Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-18 Thread Carlos Ruiz 

Hi,
It worked. Now I can make pushes.
Thanks,
Carlos

El 14/09/2017 a las 20:23, Turaga, Nitesh escribió:

Bioc-git server* (git.bioconductor.org).

Ignore the typo.


On Sep 14, 2017, at 2:20 PM, ni41435_ca  wrote:

Hi Carlos

Your ID is standardized across all your packages now to “c.ruiz”. Your key is 
the one your submitted most recently

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDEMdup9kYuv4KO5MO1lctLXl4Griu571wbbDZU+ueZHhtuEm2WBqWTC0Zp6V+rszWORQkDGcM2ym+pVMNapSbFFbCJPDG1kxXpJI+2
 …..

Please use that key to access all of your packages. You shouldn’t have to do 
anything more, please try to access the bioc-devel-git server, and let me know 
if you are able to successfully.

Best,

Nitesh



On Sep 14, 2017, at 1:30 PM, Carlos Ruiz  wrote:

Hi Nitesh,

I have checked my mail and I have 3 different SVN ids, one for each package I 
have submitted:

- r.carlos: MEAL
- c.ruiz-arenas: MultiDataSet
- c.ruiz: scoreInvHap

When I submitted MultiDataSet, I asked Bioc to consolidate my svn user. From 
then, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the next 
release, I got scoreInvHap accepted and I have now realized that I have another 
svn user. What can I do to solve it?

Thank you,

Carlos Ruiz




El jueves, 14 de septiembre de 2017, Turaga, Nitesh 
 escribió:
Hi Carlos,

Do you by any chance have 2 separate SVN id’s?

1. c.ruiz
2. c.ruiz-arenas

Best,

Nitesh



On Sep 14, 2017, at 12:17 PM, Carlos Ruiz  wrote:

Hi,
Today I definitely was able to fetch from the Bioc git. However, I cannot push. 
Here, the commands and the error:


C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream master
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to the l
ist of known hosts.
FATAL: W any packages/MEAL c.ruiz DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
origin  https://github.com/isglobal-brge/MEAL.git (fetch)
origin  https://github.com/isglobal-brge/MEAL.git (push)
upstreamg...@git.bioconductor.org:packages/MEAL.git (fetch)
upstreamg...@git.bioconductor.org:packages/MEAL.git (push)

Can you help me?

Thanks,

Carlos Ruiz


El 13/09/2017 a las 10:09, Carlos Ruiz escribió:

Hi to both,

These are the commands that I tried and the error:

$ git remote -v
origin  https://github.com/isglobal-brge/MEAL.git (fetch)
origin  https://github.com/isglobal-brge/MEAL.git (push)
upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
upstreamg...@git.bioconductor.org:packages/MEAL (push)


$  git fetch --all
Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

I think that there was a similar error in the BiocDevel list that was solved 
after sending the ssh keys. I resent the form yesterday so I hope tomorrow I'll 
be able to push. Just in case, my svn user name was c.ruiz-arenas.

Bests,
Carlos Ruiz

El 12/09/2017 a las 18:12, Shepherd, Lori escribió:

Once you submit the key you should have access.  Please provide the calls you 
are using and also the results of git remote -v



Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Carlos Ruiz 
Sent: Tuesday, September 12, 2017 12:08:15 PM
To: Shepherd, Lori
Subject: Re: Bioconductor failing package MEAL

Hi,

I am experiencing some problems with the git system. I think that i have not 
properly configured the ssh keys. I have filled again the form with the ssh 
keys (user name: c.ruiz-arenas). Once you introduced my keys in the system, 
should I do anything else to update the repo? Should I change the configuration 
on git?

Thank you,
Carlos Ruiz

El 12/09/2017 a las 17:37, Shepherd, Lori escribió:

Please update. We have temporarily added your package to the deprecation list 
as we did not hear from you and there were no updates. If you package builds 
and checks cleanly we will remove it from the list of deprecated packages.

Please also be advised we have transitioned to git. There are some useful 
information here:
http://bioconductor.org/developers/how-to/git/


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Carlos Ruiz 
Sent: Tuesday, September 12, 2017 11:28:33 AM
To: Shepherd, Lori
Subject: Re: Bioconductor failing package MEAL

Hi Lori,

I apologize for not replying you sooner but I have just finished my holidays 
today. I have

Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-15 Thread Carlos Ruiz 
Hi Nitesh,

I have checked my mail and I have 3 different SVN ids, one for each package
I have submitted:

- r.carlos: MEAL
- c.ruiz-arenas: MultiDataSet
- c.ruiz: scoreInvHap

When I submitted MultiDataSet, I asked Bioc to consolidate my svn user.
From then, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the
next release, I got scoreInvHap accepted and I have now realized that I
have another svn user. What can I do to solve it?

Thank you,

Carlos Ruiz




El jueves, 14 de septiembre de 2017, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> escribió:

> Hi Carlos,
>
> Do you by any chance have 2 separate SVN id’s?
>
> 1. c.ruiz
> 2. c.ruiz-arenas
>
> Best,
>
> Nitesh
>
>
> > On Sep 14, 2017, at 12:17 PM, Carlos Ruiz  > wrote:
> >
> > Hi,
> > Today I definitely was able to fetch from the Bioc git. However, I
> cannot push. Here, the commands and the error:
> >
> >
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream
> master
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
> to the l
> > ist of known hosts.
> > FATAL: W any packages/MEAL c.ruiz DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
> > origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> > origin  https://github.com/isglobal-brge/MEAL.git (push)
> > upstreamg...@git.bioconductor.org:packages/MEAL.git (fetch)
> > upstreamg...@git.bioconductor.org:packages/MEAL.git (push)
> >
> > Can you help me?
> >
> > Thanks,
> >
> > Carlos Ruiz
> >
> >
> > El 13/09/2017 a las 10:09, Carlos Ruiz escribió:
> >> Hi to both,
> >>
> >> These are the commands that I tried and the error:
> >>
> >> $ git remote -v
> >> origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> >> origin  https://github.com/isglobal-brge/MEAL.git (push)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (push)
> >>
> >>
> >> $  git fetch --all
> >> Fetching origin
> >> Fetching upstream
> >> Permission denied (publickey).
> >> fatal: Could not read from remote repository.
> >>
> >> Please make sure you have the correct access rights
> >> and the repository exists.
> >> error: Could not fetch upstream
> >>
> >> I think that there was a similar error in the BiocDevel list that was
> solved after sending the ssh keys. I resent the form yesterday so I hope
> tomorrow I'll be able to push. Just in case, my svn user name was
> c.ruiz-arenas.
> >>
> >> Bests,
> >> Carlos Ruiz
> >>
> >> El 12/09/2017 a las 18:12, Shepherd, Lori escribió:
> >>> Once you submit the key you should have access.  Please provide the
> calls you are using and also the results of git remote -v
> >>>
> >>>
> >>>
> >>> Lori Shepherd
> >>> Bioconductor Core Team
> >>> Roswell Park Cancer Institute
> >>> Department of Biostatistics & Bioinformatics
> >>> Elm & Carlton Streets
> >>> Buffalo, New York 14263
> >>> From: Carlos Ruiz >
> >>> Sent: Tuesday, September 12, 2017 12:08:15 PM
> >>> To: Shepherd, Lori
> >>> Subject: Re: Bioconductor failing package MEAL
> >>>
> >>> Hi,
> >>>
> >>> I am experiencing some problems with the git system. I think that i
> have not properly configured the ssh keys. I have filled again the form
> with the ssh keys (user name: c.ruiz-arenas). Once you introduced my keys
> in the system, should I do anything else to update the repo? Should I
> change the configuration on git?
> >>>
> >>> Thank you,
> >>> Carlos Ruiz
> >>>
> >>> El 12/09/2017 a las 17:37, Shepherd, Lori escribió:
>  Please update. We have temporarily added your package to the
> deprecation list as we did not hear from you and there were no updates. If
> you package builds and checks cleanly we will remove it from the list of
> deprecated packages.
> 
>  Please also be advised we have transitioned to git. There are some
> useful information here:
>  http://bioconductor.org/developers/how-to/git/
> 
> 
>  Lori Shepherd
>  Bioconductor Core Team
>  Roswell Park Cancer Institute
>  Department of Biostatistics & Bioinformatics
>  Elm & Carlton Streets
>  Buffalo, New York 14263
>  From: Carlos Ruiz >
>  Sent: Tuesday, September 12, 2017 11:28:33 AM
>  To: Shepherd, Lori
>  Subject: Re: Bioconductor failing package MEAL
> 
>  Hi Lori,
> 
>  I apologize for not replying you sooner but I have just finished my
> holidays today. I have finished the vignettes today and I only need to
> update the tests to have a fully working version again. Therefore, I expect
> to push my changes during this week.
> 
>  MEAL contains wrappers to other methods to ease

Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-15 Thread Turaga, Nitesh 
Hi Carlos

Your ID is standardized across all your packages now to “c.ruiz”. Your key is 
the one your submitted most recently 

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDEMdup9kYuv4KO5MO1lctLXl4Griu571wbbDZU+ueZHhtuEm2WBqWTC0Zp6V+rszWORQkDGcM2ym+pVMNapSbFFbCJPDG1kxXpJI+2
 …..

Please use that key to access all of your packages. You shouldn’t have to do 
anything more, please try to access the bioc-devel-git server, and let me know 
if you are able to successfully. 

Best,

Nitesh


> On Sep 14, 2017, at 1:30 PM, Carlos Ruiz  wrote:
> 
> Hi Nitesh,
> 
> I have checked my mail and I have 3 different SVN ids, one for each package I 
> have submitted:
> 
> - r.carlos: MEAL
> - c.ruiz-arenas: MultiDataSet
> - c.ruiz: scoreInvHap
> 
> When I submitted MultiDataSet, I asked Bioc to consolidate my svn user. From 
> then, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the next 
> release, I got scoreInvHap accepted and I have now realized that I have 
> another svn user. What can I do to solve it?
> 
> Thank you,
> 
> Carlos Ruiz
> 
> 
> 
> 
> El jueves, 14 de septiembre de 2017, Turaga, Nitesh 
>  escribió:
> Hi Carlos,
> 
> Do you by any chance have 2 separate SVN id’s?
> 
> 1. c.ruiz
> 2. c.ruiz-arenas
> 
> Best,
> 
> Nitesh
> 
> 
> > On Sep 14, 2017, at 12:17 PM, Carlos Ruiz  wrote:
> >
> > Hi,
> > Today I definitely was able to fetch from the Bioc git. However, I cannot 
> > push. Here, the commands and the error:
> >
> >
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream master
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> > the l
> > ist of known hosts.
> > FATAL: W any packages/MEAL c.ruiz DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
> > origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> > origin  https://github.com/isglobal-brge/MEAL.git (push)
> > upstreamg...@git.bioconductor.org:packages/MEAL.git (fetch)
> > upstreamg...@git.bioconductor.org:packages/MEAL.git (push)
> >
> > Can you help me?
> >
> > Thanks,
> >
> > Carlos Ruiz
> >
> >
> > El 13/09/2017 a las 10:09, Carlos Ruiz escribió:
> >> Hi to both,
> >>
> >> These are the commands that I tried and the error:
> >>
> >> $ git remote -v
> >> origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> >> origin  https://github.com/isglobal-brge/MEAL.git (push)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (push)
> >>
> >>
> >> $  git fetch --all
> >> Fetching origin
> >> Fetching upstream
> >> Permission denied (publickey).
> >> fatal: Could not read from remote repository.
> >>
> >> Please make sure you have the correct access rights
> >> and the repository exists.
> >> error: Could not fetch upstream
> >>
> >> I think that there was a similar error in the BiocDevel list that was 
> >> solved after sending the ssh keys. I resent the form yesterday so I hope 
> >> tomorrow I'll be able to push. Just in case, my svn user name was 
> >> c.ruiz-arenas.
> >>
> >> Bests,
> >> Carlos Ruiz
> >>
> >> El 12/09/2017 a las 18:12, Shepherd, Lori escribió:
> >>> Once you submit the key you should have access.  Please provide the calls 
> >>> you are using and also the results of git remote -v
> >>>
> >>>
> >>>
> >>> Lori Shepherd
> >>> Bioconductor Core Team
> >>> Roswell Park Cancer Institute
> >>> Department of Biostatistics & Bioinformatics
> >>> Elm & Carlton Streets
> >>> Buffalo, New York 14263
> >>> From: Carlos Ruiz 
> >>> Sent: Tuesday, September 12, 2017 12:08:15 PM
> >>> To: Shepherd, Lori
> >>> Subject: Re: Bioconductor failing package MEAL
> >>>
> >>> Hi,
> >>>
> >>> I am experiencing some problems with the git system. I think that i have 
> >>> not properly configured the ssh keys. I have filled again the form with 
> >>> the ssh keys (user name: c.ruiz-arenas). Once you introduced my keys in 
> >>> the system, should I do anything else to update the repo? Should I change 
> >>> the configuration on git?
> >>>
> >>> Thank you,
> >>> Carlos Ruiz
> >>>
> >>> El 12/09/2017 a las 17:37, Shepherd, Lori escribió:
>  Please update. We have temporarily added your package to the deprecation 
>  list as we did not hear from you and there were no updates. If you 
>  package builds and checks cleanly we will remove it from the list of 
>  deprecated packages.
> 
>  Please also be advised we have transitioned to git. There are some 
>  useful information here:
>  http://bioconductor.org/developers/how-to/git/
> 
> 
>  Lori Shepherd
>  Bioconductor Core Team
>  Roswell Park Cancer Institute
>  Department of

Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-15 Thread Turaga, Nitesh 
Bioc-git server* (git.bioconductor.org). 

Ignore the typo.

> On Sep 14, 2017, at 2:20 PM, ni41435_ca  wrote:
> 
> Hi Carlos
> 
> Your ID is standardized across all your packages now to “c.ruiz”. Your key is 
> the one your submitted most recently 
> 
> ssh-rsa 
> B3NzaC1yc2EDAQABAAABAQDEMdup9kYuv4KO5MO1lctLXl4Griu571wbbDZU+ueZHhtuEm2WBqWTC0Zp6V+rszWORQkDGcM2ym+pVMNapSbFFbCJPDG1kxXpJI+2
>  …..
> 
> Please use that key to access all of your packages. You shouldn’t have to do 
> anything more, please try to access the bioc-devel-git server, and let me 
> know if you are able to successfully. 
> 
> Best,
> 
> Nitesh
> 
> 
>> On Sep 14, 2017, at 1:30 PM, Carlos Ruiz  wrote:
>> 
>> Hi Nitesh,
>> 
>> I have checked my mail and I have 3 different SVN ids, one for each package 
>> I have submitted:
>> 
>> - r.carlos: MEAL
>> - c.ruiz-arenas: MultiDataSet
>> - c.ruiz: scoreInvHap
>> 
>> When I submitted MultiDataSet, I asked Bioc to consolidate my svn user. From 
>> then, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the next 
>> release, I got scoreInvHap accepted and I have now realized that I have 
>> another svn user. What can I do to solve it?
>> 
>> Thank you,
>> 
>> Carlos Ruiz
>> 
>> 
>> 
>> 
>> El jueves, 14 de septiembre de 2017, Turaga, Nitesh 
>>  escribió:
>> Hi Carlos,
>> 
>> Do you by any chance have 2 separate SVN id’s?
>> 
>> 1. c.ruiz
>> 2. c.ruiz-arenas
>> 
>> Best,
>> 
>> Nitesh
>> 
>> 
>>> On Sep 14, 2017, at 12:17 PM, Carlos Ruiz  wrote:
>>> 
>>> Hi,
>>> Today I definitely was able to fetch from the Bioc git. However, I cannot 
>>> push. Here, the commands and the error:
>>> 
>>> 
>>> C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream master
>>> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
>>> the l
>>> ist of known hosts.
>>> FATAL: W any packages/MEAL c.ruiz DENIED by fallthru
>>> (or you mis-spelled the reponame)
>>> fatal: Could not read from remote repository.
>>> 
>>> Please make sure you have the correct access rights
>>> and the repository exists.
>>> C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
>>> origin  https://github.com/isglobal-brge/MEAL.git (fetch)
>>> origin  https://github.com/isglobal-brge/MEAL.git (push)
>>> upstreamg...@git.bioconductor.org:packages/MEAL.git (fetch)
>>> upstreamg...@git.bioconductor.org:packages/MEAL.git (push)
>>> 
>>> Can you help me?
>>> 
>>> Thanks,
>>> 
>>> Carlos Ruiz
>>> 
>>> 
>>> El 13/09/2017 a las 10:09, Carlos Ruiz escribió:
 Hi to both,
 
 These are the commands that I tried and the error:
 
 $ git remote -v
 origin  https://github.com/isglobal-brge/MEAL.git (fetch)
 origin  https://github.com/isglobal-brge/MEAL.git (push)
 upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
 upstreamg...@git.bioconductor.org:packages/MEAL (push)
 
 
 $  git fetch --all
 Fetching origin
 Fetching upstream
 Permission denied (publickey).
 fatal: Could not read from remote repository.
 
 Please make sure you have the correct access rights
 and the repository exists.
 error: Could not fetch upstream
 
 I think that there was a similar error in the BiocDevel list that was 
 solved after sending the ssh keys. I resent the form yesterday so I hope 
 tomorrow I'll be able to push. Just in case, my svn user name was 
 c.ruiz-arenas.
 
 Bests,
 Carlos Ruiz
 
 El 12/09/2017 a las 18:12, Shepherd, Lori escribió:
> Once you submit the key you should have access.  Please provide the calls 
> you are using and also the results of git remote -v
> 
> 
> 
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> From: Carlos Ruiz 
> Sent: Tuesday, September 12, 2017 12:08:15 PM
> To: Shepherd, Lori
> Subject: Re: Bioconductor failing package MEAL
> 
> Hi,
> 
> I am experiencing some problems with the git system. I think that i have 
> not properly configured the ssh keys. I have filled again the form with 
> the ssh keys (user name: c.ruiz-arenas). Once you introduced my keys in 
> the system, should I do anything else to update the repo? Should I change 
> the configuration on git?
> 
> Thank you,
> Carlos Ruiz
> 
> El 12/09/2017 a las 17:37, Shepherd, Lori escribió:
>> Please update. We have temporarily added your package to the deprecation 
>> list as we did not hear from you and there were no updates. If you 
>> package builds and checks cleanly we will remove it from the list of 
>> deprecated packages.
>> 
>> Please also be advised we have

Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-15 Thread Turaga, Nitesh 
Hi Carlos,

Do you by any chance have 2 separate SVN id’s?

1. c.ruiz
2. c.ruiz-arenas

Best,

Nitesh


> On Sep 14, 2017, at 12:17 PM, Carlos Ruiz  wrote:
> 
> Hi, 
> Today I definitely was able to fetch from the Bioc git. However, I cannot 
> push. Here, the commands and the error:
> 
> 
> C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream master
> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> the l
> ist of known hosts.
> FATAL: W any packages/MEAL c.ruiz DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
> origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> origin  https://github.com/isglobal-brge/MEAL.git (push)
> upstreamg...@git.bioconductor.org:packages/MEAL.git (fetch)
> upstreamg...@git.bioconductor.org:packages/MEAL.git (push)
> 
> Can you help me?
> 
> Thanks, 
> 
> Carlos Ruiz
> 
> 
> El 13/09/2017 a las 10:09, Carlos Ruiz escribió:
>> Hi to both,
>> 
>> These are the commands that I tried and the error:
>> 
>> $ git remote -v
>> origin  https://github.com/isglobal-brge/MEAL.git (fetch)
>> origin  https://github.com/isglobal-brge/MEAL.git (push)
>> upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
>> upstreamg...@git.bioconductor.org:packages/MEAL (push)
>> 
>> 
>> $  git fetch --all
>> Fetching origin
>> Fetching upstream
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>> 
>> Please make sure you have the correct access rights
>> and the repository exists.
>> error: Could not fetch upstream
>> 
>> I think that there was a similar error in the BiocDevel list that was solved 
>> after sending the ssh keys. I resent the form yesterday so I hope tomorrow 
>> I'll be able to push. Just in case, my svn user name was c.ruiz-arenas.
>> 
>> Bests,
>> Carlos Ruiz
>> 
>> El 12/09/2017 a las 18:12, Shepherd, Lori escribió:
>>> Once you submit the key you should have access.  Please provide the calls 
>>> you are using and also the results of git remote -v 
>>> 
>>> 
>>> 
>>> Lori Shepherd
>>> Bioconductor Core Team
>>> Roswell Park Cancer Institute
>>> Department of Biostatistics & Bioinformatics
>>> Elm & Carlton Streets
>>> Buffalo, New York 14263
>>> From: Carlos Ruiz 
>>> Sent: Tuesday, September 12, 2017 12:08:15 PM
>>> To: Shepherd, Lori
>>> Subject: Re: Bioconductor failing package MEAL
>>>  
>>> Hi,
>>> 
>>> I am experiencing some problems with the git system. I think that i have 
>>> not properly configured the ssh keys. I have filled again the form with the 
>>> ssh keys (user name: c.ruiz-arenas). Once you introduced my keys in the 
>>> system, should I do anything else to update the repo? Should I change the 
>>> configuration on git?
>>> 
>>> Thank you,
>>> Carlos Ruiz
>>> 
>>> El 12/09/2017 a las 17:37, Shepherd, Lori escribió:
 Please update. We have temporarily added your package to the deprecation 
 list as we did not hear from you and there were no updates. If you package 
 builds and checks cleanly we will remove it from the list of deprecated 
 packages. 
 
 Please also be advised we have transitioned to git. There are some useful 
 information here: 
 http://bioconductor.org/developers/how-to/git/
 
 
 Lori Shepherd
 Bioconductor Core Team
 Roswell Park Cancer Institute
 Department of Biostatistics & Bioinformatics
 Elm & Carlton Streets
 Buffalo, New York 14263
 From: Carlos Ruiz 
 Sent: Tuesday, September 12, 2017 11:28:33 AM
 To: Shepherd, Lori
 Subject: Re: Bioconductor failing package MEAL
  
 Hi Lori,
 
 I apologize for not replying you sooner but I have just finished my 
 holidays today. I have finished the vignettes today and I only need to 
 update the tests to have a fully working version again. Therefore, I 
 expect to push my changes during this week.
 
 MEAL contains wrappers to other methods to ease performing methylation and 
 gene expression analyses. I previously created a data package to show MEAL 
 functionalities and I used it in my vignettes. We have created a new data 
 package (BRGEdata) in our group that could be used by different packages. 
 My colleague uploaded it in the submission of omicRexpsome but he is 
 experiencing some problems that are trying to solve with Martin. 
 
 Until this package is not working, the new version of MEAL will fail to 
 build the vignettes. Should I wait until BRGEdata issue is solved or can I 
 update the package without including the vignettes?
 
 Bests,
 
 2017-09-01 14:21 GMT+02:00 Shepherd, Lori :
 Dear MEAL

Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-15 Thread Turaga, Nitesh 
Hi Carlos,

Give me a till tomorrow to solve this. 

Good news is r.carlos isn’t used anywhere yet. I think this is mostly on our 
end, and not on your end. 

Best,

Nitesh

> On Sep 14, 2017, at 1:30 PM, Carlos Ruiz  wrote:
> 
> Hi Nitesh,
> 
> I have checked my mail and I have 3 different SVN ids, one for each package I 
> have submitted:
> 
> - r.carlos: MEAL
> - c.ruiz-arenas: MultiDataSet
> - c.ruiz: scoreInvHap
> 
> When I submitted MultiDataSet, I asked Bioc to consolidate my svn user. From 
> then, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the next 
> release, I got scoreInvHap accepted and I have now realized that I have 
> another svn user. What can I do to solve it?
> 
> Thank you,
> 
> Carlos Ruiz
> 
> 
> 
> 
> El jueves, 14 de septiembre de 2017, Turaga, Nitesh 
>  escribió:
> Hi Carlos,
> 
> Do you by any chance have 2 separate SVN id’s?
> 
> 1. c.ruiz
> 2. c.ruiz-arenas
> 
> Best,
> 
> Nitesh
> 
> 
> > On Sep 14, 2017, at 12:17 PM, Carlos Ruiz  wrote:
> >
> > Hi,
> > Today I definitely was able to fetch from the Bioc git. However, I cannot 
> > push. Here, the commands and the error:
> >
> >
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream master
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> > the l
> > ist of known hosts.
> > FATAL: W any packages/MEAL c.ruiz DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
> > origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> > origin  https://github.com/isglobal-brge/MEAL.git (push)
> > upstreamg...@git.bioconductor.org:packages/MEAL.git (fetch)
> > upstreamg...@git.bioconductor.org:packages/MEAL.git (push)
> >
> > Can you help me?
> >
> > Thanks,
> >
> > Carlos Ruiz
> >
> >
> > El 13/09/2017 a las 10:09, Carlos Ruiz escribió:
> >> Hi to both,
> >>
> >> These are the commands that I tried and the error:
> >>
> >> $ git remote -v
> >> origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> >> origin  https://github.com/isglobal-brge/MEAL.git (push)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (push)
> >>
> >>
> >> $  git fetch --all
> >> Fetching origin
> >> Fetching upstream
> >> Permission denied (publickey).
> >> fatal: Could not read from remote repository.
> >>
> >> Please make sure you have the correct access rights
> >> and the repository exists.
> >> error: Could not fetch upstream
> >>
> >> I think that there was a similar error in the BiocDevel list that was 
> >> solved after sending the ssh keys. I resent the form yesterday so I hope 
> >> tomorrow I'll be able to push. Just in case, my svn user name was 
> >> c.ruiz-arenas.
> >>
> >> Bests,
> >> Carlos Ruiz
> >>
> >> El 12/09/2017 a las 18:12, Shepherd, Lori escribió:
> >>> Once you submit the key you should have access.  Please provide the calls 
> >>> you are using and also the results of git remote -v
> >>>
> >>>
> >>>
> >>> Lori Shepherd
> >>> Bioconductor Core Team
> >>> Roswell Park Cancer Institute
> >>> Department of Biostatistics & Bioinformatics
> >>> Elm & Carlton Streets
> >>> Buffalo, New York 14263
> >>> From: Carlos Ruiz 
> >>> Sent: Tuesday, September 12, 2017 12:08:15 PM
> >>> To: Shepherd, Lori
> >>> Subject: Re: Bioconductor failing package MEAL
> >>>
> >>> Hi,
> >>>
> >>> I am experiencing some problems with the git system. I think that i have 
> >>> not properly configured the ssh keys. I have filled again the form with 
> >>> the ssh keys (user name: c.ruiz-arenas). Once you introduced my keys in 
> >>> the system, should I do anything else to update the repo? Should I change 
> >>> the configuration on git?
> >>>
> >>> Thank you,
> >>> Carlos Ruiz
> >>>
> >>> El 12/09/2017 a las 17:37, Shepherd, Lori escribió:
>  Please update. We have temporarily added your package to the deprecation 
>  list as we did not hear from you and there were no updates. If you 
>  package builds and checks cleanly we will remove it from the list of 
>  deprecated packages.
> 
>  Please also be advised we have transitioned to git. There are some 
>  useful information here:
>  http://bioconductor.org/developers/how-to/git/
> 
> 
>  Lori Shepherd
>  Bioconductor Core Team
>  Roswell Park Cancer Institute
>  Department of Biostatistics & Bioinformatics
>  Elm & Carlton Streets
>  Buffalo, New York 14263
>  From: Carlos Ruiz 
>  Sent: Tuesday, September 12, 2017 11:28:33 AM
>  To: Shepherd, Lori
>  Subject: Re: Bioconductor failing package MEAL
> 
>  Hi Lori,
> 
>