date:20210511

Re: [Bioc-devel] Install and check error in Windows without any relevant message

2021-05-11 Thread Hervé Pagès


Hi Ramon,

This looks like a communication problem between riesling1 and nebbiolo1. 
Hopefully this is something transient. Fingers crossed!


Cheers,
H.

On 11/05/2021 16:38, Ramon Diaz-Uriarte wrote:

To partially answer myself, on looking more carefully, the INSTALL problem
seems to happen in the call to curl.exe (i.e., not in the R package
installation itself per se). It seems this failed

C:\cygwin\bin\curl.exe -O 
http://155.52.207.165/BBS/3.13/bioc/src/contrib/OncoSimulR_2.99.94.tar.gz

even if the tar.gz is actually there. Can I assume this is probably a
transient error?



And if I understand correctly the CHECK error ("Installation failed.
See 'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00install.out' for
details") it can also be traced to a curl problem?

Best,



On Tue, 11-May-2021, at 20:15:24, Ramon Diaz-Uriarte  wrote:

Dear All,

I package I maintain (OncoSimulR), which has not experienced any changes in
the last week, has failed Install and Check (but not Build or Build bin) on
Windows
(https://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/riesling1-install.html
https://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/riesling1-checksrc.html
).

However, I do not know what to do given the error output. For Install the 
message is

curl: (52) Empty reply from server


And for Check is just

* checking whether package 'OncoSimulR' can be installed ... ERROR
Installation failed.
See 'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00install.out' for 
details.
* DONE

Status: 1 ERROR
See
   'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.

curl: (52) Empty reply from server


I do not use curl in the code. Is this a problem fetching dependencies or a
problem caused by a package I depend on?


Thanks,


R.





--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Install and check error in Windows without any relevant message

2021-05-11 Thread Ramon Diaz-Uriarte

To partially answer myself, on looking more carefully, the INSTALL problem
seems to happen in the call to curl.exe (i.e., not in the R package
installation itself per se). It seems this failed

C:\cygwin\bin\curl.exe -O 
http://155.52.207.165/BBS/3.13/bioc/src/contrib/OncoSimulR_2.99.94.tar.gz

even if the tar.gz is actually there. Can I assume this is probably a
transient error?



And if I understand correctly the CHECK error ("Installation failed.
See 'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00install.out' for
details") it can also be traced to a curl problem?

Best,



On Tue, 11-May-2021, at 20:15:24, Ramon Diaz-Uriarte  wrote:
> Dear All,
>
> I package I maintain (OncoSimulR), which has not experienced any changes in
> the last week, has failed Install and Check (but not Build or Build bin) on
> Windows
> (https://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/riesling1-install.html
> https://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/riesling1-checksrc.html
> ).
>
> However, I do not know what to do given the error output. For Install the 
> message is
>
> curl: (52) Empty reply from server
>
>
> And for Check is just
>
> * checking whether package 'OncoSimulR' can be installed ... ERROR
> Installation failed.
> See 'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00install.out' for 
> details.
> * DONE
>
> Status: 1 ERROR
> See
>   'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log'
> for details.
>
> curl: (52) Empty reply from server
>
>
> I do not use curl in the code. Is this a problem fetching dependencies or a
> problem caused by a package I depend on?
>
>
> Thanks, 
>
>
> R.


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

https://ligarto.org/rdiaz

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Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Nitesh Turaga

cc-ing bioc-devel

From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 10:13 AM
To: Johnson, Ben 
Subject: Re: BFG clean-up and reset for compartmap
That is exactly right.

I would also delete/archive non-bioconductor feature branches like dev, hg38 
etc. Only master and RELEASE_X_Y branches should be available.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 10:11 AM
To: Nitesh Turaga 
Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

Apologies for not having the github in the state it should be in. Just to 
clarify, I need to follow the steps outlined here 
(https://bioconductor.org/developers/how-to/git/sync-existing-repositories/) 
through the merges, run the BFG, and contact you again for the force reset?

Again, my apologies if these are all naïve. Thanks for your time!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503

From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:06 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

Thanks for sending the github repo.

I noticed that the repo is missing the RELEASE branches. You’ll have to sync 
this from the Bioconductor repo. I cannot merge just a orphan devel branch into 
what exists on git.bioconductor.org.

You’ll have to have sync your github repo, sync all the branches and run BFG.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 8:02 AM
To: Nitesh Turaga , bioc-devel@r-project.org 

Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503

From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503

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CAUTION: This email was sent from outside of the organization 
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Re: [Bioc-devel] Maintainer change Bioconductor packages

2021-05-11 Thread Nitesh Turaga

Hi,

I added gene-expression to get package access.

Please activate the account 
https://git.bioconductor.org/BiocCredentials/account_activation. Add “new” SSH 
keys. Change the password.

gene-expression will then have access to the package, and like I mentioned 
before the changes on the package itself will be on your end to make.

Change the maintainer email, subscribe to bioc-devel etc.

Best,

Nitesh

From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 7:59 AM
To: Pablo Moreno 
Cc: Suhaib Mohammed , maintai...@bioconductor.org 
, bioc-devel@r-project.org 
, gene-express...@ebi.ac.uk 

Subject: Re: Maintainer change Bioconductor packages
Hi,

I think this might be possible to try.

So the maintainer email again has to be changed from your end on the 
DESCRIPTION file.

As far as access goes, I can add 
gene-express...@ebi.ac.uk, on the 
BiocCredentials system. You’ll have to activate the account and add SSH keys.

gene-express...@ebi.ac.uk will also have to 
follow all the protocols of a maintainer, so someone will have to actively 
monitor it and subscribe to 
bioc-devel@r-project.org mailing list.

Best,

Nitesh

From: Pablo Moreno 
Date: Sunday, May 9, 2021 at 10:32 PM
To: Nitesh Turaga 
Cc: Suhaib Mohammed , maintai...@bioconductor.org 
, bioc-devel@r-project.org 
, gene-express...@ebi.ac.uk 

Subject: Re: Maintainer change Bioconductor packages
Dear Nitesh,

I think that in the rush of Suhaib leaving, we didn’t finalise this process.

Is it acceptable to have a group email/account as maintainer? We would have 
gene-express...@ebi.ac.uk, which email gets to all the Expression Atlas team 
members. Then we wouldn’t need to repeat the process if any of us leaves.

Thanks,
Pablo

> On 28 Jan 2021, at 18:27, Nitesh Turaga  wrote:
>
> Hi Suhaib,
>
> You are correct, the maintainer needs to be changed if you are unable to 
> maintain the package further. You need to nominate another maintainer for the 
> packages you listed.
>
> Once the new maintainer steps in,
>
> 1. Change the Maintainer or Authors@R field in the DESCRIPTION file of the 
> package to reflect the change.
>
> 2. Maintainer has to have a BiocCredentials account.
>
> 3. Maintainer has to be subscripted to bioc-devel@r-project.org mailing list.
>
> Best,
>
> Nitesh
>
>
> On 1/28/21, 7:00 AM, "Suhaib Mohammed"  wrote:
>
>To whom ever it may concern,
>
>I have been maintaining the Bioconductor R packages (ExpressionAtlas and
>ArrayExpress) of Gene Expression Atlas team at the EMBL-EBI. As I will
>be leaving EBI, I understand the maintainer needs to be changed. Could
>you point to the procedure for changing the maintainer ?
>
>Expression Atlas -
>https://bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html
>Array Express -
>https://bioconductor.org/packages/release/bioc/html/ArrayExpress.html
>
>Many thanks,
>Suhaib
>
>--
>Suhaib Mohammed, Ph.D.
>Senior Bioinformatician
>European Bioinformatics Institute (EMBL-EBI)
>European Molecular Biology Laboratory
>Wellcome Trust Genome Campus
>Hinxton, Cambridge CB10 1SD
>United Kingdom
>tel : +44-1223494296
>email: suh...@ebi.ac.uk
>

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[Bioc-devel] Install and check error in Windows without any relevant message

2021-05-11 Thread Ramon Diaz-Uriarte

Dear All,

I package I maintain (OncoSimulR), which has not experienced any changes in
the last week, has failed Install and Check (but not Build or Build bin) on
Windows
(https://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/riesling1-install.html
https://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/riesling1-checksrc.html
).

However, I do not know what to do given the error output. For Install the 
message is

curl: (52) Empty reply from server


And for Check is just

* checking whether package 'OncoSimulR' can be installed ... ERROR
Installation failed.
See 'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00install.out' for 
details.
* DONE

Status: 1 ERROR
See
  'D:/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.

curl: (52) Empty reply from server


I do not use curl in the code. Is this a problem fetching dependencies or a
problem caused by a package I depend on?


Thanks, 


R.


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

https://ligarto.org/rdiaz

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Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Nitesh Turaga

Hi,

Thanks for sending the github repo.

I noticed that the repo is missing the RELEASE branches. You’ll have to sync 
this from the Bioconductor repo. I cannot merge just a orphan devel branch into 
what exists on git.bioconductor.org.

You’ll have to have sync your github repo, sync all the branches and run BFG.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 8:02 AM
To: Nitesh Turaga , bioc-devel@r-project.org 

Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Johnson, Ben

Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


[[alternative HTML version deleted]]

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(nturaga.b...@gmail.com). Do not click links or open attachments unless you 
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Re: [Bioc-devel] BFG clean-up and reset for compartmap

2021-05-11 Thread Nitesh Turaga

Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503

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Re: [Bioc-devel] Maintainer change Bioconductor packages

2021-05-11 Thread Nitesh Turaga

Hi,

I think this might be possible to try.

So the maintainer email again has to be changed from your end on the 
DESCRIPTION file.

As far as access goes, I can add 
gene-express...@ebi.ac.uk, on the 
BiocCredentials system. You’ll have to activate the account and add SSH keys.

gene-express...@ebi.ac.uk will also have to 
follow all the protocols of a maintainer, so someone will have to actively 
monitor it and subscribe to 
bioc-devel@r-project.org mailing list.

Best,

Nitesh

From: Pablo Moreno 
Date: Sunday, May 9, 2021 at 10:32 PM
To: Nitesh Turaga 
Cc: Suhaib Mohammed , maintai...@bioconductor.org 
, bioc-devel@r-project.org 
, gene-express...@ebi.ac.uk 

Subject: Re: Maintainer change Bioconductor packages
Dear Nitesh,

I think that in the rush of Suhaib leaving, we didn’t finalise this process.

Is it acceptable to have a group email/account as maintainer? We would have 
gene-express...@ebi.ac.uk, which email gets to all the Expression Atlas team 
members. Then we wouldn’t need to repeat the process if any of us leaves.

Thanks,
Pablo

> On 28 Jan 2021, at 18:27, Nitesh Turaga  wrote:
>
> Hi Suhaib,
>
> You are correct, the maintainer needs to be changed if you are unable to 
> maintain the package further. You need to nominate another maintainer for the 
> packages you listed.
>
> Once the new maintainer steps in,
>
> 1. Change the Maintainer or Authors@R field in the DESCRIPTION file of the 
> package to reflect the change.
>
> 2. Maintainer has to have a BiocCredentials account.
>
> 3. Maintainer has to be subscripted to bioc-devel@r-project.org mailing list.
>
> Best,
>
> Nitesh
>
>
> On 1/28/21, 7:00 AM, "Suhaib Mohammed"  wrote:
>
>To whom ever it may concern,
>
>I have been maintaining the Bioconductor R packages (ExpressionAtlas and
>ArrayExpress) of Gene Expression Atlas team at the EMBL-EBI. As I will
>be leaving EBI, I understand the maintainer needs to be changed. Could
>you point to the procedure for changing the maintainer ?
>
>Expression Atlas -
>https://bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html
>Array Express -
>https://bioconductor.org/packages/release/bioc/html/ArrayExpress.html
>
>Many thanks,
>Suhaib
>
>--
>Suhaib Mohammed, Ph.D.
>Senior Bioinformatician
>European Bioinformatics Institute (EMBL-EBI)
>European Molecular Biology Laboratory
>Wellcome Trust Genome Campus
>Hinxton, Cambridge CB10 1SD
>United Kingdom
>tel : +44-1223494296
>email: suh...@ebi.ac.uk
>

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Re: [Bioc-devel] Transfer Maintainership of the Package NetSAM

2021-05-11 Thread Nitesh Turaga

Hi,

This is now done.

Please try to activate your account on BiocCredentials. 
https://git.bioconductor.org/BiocCredentials/account_activation and add SSH 
keys.

You will gain access to the package then.

Best,

Nitesh

From: Zhang, Bing 
Date: Sunday, May 9, 2021 at 5:07 PM
To: maintai...@bioconductor.org , 
bioc-devel@r-project.org 
Cc: zhiao@gmail.com 
Subject: Re: Transfer Maintainership of the Package NetSAM
Sorry, I used the wrong email address for the new maintainer. Here is the 
correct information:
First Name: Zhiao
Last Name: Shi
Email: zhiao@gmail.com

Bing

From: "Zhang, Bing" 
Date: Sunday, May 9, 2021 at 10:04 PM
To: "maintai...@bioconductor.org" , 
"bioc-devel@r-project.org" 
Cc: "justin@gmail.com" 
Subject: Transfer Maintainership of the Package NetSAM

Dear Sir or Madam,

I am the maintainer of the Bioconductor package NetSAM 
(https://bioconductor.org/packages/release/bioc/html/NetSAM.html ). My lab 
moved from the Vanderbilt University to the Baylor College of Medicine a few 
years ago, and my email address used for NetSAM was my Vanderbilt email account.

I would like to transfer the maintainership of NetSAM to a Lead Programer in my 
lab (cc�ed), please find below his contact information:
First Name: Zhiao
Last Name: Shi
Email: justin@gmail.com

Please let us know if you need additional information to make the transfer. 
Thanks!

Best regards,

Bing


Bing Zhang, Ph.D.
Professor of Molecular and Human Genetics
Breast Center
McNair Medical Institute Scholar
Cancer Prevention Research Institute of Texas (CPRIT) Scholar
Baylor College of Medicine
Houston, Texas 77030
Tel: 713-798-1443
Email: bing.zh...@bcm.edu
URL: http://www.zhang-lab.org

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Re: [Bioc-devel] Install and check error in Windows without any relevant message

Re: [Bioc-devel] Install and check error in Windows without any relevant message

Re: [Bioc-devel] BFG clean-up and reset for compartmap

Re: [Bioc-devel] Maintainer change Bioconductor packages

[Bioc-devel] Install and check error in Windows without any relevant message

Re: [Bioc-devel] BFG clean-up and reset for compartmap

Re: [Bioc-devel] BFG clean-up and reset for compartmap

Re: [Bioc-devel] BFG clean-up and reset for compartmap

Re: [Bioc-devel] Maintainer change Bioconductor packages

Re: [Bioc-devel] Transfer Maintainership of the Package NetSAM

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