Re: [Bioc-devel] destiny git mirror and SVN desynced

[Martin Morgan]

On 12/14/2016 10:47 AM, James W. MacDonald wrote:



On Wed, Dec 14, 2016 at 10:02 AM, Martin Morgan
>
wrote:



yes; the current situation is unsatisfactory.

Currently the cannonical repository is svn. The build system (and
hence packages seen by the user) don't care about the mirror. Also,
the mirror is in many ways confusing -- not the official repository,
and not the developer repository.


What is the goal as far as the repository goes? Are we transitioning to
git/github, and this is just the messy intervening period, or are we
sticking with svn and just trying to find a workable way to add git
functionality for those who prefer to work with git?


we will transition to git. Martin



--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099



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[Rd] New leap second end of 2016 / beginning 2017 (depending on TZ)

[Martin Maechler]

As R is sophisticated enough to track leap seconds,

   ?.leap.seconds

we'd need to update our codes real soon now again:

https://en.wikipedia.org/wiki/Leap_second

(and those of you who want second precision in R in 2017 need to start
working with 'R patched' or 'R devel' ...)

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Re: [Bioc-devel] destiny git mirror and SVN desynced

[James W. MacDonald]

On Wed, Dec 14, 2016 at 10:02 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

>
>>
> yes; the current situation is unsatisfactory.
>
> Currently the cannonical repository is svn. The build system (and hence
> packages seen by the user) don't care about the mirror. Also, the mirror is
> in many ways confusing -- not the official repository, and not the
> developer repository.
>

What is the goal as far as the repository goes? Are we transitioning to
git/github, and this is just the messy intervening period, or are we
sticking with svn and just trying to find a workable way to add git
functionality for those who prefer to work with git?

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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Re: [Bioc-devel] destiny git mirror and SVN desynced

[Angerer, Philipp via Bioc-devel]

hmm, this is bad. now the release branch is OK, but there seems to be problem. 

when i do git svn rebase , i get this history: 


and a git reset origin/master sends me here: 


so the git mirror and the SVN seem to have permanently desynced… 

best, philipp 


Von: "Martin Morgan"  
An: "Angerer, Philipp" , "bioc-devel" 
 
Gesendet: Mittwoch, 14. Dezember 2016 16:02:04 
Betreff: Re: [Bioc-devel] destiny git mirror and SVN desynced 

On 12/14/2016 09:27 AM, Angerer, Philipp via Bioc-devel wrote: 
> hi, 
> 
> for my package “destiny”, the master and release-3.4 branches aren’t in sync 
> between SVN and the gihub mirror. 
> 
> release-3.4 is just 2 commits behind, but the master branch has diverged. (a 
> few commits have different hashs and a few are missing on the github mirror) 
> 
> this has been really unstable so far. do you plan to offer upstream 
> repositories soon? 

yes; the current situation is unsatisfactory. 

Currently the cannonical repository is svn. The build system (and hence 
packages seen by the user) don't care about the mirror. Also, the mirror 
is in many ways confusing -- not the official repository, and not the 
developer repository. 

> 
> best regards, philipp 
> 
> 
> 
> 
> Helmholtz Zentrum Muenchen 
> 
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) 
> 
> Ingolstaedter Landstr. 1 
> 
> 85764 Neuherberg 
> 
> www.helmholtz-muenchen.de 
> 
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe 
> 
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen 
> 
> Registergericht: Amtsgericht Muenchen HRB 6466 
> 
> USt-IdNr: DE 129521671 
> 
> 
> [[alternative HTML version deleted]] 
> 
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Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

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Re: [Bioc-devel] destiny git mirror and SVN desynced

[Martin Morgan]

On 12/14/2016 09:27 AM, Angerer, Philipp via Bioc-devel wrote:

hi,

for my package “destiny”, the master and release-3.4 branches aren’t in sync 
between SVN and the gihub mirror.

release-3.4 is just 2 commits behind, but the master branch has diverged. (a 
few commits have different hashs and a few are missing on the github mirror)

this has been really unstable so far. do you plan to offer upstream 
repositories soon?


yes; the current situation is unsatisfactory.

Currently the cannonical repository is svn. The build system (and hence 
packages seen by the user) don't care about the mirror. Also, the mirror 
is in many ways confusing -- not the official repository, and not the 
developer repository.




best regards, philipp




Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671


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[Bioc-devel] destiny git mirror and SVN desynced

[Angerer, Philipp via Bioc-devel]

hi, 

for my package “destiny”, the master and release-3.4 branches aren’t in sync 
between SVN and the gihub mirror. 

release-3.4 is just 2 commits behind, but the master branch has diverged. (a 
few commits have different hashs and a few are missing on the github mirror) 

this has been really unstable so far. do you plan to offer upstream 
repositories soon? 

best regards, philipp 

 


Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671


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Re: [Rd] Check package issue on mavericks

[Gionata Bocci]

Dear Jeroen,

   Thank you very much for the time you spent checking my package; I think
I will upload the package to CRAN hoping that this will be considered as a
non-existing issue.
   Thanks again,

Gionata.

2016-12-11 18:09 GMT+01:00 Jeroen Ooms :

> I just checked your package on a mavericks VM and it seems fine, so I
> wouldn't worry about it. Probably some configuration issue on the CRAN
> server, perhaps xquartz is outdated.
>
> Unfortunately there is no easy way anymore to check on Mavericks.
> Travis used to support it, but they have deprecated mavericks (along
> with Apple and homebrew). Hopefully CRAN will update to the current
> MacOS for the next release of R.
>
>
>
>
> On Fri, Dec 9, 2016 at 3:56 PM, Gionata Bocci 
> wrote:
> >
> > Dear List,
> >
> >   I've realized that the "CRAN Checking Package" system returns some
> > Warnings for my package TR8 under "r-release-osx-x86_64-mavericks"; all
> the
> > warnings include the following message "Invalid MIT-MAGIC-COOKIE-1 key"
> > which I find a little cryptic.
> >   After some web searches, I understood that "MIT-MAGIC-COOKIE" is
> related
> > to the X server and most of the messages reporting issues with that are
> > related to R packages having problems with "mavericks" (either NOTES or
> > Warnings resulting from the "checking process").
> >   Not having a Mac available where I could try to explore this issue (and
> > not being familiar with Mac in general), I've set up a Travis CI account
> in
> > order to check whether the package was built and "checked --as-cran" on
> > both Linux (my OS) and Mac OSX (Travis is using OS X versions >= 10.10):
> it
> > looks like everything is fine, correctly built and checked.
> >   I am thus writing to ask if other developers on the list have found and
> > fixed this issue (so that I could fix that as well and tick the checkbox
> "I
> > have fixed all problems shown on the package check page" before
> submitting
> > a new version to CRAN).
> >   Best,
> >
> >
> > Gionata.
> >
> > [[alternative HTML version deleted]]
> >
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