Re: [Bioc-devel] Access to schex

[Nitesh Turaga]

Hi Saskia,

I’ve updated your email address to saskia.frey...@perkins.uwa.edu.au. 

Please activate your BiocCredentials account again, from 
https://git.bioconductor.org/BiocCredentials/account_activation. 

Another thing that could be happening is the “permissions” on your keys. 
http://bioconductor.org/developers/how-to/git/faq/ please check FAQ number #14, 
#15 and  #16 to see if those might help as well. 

Hopefully this sorts it out.


Nitesh

> On May 20, 2021, at 10:03 PM, Saskia Freytag 
>  wrote:
> 
> Hi Nitesh,
> 
> I have added multiple keys (using both my maintainer addresses), but none of 
> them seem to change anything. Could it be that there is a problem with the 
> email addresses registered to the package? It may be that a year ago we 
> changed these to make them the same between RUVcorr and schex.
> 
> Cheers,
> 
> Saskia
> 
>> On 18 May 2021, at 7:46 am, Nitesh Turaga  wrote:
>> 
>> Hi Saskia ,
>>  
>> Please try to add new keys. It’s possible you aren’t using the correct key 
>> pair to access your package.
>>  
>> Best,
>>  
>> Nitesh 
>>  
>> From: Bioc-devel  on behalf of Saskia 
>> Freytag 
>> Date: Saturday, May 15, 2021 at 8:42 PM
>> To: bioc-devel@r-project.org 
>> Subject: [Bioc-devel] Access to schex
>> 
>> Hi,
>> 
>> I am the maintainer of the schex package. I tried to update the package but 
>> when I get to the step of pushing the changes to upstream, I get the 
>> following error message:
>> FATAL: W any packages/schex SaskiaFreytag DENIED by fallthru
>> (or you mis-spelled the reponame)
>> fatal: Could not read from remote repository.
>> 
>> Please make sure you have the correct access rights
>> and the repository exists.
>> Do I need to change my ssh keys in Bioccredentials or is there something 
>> deeper going on?
>> 
>> Cheers,
>> 
>> Saskia
>> 
>> [[alternative HTML version deleted]]
>> 
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 

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Re: [Bioc-devel] Bioconductor 3.14 R Version

[Kern, Lori]

Bioconductor has two releases per year.  One spring and one fall.  The devel 
will continue to use R 4.1 for the next 6 months leading up to our Bioconductor 
fall release.  After the fall release (normally around November), we update the 
devel builders to use R devel (R 4.2) leading up to the annual R release 
(typically spring).

So short answer, no  Bioc 3.14 will also be compatible with R 4.1 and not 4.2.  
It will be the following release (?3.15) that will switch to 4.2.

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 Chris Eeles 

Sent: Friday, May 21, 2021 2:23 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bioconductor 3.14 R Version

Hello Bioc Core Team,

I noticed that currently Bioconductor 3.14 is building using R 4.1.0 beta. Will 
this be changed to R 4.2 in the future?

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network


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[Bioc-devel] Bioconductor 3.14 R Version

[Chris Eeles]

Hello Bioc Core Team,

I noticed that currently Bioconductor 3.14 is building using R 4.1.0 beta. Will 
this be changed to R 4.2 in the future?

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network


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Re: [Bioc-devel] missing GenomicScores platform availability shield for release

[Robert Castelo]

excellent, thank you so much Lori for following this up. have a nice 
weekend!!

robert.

On 21/05/2021 15:10, Kern, Lori wrote:
> I'm sorry this took so long to get back to.� �I have fixed the issue 
> with the availability badge.� This was an older badge and still used 
> numerical release values while all the other badges used release and 
> devel.� We have updated the badge location to use the release and 
> devel that is consistent with the other badges.
>
> 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 
> Robert Castelo 
> *Sent:* Wednesday, March 31, 2021 9:11 AM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] missing GenomicScores platform availability 
> shield for release
> hi,
>
> the platform availability shield for the release version of
> GenomicScores pointing here:
>
> https://secure-web.cisco.com/1k5uRLkYKb94x46c0VBX3g2O0bFWmtTPEpX_tTzr6UjSykx9XJIIiYatW_mc6PBcNAw_v2pw8UmqaVOgZYdhZszXylbRDCQvN8fyuIUBbd0B9x7sc0dh9cjTbFSt-dIiJSDS_IdDR2iRWCCWwkry0atuORg5RSurJMuOcdZmnGBAbVxhuM9lq1nIfFuqzpURRa_AV7mJwfTlJ3OnfO-9DHpo7Yd2dF_VgM9S1Z-7pQlL08lWpx7KsMDWFJEvvtuFhfXlCsx196W7GUvMDMoQnxSelXXr3c2i3vXG6vYOvcZ1muxdqx-h1s-6CP1N_rPfi/https%3A%2F%2Fbioconductor.org%2Fshields%2Favailability%2Frelease%2FGenomicScores.svg
>  
> 
>
> is missing, if i look up the same shield for another of my packages,
> it's there:
>
> https://secure-web.cisco.com/1euFKX990kz65NLpx678ArKnRM9Su1EcYOC7649jGofqndz48PyUUG_6fVdUCLdmLO0fDYX6C8JADDsvBS8tXv1uFLTMusgb1_CY8sQZgelJnhmbfmgs92n1VhKXXp48LnsDkknfN0Z8ZhpGh4QYmeU7kL3SxD-46zEvqSa04mWZDaSLUfbvQgV_5mTptKEW_2zwgpyC6j_sfuZV0sVlFT8B8jVDavofioKhCZDh-8zqmXs_ApvUUTxvyYSBmpuUXAz-1ai6uT-q5srIXAGQWjw3tmoQ4bY24Z_ZfiFRkOqaO9yQam8GS6_HCxgmWvWgk/https%3A%2F%2Fbioconductor.org%2Fshields%2Favailability%2Frelease%2Fqpgraph.svg
>  
> 
>
> if, in the case of GenomicScores, i replace 'release' by the current
> release version '3.12', then it works:
>
> https://secure-web.cisco.com/1l36aer-CBWxJKyor8kfkIMv2AsKV8oga20au0ZS7Z2_D5lhFyowepGvctR23hBu2DEtHu1QN5u3Bmvts6kUE09k0fp_ipqx55gcJDxMkkg9SxswwIuuMxm5_Go8-5p8mYjr5xUHiQsCUZ1MnEHjR_8LhI5cVoCYK4_aG76m7ZjH4KOHuLDQBzpLea9XKhWKEyG2eeE2EjKih0exRhjOy5EX8mHAjXnUDPwqAsumEporq_3iaqm_hhGinlUE9G0U5VwbrTsO9oBRMHWVXQdiYEuTIRcdJSEKDk5GLnnZRoW47M0pJM6h8RYntFSlKdMPj/https%3A%2F%2Fbioconductor.org%2Fshields%2Favailability%2F3.12%2FGenomicScores.svg
>  
> 
>
> is this inconsistency some kind of bug? should i use '3.12' instead of
> 'release' in the URL?
>
> the reason for my question is that i include this shield in my GH repo
> and noticed that the platform availability shield for the release
> version of GenomicScores disappeared at some point. i know i can fix it
> by replacing 'release' by '3.12', but of course it would be better for
> me that it would work with 'release', since then i would have to fix
> that bit in the README.md file at each new release.
>
> thanks!
>
> robert.
>
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/1lwRhIH6VEvHdmkXYGJpFgB9gAWUWAOfBl6DZCX1RkzSEeqN3J6UBXJYuwVdxR6V42f-9W4Fa7xdDg02VdUVCVr9YblN8JoYyNFQvPnc2Rj6EkDrlcNfmujIEffkasqxzpJQPM5FGdKa0o1cSWmGgc7sRJNnPllJn6VZ1vnyPw_HSX-K-TC5_jXA1o3B1ZG2B2mJJ1yHqxQC_NCVz5w1lcI1vKwiBYbz8j0ZwQhhZMyrtVRSGcHPI5IB1_Cj2ffeMTjbn2UyT6RZZ57DzfRJ63aboH3Wj4V2xf58I0P5-ljInCNn1jx5Zvx9jCGD8QVtn/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>  
> 

Re: [Bioc-devel] missing GenomicScores platform availability shield for release

[Kern, Lori]

I'm sorry this took so long to get back to.   I have fixed the issue with the 
availability badge.  This was an older badge and still used numerical release 
values while all the other badges used release and devel.  We have updated the 
badge location to use the release and devel that is consistent with the other 
badges.

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 Robert Castelo 

Sent: Wednesday, March 31, 2021 9:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] missing GenomicScores platform availability shield for 
release

hi,

the platform availability shield for the release version of
GenomicScores pointing here:

https://secure-web.cisco.com/1k5uRLkYKb94x46c0VBX3g2O0bFWmtTPEpX_tTzr6UjSykx9XJIIiYatW_mc6PBcNAw_v2pw8UmqaVOgZYdhZszXylbRDCQvN8fyuIUBbd0B9x7sc0dh9cjTbFSt-dIiJSDS_IdDR2iRWCCWwkry0atuORg5RSurJMuOcdZmnGBAbVxhuM9lq1nIfFuqzpURRa_AV7mJwfTlJ3OnfO-9DHpo7Yd2dF_VgM9S1Z-7pQlL08lWpx7KsMDWFJEvvtuFhfXlCsx196W7GUvMDMoQnxSelXXr3c2i3vXG6vYOvcZ1muxdqx-h1s-6CP1N_rPfi/https%3A%2F%2Fbioconductor.org%2Fshields%2Favailability%2Frelease%2FGenomicScores.svg

is missing, if i look up the same shield for another of my packages,
it's there:

https://secure-web.cisco.com/1euFKX990kz65NLpx678ArKnRM9Su1EcYOC7649jGofqndz48PyUUG_6fVdUCLdmLO0fDYX6C8JADDsvBS8tXv1uFLTMusgb1_CY8sQZgelJnhmbfmgs92n1VhKXXp48LnsDkknfN0Z8ZhpGh4QYmeU7kL3SxD-46zEvqSa04mWZDaSLUfbvQgV_5mTptKEW_2zwgpyC6j_sfuZV0sVlFT8B8jVDavofioKhCZDh-8zqmXs_ApvUUTxvyYSBmpuUXAz-1ai6uT-q5srIXAGQWjw3tmoQ4bY24Z_ZfiFRkOqaO9yQam8GS6_HCxgmWvWgk/https%3A%2F%2Fbioconductor.org%2Fshields%2Favailability%2Frelease%2Fqpgraph.svg

if, in the case of GenomicScores, i replace 'release' by the current
release version '3.12', then it works:

https://secure-web.cisco.com/1l36aer-CBWxJKyor8kfkIMv2AsKV8oga20au0ZS7Z2_D5lhFyowepGvctR23hBu2DEtHu1QN5u3Bmvts6kUE09k0fp_ipqx55gcJDxMkkg9SxswwIuuMxm5_Go8-5p8mYjr5xUHiQsCUZ1MnEHjR_8LhI5cVoCYK4_aG76m7ZjH4KOHuLDQBzpLea9XKhWKEyG2eeE2EjKih0exRhjOy5EX8mHAjXnUDPwqAsumEporq_3iaqm_hhGinlUE9G0U5VwbrTsO9oBRMHWVXQdiYEuTIRcdJSEKDk5GLnnZRoW47M0pJM6h8RYntFSlKdMPj/https%3A%2F%2Fbioconductor.org%2Fshields%2Favailability%2F3.12%2FGenomicScores.svg

is this inconsistency some kind of bug? should i use '3.12' instead of
'release' in the URL?

the reason for my question is that i include this shield in my GH repo
and noticed that the platform availability shield for the release
version of GenomicScores disappeared at some point. i know i can fix it
by replacing 'release' by '3.12', but of course it would be better for
me that it would work with 'release', since then i would have to fix
that bit in the README.md file at each new release.

thanks!

robert.

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Re: [Bioc-devel] EnMCB reduce dependencies

[xin wwa]

Dear Carey,
Thank you for your email!
IlluminaHumanMethylation450kanno.ilmn12.hg19 depends on minfi, so if we
load the ..anno.. package.
We will always get minfi package in the dependencies list.
Maybe we can directly reupload or include the annotation dataframe in our
package?

Regards,
Xin Yu
Ph.D. student of Biomedical Informatics
College of Bioinformatics - Huazhong Agricultural University
whirl...@gmail.com
yu...@webmail.hzau.edu.cn
tel: (+86) 186-5313-5769


Vincent Carey  于2021年5月21日周五 下午6:04写道：

> IlluminaHumanMethylation450kanno.ilmn12.hg19 is primarily
> a collection of data.frames isn't it?  I notice that the
> Illum...anno... package itself depends on minfi, which seems
> unnecessary.  But perhaps Kasper will comment.
>
> On Fri, May 21, 2021 at 5:32 AM xin wwa  wrote:
>
>> Dear Bioconductor team,
>>
>> Hi, thank you for reading my email.
>>
>> Our package has too many dependencies.
>> Therefore, we may want to reduce dependencies.
>> The main reason is that we use
>> minfi::getAnnotation("IlluminaHumanMethylation450kanno.ilmn12.hg19"). And
>> minfi package we used has lots of dependencies.
>> This is only an annotation table that contains some probe information.
>> Is there a way to load the annotation file independent of minfi package?
>>
>> Thanks in advance. Any help is appreciated!
>>
>> Regards,
>>
>> Xin Yu
>> Ph.D. student of Biomedical Informatics
>> College of Bioinformatics - Huazhong Agricultural University
>> whirl...@gmail.com
>> yu...@webmail.hzau.edu.cn
>> tel: (+86) 186-5313-5769
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>>
>
> The information in this e-mail is intended only for th...{{dropped:16}}

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Re: [Bioc-devel] EnMCB reduce dependencies

[Vincent Carey]

IlluminaHumanMethylation450kanno.ilmn12.hg19 is primarily
a collection of data.frames isn't it?  I notice that the
Illum...anno... package itself depends on minfi, which seems
unnecessary.  But perhaps Kasper will comment.

On Fri, May 21, 2021 at 5:32 AM xin wwa  wrote:

> Dear Bioconductor team,
>
> Hi, thank you for reading my email.
>
> Our package has too many dependencies.
> Therefore, we may want to reduce dependencies.
> The main reason is that we use
> minfi::getAnnotation("IlluminaHumanMethylation450kanno.ilmn12.hg19"). And
> minfi package we used has lots of dependencies.
> This is only an annotation table that contains some probe information.
> Is there a way to load the annotation file independent of minfi package?
>
> Thanks in advance. Any help is appreciated!
>
> Regards,
>
> Xin Yu
> Ph.D. student of Biomedical Informatics
> College of Bioinformatics - Huazhong Agricultural University
> whirl...@gmail.com
> yu...@webmail.hzau.edu.cn
> tel: (+86) 186-5313-5769
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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[Bioc-devel] EnMCB reduce dependencies

[xin wwa]

Dear Bioconductor team,

Hi, thank you for reading my email.

Our package has too many dependencies.
Therefore, we may want to reduce dependencies.
The main reason is that we use
minfi::getAnnotation("IlluminaHumanMethylation450kanno.ilmn12.hg19"). And
minfi package we used has lots of dependencies.
This is only an annotation table that contains some probe information.
Is there a way to load the annotation file independent of minfi package?

Thanks in advance. Any help is appreciated!

Regards,

Xin Yu
Ph.D. student of Biomedical Informatics
College of Bioinformatics - Huazhong Agricultural University
whirl...@gmail.com
yu...@webmail.hzau.edu.cn
tel: (+86) 186-5313-5769

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Access to schex

[Saskia Freytag]

Hi Nitesh,

I have added multiple keys (using both my maintainer addresses), but none of 
them seem to change anything. Could it be that there is a problem with the 
email addresses registered to the package? It may be that a year ago we changed 
these to make them the same between RUVcorr and schex.

Cheers,

Saskia

On 18 May 2021, at 7:46 am, Nitesh Turaga 
mailto:nturaga.b...@gmail.com>> wrote:

Hi Saskia ,

Please try to add new keys. It’s possible you aren’t using the correct key pair 
to access your package.

Best,

Nitesh

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Saskia Freytag 
mailto:saskia.frey...@perkins.uwa.edu.au>>
Date: Saturday, May 15, 2021 at 8:42 PM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Access to schex
Hi,

I am the maintainer of the schex package. I tried to update the package but 
when I get to the step of pushing the changes to upstream, I get the following 
error message:
FATAL: W any packages/schex SaskiaFreytag DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Do I need to change my ssh keys in Bioccredentials or is there something deeper 
going on?

Cheers,

Saskia

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