 -0800 > From: Matthew Busse <[email protected]> > Subject: [Biojava-l] Checking out code > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hello all, > > I've tried several times over the past couple days to check out code from > both of the sites, and I either receive a "Connection timed out" error from > the code.open site or a "PROPFIND of '/biojava': 502 Bad Gateway ( > http://svn.github.com)" error from the github site. > > I'm using the maven and subclipse plug-ins for eclipse, and this is the > first time Ive tried to use an SVN repository, so it's possible I'm doing > something wrong, but these errors sound like it's a connection problem. > > Thanks! > > Matthew > > > ------------------------------ > > Message: 4 > Date: Thu, 6 Jan 2011 17:04:43 -0800 > From: Andreas Prlic <[email protected]> > Subject: Re: [Biojava-l] Checking out code > To: Matthew Busse <[email protected]> > Cc: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > I just tried to reproduce a fresh checkout from github and I can > confirm, it does not work correctly any more. > > ... investigating what is going on... > > A > > > > On Thu, Jan 6, 2011 at 4:45 PM, Matthew Busse > <[email protected]> wrote: > > Hello all, > > > > I've tried several times over the past couple days to check out code from > > both of the sites, and I either receive a "Connection timed out" error > from > > the code.open site or a "PROPFIND of '/biojava': 502 Bad Gateway ( > > http://svn.github.com)" error from the github site. > > > > I'm using the maven and subclipse plug-ins for eclipse, and this is the > > first time Ive tried to use an SVN repository, so it's possible I'm doing > > something wrong, but these errors sound like it's a connection problem. > > > > Thanks! > > > > Matthew > > _______________________________________________ > > Biojava-l mailing list ?- [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > ------------------------------ > > Message: 5 > Date: Thu, 6 Jan 2011 17:06:46 -0800 > From: Andreas Prlic <[email protected]> > Subject: Re: [Biojava-l] Checking out code > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > and to follow up, I believe we are seeing this problem: > > > http://support.github.com/discussions/repos/5188-fresh-checkout-of-svn-repo-shows-dozens-of-empty-files-where-they-shouldnt-be > > > > > On Thu, Jan 6, 2011 at 5:04 PM, Andreas Prlic <[email protected]> wrote: > > I just tried to reproduce a fresh checkout from github and I can > > confirm, it does not work correctly any more. > > > > ... investigating what is going on... > > > > A > > > > > > > > On Thu, Jan 6, 2011 at 4:45 PM, Matthew Busse > > <[email protected]> wrote: > >> Hello all, > >> > >> I've tried several times over the past couple days to check out code > from > >> both of the sites, and I either receive a "Connection timed out" error > from > >> the code.open site or a "PROPFIND of '/biojava': 502 Bad Gateway ( > >> http://svn.github.com)" error from the github site. > >> > >> I'm using the maven and subclipse plug-ins for eclipse, and this is the > >> first time Ive tried to use an SVN repository, so it's possible I'm > doing > >> something wrong, but these errors sound like it's a connection problem. > >> > >> Thanks! > >> > >> Matthew > >> _______________________________________________ > >> Biojava-l mailing list ?- [email protected] > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > > > > > -- > ----------------------------------------------------------------------- > Dr. Andreas Prlic > Senior Scientist, RCSB PDB Protein Data Bank > University of California, San Diego > (+1) 858.246.0526 > ----------------------------------------------------------------------- > > > > ------------------------------ > > Message: 6 > Date: Thu, 6 Jan 2011 18:24:48 -0800 > From: Andreas Prlic <[email protected]> > Subject: [Biojava-l] github svn access issues > To: biojava-dev <[email protected]>, > [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > Seems github is currently having issues with their svn interface. As > such if you want to get hold of a copy of the latest source for the > moment there are the following two options: > > - use git rather than svn to fetch the code from github > - use Maven and get the biojava3.0.1-SNAPSHOT builds from the > http://www.biojava.org/download/maven/ repository > > Andreas > > > ------------------------------ > > Message: 7 > Date: Thu, 6 Jan 2011 21:42:50 -0500 > From: Scooter Willis <[email protected]> > Subject: Re: [Biojava-l] biojava3 getting the features from > alignedsequence > To: Hara Dilley <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hara > > Can you provide more of the code you are using that shows how you are > loading the initial sequences. > > Thanks > > Scooter > > On Thu, Jan 6, 2011 at 7:09 PM, Hara Dilley <[email protected]> wrote: > > > Hi, > > > > I would like to align a set of sequences against a scaffold and get the > > list of the modifications for each aligned sequence. > > I am using biojava3 > > I have tried to create a profile thinking that I can get the > > AlignedSequences from it but that it appears to be null. > > Here is part of my code: > > > > Profile<ProteinSequence, AminoAcidCompound> profile = > > Alignments.getMultipleSequenceAlignment(lst); > > Profile.getAlignedSequence(0); > > > > Can someone please point to an example for this or to the classes I have > to > > use. > > Thank you, > > Hara > > > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > End of Biojava-l Digest, Vol 96, Issue 5 > **************************************** > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
