Re: [Bioc-devel] NanoStringDiff package update

[Shepherd, Lori]

If you have successfully pushed to the git.bioconductor.org server (which I do 
see your changes) with a valid version bump (which the last was),  the changes 
will become available to the user on the next build of the system.  We do 
nightly builds so it should appear on the daily build report with the updated 
version within the next 24 hours


http://bioconductor.org/checkResults/3.7/bioc-LATEST/


Cheers,


Thank you for your efforts!


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Zhai, Tingting 
Sent: Thursday, January 25, 2018 6:00:57 PM
To: Shepherd, Lori
Cc: Martin Morgan; Turaga, Nitesh
Subject: Re: [Bioc-devel] NanoStringDiff package update

I think I have successfully pushed my package files with version 1.9.1 to both 
Bioconductor and GitHub repositories, and repeated for the release branch with 
version 1.8.1. So what next I should do to make my updated package available to 
users?  Thank you again for all your help!

Best wishes,
Tingting

On Thu, Jan 25, 2018 at 1:58 PM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

So you are missing the upstream remote.  I'm not exactly sure how it got 
deleted and how you have been able to push to master.

It looks like you have created a github repository for your package and should 
be following

Create a new GitHub repository tutorial:



http://bioconductor.org/developers/how-to/git/maintain-github-bioc/



using origin will push/pull to your github repository

using upstream (once it is added) will push/pull to our 
git.bioconductor.org server


You'll want to pick up the above page at step 6 for adding the upstream remote.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Zhai, Tingting mailto:tingting.z...@uky.edu>>
Sent: Thursday, January 25, 2018 1:47:51 PM
To: Shepherd, Lori
Cc: Martin Morgan; Turaga, Nitesh

Subject: Re: [Bioc-devel] NanoStringDiff package update


the results of


git remote -v :


origin g...@github.com:tingtina/NanoStringDiff.git (fetch)

origin g...@github.com:tingtina/NanoStringDiff.git (push)



I'm trying to change the version on the master branch to 1.9.1.


Thanks,

Tingting

On Thu, Jan 25, 2018 at 1:26 PM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

Can you please send the results of


git remote -v



Also please note:


The version on the master branch (devel) should be 1.9.1


The 1.8.1 will be for RELEASE_3_6


Versions are package_x.y.z   the y in devel is always odd,  y in release is 
always even, and devel y >  release y





Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Zhai, Tingting mailto:tingting.z...@uky.edu>>
Sent: Thursday, January 25, 2018 1:17:22 PM

To: Shepherd, Lori
Cc: Martin Morgan
Subject: Re: [Bioc-devel] NanoStringDiff package update

Hi Lori,
Sorry to bother you again. Now I have successfully pushed my package files with 
version 1.8.1 to both Bioconductor and GitHub repositories. But when I repeat 
for the release branch with "git push upstream RELEASE_3_6", I get following 
error:

fatal: 'upstream' does not appear to be a git repository

fatal: Could not read from remote repository.


Please make sure you have the correct access rights

and the repository exists.

Could you help me fix this out?

Thanks,
Tingting

On Thu, Jan 25, 2018 at 11:50 AM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

The current release branch is RELEASE_3_6


So the bottom section instructions would use that as the release branch:

http://bioconductor.org/developers/how-to/git/maintain-bioc-only/


I do see the changes on the git.bioconductor.org 
so your push was successful however this is one issue:


Please pay attention to version numbers. I just did a quick glance at the 
changes that were uploaded and the version number committed is less than the 
current devel version :


http://bioconductor.org/checkResults/3.7/bioc-LATEST/NanoStringDiff/malbec2-buildsrc.html


The current devel version we have is 1.9.0 and you submitted changes with 1.7.1


Please see the section on versioning

http://bioconductor.org/developers/how-to/version-numbering/

and the recent devel post

https://stat.ethz.ch/pipermail/bioc-devel/2018-January/012657.html


While your changes are on the git server the package won't be rebuild because 
of the lower Description version number. It needs to be corrected on the master 
branch to 1.9.1.


When you submit your changes on the RELEASE_3_6 branch the current version we 
have is 1.8.0 so the changes should b

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

[Martin Morgan]

On 01/24/2018 03:38 PM, Wolfgang Huber wrote:

GenomicFeatures_1.31.3 imports RMySQL.

I'm having great trouble installing RMySQL from source on a recent MacOS 
(10.13.3) with homebrew.


The package's homepage says "The 'RMySQL' package contains an old 
implementation based on legacy code from S-PLUS which being phased out. 
A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' 
package" https://cran.r-project.org/web/packages/RMySQL/index.html


So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?


Out of curiosity, is MariaDB easier to install on your system? Its 
system dependencies are described at 
https://CRAN.R-project.org/package=RMariaDB


FWIW MySQL is a relatively recent addition as a dependency to 
GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a 
much more stable solution than `makeTxDbFromBiomart()`. On the other had 
Johannes does an excellent job on the ensembldb packages, so perhaps 
this code could really be conditional with the RMySQL dependency moved 
to Suggests:


Martin



With thanks in advance-
Wolfgang

---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.hu...@embl.de
http://www.huber.embl.de

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Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

[Vincent Carey]

On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
>
>> GenomicFeatures_1.31.3 imports RMySQL.
>>
>> I'm having great trouble installing RMySQL from source on a recent MacOS
>> (10.13.3) with homebrew.
>>
>> The package's homepage says "The 'RMySQL' package contains an old
>> implementation based on legacy code from S-PLUS which being phased out. A
>> modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB'
>> package" https://cran.r-project.org/web/packages/RMySQL/index.html
>>
>> So is it time to heed that advice and migrate GenomicFeatures to RMariaDB
>> ?
>>
>
> Out of curiosity, is MariaDB easier to install on your system? Its system
> dependencies are described at https://CRAN.R-project.org/package=RMariaDB
>
> FWIW MySQL is a relatively recent addition as a dependency to
> GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a
> much more stable solution than `makeTxDbFromBiomart()`. On the other had
> Johannes does an excellent job on the ensembldb packages, so perhaps this
> code could really be conditional with the RMySQL dependency moved to
> Suggests:
>

I would vote for moving the relationship to Suggests.


>
> Martin
>
>
>> With thanks in advance-
>> Wolfgang
>>
>> ---
>> Wolfgang Huber
>> Principal Investigator, EMBL Senior Scientist
>> European Molecular Biology Laboratory (EMBL)
>> Heidelberg, Germany
>>
>> wolfgang.hu...@embl.de
>> http://www.huber.embl.de
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
>
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Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

[Tim Triche, Jr.]

Moving it to Suggests: would certainly ease installation on clusters and
such.

--t

On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
>
>> GenomicFeatures_1.31.3 imports RMySQL.
>>
>> I'm having great trouble installing RMySQL from source on a recent MacOS
>> (10.13.3) with homebrew.
>>
>> The package's homepage says "The 'RMySQL' package contains an old
>> implementation based on legacy code from S-PLUS which being phased out. A
>> modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB'
>> package" https://cran.r-project.org/web/packages/RMySQL/index.html
>>
>> So is it time to heed that advice and migrate GenomicFeatures to RMariaDB
>> ?
>>
>
> Out of curiosity, is MariaDB easier to install on your system? Its system
> dependencies are described at https://CRAN.R-project.org/package=RMariaDB
>
> FWIW MySQL is a relatively recent addition as a dependency to
> GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a
> much more stable solution than `makeTxDbFromBiomart()`. On the other had
> Johannes does an excellent job on the ensembldb packages, so perhaps this
> code could really be conditional with the RMySQL dependency moved to
> Suggests:
>
> Martin
>
>
>> With thanks in advance-
>> Wolfgang
>>
>> ---
>> Wolfgang Huber
>> Principal Investigator, EMBL Senior Scientist
>> European Molecular Biology Laboratory (EMBL)
>> Heidelberg, Germany
>>
>> wolfgang.hu...@embl.de
>> http://www.huber.embl.de
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
>
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Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Simina Boca]

Dear all,
Thank you to Sean, Lori, and Nitesh for helping me out with a package
update last year. I'm now trying to update another package, MultiMed. I
have it set up on Github https://github.com/SiminaB/MultiMed - you can see
that the contributors are Marc, Herve, and Dan Tenenbaum.
However, I get the same error as I got before when doing "git push upstream
master":
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
FATAL: W any packages/swfdr SiminaB 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.

Do I need to submit anything else or should BioC already know that I'm the
same person who is managing these packages?

Thanks so much!

Cheers,
Simina


On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Simina,
>
> Please try again now.
>
> The issue was you didn’t submit your SVN ID “s.boca”. This is needed for
> people who have been maintainers before the Git transition, to associate
> your key to the package.
>
> For new packages this issue doesn’t apply, because we just collect their
> Github IDs.
>
> Hope this helps.
>
> Best,
>
> Nitesh
>
> > On Sep 11, 2017, at 2:50 PM, Simina Boca  wrote:
> >
> > Thank you again Sean and Lori! I am now past that initial stage. I now
> have
> > to resolve merge conflicts, primarily in the DESCRIPTION file. When
> > following the instructions here http://bioconductor.org/
> > developers/how-to/git/resolve-conflicts/ however, I ended up getting the
> > error below:
> >
> > ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git push upstream master
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
> to
> > the list of known hosts.
> > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > FATAL: W any packages/swfdr SiminaB 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.
> >
> > Thank you so much!
> >
> > Best,
> > Simina
> >
> >
> > On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca 
> wrote:
> >
> >> Thank you so much Sean and Lori! For some reason I thought the ssh key
> >> part was only relevant if the package was submitted via svn, which is
> why i
> >> had overlooked those instructions initially.
> >>
> >> Cheers,
> >> Simina
> >>
> >> On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
> >> lori.sheph...@roswellpark.org> wrote:
> >>
> >>> Have you submitted your ssh key
> >>>
> >>>
> >>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
> >>> o4tNufs0ziNyNmexegNZgNieIovbAA/viewform
> >>>
> >>>  ufs0ziNyNmexegNZgNieIovbAA/viewform>
> >>> git / svn transition: ssh keys
> >>>  ufs0ziNyNmexegNZgNieIovbAA/viewform>
> >>> docs.google.com
> >>> Use this form to link your existing svn credentials with access
> >>> permissions to the new Bioconductor git repository. To do this, we
> need an
> >>> ssh public key. You might have added these to github, see
> >>> https://github.com/your-github-id.keys. Alternatively, you may provide
> >>> the ssh public key directly, e.g., copy-pasting ~/.ssh/id_rsa.pub. To
> >>> generate ssh key pairs, see https://help.github.com/articl
> >>> es/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/
> >>>
> >>>
> >>>
> >>>
> >>> Lori Shepherd
> >>>
> >>> Bioconductor Core Team
> >>>
> >>> Roswell Park Cancer Institute
> >>>
> >>> Department of Biostatistics & Bioinformatics
> >>>
> >>> Elm & Carlton Streets
> >>>
> >>> Buffalo, New York 14263
> >>> --
> >>> *From:* Bioc-devel  on behalf of
> >>> Simina Boca 
> >>> *Sent:* Tuesday, September 5, 2017 11:40:37 PM
> >>> *To:* bioc-devel@r-project.org
> >>> *Subject:* [Bioc-devel] updating Bioconductor package that is already
> on
> >>> Github
> >>>
> >>> Dear all,
> >>>
> >>> I hope this isn't a duplicate of another question. Here goes:
> >>>
> >>> - I would like to update my swfdr package, which is already on
> >>> Bioconductor. It is also on Github and my submission process was via
> >>> opening an issue at https://github.com/Bioconducto
> >>> r/Contributions/issues/213
> >>>
> >>> - At this point there are some slight differences between the Github
> and
> >>> Bioconductor versions, for example the Bioconductor version number got
> >>> automatically bumped to 1.0.0 upon acceptance
> >>>
> >>> - I would like to first synchronize what is on Github to have the
> current
> >>> version that is on Bioconductor before updating and also include any
> >>> updates in the next version of the package on Bioconductor
> >>>
> >>> - I did "git remote add upstream g...@git.bioconductor.org:packa
> >

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

[Hervé Pagès]

Yep, moving RMySQL to Suggests makes sense. Will do. Also migrating to
RMariaDB is on the TODO list.

Note that the current problem of RMySQL being hard to install on Mac is
only because CRAN doesn't provide an RMySQL binary for R 3.5 yet:

  https://cran.r-project.org/web/packages/RMySQL/index.html

For the record, we had a similar situation one year ago when R 3.4 was
in development: CRAN started to build package binaries for Mac a few
weeks only before the release of R 3.4.0. Not ideal :-/

H.

On 01/26/2018 07:35 AM, Tim Triche, Jr. wrote:

Moving it to Suggests: would certainly ease installation on clusters and
such.

--t

On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:


On 01/24/2018 03:38 PM, Wolfgang Huber wrote:


GenomicFeatures_1.31.3 imports RMySQL.

I'm having great trouble installing RMySQL from source on a recent MacOS
(10.13.3) with homebrew.

The package's homepage says "The 'RMySQL' package contains an old
implementation based on legacy code from S-PLUS which being phased out. A
modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB'
package" 
https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_RMySQL_index.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=VnqaJPDwlPTUg8EwcI-uhm0UISQ6z5Cf7Ml5yb71KOI&e=

So is it time to heed that advice and migrate GenomicFeatures to RMariaDB
?



Out of curiosity, is MariaDB easier to install on your system? Its system
dependencies are described at 
https://urldefense.proofpoint.com/v2/url?u=https-3A__CRAN.R-2Dproject.org_package-3DRMariaDB&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=ENePjXHv_uoxwPiSLsoj0K0M4yAzHXPCDLsnTpoURJ8&e=

FWIW MySQL is a relatively recent addition as a dependency to
GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a
much more stable solution than `makeTxDbFromBiomart()`. On the other had
Johannes does an excellent job on the ensembldb packages, so perhaps this
code could really be conditional with the RMySQL dependency moved to
Suggests:

Martin



With thanks in advance-
Wolfgang

---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.hu...@embl.de
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.huber.embl.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=vWnZbbUZzkP2WNC8YkvlMDP2U8YILpmkr0tD2i56_gs&e=

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Simina Boca]

Thank you Nitesh! Where should I use the private key? I only see the public
key mentioned here:
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Sorry
if I'm missing something very obvious!

Best,
Simina

On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi
>
> You are using the wrong key.
>
> The key we have on file for you is
>
> ssh-rsa B3NzaC1yc2EDAQABAAACAQDk1ywCtjVfC0wewYRCvzEiAac3so7n
> nRISC6xj3RkEerAUaOHHSA2RjlrG60TYjnEZGPyeN79oKNDP0NhCelsNR2us
> gviCVeS04Qs2RhyzQVf5iNP/pJIBt21pwIvsW3CBqB1bTECUG8E9pK
> 3Gtm77uyRAwLImJtH1RioJ1JpGWKZ0r0ZU0O9c//zwr+Ae8OB94kSEuQ0yTXZj1nHfzL3vHsDt
> I8SsF3UE22RhS/sClW7s3raAlGNbmVdURZ2726JW2jIm40jeLDScdfO8UGEr5bWgVo7bnl6bzY
> UBsS2l8I2DZZHKIC+A1wBngNFpKNJ6dTpKzadkRudGbvU5q
> cIoX2zQNGzs/IyTh3LnX1TbCR1TbG/zC1BwoLB64yyjYI0O2nb+
> ZhhRyXyoljX6AtoMgr16vwUfO+ts3HoD060WTFx29jucqV8rtYXNhDzZmqQs8Z5Ajk++
> 8A0x7fxtuAR1FTVNByaTmH3PAIW6WU9wXXpQEz72mSm7FpQgQDkOfjRBQKqR
> nGbhaay8qltMYaqzjQLA8pBl7YIa5Km5UvyvV2DbAHS0B1R8w7c8L3kmPj5M
> PJZdAcRc6Nc0ByE4pYVwv8mosMB4gt12Lzuj0hz5ID9SDUPq8QghGJiWhVyb
> ZpKafu8VQ7E5QvqBC6DHhpKhdodt16BymxkEWk380yODUQ==
>
>
> You should use a private key corresponding to that public key.
>
> Best,
>
> Nitesh
>
> > On Jan 26, 2018, at 12:05 PM, Simina Boca  wrote:
> >
> > Dear all,
> > Thank you to Sean, Lori, and Nitesh for helping me out with a package
> update last year. I'm now trying to update another package, MultiMed. I
> have it set up on Github https://github.com/SiminaB/MultiMed - you can
> see that the contributors are Marc, Herve, and Dan Tenenbaum.
> > However, I get the same error as I got before when doing "git push
> upstream master":
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
> to the list of known hosts.
> > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > FATAL: W any packages/swfdr SiminaB 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.
> >
> > Do I need to submit anything else or should BioC already know that I'm
> the same person who is managing these packages?
> >
> > Thanks so much!
> >
> > Cheers,
> > Simina
> >
> >
> > On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
> > Hi Simina,
> >
> > Please try again now.
> >
> > The issue was you didn’t submit your SVN ID “s.boca”. This is needed for
> people who have been maintainers before the Git transition, to associate
> your key to the package.
> >
> > For new packages this issue doesn’t apply, because we just collect their
> Github IDs.
> >
> > Hope this helps.
> >
> > Best,
> >
> > Nitesh
> >
> > > On Sep 11, 2017, at 2:50 PM, Simina Boca 
> wrote:
> > >
> > > Thank you again Sean and Lori! I am now past that initial stage. I now
> have
> > > to resolve merge conflicts, primarily in the DESCRIPTION file. When
> > > following the instructions here http://bioconductor.org/
> > > developers/how-to/git/resolve-conflicts/ however, I ended up getting
> the
> > > error below:
> > >
> > > ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git push upstream
> master
> > > Warning: Permanently added 'git.bioconductor.org,34.192.48.227'
> (ECDSA) to
> > > the list of known hosts.
> > > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > > FATAL: W any packages/swfdr SiminaB 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.
> > >
> > > Thank you so much!
> > >
> > > Best,
> > > Simina
> > >
> > >
> > > On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca 
> wrote:
> > >
> > >> Thank you so much Sean and Lori! For some reason I thought the ssh key
> > >> part was only relevant if the package was submitted via svn, which is
> why i
> > >> had overlooked those instructions initially.
> > >>
> > >> Cheers,
> > >> Simina
> > >>
> > >> On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
> > >> lori.sheph...@roswellpark.org> wrote:
> > >>
> > >>> Have you submitted your ssh key
> > >>>
> > >>>
> > >>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
> > >>> o4tNufs0ziNyNmexegNZgNieIovbAA/viewform
> > >>>
> > >>>  ufs0ziNyNmexegNZgNieIovbAA/viewform>
> > >>> git / svn transition: ssh keys
> > >>>  ufs0ziNyNmexegNZgNieIovbAA/viewform>
> > >>> docs.google.com
> > >>> Use this form to link your existing svn credentials with access
> > >>> permissions to the new Bioconductor git repository. To do this, we
> need an
> > >>> ssh public key. You might have added these to github, see
> > >>> https://github.com/your-github-id.keys. Alternatively, you may
> provide
> > >>> the ssh public key directly, e.g., copy-pasting ~/.ssh

Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Turaga, Nitesh]

Hi

You are using the wrong key.

The key we have on file for you is

ssh-rsa 
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


You should use a private key corresponding to that public key.

Best,

Nitesh 

> On Jan 26, 2018, at 12:05 PM, Simina Boca  wrote:
> 
> Dear all,
> Thank you to Sean, Lori, and Nitesh for helping me out with a package update 
> last year. I'm now trying to update another package, MultiMed. I have it set 
> up on Github https://github.com/SiminaB/MultiMed - you can see that the 
> contributors are Marc, Herve, and Dan Tenenbaum.
> However, I get the same error as I got before when doing "git push upstream 
> master":
> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> the list of known hosts.
> Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> FATAL: W any packages/swfdr SiminaB 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.
> 
> Do I need to submit anything else or should BioC already know that I'm the 
> same person who is managing these packages?
> 
> Thanks so much!
> 
> Cheers,
> Simina
> 
> 
> On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh 
>  wrote:
> Hi Simina,
> 
> Please try again now.
> 
> The issue was you didn’t submit your SVN ID “s.boca”. This is needed for 
> people who have been maintainers before the Git transition, to associate your 
> key to the package.
> 
> For new packages this issue doesn’t apply, because we just collect their 
> Github IDs.
> 
> Hope this helps.
> 
> Best,
> 
> Nitesh
> 
> > On Sep 11, 2017, at 2:50 PM, Simina Boca  wrote:
> >
> > Thank you again Sean and Lori! I am now past that initial stage. I now have
> > to resolve merge conflicts, primarily in the DESCRIPTION file. When
> > following the instructions here http://bioconductor.org/
> > developers/how-to/git/resolve-conflicts/ however, I ended up getting the
> > error below:
> >
> > ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git push upstream master
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
> > the list of known hosts.
> > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > FATAL: W any packages/swfdr SiminaB 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.
> >
> > Thank you so much!
> >
> > Best,
> > Simina
> >
> >
> > On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca  wrote:
> >
> >> Thank you so much Sean and Lori! For some reason I thought the ssh key
> >> part was only relevant if the package was submitted via svn, which is why i
> >> had overlooked those instructions initially.
> >>
> >> Cheers,
> >> Simina
> >>
> >> On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
> >> lori.sheph...@roswellpark.org> wrote:
> >>
> >>> Have you submitted your ssh key
> >>>
> >>>
> >>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
> >>> o4tNufs0ziNyNmexegNZgNieIovbAA/viewform
> >>>
> >>> 
> >>> git / svn transition: ssh keys
> >>> 
> >>> docs.google.com
> >>> Use this form to link your existing svn credentials with access
> >>> permissions to the new Bioconductor git repository. To do this, we need an
> >>> ssh public key. You might have added these to github, see
> >>> https://github.com/your-github-id.keys. Alternatively, you may provide
> >>> the ssh public key directly, e.g., copy-pasting ~/.ssh/id_rsa.pub. To
> >>> generate ssh key pairs, see https://help.github.com/articl
> >>> es/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/
> >>>
> >>>
> >>>
> >>>
> >>> Lori Shepherd
> >>>
> >>> Bioconductor Core Team
> >>>
> >>> Roswell Park Cancer Institute
> >>>
> >>> Department of Biostatistics & Bioinformatics
> >>>
> >>> Elm & Carlton Streets
> >>>
> >>> Buffalo, New York 14263
> >>> --
> >>> *From:* Bioc-devel  on behalf of
> >>> Simina Boca 
> >>> *Sent:* Tuesday, September 5, 2017 11:40:37 PM
> >>> *To:* bioc-devel@r-project.o

Re: [Bioc-devel] updating Bioconductor package that is already on Github

[Turaga, Nitesh]

Hi Simina,

I’m assuming your keys are stored in the folder “.ssh”. If that is the case, 
try,

 ssh-keygen -y -e -f 

That command will print out a public key. If that public key is the same as the 
one I’ve sent you, they you can use that. (Remember that public keys, don’t 
have “.pub” ending. If your public key is called “id_rsa.pub” then your private 
key is most likely, “id_rsa”). 

If you have to configure your git login, please follow the link below to make 
sure that the same key is used

http://bioconductor.org/developers/how-to/git/faq/

Best,

Nitesh 


> On Jan 26, 2018, at 12:36 PM, Simina Boca  wrote:
> 
> Thank you Nitesh! Where should I use the private key? I only see the public 
> key mentioned here: 
> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Sorry if 
> I'm missing something very obvious!
> 
> Best,
> Simina
> 
> On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh 
>  wrote:
> Hi
> 
> You are using the wrong key.
> 
> The key we have on file for you is
> 
> ssh-rsa 
> 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
> 
> 
> You should use a private key corresponding to that public key.
> 
> Best,
> 
> Nitesh
> 
> > On Jan 26, 2018, at 12:05 PM, Simina Boca  wrote:
> >
> > Dear all,
> > Thank you to Sean, Lori, and Nitesh for helping me out with a package 
> > update last year. I'm now trying to update another package, MultiMed. I 
> > have it set up on Github https://github.com/SiminaB/MultiMed - you can see 
> > that the contributors are Marc, Herve, and Dan Tenenbaum.
> > However, I get the same error as I got before when doing "git push upstream 
> > master":
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to 
> > the list of known hosts.
> > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > FATAL: W any packages/swfdr SiminaB 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.
> >
> > Do I need to submit anything else or should BioC already know that I'm the 
> > same person who is managing these packages?
> >
> > Thanks so much!
> >
> > Cheers,
> > Simina
> >
> >
> > On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh 
> >  wrote:
> > Hi Simina,
> >
> > Please try again now.
> >
> > The issue was you didn’t submit your SVN ID “s.boca”. This is needed for 
> > people who have been maintainers before the Git transition, to associate 
> > your key to the package.
> >
> > For new packages this issue doesn’t apply, because we just collect their 
> > Github IDs.
> >
> > Hope this helps.
> >
> > Best,
> >
> > Nitesh
> >
> > > On Sep 11, 2017, at 2:50 PM, Simina Boca  wrote:
> > >
> > > Thank you again Sean and Lori! I am now past that initial stage. I now 
> > > have
> > > to resolve merge conflicts, primarily in the DESCRIPTION file. When
> > > following the instructions here http://bioconductor.org/
> > > developers/how-to/git/resolve-conflicts/ however, I ended up getting the
> > > error below:
> > >
> > > ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git push upstream master
> > > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
> > > the list of known hosts.
> > > Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
> > > FATAL: W any packages/swfdr SiminaB 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.
> > >
> > > Thank you so much!
> > >
> > > Best,
> > > Simina
> > >
> > >
> > > On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca  
> > > wrote:
> > >
> > >> Thank you so much Sean and Lori! For some reason I thought the ssh key
> > >> part was only relevant if the package was submitted via svn, which is 
> > >> why i
> > >> had overlooked those instructions initially.
> > >>
> > >> Cheers,
> > >> Simina
> > >>
> > >> On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
> > >> lori.sheph...@roswellpark.org> wrote:
> > >>
> > >>> Have you submitted your ssh key
> > >>>
> > >>>
> > >>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
> > >>> o4tNufs0ziNyNmexegNZgNieIovbAA/viewform
> > >>>
> > >>> 

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

[Wolfgang Huber]

26.1.18 14:59, Martin Morgan scripsit:

On 01/24/2018 03:38 PM, Wolfgang Huber wrote:

GenomicFeatures_1.31.3 imports RMySQL.

I'm having great trouble installing RMySQL from source on a recent 
MacOS (10.13.3) with homebrew.


The package's homepage says "The 'RMySQL' package contains an old 
implementation based on legacy code from S-PLUS which being phased 
out. A modern 'MySQL' client based on 'Rcpp' is available from the 
'RMariaDB' package" 
https://cran.r-project.org/web/packages/RMySQL/index.html


So is it time to heed that advice and migrate GenomicFeatures to 
RMariaDB ?


Out of curiosity, is MariaDB easier to install on your system? Its 
system dependencies are described at 
https://CRAN.R-project.org/package=RMariaDB


I have no problems installing RMariaDB on MacOS (10.13.3) on an R-devel 
from source, after installing mariadb-connector-c with homebrew.


OTOH, I have not figured out a way to install RMySQL neither on my 
R-devel from source (various complaints about missing .h files) nor on a 
binary R 3.4.2 with the binary package download (complaints about 
missing system libraries / wrong versions).


Thanks and kind regards
Wolfgang

FWIW MySQL is a relatively recent addition as a dependency to 
GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a 
much more stable solution than `makeTxDbFromBiomart()`. On the other had 
Johannes does an excellent job on the ensembldb packages, so perhaps 
this code could really be conditional with the RMySQL dependency moved 
to Suggests:


Martin



With thanks in advance-
Wolfgang

---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.hu...@embl.de
http://www.huber.embl.de

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This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee 
or agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have 
received this message in error, please notify the sender immediately by 
e-mail and delete this email message from your computer. Thank you.


--
With thanks in advance-
Wolfgang

---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.hu...@embl.de
http://www.huber.embl.de

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Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

[Kasper Daniel Hansen]

As an alternative to Suggests, perhaps make a GenomicFeaturesBuildTools.
 Not sure if it is better or worse, just different

On Fri, Jan 26, 2018 at 2:39 PM, Wolfgang Huber 
wrote:

>
>
> 26.1.18 14:59, Martin Morgan scripsit:
>
>> On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
>>
>>> GenomicFeatures_1.31.3 imports RMySQL.
>>>
>>> I'm having great trouble installing RMySQL from source on a recent MacOS
>>> (10.13.3) with homebrew.
>>>
>>> The package's homepage says "The 'RMySQL' package contains an old
>>> implementation based on legacy code from S-PLUS which being phased out. A
>>> modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB'
>>> package" https://cran.r-project.org/web/packages/RMySQL/index.html
>>>
>>> So is it time to heed that advice and migrate GenomicFeatures to
>>> RMariaDB ?
>>>
>>
>> Out of curiosity, is MariaDB easier to install on your system? Its system
>> dependencies are described at https://CRAN.R-project.org/package=RMariaDB
>>
>
> I have no problems installing RMariaDB on MacOS (10.13.3) on an R-devel
> from source, after installing mariadb-connector-c with homebrew.
>
> OTOH, I have not figured out a way to install RMySQL neither on my R-devel
> from source (various complaints about missing .h files) nor on a binary R
> 3.4.2 with the binary package download (complaints about missing system
> libraries / wrong versions).
>
> Thanks and kind regards
> Wolfgang
>
> FWIW MySQL is a relatively recent addition as a dependency to
>> GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a
>> much more stable solution than `makeTxDbFromBiomart()`. On the other had
>> Johannes does an excellent job on the ensembldb packages, so perhaps this
>> code could really be conditional with the RMySQL dependency moved to
>> Suggests:
>>
>> Martin
>>
>>
>>> With thanks in advance-
>>> Wolfgang
>>>
>>> ---
>>> Wolfgang Huber
>>> Principal Investigator, EMBL Senior Scientist
>>> European Molecular Biology Laboratory (EMBL)
>>> Heidelberg, Germany
>>>
>>> wolfgang.hu...@embl.de
>>> http://www.huber.embl.de
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information.  If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited.  If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>>
>
> --
> With thanks in advance-
> Wolfgang
>
> ---
> Wolfgang Huber
> Principal Investigator, EMBL Senior Scientist
> European Molecular Biology Laboratory (EMBL)
> Heidelberg, Germany
>
> wolfgang.hu...@embl.de
> http://www.huber.embl.de
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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