Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi Stefano,

Thank you for your share.

Jianhong.

From: Stefano de Pretis 
Date: Friday, April 17, 2020 at 3:18 PM
To: "Jianhong Ou, Ph.D." 
Cc: "bioc-devel@r-project.org" 
Subject: Re: [Bioc-devel] Got timeout for machv2 BUILD

HI,

We solved a similar issue for the INSPEcT package avoiding the parallelization 
in the computation of examples and vignettes. In our case it caused the timeout 
in the Windows environment.

Best,
Stefano

Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D. 
mailto:jianhong...@duke.edu>> ha scritto:
Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.

From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



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] Got timeout for machv2 BUILD

[Hervé Pagès]

For some reasons the generation of the plots in the vignette is VERY 
slow on machv2. 'R CMD build' actually completed... after 6h! This is 
still under investigation.


Best,
H.


On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:

Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.

From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org 
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



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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--
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] Got timeout for machv2 BUILD

[Stefano de Pretis]

HI,

We solved a similar issue for the INSPEcT package avoiding the
parallelization in the computation of examples and vignettes. In our case
it caused the timeout in the Windows environment.

Best,
Stefano

Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D. <
jianhong...@duke.edu> ha scritto:

> Hi,
>
> I got timeout for my package motifStack in machv2. But I don't know what
> cuased the issue.
>
> Any help would be greatly appreciated.
>
> Jianhong.
> 
> From: Jianhong Ou, Ph.D.
> Sent: Wednesday, April 15, 2020 7:53 AM
> To: bioc-devel@r-project.org 
> Subject: Got timeout for machv2 BUILD
>
> Hi,
>
> Hope you are doing well.
>
> I got timeout for my package motifStack in machv2. The ellapsedTime is
> 2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1
> seconds. I have limited information how to debug.
> Could you share your suggestion? Thank you.
>
>
>
> 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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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.

From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org 
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



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] Nominations for Bioconductor Awards!

[Shepherd, Lori]

Yikes!  Sorry everyone.  That did not format like I thought it would!

Let's recap:


Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of specific criteria.  The deadline for nominations is June 15!
Please see the support site announcement for the links with more information as 
well as the nomination form


https://support.bioconductor.org/p/130094/



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 Shepherd, Lori 

Sent: Friday, April 17, 2020 1:37 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Nominations for Bioconductor Awards!

Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of the criteria found at:  
https://secure-web.cisco.com/16tUFz5Y9fiV3wv_pZMAWX8bU4HXzuPOui85-nQ6NxdiPfAd9AGquEUvWb6C-LqP7Yon62aBX8ULdJ8idAqvXqfsS_80ScouEVrCiYdbsjwPmqVEbnGoAIln4gcIdTSltcXdtZqN-SrpDdJ6V6xiB1LzQMUtGkSIQQOK0X37ra7bPWibIkPd2WsBLOzOazj46TnTNdgTH2udZ-EV99vyCBNSU-6hxSFMVD1JaO0xxTHknOWiTg8zKGBRgQfMmGNrGMj9W2UN-O9HYRD-hYd7fveCzPkaRvBnIl3inUB37KohceYdqJ8OfRdo9efhwHjq7MJPEWCxzuPDs4fppgD4R_w/https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1ccXPFc_bGZoW3DgfgXf13_4i5TXySvXQCdRR8UJr__I%2Fedit.

Please fill out the nomination form by June 15 : 
https://secure-web.cisco.com/1xiPaCt8pwJs16iKlj7jvaYfJRuP-w9MsvNcZNvld32dl1SpBeEFARwBSlrUJXVOXsfzBL4GIhwPelo-KTR-VUpxPNz9UDtDERtyuf6l1El6gEPTLcOq8K1SF_3MogKWaY6dWWiMfhD43WIzp_VYutvmEhB1vW3JbN9QJkXBkfOC9KUqOPsypOz6Ppj4zSuGJsJt6g2iiPit6j_nrEPTKKHxXHa9zfcfYga9asnMOvYvKeqW4szgu3T-sfVaCWjw2Jl-YIN9jFdGmAmLDc3ki0_x-CCZEyJMLAVFYBpXivjgUUOar5_hewa3T0s6Ift_kLY_qQL5sO2Lia8vQDZ-guw/https%3A%2F%2Fdocs.google.com%2Fforms%2Fd%2Fe%2F1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw%2Fviewform



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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[Bioc-devel] Nominations for Bioconductor Awards!

[Shepherd, Lori]

Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of the criteria found at:  
https://docs.google.com/document/d/1ccXPFc_bGZoW3DgfgXf13_4i5TXySvXQCdRR8UJr__I/edit.

Please fill out the nomination form by June 15 : 
https://docs.google.com/forms/d/e/1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw/viewform



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] regarding imports github R packages, in new R package's description file

[Krishan Gupta]

Ya so I can include git hub packages, in cran submission policy.
*Thanks and Regards*

*Krishan Gupta*

*PhD16008PhD Scholar*




On Fri, Apr 17, 2020 at 10:23 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> This mailing list is for Bioconductor package development and Bioconductor
> submissions not CRAN.
>
> Bioconductor only allows dependencies from CRAN or Bioconductor and does
> not allow github only repositories.
>
> If you indeed meant to submit to CRAN you should check with CRAN's
> submission policies on what they allow:
> https://cran.r-project.org/web/packages/policies.html
>
>
>
> 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
> Krishan Gupta 
> *Sent:* Friday, April 17, 2020 12:45 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] regarding imports github R packages, in new R
> package's description file
>
> I want to build a new package to submit on CRAN, but my package has
> two dependencies harmony and iCTC which are available only on github.
> So now I can import these dependencies in description files.
> Imports:
> BiocManager,
> caret,
> klaR,
> randomForest,
> gbm,
> devtools,
> harmony,
> iCTC
> I did as shown above but I got an error,
> checking package dependencies ... ERROR
> Packages required but not available: 'harmony', 'iCTC'
> How can I resolve the error?
> *Thanks and Regards*
>
> *Krishan Gupta*
>
> *PhD16008PhD Scholar*
>
> [[alternative HTML version deleted]]
>
> ___
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>
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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.

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Re: [Bioc-devel] regarding imports github R packages, in new R package's description file

[Shepherd, Lori]

This mailing list is for Bioconductor package development and Bioconductor 
submissions not CRAN.

Bioconductor only allows dependencies from CRAN or Bioconductor and does not 
allow github only repositories.

If you indeed meant to submit to CRAN you should check with CRAN's submission 
policies on what they allow:
https://cran.r-project.org/web/packages/policies.html




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 Krishan Gupta 

Sent: Friday, April 17, 2020 12:45 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] regarding imports github R packages, in new R package's 
description file

I want to build a new package to submit on CRAN, but my package has
two dependencies harmony and iCTC which are available only on github.
So now I can import these dependencies in description files.
Imports:
BiocManager,
caret,
klaR,
randomForest,
gbm,
devtools,
harmony,
iCTC
I did as shown above but I got an error,
checking package dependencies ... ERROR
Packages required but not available: 'harmony', 'iCTC'
How can I resolve the error?
*Thanks and Regards*

*Krishan Gupta*

*PhD16008PhD Scholar*

[[alternative HTML version deleted]]

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[Bioc-devel] regarding imports github R packages, in new R package's description file

[Krishan Gupta]

I want to build a new package to submit on CRAN, but my package has
two dependencies harmony and iCTC which are available only on github.
So now I can import these dependencies in description files.
Imports:
BiocManager,
caret,
klaR,
randomForest,
gbm,
devtools,
harmony,
iCTC
I did as shown above but I got an error,
checking package dependencies ... ERROR
Packages required but not available: 'harmony', 'iCTC'
How can I resolve the error?
*Thanks and Regards*

*Krishan Gupta*

*PhD16008PhD Scholar*

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Question for building error

[Shepherd, Lori]

 The current ERROR
"polygon edge not found"
is  a Bioconductor builder issue having to do with fonts not being found.

We are working on a solution but for now you can ignore.


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 Yang,Peng 

Sent: Friday, April 17, 2020 12:26 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Question for building error

Dear Bioconductor team,

I met a building errors for our package, DeMixT 1.3.6, under Mac OS planform on 
Apr 16th. And it shows failed to create vignettes.

Since R 4.0.0 no longer support OpenMP, I disabled OpenMP under Mac version and 
it passed the building process after I committed the change on Apr 12th.

However, I did not see the specific reason why failed to create vignettes this 
time, may I ask how can I fix this issue?

Thank you so much,
Peng

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[Bioc-devel] Question for building error

[Yang,Peng]

Dear Bioconductor team,

I met a building errors for our package, DeMixT 1.3.6, under Mac OS planform on 
Apr 16th. And it shows failed to create vignettes.

Since R 4.0.0 no longer support OpenMP, I disabled OpenMP under Mac version and 
it passed the building process after I committed the change on Apr 12th.

However, I did not see the specific reason why failed to create vignettes this 
time, may I ask how can I fix this issue?

Thank you so much,
Peng

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Re: [Bioc-devel] Transfer Maintainership of a Package ClusterJudge

[Turaga, Nitesh]

Hi Adrian, 

You have to first activate your BiocCredentials account 
https://git.bioconductor.org/BiocCredentials/. 

Once you activate your account, you should be able to log in and add some SSH 
keys. You'll be given access to the system once you add your SSH keys. 

Also, please change the email address in the DESCRIPTION file of the package.

Should you have any questions on how to manage your repository, please check 
http://bioconductor.org/developers/how-to/git/.

Best,

Nitesh 

On 4/16/20, 3:03 PM, "Bioc-devel on behalf of Adrian Pasculescu" 
 wrote:

Hi ,

I am the original maintainer of the ClusterJudge but my original email
address (pascule...@lunenfeld.ca) is no longer valid.
I need to continue maintaining the package under the new email address:
a.pascule...@gmail.com
I created a new github repo: 
https://secure-web.cisco.com/1sCaxjhRuZo99ozJCU75a7QnU1lswB29hIn0hqXYOOmXbgcoUdfMsNaSCUiaujM5gog_RQ1pJYSpkT1uMQwp2ppyjUcoAnd-TAc0JmPaR1paAqVX01mx7JBimm5taYpBaOmJlELUk-gs13gE29icKPvpzVOG6ZQ6jcIA-G7rT6roMO_qrZXfjG2EuoDcW9aIFYgp2X6ph7MZCB1Hyp8SumsT197WMNa_qGUFJ4QmPekX14fj8gNH1_1xx-yp-tkHQe8Ts2E88-EBYJdxwIoT3DLxRWbfe4E4UO1FDW6KbNsuxBIZi6_PHm0h8YJxO3hSkZxgfa2jnmufgid_z9eFTTg/https%3A%2F%2Fgithub.com%2Fapasculescu%2FClusterJudge
However I cannot update the package as I am not recognized by bioconductor.

I cannot re-register to bioconductor under the new email address since the
original DESCRIPTION of the ClusterJudge (and the bioconductor database of
maintainers) contains my old and inactive email address.

Can you please help and indicate what are my next steps,
Many thanks,
Adrian Pasculescu
(see also some previous email related to the subject)

-- Forwarded message -
De : Hervé Pagès 
Date: mer. 15 avr. 2020 à 22:29
Subject: Re: ClusterJudge bioconductor package
To: Adrian Pasculescu 
Cc: Frederick Roth 


Hi Adrian,

You're looking at the wrong place. The web hook is for triggering builds
during the package submission process. We're way past this ;-)

One the package is accepted and added to git.bioconductor.org, you need
to push your changes to git.bioconductor.org in addition to pushing them
to your GitHub repo. See our documentation here

https://secure-web.cisco.com/1tt0anS6Ry8ADw1Qx4iLhGwW5C4oOroYjPEnwi2d1gnYurIieI1wDpHup0lBDQc29xE01gZkqZl-WQ9xtpjd7cdNCK5gpkHtaYP_bBgnj8OyWa_awl1BVqfjLcScn4RhijJWETu4IKRofCH4WTJaCTOjcfXjxfou1U-2BxPLfbWGNo_-Si-rL1Yyw3M5zeqPQWqTAbJRtC5sgcprXigibqGvWmSGJ6TgY2cPIgLxIhGsFW12GgdRTH-d43qQOkw4bFxl9PYen_QWzTbDoYgmMoNlpevupHksXGkIq4-WUcWow2d15W1yZWnfK5BlVVK1FDAANkkochiV6fwV-936lRl-_mvFAoSiUPr8DD32TLdk/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2F
 for the details.

Any further question related to how to maintain/update your package
should be asked on the bioc-devel mailing list.

Thanks,
H.

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Re: [Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

[Shepherd, Lori]

Firstly,  macv2 is R devel so to accurately test  you should be using R 4.0.0  
with Bioc 3.11 packages.

However, this ERROR is  a Bioconductor builder issue having to do with fonts 
not being found.  We are working on a solution but for now you can ignore.


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 Koustav Pal 

Sent: Friday, April 17, 2020 8:18 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

Hi,

My package, HiCBricks is showing failed builds on the Mac builder macv2.

I have checked the packaged on my Mac running Catalina 10.15 and R 3.6.1. The 
build is ok.

Also, GitHub travis-ci build reports are fine.

The error message is �polygon edge not found�

Any help is much appreciated.

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu




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[Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

[Koustav Pal]

Hi,

My package, HiCBricks is showing failed builds on the Mac builder macv2.

I have checked the packaged on my Mac running Catalina 10.15 and R 3.6.1. The 
build is ok.

Also, GitHub travis-ci build reports are fine. 

The error message is “polygon edge not found”

Any help is much appreciated.

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu




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