[Bioc-devel] Maintainer for preciseTAD

[Mikhail Dozmorov]

Hi,
I noted our package https://bioconductor.org/packages/preciseTAD/ shows
build error. This is because https://CRAN.R-project.org/package=DMwR was
removed. Please, add me as a maintainer to the preciseTAD repo. Spiro
should remain a maintainer, but he is getting harder to reach after
graduation.

Thanks,
Mikhail

---
Mikhail Dozmorov, Ph.D.
Department of Biostatistics, VCU
E-mail:  mdozmo...@vcu.edu
Phone: 804-827-2055

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Re: [Bioc-devel] Log in to the BiocCredentials app

[mauro castro]

Hi Nitesh,

I was surprised that my account had never been activated; maybe I was
using some pre-git settings, until something stopped working.

Anyhow, I just activated the BiocCredentials and it's working now.

Many thanks,

Mauro

On Tue, 4 May 2021 at 14:34, Nitesh Turaga  wrote:
>
> Hi Mauro,
>
>
>
> I just checked and you’ve never activated your account. You should try to 
> activate it before you do anything else.
>
>
>
> Best,
>
>
>
> Nitesh
>
>
>
> From: mauro castro 
> Date: Tuesday, May 4, 2021 at 1:31 PM
> To: Nitesh Turaga 
> Cc: Bioc-devel 
> Subject: Re: [Bioc-devel] Log in to the BiocCredentials app
>
> Hi Nitesh,
>
> Thank you for your email. I tried to do the password reset again, but
> still haven't received an email from maintai...@bioconductor.org (and
> also not in the spam box).
>
> I tried the BiocCredentials app as in the attached print screen, using
> the same email from my r-project.org mailing list membership, and
> informed in my packages.
>
> I don't know if this problem is some "shadow" from a time before the
> git transition, so I revised my emails and found my very 1st
> credential, the subversion user ID was "m.castro"; not sure if this
> information would help to identify the problem. Sorry to bother you
> with this apparent simple problem, but I dont know why this is
> happening.
>
> Many thanks,
>
> Mauro
>
> On Tue, 4 May 2021 at 10:02, Nitesh Turaga  wrote:
> >
> > Hi
> >
> >
> >
> > Have you checked your Spam or junk mail?
> >
> >
> >
> > You should have received an email from maintai...@bioconductor.org -  
> > Bioconductor git credentials administrator.
> >
> >
> >
> > If it’s being filtered or something, could you please try to do the 
> > password reset again? I checked our end, and everything seems to be in 
> > place.
> >
> >
> >
> > Best,
> >
> >
> >
> > Nitesh
> >
> >
> >
> > From: Bioc-devel  on behalf of mauro 
> > castro 
> > Date: Tuesday, May 4, 2021 at 8:48 AM
> > To: Bioc-devel 
> > Subject: [Bioc-devel] Log in to the BiocCredentials app
> >
> > Hi All,
> >
> > I’m a Bioconductor package maintainer, but I could not log in to the
> > BiocCredentials app to submit a new SSH public key. A already tried to
> > reset the password, but I didn't receive any email with instructions
> > for setting a password.
> >
> > https://git.bioconductor.org/BiocCredentials/password_reset/
> >
> > The email I entered is the same associated with all my packages
> > (mauro.a.cas...@gmail.com). Here a list of packages for which I am
> > maintainer:
> > - RedeR, RTN, RTNduals, RTNsurvival, geneplast, Fletcher2013a, Fletcher2013b
> >
> > Please, let me know if I am missing any steps.
> >
> > Many thanks,
> >
> > Mauro
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Log in to the BiocCredentials app

[Nitesh Turaga]

Hi Mauro,

I just checked and you�ve never activated your account. You should try to 
activate it before you do anything else.

Best,

Nitesh

From: mauro castro 
Date: Tuesday, May 4, 2021 at 1:31 PM
To: Nitesh Turaga 
Cc: Bioc-devel 
Subject: Re: [Bioc-devel] Log in to the BiocCredentials app
Hi Nitesh,

Thank you for your email. I tried to do the password reset again, but
still haven't received an email from maintai...@bioconductor.org (and
also not in the spam box).

I tried the BiocCredentials app as in the attached print screen, using
the same email from my r-project.org mailing list membership, and
informed in my packages.

I don't know if this problem is some "shadow" from a time before the
git transition, so I revised my emails and found my very 1st
credential, the subversion user ID was "m.castro"; not sure if this
information would help to identify the problem. Sorry to bother you
with this apparent simple problem, but I dont know why this is
happening.

Many thanks,

Mauro

On Tue, 4 May 2021 at 10:02, Nitesh Turaga  wrote:
>
> Hi
>
>
>
> Have you checked your Spam or junk mail?
>
>
>
> You should have received an email from maintai...@bioconductor.org -  
> Bioconductor git credentials administrator.
>
>
>
> If it�s being filtered or something, could you please try to do the password 
> reset again? I checked our end, and everything seems to be in place.
>
>
>
> Best,
>
>
>
> Nitesh
>
>
>
> From: Bioc-devel  on behalf of mauro castro 
> 
> Date: Tuesday, May 4, 2021 at 8:48 AM
> To: Bioc-devel 
> Subject: [Bioc-devel] Log in to the BiocCredentials app
>
> Hi All,
>
> I�m a Bioconductor package maintainer, but I could not log in to the
> BiocCredentials app to submit a new SSH public key. A already tried to
> reset the password, but I didn't receive any email with instructions
> for setting a password.
>
> https://git.bioconductor.org/BiocCredentials/password_reset/
>
> The email I entered is the same associated with all my packages
> (mauro.a.cas...@gmail.com). Here a list of packages for which I am
> maintainer:
> - RedeR, RTN, RTNduals, RTNsurvival, geneplast, Fletcher2013a, Fletcher2013b
>
> Please, let me know if I am missing any steps.
>
> Many thanks,
>
> Mauro
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Log in to the BiocCredentials app

[mauro castro]

Hi Nitesh,

Thank you for your email. I tried to do the password reset again, but
still haven't received an email from maintai...@bioconductor.org (and
also not in the spam box).

I tried the BiocCredentials app as in the attached print screen, using
the same email from my r-project.org mailing list membership, and
informed in my packages.

I don't know if this problem is some "shadow" from a time before the
git transition, so I revised my emails and found my very 1st
credential, the subversion user ID was "m.castro"; not sure if this
information would help to identify the problem. Sorry to bother you
with this apparent simple problem, but I dont know why this is
happening.

Many thanks,

Mauro

On Tue, 4 May 2021 at 10:02, Nitesh Turaga  wrote:
>
> Hi
>
>
>
> Have you checked your Spam or junk mail?
>
>
>
> You should have received an email from maintai...@bioconductor.org -  
> Bioconductor git credentials administrator.
>
>
>
> If it’s being filtered or something, could you please try to do the password 
> reset again? I checked our end, and everything seems to be in place.
>
>
>
> Best,
>
>
>
> Nitesh
>
>
>
> From: Bioc-devel  on behalf of mauro castro 
> 
> Date: Tuesday, May 4, 2021 at 8:48 AM
> To: Bioc-devel 
> Subject: [Bioc-devel] Log in to the BiocCredentials app
>
> Hi All,
>
> I’m a Bioconductor package maintainer, but I could not log in to the
> BiocCredentials app to submit a new SSH public key. A already tried to
> reset the password, but I didn't receive any email with instructions
> for setting a password.
>
> https://git.bioconductor.org/BiocCredentials/password_reset/
>
> The email I entered is the same associated with all my packages
> (mauro.a.cas...@gmail.com). Here a list of packages for which I am
> maintainer:
> - RedeR, RTN, RTNduals, RTNsurvival, geneplast, Fletcher2013a, Fletcher2013b
>
> Please, let me know if I am missing any steps.
>
> Many thanks,
>
> Mauro
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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Re: [Bioc-devel] Can anyone reproduce this? Possible bug or typo in BiocManager:::.version_map() or upstream

[Martin Morgan]

It's because Bioconductor won't be building (supporting) R-4.2 (R-devel) until 
six months from now, even in the 'devel' branch of Bioconductor. Bioc 3.14 
(once it becomes available after the Bioconductor release) will use R 4.1 and 
the table will be updated to have line 34 as 3.14 / 4.1. There will be an entry 
3.15/4.2/future, but there won't be a 3.15...

Martin

On 5/4/21, 8:21 AM, "Bioc-devel on behalf of Wolfgang Huber" 
 wrote:

Hi,

I get

 > BiocManager::install()
Error: Bioconductor version '3.13' requires R version '4.1'; R version is 
too new; see
  https://bioconductor.org/install

and this appears to be because of the last line in

> BiocManager:::.version_map()
   BiocR  BiocStatus RSPM MRAN
…(29 lines omitted)….
30 3.10  3.6 out-of-date  
31 3.11  4.0 out-of-date  
32 3.12  4.0 release  
33 3.13  4.1   devel  
34 3.13  4.2  future  

Shouldn’t it say “3.14” in the second element of the last line?


> sessionInfo()
R Under development (unstable) (2021-05-04 r80261)
Platform: x86_64-apple-darwin20.4.0 (64-bit)
Running under: macOS Big Sur 11.3

Matrix products: default
BLAS:   /Users/whuber/R/lib/libRblas.dylib
LAPACK: /Users/whuber/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocManager_1.30.12 fortunes_1.5-4

loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0

and I seem to have the most recent version of BiocManager as of today’s 
https://cran.r-project.org/web/packages/BiocManager/index.html 

——

Btw the result of

> BiocManager:::.get_R_version()
[1] ‘4.2.0’

is probably technically not correct, as it’s r-devel.

Kind regards
Wolfgang

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Re: [Bioc-devel] Build error on Mac re: Arial font and polygon edges

[Shraddha Pai]

Good morning Hervé,
Thank you - I checked Monday am, and sure enough those errors were resolved.
Best,Shraddha

On Fri, Apr 30, 2021 at 8:51 PM Hervé Pagès 
wrote:

> Hi Shraddha,
>
> Hundreds of Bioconductor packages are affected since yesterday. Please
> ignore.
>
> Today we've upgraded R to R 4.1 alpha on machv2, and made a tweak to the
> setup, so hopefully these errors will be gone on tomorrow's report.
>
> Best,
> H.
>
> On 4/30/21 2:46 PM, Shraddha Pai wrote:
> > Hello BioC community,
> > My package netDx is building correctly on Linux but has the following
> > issues on Mac:
> > When running the vignette BuildPredictor.Rmd,
> > 1) we get the error: Warning in doTryCatch(return(expr), name, parentenv,
> > handler) :
> >
> >no font could be found for family "Arial"
> >
> > 2) the vignette then ends with the error:
> >
> > Error: processing vignette 'BuildPredictor.Rmd' failed with diagnostics:
> >
> > polygon edge not found
> >
> >
> > Why would the package have this error on Macs and not on Linux machines?
> > And the error had not previously occurred. It seems to have occurred with
> > an old vignette (not the one I recently added).
> >
> >
> > One thing I had to change recently was to change the vignette building
> > method for all vignettes, from knitr::knitr to knitr::rmarkdown, but I
> only
> > did it because I was getting a never-before-seen vignette building
> related
> > error for which I found this solution. Was this change a mistake?
> >
> >
> > Any thoughts would be appreciated.
> >
> > Thanks,
> > Shraddha
> >
> > --
> >
> > *Shraddha Pai, PhD*
> > Independent Investigator
> > shraddhapai.com; @spaiglass on Twitter
> >
> >
> > *Ontario Institute for Cancer Research*
> > MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada
> M5G
> > 0A3
> > *@OICR_news*  | *www.oicr.on.ca*
> > 
> >
> >
> >
> > *Collaborate. Translate. Change lives.*
> >
> >
> >
> > This message and any attachments may contain confidentia...{{dropped:11}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>

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Re: [Bioc-devel] Log in to the BiocCredentials app

[Nitesh Turaga]

Hi

Have you checked your Spam or junk mail?

You should have received an email from 
maintai...@bioconductor.org -  Bioconductor 
git credentials administrator.

If it�s being filtered or something, could you please try to do the password 
reset again? I checked our end, and everything seems to be in place.

Best,

Nitesh

From: Bioc-devel  on behalf of mauro castro 

Date: Tuesday, May 4, 2021 at 8:48 AM
To: Bioc-devel 
Subject: [Bioc-devel] Log in to the BiocCredentials app
Hi All,

I�m a Bioconductor package maintainer, but I could not log in to the
BiocCredentials app to submit a new SSH public key. A already tried to
reset the password, but I didn't receive any email with instructions
for setting a password.

https://git.bioconductor.org/BiocCredentials/password_reset/

The email I entered is the same associated with all my packages
(mauro.a.cas...@gmail.com). Here a list of packages for which I am
maintainer:
- RedeR, RTN, RTNduals, RTNsurvival, geneplast, Fletcher2013a, Fletcher2013b

Please, let me know if I am missing any steps.

Many thanks,

Mauro

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Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

[Nitesh Turaga]

Hi,

The branch your linked is going to be the upcoming RELEASE_3_13 branch and 
currently �devel� (master branch).

I�m not sure how to help you as far as debugging the error goes, the best way 
is first try to be able to reproduce it on your local machine. You can also add 
a statement to avoid running the example if the OS is recognized as a mac 
(https://stat.ethz.ch/R-manual/R-patched/library/base/html/Platform.html)

```
if (.Platform$OS.type == �darwin�) ## maybe it�s just �unix� now
```

But this should be directed in a separate thread as question, it seems it has 
nothing to do with the RELEASE_3_12 branch freeze and discussion on this thread 
will lead to confusion.

Best,

Nitesh


From: Waldir Leoncio Netto 
Date: Tuesday, May 4, 2021 at 1:20 AM
To: bioc-devel@r-project.org , nturaga.b...@gmail.com 

Subject: Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 
branch freeze
Dear Nitesh,

What happens to packages presenting a check error (e.g. 
cellmigRation
 installs and builds on all supported OSs, but fails on macOS while checking a 
function example)? I've been working on solving that, but there can only be so 
much progress when using daily builds as a gauge.

Best regards,
Waldir

ma., 03.05.2021 kl. 17.07 +, skrev Nitesh Turaga:
Today - May 3, 2021.

My apologies.

Nitesh

From: Nitesh Turaga mailto:nturaga.b...@gmail.com>>
Date: Monday, May 3, 2021 at 1:04 PM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: Bioconductor Release Announcement: RELEASE_3_12 branch freeze
Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in 
http://bioconductor.org/developers/release-schedule/.

Today (April 14th 2020) at 2pm EDT, I will freeze the commits to the 
RELEASE_3_12 branch in Bioconductor. This is for all packages (software, 
data-experiment and workflow).

After 2pm today, you will not be able to push to the RELEASE_3_12 branch.

Best regards,

Nitesh Turaga


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[Bioc-devel] Log in to the BiocCredentials app

[mauro castro]

Hi All,

I’m a Bioconductor package maintainer, but I could not log in to the
BiocCredentials app to submit a new SSH public key. A already tried to
reset the password, but I didn't receive any email with instructions
for setting a password.

https://git.bioconductor.org/BiocCredentials/password_reset/

The email I entered is the same associated with all my packages
(mauro.a.cas...@gmail.com). Here a list of packages for which I am
maintainer:
- RedeR, RTN, RTNduals, RTNsurvival, geneplast, Fletcher2013a, Fletcher2013b

Please, let me know if I am missing any steps.

Many thanks,

Mauro

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[Bioc-devel] Can anyone reproduce this? Possible bug or typo in BiocManager:::.version_map() or upstream

[Wolfgang Huber]

Hi,

I get

 > BiocManager::install()
Error: Bioconductor version '3.13' requires R version '4.1'; R version is too 
new; see
  https://bioconductor.org/install

and this appears to be because of the last line in

> BiocManager:::.version_map()
   BiocR  BiocStatus RSPM MRAN
…(29 lines omitted)….
30 3.10  3.6 out-of-date  
31 3.11  4.0 out-of-date  
32 3.12  4.0 release  
33 3.13  4.1   devel  
34 3.13  4.2  future  

Shouldn’t it say “3.14” in the second element of the last line?


> sessionInfo()
R Under development (unstable) (2021-05-04 r80261)
Platform: x86_64-apple-darwin20.4.0 (64-bit)
Running under: macOS Big Sur 11.3

Matrix products: default
BLAS:   /Users/whuber/R/lib/libRblas.dylib
LAPACK: /Users/whuber/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocManager_1.30.12 fortunes_1.5-4

loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0

and I seem to have the most recent version of BiocManager as of today’s 
https://cran.r-project.org/web/packages/BiocManager/index.html 

——

Btw the result of

> BiocManager:::.get_R_version()
[1] ‘4.2.0’

is probably technically not correct, as it’s r-devel.

Kind regards
Wolfgang

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Re: [Bioc-devel] Cannot find my package "interacCircos" on check results of BioC3.13

[Kern, Lori]

It looks like the package was just put through the final steps of addition 
yesterday.  I expect it to show up on the nightly builds in either today or 
tomorrow's build report.  If it does not please follow up again.

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 $BVCE/(B 

Sent: Tuesday, May 4, 2021 2:22 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Cannot find my package "interacCircos" on check results 
of BioC3.13

Hello,

I$B!G(Bm the maintainer of $B!H(BinteracCircos$B!I(B, which should be 
accepted two weeks ago.

However, I still cannot find the build results of $B!H(BinteracCircos$B!I(B 
on the latest nightly build of BioC3.13, which should be available at 
https://secure-web.cisco.com/1Ofrl_4AwDcI525L9tXuxWqdq5dNGjTxLRpPwV-SxmzeabQkmD41V2H_rh_586luAkabNI3waWaVljCT6KJjNDAK96mJmC_85-vMKicxhg37f1EsncH9bozC3FhHqdKE23PCNR4D4ULmTQPabc6JDS0L0XFmurq6QTe3ep9Oml-Hu7_bFuyrHYIQPkIcTVUJWfvO9mza8iL1VvaZNEZYk32wv0wqtR6D_BGMYiYly0j_Ch2qUglY14R_X-VU5a7LKEYUps-V4tvfXRo1qu9xaXTK85ia7w-TRFfqRP3dlMD9JCQ3xyI4C9972BhlRUuud/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F
 


If anyone know why this package still not available online, please let me know.

Best
Zhe
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Re: [Bioc-devel] Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment

[Martin Morgan]

This is because of a change in base R

  
https://github.com/wch/r-source/blob/9ad27a744572fca453665e97110ded41a2680a57/doc/NEWS.Rd#L257

It can be reproduced by using a recent version R-4-1.

Looking at your code, I guess it is at

  
https://code.bioconductor.org/browse/IsoCorrectoRGUI/blob/master/R/IsoCorrectionGUI.R#L30

that things start to run into trouble -- probably instead you want to create a 
'package local' environment, e.g., 

   isoCorrectionGUIEnvironment <- new.env()

as the very first line in this file, and use that for storing these variables.

Martin



On 5/4/21, 12:36 AM, "Bioc-devel on behalf of Christian Kohler" 
 wrote:

Hello BioC community,

I am the maintainer of the IsoCorrectoRGUI package.
Starting with April 30th, problems are reported in the Multiple platform 
build/check report for BioC3.13 (Linux, Windows Server as well as macOS) 
though IsoCorrectoRGUIs code base did not change since end of October 2020.

The relevant part of the error message is shown below:

* checking examples ... ERROR
Running examples in ‘IsoCorrectoRGUI-Ex.R’ failed
The error most likely occurred in:

 > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: IsoCorrectionGUI
 > ### Title: Graphical User Interface for IsoCorrectoR
 > ### Aliases: IsoCorrectionGUI
 >
 > ### ** Examples
 >
 >
 >  IsoCorrectionGUI()
Error in baseEnvRef$continueIsoCorrection <- TRUE :
   cannot add binding of 'continueIsoCorrection' to the base environment
Calls: IsoCorrectionGUI -> initGUI
Execution halted

Frankly speaking, at the moment I have no clue why the CHECK procedure 
fails from one day to the next. Does this reflect a conflict with R 
4.1.0 alpha internals?
Any insight would be greatly appreciated as the deadline for passing R 
CMD check is in a couple of days.

If anyone knows why this could be happening or if it is likely to sort 
itself in the next build please let me know.


Thanks,

Christian

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[Bioc-devel] Cannot find my package "interacCircos" on check results of BioC3.13

[崔哲]

Hello,

I’m the maintainer of “interacCircos”, which should be accepted two weeks ago. 

However, I still cannot find the build results of “interacCircos” on the latest 
nightly build of BioC3.13, which should be available at 
https://bioconductor.org/checkResults/ 

If anyone know why this package still not available online, please let me know.

Best
Zhe
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