[Bioc-devel] updating Bioconductor package that is already on Github

Thanks so much Nitesh! I had submitted my public key last time I did this
(a few months ago) so I thought I didn't have to do it again. However, for
whatever reason, the public key you sent is a bit different from mine (not
sure why, since I haven't generated any more since then). In any case, I
just used the google form to submit my public key.

Cheers,
Simina

On Fri, Jan 26, 2018 at 12:44 PM, Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:

Hi Simina,

I?m assuming your keys are stored in the folder ?.ssh?. If that is the
case, try,

         ssh-keygen -y -e -f <private_key>

That command will print out a public key. If that public key is the same
as the one I?ve sent you, they you can use that. (Remember that public
keys, don?t have ?.pub? ending. If your public key is called ?id_rsa.pub?
then your private key is most likely, ?id_rsa?).

If you have to configure your git login, please follow the link below to
make sure that the same key is used

http://bioconductor.org/developers/how-to/git/faq/

Best,

Nitesh

On Jan 26, 2018, at 12:36 PM, Simina Boca <smb310 at georgetown.edu>

wrote:

Thank you Nitesh! Where should I use the private key? I only see the

public key mentioned here: http://bioconductor.org/develo
pers/how-to/git/maintain-github-bioc/ Sorry if I'm missing something
very obvious!

Best,
Simina

On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh <

Nitesh.Turaga at roswellpark.org> wrote:

Hi

You are using the wrong key.

The key we have on file for you is

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAACAQDk1ywCtjVfC0wewYRCvzEiAac3so7n

nRISC6xj3RkEerAUaOHHSA2RjlrG60TYjnEZGPyeN79oKNDP0NhCelsNR2us
gviCVeS04Qs2RhyzQVf5iNP/pJIBt21pwIvsW3CBqB1bTECUG8E9pK3Gtm77
uyRAwLImJtH1RioJ1JpGWKZ0r0ZU0O9c//zwr+Ae8OB94kSEuQ0yTXZj1nHf
zL3vHsDtI8SsF3UE22RhS/sClW7s3raAlGNbmVdURZ2726JW2jIm40jeLDSc
dfO8UGEr5bWgVo7bnl6bzYUBsS2l8I2DZZHKIC+A1wBngNFpKNJ6dTpKzadk
RudGbvU5qcIoX2zQNGzs/IyTh3LnX1TbCR1TbG/zC1BwoLB64yy
jYI0O2nb+ZhhRyXyoljX6AtoMgr16vwUfO+ts3HoD060WTFx29jucqV8rtYX
NhDzZmqQs8Z5Ajk++8A0x7fxtuAR1FTVNByaTmH3PAIW6WU9wXXpQEz72mSm
7FpQgQDkOfjRBQKqRnGbhaay8qltMYaqzjQLA8pBl7YIa5Km5UvyvV2DbAHS
0B1R8w7c8L3kmPj5MPJZdAcRc6Nc0ByE4pYVwv8mosMB4gt12Lzuj0hz5ID9
SDUPq8QghGJiWhVybZpKafu8VQ7E5QvqBC6DHhpKhdodt16BymxkEWk380yODUQ==

You should use a private key corresponding to that public key.

Best,

Nitesh

On Jan 26, 2018, at 12:05 PM, Simina Boca <smb310 at georgetown.edu>

wrote:

Dear all,
Thank you to Sean, Lori, and Nitesh for helping me out with a package

update last year. I'm now trying to update another package, MultiMed. I
have it set up on Github https://github.com/SiminaB/MultiMed - you can
see that the contributors are Marc, Herve, and Dan Tenenbaum.

However, I get the same error as I got before when doing "git push

upstream master":

Warning: Permanently added 'git.bioconductor.org,34.192.48.227'

(ECDSA) to the list of known hosts.

Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
FATAL: W any packages/swfdr SiminaB 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 submit anything else or should BioC already know that

I'm the same person who is managing these packages?

Thanks so much!

Cheers,
Simina


On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh <

Nitesh.Turaga at roswellpark.org> wrote:

Hi Simina,

Please try again now.

The issue was you didn?t submit your SVN ID ?s.boca?. This is needed

for people who have been maintainers before the Git transition, to
associate your key to the package.

For new packages this issue doesn?t apply, because we just collect

their Github IDs.

Hope this helps.

Best,

Nitesh

On Sep 11, 2017, at 2:50 PM, Simina Boca <smb310 at georgetown.edu>

wrote:

Thank you again Sean and Lori! I am now past that initial stage. I

now have

to resolve merge conflicts, primarily in the DESCRIPTION file. When
following the instructions here http://bioconductor.org/
developers/how-to/git/resolve-conflicts/ however, I ended up

getting the

error below:

~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git push upstream

master

Warning: Permanently added 'git.bioconductor.org,34.192.48.227'

(ECDSA) to

the list of known hosts.
Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
FATAL: W any packages/swfdr SiminaB 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.

Thank you so much!

Best,
Simina


On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca <smb310 at georgetown.edu>

wrote:

Thank you so much Sean and Lori! For some reason I thought the ssh

key

part was only relevant if the package was submitted via svn, which

is why i

had overlooked those instructions initially.

Cheers,
Simina

On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:

Have you submitted your ssh key


https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
o4tNufs0ziNyNmexegNZgNieIovbAA/viewform

<https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480

vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>

git / svn transition: ssh keys
<https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480

vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>

docs.google.com
Use this form to link your existing svn credentials with access
permissions to the new Bioconductor git repository. To do this,

we need an

ssh public key. You might have added these to github, see
https://github.com/your-github-id.keys. Alternatively, you may

provide

the ssh public key directly, e.g., copy-pasting

~/.ssh/id_rsa.pub. To

generate ssh key pairs, see https://help.github.com/articl
es/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
------------------------------
*From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf

of

Simina Boca <smb310 at georgetown.edu>
*Sent:* Tuesday, September 5, 2017 11:40:37 PM
*To:* bioc-devel at r-project.org
*Subject:* [Bioc-devel] updating Bioconductor package that is

already on

Github

Dear all,

I hope this isn't a duplicate of another question. Here goes:

- I would like to update my swfdr package, which is already on
Bioconductor. It is also on Github and my submission process was

via

opening an issue at https://github.com/Bioconducto
r/Contributions/issues/213

- At this point there are some slight differences between the

Github and

Bioconductor versions, for example the Bioconductor version

number got

automatically bumped to 1.0.0 upon acceptance

- I would like to first synchronize what is on Github to have the

current

version that is on Bioconductor before updating and also include

any

updates in the next version of the package on Bioconductor

- I did "git remote add upstream git at git.bioconductor.org:packa
ges/swfdr.git"
as per some of the instructions for developers, so that now I

have:

~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git remote -v
origin  https://github.com/leekgroup/swfdr.git (fetch)
origin  https://github.com/leekgroup/swfdr.git (push)
upstream        git at git.bioconductor.org:packages/swfdr.git

(fetch)

upstream        git at git.bioconductor.org:packages/swfdr.git

(push)

*but* when I try to fetch upstream content, via:
git fetch upstream

I get an error:
~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git fetch upstream
Warning: Permanently added 'git.bioconductor.org,34.192.48.227'

(ECDSA)

to
the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights

Am I missing something here? Alternatively, I suppose I can just

make the

changes I want and simply open another issue, although it would

be nice to

have an easy to sync it with what is already on Bioconductor.

Thank you in advance for your help and I apologize if I missed

anything

obvious!

Cheers,
Simina

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics |
Georgetown
University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive

Cancer

Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

       [[alternative HTML version deleted]]

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 prohibited. If you

have

received this message in error, please notify the sender

immediately by

e-mail and delete this email message from your computer. Thank

you.

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics |
Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive

Cancer

Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics |

Georgetown

University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive

Cancer Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

      [[alternative HTML version deleted]]

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 prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics |

Georgetown University Medical Center

Cancer Prevention and Control Program | Lombardi Comprehensive Cancer

Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

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 prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics |

Georgetown University Medical Center

Cancer Prevention and Control Program | Lombardi Comprehensive Cancer

Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

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 prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics |
Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca