[Bioc-devel] orthogene: killed while reading tree

2023-04-05 Thread Brian Schilder 
Hi everyone,

After some pushes upstream to my package 
orthogene, 
I noticed that the release version (3.16) is failing on the server because it 
was �Killed� midway through. But I can�t see any details that explain why or 
how it was killed.
http://bioconductor.org/checkResults/release/bioc-LATEST/orthogene/nebbiolo2-checksrc.html

The only thing I know is that is occurs at the step where a large tree (147k 
species, stored as a 5.3Mb newick file) is being read into R with ape::read.tree
https://github.com/neurogenomics/orthogene/blob/4e41e6322507a929562fc77cbdc602bc084a34bf/R/prepare_tree.R#L115

Oddly, this same code seems to work fine on devel (3.17):
http://bioconductor.org/packages/3.17/bioc/html/orthogene.html

Anyone know why this might be?

Thanks in advance,
Brian
___
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
CV | https://bschilder.github.io/CV/CV
LinkedIn | 
linkedin.com/in/brian-schilder
Twitter | twitter.com/BMSchilder
Lab | neurogenomics.co.uk
UK DRI | www.ukdri.ac.uk

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out

2023-04-05 Thread Aditya Bhagwat via Bioc-devel 

Dear Lori and Sarvesh,

The proxy server at our institute was blocking ssh.
Sorry for bothering you with that, it's working now : )

Thankyou very much for the help!

Aditya


It looks like it reads /etc/ssh/ssh_config but doesn't actually try  
a ssh key.  Perhaps try regenerating a ssh key and adding new or  
check the setting in the ssh_config that it is refrencing.



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: aditya.bhag...@uni-marburg.de 
Sent: Wednesday, April 5, 2023 8:56 AM
To: Kern, Lori 
Cc: Sarvesh Nikumbh ;  
bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Fixing autonomics - ssh: connect to host  
git.bioconductor.org port 22: Connection timed out


Thank you very much Lori,

$ git remote -v
origin   
https://secure-web.cisco.com/12mXJ65QixB3NHWkG2clCIt7EuA2ogRSnpCZg2WeBlyKGEe4fCwN92cdYjCXrFEtq8jL9iIpV73weH_1i_U2R1QIgyH1_W4Kb7UGXF3UHvaEuQrElOxLsUMx9R4deNWl0EK9GPJqm2JSSNcjVom1A3ncR7heM9u5_H7hT7FBmKI-zgJm3yhzOBDbhNZraG9LArQLtPzA9WNOZb5ZPbKSGtptjQpk9GncgSkYtYJWMhjOqLQgkOt8PQQrsM96P4Hose38bllGfYhD4bu9M9-MHqRzVI0gY-bK4r0fndo1IA9OAooTEl8_1UG7z8Ec9644p/https%3A%2F%2Fgithub.com%2Fbhagwataditya%2Fautonomics.git  
(fetch)
origin   
https://secure-web.cisco.com/12mXJ65QixB3NHWkG2clCIt7EuA2ogRSnpCZg2WeBlyKGEe4fCwN92cdYjCXrFEtq8jL9iIpV73weH_1i_U2R1QIgyH1_W4Kb7UGXF3UHvaEuQrElOxLsUMx9R4deNWl0EK9GPJqm2JSSNcjVom1A3ncR7heM9u5_H7hT7FBmKI-zgJm3yhzOBDbhNZraG9LArQLtPzA9WNOZb5ZPbKSGtptjQpk9GncgSkYtYJWMhjOqLQgkOt8PQQrsM96P4Hose38bllGfYhD4bu9M9-MHqRzVI0gY-bK4r0fndo1IA9OAooTEl8_1UG7z8Ec9644p/https%3A%2F%2Fgithub.com%2Fbhagwataditya%2Fautonomics.git  
(push)

upstreamg...@git.bioconductor.org:packages/autonomics.git (fetch)
upstreamg...@git.bioconductor.org:packages/autonomics.git (push)

$ ssh -T -v g...@git.bioconductor.org
OpenSSH_8.8p1, OpenSSL 1.1.1m  14 Dec 2021
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22.
debug1: connect to address 34.192.48.227 port 22: Connection timed out
ssh: connect to host git.bioconductor.org port 22: Connection timed out

I also went through the troubleshooting FAQ but so far could not
identify the cause.

The ssh key that I have on my machine is there in BiocCredentials.
I noticed that it was not in my github account, which I have now added.
That didnt seem to make a difference though.

Thank you very much for helping.

Aditya



It would help to show some of the commands and output in the FAQ for
git help and working through some of the trouleshooting there.

http://secure-web.cisco.com/18MFSeHzZZB_WuIlGDqlzJdFRKETumUZjeCtSgSrANYmR9CyDbS-RMo8AVTsDgJKleT8dp9w9QTrX9eiy0thyU3IL8BCWxDa550ejaMKUoVKvybRr8chTr3WQqgYudsSKXSv-GvtBRgs2YuhV4R5GZGK3qJ34BxkHYk2lPkkYGywLSuMzYSP-MQshj85idbKgtIJ7GSLyNVnPjwm3vA9SpP6T9_6rTWyDbly5cmSvREZISPzhTEBnPX3m5lSozzqjCOWNHqUASmQLoCjJlWGSJZjKNp7gx2pS5lsOGvr2CYtE5TQao2-3h9u0x4FihANR/http%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23faq

Particularly showing your
git remote  -v

and trying


 ssh -T -v g...@git.bioconductor.org




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
Aditya Bhagwat via Bioc-devel 
Sent: Wednesday, April 5, 2023 7:33 AM
To: Sarvesh Nikumbh 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Fixing autonomics - ssh: connect to host
git.bioconductor.org port 22: Connection timed out

Thank you very much Sarvesh, lovely also to hear from you - how are you? .

I had indeed failed to do these branch renamings which I now have.
Unfortunately, my ssh issue remains:

git push upstream devel
ssh: connect to host git.bioconductor.org port 22: Connection timed out
fatal: Could not read from remote repository.

Dear BioC team, could you help out, am a bit at loss here ?

Thank you very much,

Aditya




Hi Aditya,

Can you check if this is due to the recent branch name changes: default
branch name changed from 'main' to 'devel'
This was announced on the mailing-list, and also on this blogpost:
https://secure-web.cisco.com/1n72fvF59dD6BZtBdt6wi9Th7fr3G7_rRtSP9FgXzBRpHnSq-VrSgmyZlsAZ4KjMK-pSsxbs9F2zruBwHjVrdFmi4KD7vdnC-vhDy3qDgan2xX9UGFvUBU0MvtXSbXn-0RJfroqoyy3xj4ETCHFaoJ6cPKaoO-tqdefMvlf5zDYW5d4V0RKW61PLY4Qy0F_vqKxqQ2aTb_0DxWbnYs-I84vMG_6QA2TWTUGyFqE9D9gbvVQMu5GMxw6G7t7xZF_BUpdUBrgPEQKJEkundypNCsh3Of95OHse3VzpxIPUn-8j8QCV8ZgC8aZ-tVcnokUlF/https%3A%2F%2Fbioconductor.github.io%2Fbiocblog%2Fposts%2F2023-03-01-transition-to-devel%2F

Sarvesh

On Tue, 4 Apr 2023 at 19:38, Aditya Bhagwat via Bioc-devel <
bioc-devel@r-project.org> wrote:


Dear BioC team,

I am having the same error as many others (the missing BiocStyle
issue) and I wanted to fix it. But I somehow

Re: [Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out

2023-04-05 Thread Kern, Lori 
It would help to show some of the commands and output in the FAQ for git help 
and working through some of the trouleshooting there.

http://contributions.bioconductor.org/git-version-control.html#faq

Particularly showing your
git remote  -v

and trying


 ssh -T -v g...@git.bioconductor.org




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 Aditya Bhagwat 
via Bioc-devel 
Sent: Wednesday, April 5, 2023 7:33 AM
To: Sarvesh Nikumbh 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Fixing autonomics - ssh: connect to host 
git.bioconductor.org port 22: Connection timed out

Thank you very much Sarvesh, lovely also to hear from you - how are you? .

I had indeed failed to do these branch renamings which I now have.
Unfortunately, my ssh issue remains:

git push upstream devel
ssh: connect to host git.bioconductor.org port 22: Connection timed out
fatal: Could not read from remote repository.

Dear BioC team, could you help out, am a bit at loss here ?

Thank you very much,

Aditya



> Hi Aditya,
>
> Can you check if this is due to the recent branch name changes: default
> branch name changed from 'main' to 'devel'
> This was announced on the mailing-list, and also on this blogpost:
> https://secure-web.cisco.com/1n72fvF59dD6BZtBdt6wi9Th7fr3G7_rRtSP9FgXzBRpHnSq-VrSgmyZlsAZ4KjMK-pSsxbs9F2zruBwHjVrdFmi4KD7vdnC-vhDy3qDgan2xX9UGFvUBU0MvtXSbXn-0RJfroqoyy3xj4ETCHFaoJ6cPKaoO-tqdefMvlf5zDYW5d4V0RKW61PLY4Qy0F_vqKxqQ2aTb_0DxWbnYs-I84vMG_6QA2TWTUGyFqE9D9gbvVQMu5GMxw6G7t7xZF_BUpdUBrgPEQKJEkundypNCsh3Of95OHse3VzpxIPUn-8j8QCV8ZgC8aZ-tVcnokUlF/https%3A%2F%2Fbioconductor.github.io%2Fbiocblog%2Fposts%2F2023-03-01-transition-to-devel%2F
>
> Sarvesh
>
> On Tue, 4 Apr 2023 at 19:38, Aditya Bhagwat via Bioc-devel <
> bioc-devel@r-project.org> wrote:
>
>> Dear BioC team,
>>
>> I am having the same error as many others (the missing BiocStyle
>> issue) and I wanted to fix it. But I somehow am not getting into
>> git.bioconductor.org anymore :
>>
>> $ git fetch --all
>> Fetching origin
>> Fetching upstream
>> ssh: connect to host git.bioconductor.org port 22: Connection timed out
>> fatal: Could not read from remote repository.
>> Please make sure you have the correct access rights
>> and the repository exists.
>> error: could not fetch upstream
>>
>> I checked BiocCredentials and my public key is visible there.
>>
>> What else could this be ? I changed institutes since my last push, in
>> my current setup things go through a proxyserver, could that be the
>> reason?
>>
>> Thank you for feedback.
>>
>> Aditya
>>
>>
>> --
>> Aditya Bhagwat
>> Statistics � Bioinformatics � Data Science
>> Translational Proteomics � Philipps-University Marburg
>> Karl-von-Frisch-Str 2 � 35043 Marburg � Germany
>> Tel.: +49 6421 28 27403
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://secure-web.cisco.com/1WSmgk-KPuAvx2yiy7_CfLoJSFFXcVGygfQznt_qB7SQzYIOTZOS1jnbIlMfheyKx9-wSPjP2sVqdPJJNmmvga9wi8cTqmeUh9t1N_wRtyS0YXMH081klK8t7HHOsECW405BsZJMDrRD9Xae5g0NPzAyPh5a48WuH2iXg5nt8JtuUYOU4F2XbFwGqtaIdpGPU-i4DCuMaSTuyiOpGBc5SQaAnixj9Ghn0ybCbegKZobuyDSZ2cOw0iRcWcgLYgYYZHm07c0yilexca5YctM5QZp-Ex-opMf-2lqTxelW3hks2aPaGG-GOCGpv9K9gwQTL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>>
>
>
> --
>
> thanks!
> -Sarvesh
>
> 
> Q: Why is this email five sentences or less?
> A: 
> http://secure-web.cisco.com/1LnTiYl4U5aiZv9MUQP8HFGMMtS3dII6KIIXyAig8z_4ahFQ0zUCrVtQOST4Lh8XxFx_GJAQU8xO_Pml_jbz64SSaRt9i30NzqAGq_Fn8b5JHMV8Fj8S2TmKYbAz2K-1-ivKeePv2HupVikTt9AZhVI8QlecwemzZ_o8gUDicwVcdIdyeFKoACKmqNeiCqFeRluTyb16JeQCYOVJF-yOj5ATVrJAS2A7000VwaREP1pyZKLeSkJJeEcV7607ZULhbMBzrYIPjB8lZ00_aupQ_5rhrSh0ETTBFNyO8LEzwq1psweEQErRCNWBO3dOqvBXN/http%3A%2F%2Ffive.sentenc.es



--
Aditya Bhagwat
Statistics � Bioinformatics � Data Science
Translational Proteomics � Philipps-University Marburg
Karl-von-Frisch-Str 2 � 35043 Marburg � Germany
Tel.: +49 6421 28 27403

___
Bioc-devel@r-project.org mailing list
https://secure-web.cisco.com/1WSmgk-KPuAvx2yiy7_CfLoJSFFXcVGygfQznt_qB7SQzYIOTZOS1jnbIlMfheyKx9-wSPjP2sVqdPJJNmmvga9wi8cTqmeUh9t1N_wRtyS0YXMH081klK8t7HHOsECW405BsZJMDrRD9Xae5g0NPzAyPh5a48WuH2iXg5nt8JtuUYOU4F2XbFwGqtaIdpGPU-i4DCuMaSTuyiOpGBc5SQaAnixj9Ghn0ybCbegKZobuyDSZ2cOw0iRcWcgLYgYYZHm07c0yilexca5YctM5QZp-Ex-opMf-2lqTxelW3hks2aPaGG-GOCGpv9K9gwQTL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



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

Re: [Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out

2023-04-05 Thread Aditya Bhagwat via Bioc-devel 

Thank you very much Sarvesh, lovely also to hear from you - how are you? .

I had indeed failed to do these branch renamings which I now have.
Unfortunately, my ssh issue remains:

git push upstream devel
ssh: connect to host git.bioconductor.org port 22: Connection timed out
fatal: Could not read from remote repository.

Dear BioC team, could you help out, am a bit at loss here ?

Thank you very much,

Aditya




Hi Aditya,

Can you check if this is due to the recent branch name changes: default
branch name changed from 'main' to 'devel'
This was announced on the mailing-list, and also on this blogpost:
https://bioconductor.github.io/biocblog/posts/2023-03-01-transition-to-devel/

Sarvesh

On Tue, 4 Apr 2023 at 19:38, Aditya Bhagwat via Bioc-devel <
bioc-devel@r-project.org> wrote:


Dear BioC team,

I am having the same error as many others (the missing BiocStyle
issue) and I wanted to fix it. But I somehow am not getting into
git.bioconductor.org anymore :

$ git fetch --all
Fetching origin
Fetching upstream
ssh: connect to host git.bioconductor.org port 22: Connection timed out
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
error: could not fetch upstream

I checked BiocCredentials and my public key is visible there.

What else could this be ? I changed institutes since my last push, in
my current setup things go through a proxyserver, could that be the
reason?

Thank you for feedback.

Aditya


--
Aditya Bhagwat
Statistics ∙ Bioinformatics ∙ Data Science
Translational Proteomics ∙ Philipps-University Marburg
Karl-von-Frisch-Str 2 ∙ 35043 Marburg ∙ Germany
Tel.: +49 6421 28 27403

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel




--

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es




--
Aditya Bhagwat
Statistics ∙ Bioinformatics ∙ Data Science
Translational Proteomics ∙ Philipps-University Marburg
Karl-von-Frisch-Str 2 ∙ 35043 Marburg ∙ Germany
Tel.: +49 6421 28 27403

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out

2023-04-05 Thread Sarvesh Nikumbh 
Hi Aditya,

Can you check if this is due to the recent branch name changes: default
branch name changed from 'main' to 'devel'
This was announced on the mailing-list, and also on this blogpost:
https://bioconductor.github.io/biocblog/posts/2023-03-01-transition-to-devel/

Sarvesh

On Tue, 4 Apr 2023 at 19:38, Aditya Bhagwat via Bioc-devel <
bioc-devel@r-project.org> wrote:

> Dear BioC team,
>
> I am having the same error as many others (the missing BiocStyle
> issue) and I wanted to fix it. But I somehow am not getting into
> git.bioconductor.org anymore :
>
> $ git fetch --all
> Fetching origin
> Fetching upstream
> ssh: connect to host git.bioconductor.org port 22: Connection timed out
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> error: could not fetch upstream
>
> I checked BiocCredentials and my public key is visible there.
>
> What else could this be ? I changed institutes since my last push, in
> my current setup things go through a proxyserver, could that be the
> reason?
>
> Thank you for feedback.
>
> Aditya
>
>
> --
> Aditya Bhagwat
> Statistics ∙ Bioinformatics ∙ Data Science
> Translational Proteomics ∙ Philipps-University Marburg
> Karl-von-Frisch-Str 2 ∙ 35043 Marburg ∙ Germany
> Tel.: +49 6421 28 27403
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel