Re: [Debian-med-packaging] Progress on the BioJava Front

[Charles Plessy-12]

Le Sun, Jul 13, 2008 at 06:15:27PM +0200, Steffen Moeller a écrit :

>
> I am writing to inform you that the active management of biojava and
> bytecode is on pkg-escience.alioth.debian.org, not on the debian-med
> site. Why is that? Because of a long time goal of mine to provide
> everything for a Debian package of Taverna.sf.net and that requires
> biojava. pkg-escience aims at streamlining the preparation of software
> for that cause.
>
> Once the package is due to be uploaded I am not so certain that it
> indeed should reside with pkg-java. Debian-med might indeed be a better
> place or pkg-java. I can't tell and don't care much either  :)

Hi Steffen,

I am so sorry that I did not find time to test your recent work...

Since pkg-escience is very Java oriented, it can make sense to cluster
the programs in a separate repository if it can attract more
developpers. It was a nice idea to add a link to the package from the
pkg-escience SVN in Debian-Med's, but as a result it is not possible
anymore to make a full checkout if one does not have write access to
both repositories.

I just have requested to the Alioth admins to make Debian Med's SVN
repository write-accessible to all DDs (as we discussed this and nobody
raised objections)
https://alioth.debian.org/tracker/index.php?func=detail&aid=310947&group_id=1&atid=200001
Maybe you can do the same for pkg-escience?

(by the way, I do not use the "charles-guest" account anymore, can you
replace it by "plessy"?)

Have a nice day,

--
Charles

--
Charles Plessy
Debian-Med packaging team,
Tsurumi, Kanagawa, Japan


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[Andreas Tille]

On Tue, 15 Jul 2008, Charles Plessy wrote:

> as a result it is not possible
> anymore to make a full checkout if one does not have write access to
> both repositories.

Huh, why this?  Isn't checkout readonly???  I had no problems at all
and I do not think that I have write access to pkg-escience

> I just have requested to the Alioth admins to make Debian Med's SVN
> repository write-accessible to all DDs (as we discussed this and nobody
> raised objections)
> https://alioth.debian.org/tracker/index.php?func=detail&aid=310947&group_id=1&atid=200001

Well, I do not have objections - but I do not think that this is really
needed to solve this problem - it is just not logical.

Kind regards

         Andreas.

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http://fam-tille.de


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[Charles Plessy-12]

Le Tue, Jul 15, 2008 at 04:22:42PM +0200, Andreas Tille a écrit :
> On Tue, 15 Jul 2008, Charles Plessy wrote:
>
> >as a result it is not possible
> >anymore to make a full checkout if one does not have write access to
> >both repositories.
>
> Huh, why this?  Isn't checkout readonly???  I had no problems at all
> and I do not think that I have write access to pkg-escience

Hi Andreas,

then I must have a problem on the local side:

sorbet【packages】$ LC_ALL=C svn update

Fetching external item into 'med-doc/trunk/05_biomed_bio'
External at revision 982.


Fetching external item into 'biojava/BioJava'
Password:


As you see, it asks me a password, and the Alioth one is not accepted. I
thought it was sort of write access-related. Does anybody have another
hypothesis ?


--
Charles Plessy
Debian-Med packaging team,
Tsurumi, Kanagawa, Japan


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[Andreas Tille]

On Wed, 16 Jul 2008, Charles Plessy wrote:

> Fetching external item into 'biojava/BioJava'
> Password:
>
>
> As you see, it asks me a password, and the Alioth one is not accepted. I
> thought it was sort of write access-related. Does anybody have another
> hypothesis ?

No, it's just strange ...

Kind regards

          Andreas.

--
http://fam-tille.de


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[Manuel Prinz-2]

Hi Charles!

Am Mittwoch, den 16.07.2008, 08:50 +0900 schrieb Charles Plessy:
> then I must have a problem on the local side:
>
> sorbet【packages】$ LC_ALL=C svn update
> [...]
> As you see, it asks me a password, and the Alioth one is not accepted. I
> thought it was sort of write access-related. Does anybody have another
> hypothesis ?

This is weird. What does

    cat .svn/entries | grep debian.org

say?

Best regards
Manuel

[Charles Plessy-12]

Hi Manuel, thank you for the help!

Le Thu, Jul 17, 2008 at 12:36:07PM +0200, Manuel Prinz a écrit :

> Am Mittwoch, den 16.07.2008, 08:50 +0900 schrieb Charles Plessy:
> > sorbet【packages】$ LC_ALL=C svn update
> > [...]
> > As you see, it asks me a password, and the Alioth one is not accepted. I
> > thought it was sort of write access-related. Does anybody have another
> > hypothesis ?
>
> This is weird. What does
>     cat .svn/entries | grep debian.org
> say?

sorbet【biojava】$ cat .svn/entries | grep debian.org
svn+ssh://plessy@.../svn/debian-med/trunk/packages/biojava
svn+ssh://plessy@.../svn/debian-med

Actually, there is also:

sorbet【biojava】$ cat .svn/dir-prop-base | grep debian.org
BioJava svn+ssh://svn.debian.org/svn/pkg-escience/biojava/

and

sorbet【biojava】$ env | grep USER
USER=charles
USERNAME=charles

So probably what happens is that svn tries to connect to alioth as
"charles", and as I only have keys for "plessy", requests a password.

Strangely correcting dir-prop-base does not work:

sorbet【biojava】$ cat .svn/dir-prop-base | grep debian.org
BioJava svn+ssh://plessy@.../svn/pkg-escience/biojava/
sorbet【biojava】$ LC_ALL=C svn update
svn: Failed to load properties from disk
svn: Can't parse '.svn/dir-prop-base'
svn: Malformed file

Any idea ?

--
Charles Plessy
Debian-Med packaging team,
Tsurumi, Kanagawa, Japan


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[Manuel Prinz-2]

Am Donnerstag, den 17.07.2008, 23:15 +0900 schrieb Charles Plessy:
> Strangely correcting dir-prop-base does not work:

Files in .svn are like the repo database and should not be changed by
hand.

> sorbet【biojava】$ cat .svn/dir-prop-base | grep debian.org
> BioJava svn+ssh://plessy@.../svn/pkg-escience/biojava/
> sorbet【biojava】$ LC_ALL=C svn update
> svn: Failed to load properties from disk
> svn: Can't parse '.svn/dir-prop-base'
> svn: Malformed file
>
> Any idea ?

Yes. You probably broke your working copy by editing this file but maybe
it can be reverted. In general, you can easily relocate the repo by
using:

switch --relocate FROM TO

("Relocation" means all changes in the repository path here. Changing
the username is a change of the path as well, since the URI changes.)

You should try to revert the change you made to dir-prop-base and then
call

switch --relocate svn+ssh://svn.debian.org/svn/pkg-escience/biojava/ \
  svn+ssh://plessy@.../svn/pkg-escience/biojava/

After another "svn update", all should be fine. Hope that does the trick
for you!

Best regards
Manuel

[Charles Plessy-12]

Le Thu, Jul 17, 2008 at 04:30:19PM +0200, Manuel Prinz a écrit :
>
> You should try to revert the change you made to dir-prop-base and then
> call
>
> switch --relocate svn+ssh://svn.debian.org/svn/pkg-escience/biojava/ \
>   svn+ssh://plessy@.../svn/pkg-escience/biojava/

Hi Manuel,

unfortunately it did not work.

Furthermore, I tried to make a fresh checkout and was asked again
for my password, either with
`svn co svn+ssh://plessy@.../svn/debian-med/' or
`svn co svn+ssh://plessy@.../svn/debian-med/'.

So the problem lies outside the svn tree, somewhere in my configuration
or my alioth account...

Does everybody manage to make a fresh checkout ?

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan


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[Steffen Moeller-3]

Hi,

Charles Plessy wrote:

> Le Thu, Jul 17, 2008 at 04:30:19PM +0200, Manuel Prinz a écrit :
>> You should try to revert the change you made to dir-prop-base and then
>> call
>>
>> switch --relocate svn+ssh://svn.debian.org/svn/pkg-escience/biojava/ \
>>   svn+ssh://plessy@.../svn/pkg-escience/biojava/
>
> Hi Manuel,
>
> unfortunately it did not work.
>
> Furthermore, I tried to make a fresh checkout and was asked again
> for my password, either with
> `svn co svn+ssh://plessy@.../svn/debian-med/' or
> `svn co svn+ssh://plessy@.../svn/debian-med/'.
>
> So the problem lies outside the svn tree, somewhere in my configuration
> or my alioth account...

should we not just remove that BioJava directory from debian-med? A reference to pkg-escience on the alioth and wiki pages should be sufficient.

Cheers,

Steffen


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[Andreas Tille]

On Tue, 22 Jul 2008, Steffen Moeller wrote:

> should we not just remove that BioJava directory from debian-med? A reference to pkg-escience on the alioth and wiki pages should be sufficient.

I don't think so.  I just learned that these svn external references are
*very* handy because it works transparently (*if* it works) and you can not
be beaten by outdated / unmaintained Wiki pages.

Kind regards

        Andreas.

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[Manuel Prinz-2]

Am Dienstag, den 22.07.2008, 13:14 +0900 schrieb Charles Plessy:
> Furthermore, I tried to make a fresh checkout and was asked again
> for my password, either with
> `svn co svn+ssh://plessy@.../svn/debian-med/' or
> `svn co svn+ssh://plessy@.../svn/debian-med/'.
>
> So the problem lies outside the svn tree, somewhere in my configuration
> or my alioth account...
>
> Does everybody manage to make a fresh checkout ?

I tried both anonymous and login checkout:

svn co svn://svn.debian.org/svn/debian-med/
svn co svn+ssh://$USER@.../svn/debian-med/

Both worked fine for me. (I had to type the password twice on the later
run.) I can't really think of anything that should prevent it from
working. You could check if you got a recent key of Alioth since all of
them were exchanged. If you do not see a huge warning when you login to
Alioth via SSH it should be all fine, though. (alioth.debian.org and
svn.debian.org are the same machine, so this is not an issue.)

Best regards
Manuel

[Charles Plessy-12]

Le Tue, Jul 22, 2008 at 02:44:38PM +0200, Manuel Prinz a écrit :
> I tried both anonymous and login checkout:
>
> svn co svn://svn.debian.org/svn/debian-med/
> svn co svn+ssh://$USER@.../svn/debian-med/
>
> Both worked fine for me.

Interesting... even the read-only checkout asks me for a password...

My Alioth key is secure and up-to-date: if the connection would be made
on my account, I would be requested my key's passphrase, not my
password.

I am a bit clueless...

--
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan


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