[Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?

[Johannes Griss]

Hi everyone,

For a while the build system reported an error that our ReactomeGSA 
package cannot be build due to the missing dependency of the 
"ReactomeGSA.data" package which is required to build the vignettes and 
is listed in the "Suggests" section.


ReactomeGSA.data seems to building fine though but depends on ReactomeGSA.

Unfortunately, I cannot figure out how I could solve this issue.

Thanks for your help!

Kind regards,
Johannes

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EpiCompare: transferring maintainership

[Kern, Lori via Bioc-devel]

We will need to create a BiocCredentials account for Tom Roberts if he does not 
have one yet.  We would need to know what email Tom would like for access there 
as well as if they have a github id?   I can create the account and allow 
access.
After access to the package, it will be up to the new maintainer to change the 
DESCRIPTION file and push to git.bioconductor.org.  It will also be good to 
sign up both here on the bioc-devel mailing list as well as the support site.

Cheers,


Lori Shepherd - Kern

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 Sera Choi 

Sent: Friday, November 3, 2023 11:17 AM
To: bioc-devel@r-project.org 
Cc: Skene, Nathan G ; tomroberts.wor...@gmail.com 

Subject: [Bioc-devel] EpiCompare: transferring maintainership

Hi Bioconductor team,

I'm currently the maintainer of Bioconductor package, EpiCompare. I'm
writing to request transfer of maintainership to Tom Roberts (
tomroberts.wor...@gmail.com). Please could you let me know what is
required?

Thanks so much!

Best wishes,
Sera

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://secure-web.cisco.com/1NuXUVjoaINoIA1htxsUQNr5ZDqBmToryd5xjLclHNtpLUmQ17ToNQyYUOKx4FH7xrGp3xtTg2Wq984tLlCIlRNtp4dBX82Ik708nCdGXir9H5QM2AgGDYYL4MuUbh1iMBc78sZW2QCB_o1j_JU147uAsd2AqMm801N2Pc6b9dakNzFsUYhfZ8-1Uk9sDkI8Qvp2mbu6-0cqDpdNmi1SNrpFNvw7FRJdHRh-QwSThC5VxLzIVjIYCk2vJ_zvp9u8reWB0BskqmNpcjXaxjbvKEV4UhPhkL2OIyCarMjiLalI78G7VPas3uhG_p0HNrxtE/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] EpiCompare: transferring maintainership

[Sera Choi]

Hi Bioconductor team,

I'm currently the maintainer of Bioconductor package, EpiCompare. I'm
writing to request transfer of maintainership to Tom Roberts (
tomroberts.wor...@gmail.com). Please could you let me know what is
required?

Thanks so much!

Best wishes,
Sera

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] gwasurvivr is looking for a new owner/maintainer

[Abbas Rizvi]

Ali - I'll email you separately!

If any other folks are interested, please still inquire as we figure out
the ownership handoff.

Thank you!

Abbas

On Fri, Nov 3, 2023 at 9:01 AM Ali Sajid Imami 
wrote:

> I am definitely interested, as I am working heavily with GWAS data now.
>
> > On Nov 3, 2023, at 8:36 AM, Abbas Rizvi  wrote:
> >
> > Dear Bioconductor Developers,
> >
> > We are looking for a new primary owner for gwasurvivr
> >  >.
> > This package allows users to build multivariate Cox models on
> typed/imputed
> > GWAS data. It seems to have quite a few regular users and has been cited
> > <
> https://scholar.google.ca/scholar?oi=bibs=en=770317402630660857>
> for
> > a number of research projects. We don't have time to support this
> > project/package any longer.
> >
> > Revamping this package and expanding its usage could be an excellent part
> > of one's MS or PhD projects. I am happy to onboard anyone to the package
> > code base and work with them on the needs and feature updates that are
> > needed.
> >
> > Please let me know if you are interested.
> >
> > - Abbas
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] gwasurvivr is looking for a new owner/maintainer

[Abbas Rizvi]

Dear Bioconductor Developers,

We are looking for a new primary owner for gwasurvivr
.
This package allows users to build multivariate Cox models on typed/imputed
GWAS data. It seems to have quite a few regular users and has been cited
 for
a number of research projects. We don't have time to support this
project/package any longer.

Revamping this package and expanding its usage could be an excellent part
of one's MS or PhD projects. I am happy to onboard anyone to the package
code base and work with them on the needs and feature updates that are
needed.

Please let me know if you are interested.

- Abbas

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Add a package to BiocCredentials

[Yunshun Chen via Bioc-devel]

Hi Lori,

Thanks for that.

Yes, I can confirm that Mengbo Li is one of the scider authors and maintainers. 
Could you please grant Mengbo access to scider on Bioc git?

Best,
Yunshun


From: Kern, Lori 
Sent: Friday, November 3, 2023 22:15
To: bioc-devel@r-project.org ; Mengbo Li 

Cc: Yunshun Chen 
Subject: Re: Add a package to BiocCredentials

Yunchun Chen as the current maintainer can you please confirm this request?


Lori Shepherd - Kern

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 Mengbo Li via 
Bioc-devel 
Sent: Friday, November 3, 2023 5:12 AM
To: bioc-devel@r-project.org 
Cc: Yunshun Chen 
Subject: [Bioc-devel] Add a package to BiocCredentials

Dear core team,

Hope this email finds you well. Could I please have scider 
(https://secure-web.cisco.com/1Dl9WFFykg45Tdw8lYQGZVVBEqpo7LEB9FTe9nej7_P_i8sLW6ap8WOz2vz7pAMkhqULPLN5QgVJVB5N0RcA_MROioNJwneusXiG9NpAlL_Uw3_pDoE3zOuEYLdI4-Cv6SUn3kaHkB9SCDdDAkB19x8Jmm2eVXfiihblp-aD8d4jCLzUAmIJT_GQWLboOxjeJvq-7EGiRTZOi8Q0PEKKn7z3x0-i2qg5EjBXmHYTr4UyBE3KiMfcRdIdhnQNG-Cx35FhF94_SUbBQvBLfKi6q2shhOJhMSA9QqghhPiqYGMUJ6pPh2kj96KirwVBG8qrT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fscider.html)
 added to my Bioc git credentials? The email address is 
li...@wehi.edu.au. I have also cc-ed the current 
maintainer of the package.

Many thanks,
Mengbo

[WEHI Logo]


Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia

http://secure-web.cisco.com/1K1BiFTNEdSY2DDCe1DG2wQiBjEPrfF7izI_9faFlAsvTibbBQmbrS0ykAuNo6hr-20mDZTQBPrij2XVAyMkf7m44YLxPiMirDXId6PfTjChBJJVxa24agUcGv90AcmDp8apyf0V2Y0KxVcoUgDw-gSX0Z4V-WPFArWvGU-YahlmmKwAMLXj-1v4KOGi9nJLZTyPZm0nVJj99GkRp_VTP4x4Wkzrb9bFqq_m7EU5623y7b7CwkZsvcn3JcCgqDTwOB3eJjvdoXqigHj8S1w1k39vj6DNzYBppFd8mY7QrClfLLh_NFsLPmewTUqmyKjBC/http%3A%2F%2Fwww.wehi.edu.au

Twitter
  |  
Facebook
  |  
Instagram
  |  
Youtube
  |  
LinkedIn


WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional 
owners of the land where our campuses are located and the continuing connection 
to country and community.

Private and confidential
The content of this e-mail and any attachments may be private and confidential, 
intended only for use of the individual or entity named. If you are not the 
intended recipient of this message you must not read, forward, print, copy, 
disclose, use or store in 

Re: [Bioc-devel] Add a package to BiocCredentials

[Kern, Lori via Bioc-devel]

Yunchun Chen as the current maintainer can you please confirm this request?


Lori Shepherd - Kern

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 Mengbo Li via 
Bioc-devel 
Sent: Friday, November 3, 2023 5:12 AM
To: bioc-devel@r-project.org 
Cc: Yunshun Chen 
Subject: [Bioc-devel] Add a package to BiocCredentials

Dear core team,

Hope this email finds you well. Could I please have scider 
(https://secure-web.cisco.com/1Dl9WFFykg45Tdw8lYQGZVVBEqpo7LEB9FTe9nej7_P_i8sLW6ap8WOz2vz7pAMkhqULPLN5QgVJVB5N0RcA_MROioNJwneusXiG9NpAlL_Uw3_pDoE3zOuEYLdI4-Cv6SUn3kaHkB9SCDdDAkB19x8Jmm2eVXfiihblp-aD8d4jCLzUAmIJT_GQWLboOxjeJvq-7EGiRTZOi8Q0PEKKn7z3x0-i2qg5EjBXmHYTr4UyBE3KiMfcRdIdhnQNG-Cx35FhF94_SUbBQvBLfKi6q2shhOJhMSA9QqghhPiqYGMUJ6pPh2kj96KirwVBG8qrT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fscider.html)
 added to my Bioc git credentials? The email address is 
li...@wehi.edu.au. I have also cc-ed the current 
maintainer of the package.

Many thanks,
Mengbo

[WEHI Logo]


Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia

http://secure-web.cisco.com/1K1BiFTNEdSY2DDCe1DG2wQiBjEPrfF7izI_9faFlAsvTibbBQmbrS0ykAuNo6hr-20mDZTQBPrij2XVAyMkf7m44YLxPiMirDXId6PfTjChBJJVxa24agUcGv90AcmDp8apyf0V2Y0KxVcoUgDw-gSX0Z4V-WPFArWvGU-YahlmmKwAMLXj-1v4KOGi9nJLZTyPZm0nVJj99GkRp_VTP4x4Wkzrb9bFqq_m7EU5623y7b7CwkZsvcn3JcCgqDTwOB3eJjvdoXqigHj8S1w1k39vj6DNzYBppFd8mY7QrClfLLh_NFsLPmewTUqmyKjBC/http%3A%2F%2Fwww.wehi.edu.au

Twitter
  |  
Facebook
  |  
Instagram
  |  
Youtube
  |  
LinkedIn


WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional 
owners of the land where our campuses are located and the continuing connection 
to country and community.

Private and confidential
The content of this e-mail and any attachments may be private and confidential, 
intended only for use of the individual or entity named. If you are not the 
intended recipient of this message you must not read, forward, print, copy, 
disclose, use or store in any way the information this e-mail or any attachment 
contains. If you are not the intended recipient, please notify the sender 
immediately and delete or destroy all copies of this e-mail and any attachment.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list

[Bioc-devel] Add a package to BiocCredentials

[Mengbo Li via Bioc-devel]

Dear core team,

Hope this email finds you well. Could I please have scider 
(https://bioconductor.org/packages/release/bioc/html/scider.html) added to my 
Bioc git credentials? The email address is 
li...@wehi.edu.au. I have also cc-ed the current 
maintainer of the package.

Many thanks,
Mengbo

[WEHI Logo]


Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia

www.wehi.edu.au

Twitter  |  
Facebook  |  
Instagram  |  
Youtube  |  
LinkedIn


WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional 
owners of the land where our campuses are located and the continuing connection 
to country and community.

Private and confidential
The content of this e-mail and any attachments may be private and confidential, 
intended only for use of the individual or entity named. If you are not the 
intended recipient of this message you must not read, forward, print, copy, 
disclose, use or store in any way the information this e-mail or any attachment 
contains. If you are not the intended recipient, please notify the sender 
immediately and delete or destroy all copies of this e-mail and any attachment.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] problems when updating MOSim package

[Sonia Tarazona]

Dear Lori,

We have made some changes in the MOSim package and we are now trying to
update the package in Bioconductor.

However, we cannot make it. This is the error message we get:

PS W:\MOSim> git push upstream devel
g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

However, we could do it last time with the same computer and credentials.
We have checked the ssh keys in my computer, GitHub and Bioconductor and
everything seems to be fine.

Could you help us with this?

Thanks,

Sonia Tarazona

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel