Re: [Bioc-devel] git credential problem

[Liu, Qian]

Hi Nitesh,

Thanks and I can login now and see the details in BiocCredentials account. I 
will change the maintainer email in my package also.

Best,
Qian

From: Bioc-devel  on behalf of Nitesh Turaga 

Sent: Tuesday, November 10, 2020 10:34 AM
To: Qian Liu ; Kern, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] git credential problem

Hi Qian,

You should have access to the package using qian@roswellpark.org 
. You should be able to login to your 
BiocCredentials account and check if you have access. Everything on our end 
looks fine.

You should change the DESCRIPTION in your package to say 
qian@roswellpark.org  instead fo the 
buffalo.edu 

 address.

Best,

Nitesh

> On Nov 9, 2020, at 9:50 PM, Qian Liu  wrote:
>
> Dear Bioc,
>
> I was trying to fix the SQLDataFrame building error, but it says I don't
> have correct access right. Since I am using a different computer, so I
> followed the step 1 in this link:
> http://secure-web.cisco.com/1kBXPwKQ9XzoGxCtVVGYHcbvnmiob1CR6ELUMPtYSkYPl6gmOoHnA5ch3QvaGPr2UGypYThMH2ahDLVR1NRG3mBp5hCntF5QxGC2rTvgl3QilEGrDVn1MwVQlysjsuURr0Ksn82ckimHSPvkKgxij7WoJACs2UFNnmz-JxqY2ThmfCgpCtF2bDvd8exuSLW63qHkrsKPOPWTvkkgRKU2zArxR2eVISaYNmsixlBDtFV4bhpVUKZ0N3QpFeE2QD5iY1rSMh8qb_jybvLREH_7aI8ATsAL6MyPVyipRRbh-UoPq4PBcWMVkLwKNQtlpBKek/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fmaintain-bioc-only%2F,
>  but the
> Bioconductor git credential page shows:
>
> ql...@buffalo.edu is not associated with a maintainer of a Bioconductor
> package. Please check the spelling or contact bioc-devel@r-project.org for
> help.
> qian@roswellpark.org is not associated with a maintainer of a
> Bioconductor package. Please check the spelling or contact
> bioc-devel@r-project.org for help.
>
> Please suggest how to proceed. Thanks!
>
> Best,
> Qian
>
>[[alternative HTML version deleted]]
>
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Re: [Bioc-devel] git credential problem

[Nitesh Turaga]

Hi Qian,

You should have access to the package using qian@roswellpark.org 
. You should be able to login to your 
BiocCredentials account and check if you have access. Everything on our end 
looks fine. 

You should change the DESCRIPTION in your package to say 
qian@roswellpark.org  instead fo the 
buffalo.edu  address. 

Best,

Nitesh 

> On Nov 9, 2020, at 9:50 PM, Qian Liu  wrote:
> 
> Dear Bioc,
> 
> I was trying to fix the SQLDataFrame building error, but it says I don't
> have correct access right. Since I am using a different computer, so I
> followed the step 1 in this link:
> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, but the
> Bioconductor git credential page shows:
> 
> ql...@buffalo.edu is not associated with a maintainer of a Bioconductor
> package. Please check the spelling or contact bioc-devel@r-project.org for
> help.
> qian@roswellpark.org is not associated with a maintainer of a
> Bioconductor package. Please check the spelling or contact
> bioc-devel@r-project.org for help.
> 
> Please suggest how to proceed. Thanks!
> 
> Best,
> Qian
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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Re: [Bioc-devel] Acceptable dataset origins besides ExperimentHub

[Kern, Lori]

Including this data should be okay.  The benefit of the ExperimentHub package 
would be to allow broader use of the data beyond your package to the 
Bioconductor community at large.If you include the data from the site,  I 
would strongly, strongly suggest implementing a caching mechanism 
(ExperimentHub does this already in the backend)  so that if the public server 
goes down or has connectivity issues, any previously cached version could be 
utilized  (I'm bias but see BiocFileCache)



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sean Davis 

Sent: Tuesday, November 10, 2020 7:29 AM
To: Hector Gracia 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Acceptable dataset origins besides ExperimentHub

Hi, Hector.

While an "unofficial" answer, there are many packages that access data from
public repositories, so using an EBI-supported repository and FTP site
seems perfectly acceptable to me.

Sean

ᐧ

On Tue, Nov 10, 2020 at 5:54 AM Hector Gracia 
wrote:

> Recently our package AlpsNMR was accepted in Bioconductor
> https://secure-web.cisco.com/1QVyrCOoYojsO56K9awpCpiKlq4s6e6G9Ge_d2An_SuDgWlzM-MlYzxEysc-Y7SuG5Udcl6X2SKaZpUe9Z9D3S36GdqsSexPj2VVXSG9UoIvIzyHGV1C4gmIsQ2OyggbYCLelhaW5Vhk_tOZqQg1t_OLQCIOwM7k05edN1JtOMDMObKi0JG8SRt66UgRyG_urIe_hcCt17o6dwDheJBapQQLY6zEtlcij57JGzGB6CtgnKsuPzV7vBxNUbl85mCu83TbmuFPOWJRTm2Otyw2BeeWgZapUluBSXDYnNSe_iJ_3sqY815LFDgEFuZ1Ry1yZyw98GWjzUy7S1rEl4_bMuQ/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FAlpsNMR.html
>
> For pass the review process we had to remove a dataset that was stored in
> Dropbox and that was used in one long tutorial about the package.
>
> Besides create an ExperimentHub package with this data, is there other
> ways to include this data in the package tutorial?
>
> I ask it because the dataset is public available in metabolights ftp and i
> like to know if this ftp can be considered as dedicated server that ensure
> logevity of the data
> ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS242/
>
> Or if the only way to do this is create a data package in ExperimentHub
>
> Thanks
>
> Enviado desde 
> Correo
>  para
> Windows 10
>
>
>
>
> Aquest correu electr?nic cont? informaci? confidencial emparada pel secret
> professional. Qualsevol reproducci?, distribuci? o divulgaci? del seu
> contingut estan estrictament prohibides. Si vost? no ?s el destinatari, li
> preguem no faci difusi? ni copi? el seu contingut i ens ho notifiqui el m?s
> aviat possible a l'adre?a dataprotect...@ibecbarcelona.eu
> Este correo electr?nico contiene informaci?n confidencial amparada por el
> secreto profesional. Cualquier reproducci?n, distribuci?n o divulgaci?n de
> su contenido est?n estrictamente prohibidas. Si usted no es el
> destinatario, le rogamos no difunda ni copie su contenido y nos lo
> notifique de inmediato a la direcci?n dataprotect...@ibecbarcelona.eu
> This electronic transmission contains confidential information covered by
> professional secrecy. Any reproduction, distribution or disclosure of its
> contents is strictly prohibited. If you are not the intended recipient, you
> are kindly requested not to disseminate nor to copy this transmission and
> to notify us as soon as possible by email to
> dataprotect...@ibecbarcelona.eu .
>
> [[alternative HTML version deleted]]
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>


--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892

[Bioc-devel] Acceptable dataset origins besides ExperimentHub

[Hector Gracia]

Recently our package AlpsNMR was accepted in Bioconductor
https://bioconductor.org/packages/devel/bioc/html/AlpsNMR.html

For pass the review process we had to remove a dataset that was stored in 
Dropbox and that was used in one long tutorial about the package.

Besides create an ExperimentHub package with this data, is there other ways to 
include this data in the package tutorial?

I ask it because the dataset is public available in metabolights ftp and i like 
to know if this ftp can be considered as dedicated server that ensure logevity 
of the data
ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS242/

Or if the only way to do this is create a data package in ExperimentHub

Thanks

Enviado desde Correo para 
Windows 10




Aquest correu electr?nic cont? informaci? confidencial emparada pel secret 
professional. Qualsevol reproducci?, distribuci? o divulgaci? del seu contingut 
estan estrictament prohibides. Si vost? no ?s el destinatari, li preguem no 
faci difusi? ni copi? el seu contingut i ens ho notifiqui el m?s aviat possible 
a l'adre?a dataprotect...@ibecbarcelona.eu
Este correo electr?nico contiene informaci?n confidencial amparada por el 
secreto profesional. Cualquier reproducci?n, distribuci?n o divulgaci?n de su 
contenido est?n estrictamente prohibidas. Si usted no es el destinatario, le 
rogamos no difunda ni copie su contenido y nos lo notifique de inmediato a la 
direcci?n dataprotect...@ibecbarcelona.eu
This electronic transmission contains confidential information covered by 
professional secrecy. Any reproduction, distribution or disclosure of its 
contents is strictly prohibited. If you are not the intended recipient, you are 
kindly requested not to disseminate nor to copy this transmission and to notify 
us as soon as possible by email to dataprotect...@ibecbarcelona.eu .

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