[Bioc-devel] EXTERNAL: troubles with fetching Bioconductor github

[Felix Ernst]

Hi all,

I had a problem accessing git using bioconductor yesterday as well from a Windows
1803 PC. With the same PC it worked in March, but not now.

The last bit about the version is important since the OpenSSH form Microsoft
is apparently in 1803 the default. I don't know, how the setup was
previously. 

How I diagnosed the problem:
- ssh-add -l does not show previously added keys (powershell or git bash
terminal in rstudio)
- re-adding keys works and is persistent after a restart without a .bashrc
script or anything ()
- ssh -T works
- git fetch does not

The last two information means, that there are to key stores at play.

There are two solutions, which worked for me:
- copy and rename the key file to ~/.ssh/id_rsa (git finds it then and ask
for passphrase. The config file in ~/.ssh/ was ignored)
- change core.sshCommand option in .gitconfig to
"C:/Windows/System32/OpenSSH/ssh.exe" (git uses the stored keys added with
ssh-add)

I don't know, where I found all the bits of information, but it was
basically a lot of googling. I am also not sure, whether this a specific
problem to my machine or a general Windows 1803 issue. I am also not sure,
what the underlying cause for the behaviour is. It is more a fix for the
symptom, not a cure.

Hope this helps some people.

Best regards,
Felix

---
Felix Ernst, PhD
Université Libre de Bruxelles
RNA MOLECULAR BIOLOGY
BIOPARK Charleroi Brussels-South CAMPUS
Rue Profs Jeener & Brachet, 12
B-6041 Charleroi - Gosselies
BELGIUM
+32(2)650 9774 (office phone)
felix.ernst using ulb.ac.be



-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Turaga,
Nitesh
Sent: Freitag, 3. August 2018 12:21
To: Piotr <piotr.dittwald using gmail.com>
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] EXTERNAL: troubles with fetching Bioconductor
github

No, I'm not aware of any such issues.

Maybe someone else in the community can chip in with some information about
this.

Best,

Nitesh

Get Outlook for Android<https://aka.ms/ghei36>

________________________________
From: Piotr <piotr.dittwald using gmail.com>
Sent: Friday, August 3, 2018 5:22:23 AM
To: Turaga, Nitesh
Cc: bioc-devel using r-project.org
Subject: Re: EXTERNAL: [Bioc-devel] troubles with fetching Bioconductor
github

Dear Nitesh,
now works ok, although I did not change anything.
maybe there is a time when I should not connect with Bioconductor git?


Piotr

On Thu, Aug 2, 2018 at 11:35 PM Turaga, Nitesh
<Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
Please copy the result of this,

        git remote -v

and send it to us so we have more information.

http://bioconductor.org/developers/how-to/git/faq/ , check #14

Best,

Nitesh

> On Aug 2, 2018, at 5:14 PM, Piotr
<piotr.dittwald using gmail.com<mailto:piotr.dittwald using gmail.com>> wrote:
>
> Dear All,
>
> I try to follow instruction here:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositor
> ies/
>
> however, I find the following
> git fetch --all
> Fetching origin
> Fetching upstream
> sign_and_send_pubkey: signing failed: agent refused operation 
> Permission denied (publickey).
> 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 have correct ssh keys and I am almost sure about 1 hr ago it worked.
> What might have happened?
>
> I created new ssh key but it is still not working
>
> Kind regards,
> Piotr
>
>       [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list 
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