flowCL - svn conversion to Github
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Last seen 3.5 years ago

Hello, I am having a lot of difficulties with getting my updated version of flowCL on bioconductor. My issue is mainly about the following error message:

permission denied (publickey)
fatal: Could not read from remote repository.

Below is my conversation with Github. They say it is an issue with Bioconductor.

Also I noticed today that the flowCL bioconductor mirror is not working: https://github.com/Bioconductor-mirror/flowCL

I have the newest flowCL code on my Github here: https://github.com/jmeskas/flowCL

Perhaps the reason for the mirror to be disabled is because my package has not been working for a few months. I have been in contact with Lori Shephard from Bioconductor about not removing flowCL and giving me more time.

I have tried both: "http://bioconductor.org/developers/how-to/git/maintain-bioc-only/" and "http://bioconductor.org/developers/how-to/git/sync-existing-repositories/". But both are giving similar errors/issues.

Thank you,



Hi Justin,

Thanks for sending that over! From your output, it looks like you're successfully connecting to GitHub's servers via SSH:

Hi jmeskas! You've successfully authenticated, but GitHub does not provide shell access.

Looking at your upstream output from git remote -v, the repository you're trying to fetch from is on git.bioconductor.org and not github.com. Since your connection to GitHub appears to be fine, I'm afraid there's not much else we can do on our end – I recommend consulting Bioconductor's support for further assistance.


That being said, the tips in the article Shawna linked might still be useful if you can figure out how they apply to Bioconductor – the first thing I'd check would be to ensure your SSH public key is set up on Bioconductor.

I hope that helps clarify things! Feel free to let us know if you have any other questions specific to GitHub.



Hi Shawna,

Thank you for your quick reply. I hadn't gone through the link you sent me. I have now. The part titled "Verify the public key is attached to your account​" doesn't seem to be working. I get the following:

jmeskas@bioinfo20l:/code/Projects/Packages/flowCL_github/flowCL$ ssh-add -l -E md5
The agent has no identities.
jmeskas@bioinfo20l:/code/Projects/Packages/flowCL_github/flowCL$ ssh-add -l
The agent has no identities.

​The printouts you asked for are below.

Thank you for your help,


ssh -vT git@github.com

jmeskas@bioinfo20l:/code/Projects/Packages/flowCL_github/flowCL$ ssh -vT git@github.com
OpenSSH_6.6.1, OpenSSL 1.0.1f 6 Jan 2014
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: Applying options for *
debug1: Connecting to github.com [] port 22.
debug1: Connection established.
debug1: identity file /home/CRC/jmeskas/.ssh/id_rsa type 1
debug1: identity file /home/CRC/jmeskas/.ssh/id_rsa-cert type -1
debug1: identity file /home/CRC/jmeskas/.ssh/id_dsa type 2
debug1: identity file /home/CRC/jmeskas/.ssh/id_dsa-cert type -1
debug1: identity file /home/CRC/jmeskas/.ssh/id_ecdsa type -1
debug1: identity file /home/CRC/jmeskas/.ssh/id_ecdsa-cert type -1
debug1: identity file /home/CRC/jmeskas/.ssh/id_ed25519 type -1
debug1: identity file /home/CRC/jmeskas/.ssh/id_ed25519-cert type -1
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_6.6.1p1 Ubuntu-2ubuntu2.8
debug1: Remote protocol version 2.0, remote software version libssh_0.7.0
debug1: no match: libssh_0.7.0
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug1: kex: server->client aes128-ctr hmac-sha1 none
debug1: kex: client->server aes128-ctr hmac-sha1 none
debug1: sending SSH2_MSG_KEX_ECDH_INIT
debug1: expecting SSH2_MSG_KEX_ECDH_REPLY
debug1: Server host key: RSA 16:27:ac:a5:76:28:2d:36:63:1b:56:4d:eb:df:a6:48
debug1: Host 'github.com' is known and matches the RSA host key.
debug1: Found key in /home/CRC/jmeskas/.ssh/known_hosts:21
debug1: ssh_rsa_verify: signature correct
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug1: Authentications that can continue: publickey
debug1: Next authentication method: publickey
debug1: Offering RSA public key: /home/CRC/jmeskas/.ssh/id_rsa
debug1: Server accepts key: pkalg ssh-rsa blen 535
debug1: key_parse_private2: missing begin marker
debug1: key_parse_private_pem: PEM_read_PrivateKey failed
debug1: read PEM private key done: type 
Enter passphrase for key '/home/CRC/jmeskas/.ssh/id_rsa':
debug1: key_parse_private2: missing begin marker
debug1: read PEM private key done: type RSA
debug1: Authentication succeeded (publickey).
Authenticated to github.com ([]:22).
debug1: channel 0: new [client-session]
debug1: Entering interactive session.
debug1: Sending environment.
debug1: Sending env LANG = en_CA.UTF-8
Hi jmeskas! You've successfully authenticated, but GitHub does not provide shell access.
debug1: client_input_channel_req: channel 0 rtype exit-status reply 0
debug1: channel 0: free: client-session, nchannels 1
Transferred: sent 4080, received 2112 bytes, in 0.1 seconds
Bytes per second: sent 30113.4, received 15588.1
debug1: Exit status 1

git remote -v

origin https://github.com/jmeskas/flowCL.git (fetch)
origin https://github.com/jmeskas/flowCL.git (push)
upstream git@git.bioconductor.org:packages/flowCL.git (fetch)
upstream git@git.bioconductor.org:packages/flowCL.git (push)

ssh-add -l

jmeskas@bioinfo20l:/code/Projects/Packages/flowCL_github/flowCL$ ssh-add -l
The agent has no identities.

ssh-keygen -E md5 -lf ~/.ssh/id_rsa.pub

jmeskas@bioinfo20l:/code/Projects/Packages/flowCL_github/flowCL$ ssh-keygen -E md5 -lf ~/.ssh/id_rsa.pub
unknown option -- E
usage: ssh-keygen [options]
-A Generate non-existent host keys for all key types.

flowCL git-svn bridge github • 534 views
Entering edit mode
Last seen 3 months ago
United States

Hi Justin,

The Bioconductor-mirror has been deprecated and removed. See this post to follow -- https://stat.ethz.ch/pipermail/bioc-devel/2017-August/011329.html 

Please submit your key to https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5YyQm5UD4pcs1dhEs/edit. As pointed out in the FAQ section on our website for the new GIT server http://bioconductor.org/developers/how-to/git/faq (Point #3). 

Once you submit, we'll accept your key, and you will get access. You have to submit your SVN ID (which was given to you previously) in that google form, so that the application can correctly link your package to your SVN ID. 




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