Re: [Bioc-devel] Force Package Update after Removing Large Files from .git History

2021-05-06 Thread Gabriel Odom 
Thank you Nitesh.
Our next step is then to push a version bump to trigger the re-build?
Our contribution issue is still listed as ERROR at this time 
(https://github.com/Bioconductor/Contributions/issues/2064).

On May 6, 2021, at 10:28 AM, Nitesh Turaga 
mailto:nturaga.b...@gmail.com>> wrote:


Note: This message originated from outside the FIU Faculty/Staff email system.

Hi Gabriel,

Thanks for taking the time to fix the package size to < 5MB.

I’ve synced your package repo on 
git.bioconductor.org. You should be good to go 
now.

If you have any further questions on this, please feel free to reply to this 
thread.

Best,

Nitesh

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Gabriel Odom mailto:go...@fiu.edu>>
Date: Thursday, May 6, 2021 at 9:47 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Cc: Fernanda Veitzman mailto:fveit...@fiu.edu>>, Chedraoui 
Silva, Tiago mailto:txs...@med.miami.edu>>
Subject: [Bioc-devel] Force Package Update after Removing Large Files from .git 
History
Dear Bioconductor Team,

We are submitting the package coMethDMR 
(https://github.com/Bioconductor/Contributions/issues/2064)
 and we have fixed all errors and warnings listed in the multi-system build 
report.
One error was that the package was too large. We followed the steps to use BFG 
here 
(https://bioconductor.org/developers/how-to/git/remove-large-data/),
 and we have successfully reduced the package size to <5Mb in our GitHub 
repository. However, according to those instructions, force pushes are not 
allowed to the upstream branch, and we are to contact you for help.
Please advise.

Thanks in advance,
Gabriel

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Re: [Bioc-devel] Force Package Update after Removing Large Files from .git History

2021-05-06 Thread Nitesh Turaga 
Hi Gabriel,

Thanks for taking the time to fix the package size to < 5MB.

I�ve synced your package repo on git.bioconductor.org. You should be good to go 
now.

If you have any further questions on this, please feel free to reply to this 
thread.

Best,

Nitesh

From: Bioc-devel  on behalf of Gabriel Odom 

Date: Thursday, May 6, 2021 at 9:47 AM
To: bioc-devel@r-project.org 
Cc: Fernanda Veitzman , Chedraoui Silva, Tiago 

Subject: [Bioc-devel] Force Package Update after Removing Large Files from .git 
History
Dear Bioconductor Team,

We are submitting the package coMethDMR 
(https://github.com/Bioconductor/Contributions/issues/2064) and we have fixed 
all errors and warnings listed in the multi-system build report.
One error was that the package was too large. We followed the steps to use BFG 
here (https://bioconductor.org/developers/how-to/git/remove-large-data/), and 
we have successfully reduced the package size to <5Mb in our GitHub repository. 
However, according to those instructions, force pushes are not allowed to the 
upstream branch, and we are to contact you for help.
Please advise.

Thanks in advance,
Gabriel

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[Bioc-devel] Force Package Update after Removing Large Files from .git History

2021-05-06 Thread Gabriel Odom 
Dear Bioconductor Team,

We are submitting the package coMethDMR 
(https://github.com/Bioconductor/Contributions/issues/2064) and we have fixed 
all errors and warnings listed in the multi-system build report.
One error was that the package was too large. We followed the steps to use BFG 
here (https://bioconductor.org/developers/how-to/git/remove-large-data/), and 
we have successfully reduced the package size to <5Mb in our GitHub repository. 
However, according to those instructions, force pushes are not allowed to the 
upstream branch, and we are to contact you for help.
Please advise.

Thanks in advance,
Gabriel

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Bioc Git credentials

2021-05-06 Thread Leonard Goldstein 
Great, thanks!

Leonard

On Mon, May 3, 2021 at 11:53 PM Nitesh Turaga 
wrote:

> Hi Leonard,
>
>
>
> I’ve changed your email now, you should be able to activate your account.
>
>
>
> The email listed was to a gene.com email address.
>
>
>
> Add new SSH keys if you don’t have the old key pairs.
>
>
>
> Best,
>
>
>
> Nitesh
>
>
>
> *From: *Bioc-devel  on behalf of
> Leonard Goldstein 
> *Date: *Sunday, May 2, 2021 at 10:06 PM
> *To: *bioc-devel@r-project.org 
> *Subject: *[Bioc-devel] Bioc Git credentials
>
> Hi,
>
> I'm maintaining the SGSeq Bioc package and recently changed the maintainer
> email address. I'm trying to activate a new account for Git credentials
> here
> , but
> get
> the following error message:
>
> ldgoldst...@gmail.com is not associated with a maintainer of a
> Bioconductor
> package. Please check the spelling or contact bioc-devel@r-project.org for
> help.
>
> Thanks for your help.
>
> Leonard
>
> [[alternative HTML version deleted]]
>
> ___
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>

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[Bioc-devel] Question about IRanges for coordinates greater than 536870912

2021-05-06 Thread Jianhong Ou, Ph.D. 
Hi All,

Recently I encountered issues with IRanges that the coordinates greater than 
536870912. Is there any easy solution to extract the information from bam file 
for the range greater than 2^29 via Rsamtools or GenomicAlignments?

And does Rsamtools support CRAI or CSI index formats?

Thank you in advance for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}

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Re: [Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

2021-05-06 Thread Jianhong Ou, Ph.D. 
Hi Lori,

Thank you so much for the message.

Jianhong.

From: Kern, Lori 
Sent: Thursday, May 6, 2021 8:09 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org 

Subject: Re: How to repeat the error: shape of 'skeleton' is not compatible 
with 'NROW(flesh)'

This is a known issue with a recent push to IRanges.  The maintainers are aware 
and working on a fix.  You can follow the reported issue
https://github.com/Bioconductor/IRanges/issues/40

It should get resolved on its own shortly.

Cheers,


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 Jianhong Ou, 
Ph.D. 
Sent: Thursday, May 6, 2021 7:50 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] How to repeat the error: shape of 'skeleton' is not 
compatible with 'NROW(flesh)'

Hi all,

In most recent build I got error message:

shape of 'skeleton' is not compatible with 'NROW(flesh)'

And I have trouble in repeating the error by 
Bioconductor/bioconductor_docker:devel.

I am asking will the bioconductor_docker will update soon or I should install 
the newest development version R by myself.

Thank you for your help.

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

2021-05-06 Thread Kern, Lori 
This is a known issue with a recent push to IRanges.  The maintainers are aware 
and working on a fix.  You can follow the reported issue
https://github.com/Bioconductor/IRanges/issues/40

It should get resolved on its own shortly.

Cheers,


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 Jianhong Ou, 
Ph.D. 
Sent: Thursday, May 6, 2021 7:50 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] How to repeat the error: shape of 'skeleton' is not 
compatible with 'NROW(flesh)'

Hi all,

In most recent build I got error message:

shape of 'skeleton' is not compatible with 'NROW(flesh)'

And I have trouble in repeating the error by 
Bioconductor/bioconductor_docker:devel.

I am asking will the bioconductor_docker will update soon or I should install 
the newest development version R by myself.

Thank you for your help.

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:23}}

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Re: [Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?"

2021-05-06 Thread Kern, Lori 
A new version of RcppParallel was pushed to CRAN yesterday. The builders should 
pick this up automatically and we hope it should resolve in the next day or 
two. If it does not we will follow up.

Thank you for the report.

Cheers,


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 stefano 

Sent: Wednesday, May 5, 2021 8:55 PM
To: bioc-devel 
Subject: [Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: 
maybe not installed for this architecture?"

Hello,

the package ppcseq fails on windows build (Multiple platform build/check
report for BioC 3.13 - INSTALL report for ppcseq on riesling1
(bioconductor.org)
)
because of the lack of RcppParallel in the windows build.

Any chance this can be fixed?

Thanks a lot.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544

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[Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

2021-05-06 Thread Jianhong Ou, Ph.D. 
Hi all,

In most recent build I got error message:

shape of 'skeleton' is not compatible with 'NROW(flesh)'

And I have trouble in repeating the error by 
Bioconductor/bioconductor_docker:devel.

I am asking will the bioconductor_docker will update soon or I should install 
the newest development version R by myself.

Thank you for your help.

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}

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