Re: [Bioc-devel] magpie package failing unit test

2023-09-25 Thread Martin Grigorov 
Dear Daoyu,

I can reproduce the test failure at kunpeng2 build runner!
I'd be happy to test any suggestions you might have!

Regards,
Martin

On Fri, Sep 22, 2023 at 6:34 PM Daoyu Duan  wrote:

> Dear Bioconductor team,
>
> I have received emails that my package "magpie" is failing the unit test
> in devel, but I have not made any changes after the last release where the
> unit test passed. I tried to investigate this issue but the unit test
> passed on my local machines (MacOS and Windows) and was not able to
> replicate the error. Are there any possible reasons for this to happen?
> Thank you so much for any suggestions!
>
> Best regards,
>
> Daoyu
>
> [[alternative HTML version deleted]]
>
> ___
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>

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[Bioc-devel] Lost access to my email

2023-09-25 Thread Stefan Graw 
Dear Bioconductor team,

During grad school, I submitted the package pwrEWAS to Bioconductor (
https://bioconductor.org/packages/release/bioc/html/pwrEWAS.html). However,
I don't have access to the email account (shg...@uams.edu) associated with
the packages anymore, and I was made aware by my former mentor that there
are some updates required.

Is there a way for me to change my email associated with the package? I am
currently unable to login.

Thank you,
Stefan Graw

[[alternative HTML version deleted]]

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Re: [Bioc-devel] magpie package failing unit test

2023-09-25 Thread Kern, Lori via Bioc-devel 
For What it's worth,  I can also reproduce this locally.  Please make sure you 
are using the correct version of R (4.3.1 Patched) and that all your packages 
are up-to-date with BiocManager::install and BiocManager::valid.


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 Martin 
Grigorov 
Sent: Monday, September 25, 2023 6:48 AM
To: Daoyu Duan 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] magpie package failing unit test

Dear Daoyu,

I can reproduce the test failure at kunpeng2 build runner!
I'd be happy to test any suggestions you might have!

Regards,
Martin

On Fri, Sep 22, 2023 at 6:34 PM Daoyu Duan  wrote:

> Dear Bioconductor team,
>
> I have received emails that my package "magpie" is failing the unit test
> in devel, but I have not made any changes after the last release where the
> unit test passed. I tried to investigate this issue but the unit test
> passed on my local machines (MacOS and Windows) and was not able to
> replicate the error. Are there any possible reasons for this to happen?
> Thank you so much for any suggestions!
>
> Best regards,
>
> Daoyu
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
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>

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Re: [Bioc-devel] Lost access to my email

2023-09-25 Thread Kern, Lori via Bioc-devel 
Just to confirm you no longer have access to shg...@uams.edu?


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 Stefan Graw 

Sent: Sunday, September 24, 2023 3:07 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Lost access to my email

Dear Bioconductor team,

During grad school, I submitted the package pwrEWAS to Bioconductor (
https://secure-web.cisco.com/1a1P0Sfg0V2lZ3iwLEUb14u_G5COUw7XFJgjGy1NLY5UKpBIqIUBKzk8wnn2I3cLRmXbPRfwc0EK0G4XzXMwhgH73O3P613m8rJuRl4MdiEIztjNSjdmbL9BsC-58b0NYj3y54gQndz_SNhM7vE6_sGri9C-b78cPU0Z61rNhg-Hnh3wmpCG_m7RSes-vNCTV1uEIUh0Xf8AQaiDVmbu1spL2sr0bGugw9ff_y7VJK3MDyug_Le_owApKQiFYIH3eVwyhUzBKHzPRgkvyPzAvNBXYPm41mnX6jH_gqGiQeikSUom0VG5cj1A-u6aHQpah/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FpwrEWAS.html).
 However,
I don't have access to the email account (shg...@uams.edu) associated with
the packages anymore, and I was made aware by my former mentor that there
are some updates required.

Is there a way for me to change my email associated with the package? I am
currently unable to login.

Thank you,
Stefan Graw

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] Lost access to my email

2023-09-25 Thread Kern, Lori via Bioc-devel 
I will be in touch off list about resetting your BiocCredentials account so you 
can manage your ssh keys for access to the packages.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Kern, Lori 
Sent: Monday, September 25, 2023 8:02 AM
To: Stefan Graw ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Lost access to my email

Just to confirm you no longer have access to shg...@uams.edu?


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 Stefan Graw 

Sent: Sunday, September 24, 2023 3:07 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Lost access to my email

Dear Bioconductor team,

During grad school, I submitted the package pwrEWAS to Bioconductor (
https://secure-web.cisco.com/1a1P0Sfg0V2lZ3iwLEUb14u_G5COUw7XFJgjGy1NLY5UKpBIqIUBKzk8wnn2I3cLRmXbPRfwc0EK0G4XzXMwhgH73O3P613m8rJuRl4MdiEIztjNSjdmbL9BsC-58b0NYj3y54gQndz_SNhM7vE6_sGri9C-b78cPU0Z61rNhg-Hnh3wmpCG_m7RSes-vNCTV1uEIUh0Xf8AQaiDVmbu1spL2sr0bGugw9ff_y7VJK3MDyug_Le_owApKQiFYIH3eVwyhUzBKHzPRgkvyPzAvNBXYPm41mnX6jH_gqGiQeikSUom0VG5cj1A-u6aHQpah/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FpwrEWAS.html).
 However,
I don't have access to the email account (shg...@uams.edu) associated with
the packages anymore, and I was made aware by my former mentor that there
are some updates required.

Is there a way for me to change my email associated with the package? I am
currently unable to login.

Thank you,
Stefan Graw

[[alternative HTML version deleted]]

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Re: [Bioc-devel] magpie package failing unit test

2023-09-25 Thread Daoyu Duan 
Hi Martin and Lori,

Thank you for helping test it! I will check the version of R and packages,
and try to fix it !

Thank you,

Daoyu

On Mon, Sep 25, 2023 at 7:52 AM Kern, Lori 
wrote:

> For What it's worth,  I can also reproduce this locally.  Please make sure
> you are using the correct version of R (4.3.1 Patched) and that all your
> packages are up-to-date with BiocManager::install and BiocManager::valid.
>
> 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 Martin
> Grigorov 
> *Sent:* Monday, September 25, 2023 6:48 AM
> *To:* Daoyu Duan 
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] magpie package failing unit test
>
> Dear Daoyu,
>
> I can reproduce the test failure at kunpeng2 build runner!
> I'd be happy to test any suggestions you might have!
>
> Regards,
> Martin
>
> On Fri, Sep 22, 2023 at 6:34 PM Daoyu Duan  wrote:
>
> > Dear Bioconductor team,
> >
> > I have received emails that my package "magpie" is failing the unit test
> > in devel, but I have not made any changes after the last release where
> the
> > unit test passed. I tried to investigate this issue but the unit test
> > passed on my local machines (MacOS and Windows) and was not able to
> > replicate the error. Are there any possible reasons for this to happen?
> > Thank you so much for any suggestions!
> >
> > Best regards,
> >
> > Daoyu
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://secure-web.cisco.com/1DI3X5mPa4-97d7g5-ZbYnB2O_J802PlUWd-7TwtVWJo0eoekPmh3Z2eWVFU4OiUqm6e0zlLCK7VasPasuWqmlduH4CJUCWvAVno4LCg9id8Gl0Lo02HiFpa2V7177JcUn1U8rcOChMNCvJTB6SRQmIDLW1WDc4S_U6yHOJsTYJRcNve_9T7wO-dGiwHWzHGoGQ1QCa6tohNz50fLfMBtTV_CDVREd7ZyA2vyvXF8akaJQ0vEJejG8jU9E3G2ddJw9SfklwH5CdXCFtV94QskDigycBCL-c4oe_Sym7a9Pwe7JKvH-xZ4x-a1Y3envuAA/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
>
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> received this message in error, please notify the sender immediately by
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Re: [Bioc-devel] KEGGREST is broken and has a long reverse-dependency chain.

2023-09-25 Thread Ramos Perez, Marcel via Bioc-devel 
Thank you for the fix.
I have updated the package.

Best,

Marcel

On 9/21/23 7:12 PM, Ali Sajid Imami wrote:

I'll take a look. I rely on KEGGREST a lot.


Regards,
Dr. Ali Sajid Imami
LinkedIn 



On Thu, Sep 21, 2023 at 7:02 PM Charles Plessy 

wrote:



Dear all,

yesterday I reported on GitHub that the regression tests of KEGGREST
fail because the KEGGREST:::.get.tmp.url function can not parse
www.kegg.jp pages anymore.

https://github.com/Bioconductor/KEGGREST/issues/21

This is a problem in Debian because 1) we do not allow the Bioconductor
packages that we redistribute to fail their tests and 2) the
reverse-dependency chain of KEGGREST is heavy.

KEGGREST <- AnnotationDbi <- GenomicFeatures <- lots of other packages

I am not familiar with KEGG enough to grasp what KEGGREST:::.get.tmp.url
was looking for.  But I was wondering if this bug would be a low-hanging
fruit for somebody else in this list?

Have a nice day,

Charles Plessy

--
Charles Plessy - - ~ ~ ~ ~ ~  ~ ~ ~ ~ ~ - - 
charles.ple...@oist.jp
Okinawa  Institute  of  Science  and  Technology  Graduate  University
Senior staff scientist ~~ Luscombe Unit ~~ https://groups.oist.jp/grsu
Toots from work - ~~  ~~ - https://fediscience.org/@charles_plessy

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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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