Re: [Bioc-devel] Could not read from remote repository

2020-05-05 Thread Nitesh Turaga 
I'm wondering if you are trying to connect from a IP address which is blocked 
by our server or your institutional/home firewall.

Do you mind telling me where you are trying to access this from?

Nitesh 

> On May 4, 2020, at 9:49 PM, Yingxin Lin  wrote:
> 
> Hi, 
>  
> Thank you for your suggestion! However it still doesn’t work (same error).
>  
> Best regards,
> Yingxin
>  
> From: "Chengyang.Ji12" 
> Date: Tuesday, 5 May 2020 at 11:44 am
> To: Yingxin Lin , Nitesh Turaga 
> , "bioc-devel@r-project.org" 
> 
> Subject: RE: [Bioc-devel] Could not read from remote repository
>  
> Try ‘git remote set-url upstream 
> g...@git.bioconductor.org:packages/scClassify.git’
>  
> Sent from Mail for Windows 10
>  
> From: Yingxin Lin
> Sent: 05 May 2020 08:17
> To: Nitesh Turaga; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Could not read from remote repository
>  
> Hi Nitesh,
> 
> I have created another ssh key. But the same error still comes up. Are there 
> any other way I could fix the problem. Thank you!
> 
> Best regards,
> Yingxin
> 
> On 5/5/20, 1:20 am, "Nitesh Turaga"  wrote:
> 
> Hi,
> 
> Everything looks fine. It's very unusual to see that you are getting RW 
> permissions shown from `ssh -T` and you are not able to access your package. 
> 
> It could be a firewall / transient issue with your internet. But, just 
> for the sake of it could you try adding another SSH key to your 
> BiocCredentials account and then trying once again. 
> 
> Best,
> 
> Nitesh 
> 
> On 5/4/20, 11:17 AM, "Yingxin Lin"  wrote:
> 
>  Dear Nitesh,
> 
> Thank you very much for the reply. I have attached my current config 
> file and git remote screenshots. Hope this would help you to target the 
> issues.
> 
> Best regards,
> Yingxin
> 
> 
> On 5/5/20, 1:11 am, "Nitesh Turaga"  wrote:
> 
> You must be using the wrong SSH key most likely. 
> 
> If you have R W access it means the key exists but when you try 
> to "fetch" via git, it's using the wrong key. You can set up your config file 
> if you identify which SSH key is correct. 
> 
> Your git remote is malformed(formatting), if you resend it to me, 
> I can take a better look at it. 
> 
> Best,
> 
> Nitesh
> 
> On 5/3/20, 10:37 PM, "Bioc-devel on behalf of Yingxin Lin" 
>  
> wrote:
> 
> Hi,
> 
> I am trying to follow the guideline to sync the existing 
> repositories of my package scClassify, but I got the following error:
> 
> 
> (base) 192-168-1-112:scClassify yingxinlin$ git fetch --all
> Fetching origin
> From 
> https://protect-au.mimecast.com/s/KzPLCP7LAXf9y0OESzJTPV?domain=github.com
> * branchmaster -> FETCH_HEAD
> Fetching upstream
> FATAL: invalid repo name: 'packages/scClassify.git' -X -C 
> -oForwardX11Timeout=596h -oXauthLocation=/opt/X11/bin/xauth -p 12022 
> localhost'
> 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
> 
> And I have checked ssh -T 
> g...@git.bioconductor.org, which indicates 
> that I have R and W access for scClassify. The “~/.ssh/config” file is set as 
> point 15 mentioned in 
> https://protect-au.mimecast.com/s/RzOECQnMBZfgzX8jCP6fFP?domain=bioconductor.org.
> 
> Below is my remote setting:
> (base) 192-168-1-112:scClassify yingxinlin$ git remote -v
> origin  
> https://protect-au.mimecast.com/s/miZqCROND2uo7GJqHPsE2g?domain=github.com 
> (fetch)
> origin  
> https://protect-au.mimecast.com/s/miZqCROND2uo7GJqHPsE2g?domain=github.com 
> (push)
> upstream
> g...@git.bioconductor.org:packages/scClassify.git
>  (fetch)
> upstream
> g...@git.bioconductor.org:packages/scClassify.git
>  (push)
> 
> 
> I am wondering if you could provide some suggestions on how I 
> can resolve these issues. Thank you in advance!
> 
> Best regards,
> Yingxin Lin
> 
> 
> 
>  [[alternative HTML version deleted]]
> 
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> https://protect-au.mimecast.com/s/oSWnCVARKgCmO27oHJj7UB?domain=stat.ethz.ch
> 
> 
> 
> 
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Re: [Bioc-devel] Could not read from remote repository

2020-05-05 Thread Yingxin Lin 
Hi Nitesh,

I am accessing this from my home in Sydney Australia. I could probably try to 
remote access my university computer tomorrow (the University of Sydney).

Best wishes,
Yingxin

On 5/5/20, 11:47 pm, "Nitesh Turaga"  wrote:

I'm wondering if you are trying to connect from a IP address which is 
blocked by our server or your institutional/home firewall.

Do you mind telling me where you are trying to access this from?

Nitesh 

> On May 4, 2020, at 9:49 PM, Yingxin Lin  wrote:
> 
> Hi, 
>  
> Thank you for your suggestion! However it still doesn’t work (same error).
>  
> Best regards,
> Yingxin
>  
> From: "Chengyang.Ji12" 
> Date: Tuesday, 5 May 2020 at 11:44 am
> To: Yingxin Lin , Nitesh Turaga 
, "bioc-devel@r-project.org" 
> Subject: RE: [Bioc-devel] Could not read from remote repository
>  
> Try ‘git remote set-url upstream 
g...@git.bioconductor.org:packages/scClassify.git’
>  
> Sent from Mail for Windows 10
>  
> From: Yingxin Lin
> Sent: 05 May 2020 08:17
> To: Nitesh Turaga; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Could not read from remote repository
>  
> Hi Nitesh,
> 
> I have created another ssh key. But the same error still comes up. Are 
there any other way I could fix the problem. Thank you!
> 
> Best regards,
> Yingxin
> 
> On 5/5/20, 1:20 am, "Nitesh Turaga"  wrote:
> 
> Hi,
> 
> Everything looks fine. It's very unusual to see that you are getting 
RW permissions shown from `ssh -T` and you are not able to access your package. 
> 
> It could be a firewall / transient issue with your internet. But, 
just for the sake of it could you try adding another SSH key to your 
BiocCredentials account and then trying once again. 
> 
> Best,
> 
> Nitesh 
> 
> On 5/4/20, 11:17 AM, "Yingxin Lin"  wrote:
> 
>  Dear Nitesh,
> 
> Thank you very much for the reply. I have attached my current 
config file and git remote screenshots. Hope this would help you to target the 
issues.
> 
> Best regards,
> Yingxin
> 
> 
> On 5/5/20, 1:11 am, "Nitesh Turaga"  
wrote:
> 
> You must be using the wrong SSH key most likely. 
> 
> If you have R W access it means the key exists but when you 
try to "fetch" via git, it's using the wrong key. You can set up your config 
file if you identify which SSH key is correct. 
> 
> Your git remote is malformed(formatting), if you resend it to 
me, I can take a better look at it. 
> 
> Best,
> 
> Nitesh
> 
> On 5/3/20, 10:37 PM, "Bioc-devel on behalf of Yingxin Lin" 
 wrote:
> 
> Hi,
> 
> I am trying to follow the guideline to sync the existing 
repositories of my package scClassify, but I got the following error:
> 
> 
> (base) 192-168-1-112:scClassify yingxinlin$ git fetch 
--all
> Fetching origin
> From 
https://protect-au.mimecast.com/s/KFlOCROND2uoxgLjh94fIZ?domain=github.com
> * branchmaster -> FETCH_HEAD
> Fetching upstream
> FATAL: invalid repo name: 'packages/scClassify.git' -X -C 
-oForwardX11Timeout=596h -oXauthLocation=/opt/X11/bin/xauth -p 12022 localhost'
> 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
> 
> And I have checked ssh -T 
g...@git.bioconductor.org, which indicates 
that I have R and W access for scClassify. The “~/.ssh/config” file is set as 
point 15 mentioned in 
https://protect-au.mimecast.com/s/2uytCVARKgCmYPANczi9Vw?domain=bioconductor.org.
> 
> Below is my remote setting:
> (base) 192-168-1-112:scClassify yingxinlin$ git remote -v
> origin  
https://protect-au.mimecast.com/s/cl6pCWLVXkUZVyBRhKT2GS?domain=github.com 
(fetch)
> origin  
https://protect-au.mimecast.com/s/cl6pCWLVXkUZVyBRhKT2GS?domain=github.com 
(push)
> upstream
g...@git.bioconductor.org:packages/scClassify.git
 (fetch)
> upstream
g...@git.bioconductor.org:packages/scClassify.git
 (push)
> 
> 
> I am wondering if you could provide some suggestions on 
how I can resolve these issues. Than

[Bioc-devel] 3.11 builds: no new report since last Friday

2020-05-05 Thread Hervé Pagès 

Fellow Bioconductor developers,

The release builds (3.11 builds) are experiencing problems since last 
Friday (April 30) which is why the latest published report is still from 
that day:


  https://bioconductor.org/checkResults/3.11/bioc-LATEST/

We're working on it and hopefully we'll get a new report before the end 
of the week.


Thanks for your comprehension and sorry for the inconvenience.

Best,
H.

--
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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