[Bioc-devel] CRAN dependency missing

Hello, The package GoogleGenomics has been failing the CHECK stage because of a missing CRAN dependency (RProtoBuf ) in the Suggests section.

Re: [Bioc-devel] git and public keys

Good day, Is the private key in a location other than the default SSH key folders? If so, use the ssh-add command to have the SSH agent know about it. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

Re: [Bioc-devel] REMP package commit and update

Thank you Martin. I tried again and here are the outputs: yzk256@FSMMJ047AEV MINGW64 /d/Box Sync/Bioconductor/REMP (master) $ git checkout RELEASE_3_5 Branch RELEASE_3_5 set up to track remote branch RELEASE_3_5 from upstream. Switched to a new branch 'RELEASE_3_5' yzk256@FSMMJ047AEV MINGW64 /d/B

Re: [Bioc-devel] REMP package commit and update

On 08/22/2017 06:45 PM, Yinan Zheng wrote: Hi Martin, I have moved my package “REMP” maintenance workflow to git source control as instructed and I committed a few bug fixes to both devel and release last week. Everything works well. Just wonder which site and how long will I be able to see t

[Bioc-devel] REMP package commit and update

Hi Martin, I have moved my package "REMP" maintenance workflow to git source control as instructed and I committed a few bug fixes to both devel and release last week. Everything works well. Just wonder which site and how long will I be able to see the changes take effect. Thanks. Yinan Zhen

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

On 08/22/2017 04:33 PM, Andrzej Oleś wrote: Hi Martin, Nitesh, thanks for recreating the EBImage repo! I've noticed that even though the operation helped to fix one commit where the user was previously unknown: commit b67438e41b9b7dc62db8c403ee8afd673bd5c0a0 Author: unknown mailto:

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Hi Martin, Nitesh, thanks for recreating the EBImage repo! I've noticed that even though the operation helped to fix one commit where the user was previously unknown: commit b67438e41b9b7dc62db8c403ee8afd673bd5c0a0 Author: unknown Date: Fri Apr 21 13:47:14 2006 + JWM:Added

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Never mind. It's all Patrick Aboyoun, for whom I think this should persist. Jim On Tue, Aug 22, 2017 at 4:13 PM, James W. MacDonald wrote: > Hi Martin and Nitesh, > > > On Tue, Aug 22, 2017 at 10:09 AM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > >> Thanks for your patience. We up

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Hi Martin and Nitesh, On Tue, Aug 22, 2017 at 10:09 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > Thanks for your patience. We updated the repositories below; if you cloned > one of these repositories, you will need to DELETE your clone, and create a > new clone. If you have added

[Bioc-devel] IP blocking on web site

Hi, We're increasing security on the web site, www.bioconductor.org, to prevent http flooding and other attacks. Over the past week I've been monitoring a rule that identifies IPs making > 400 requests per minute. It looks like this is catching just rogue IPs (good

Re: [Bioc-devel] ViennaRNA and Biopython in R package

On 08/21/2017 06:39 PM, carl fakhry wrote: Hi Martin, I wrote an R package which has functions that invoke system commands. Part of the system commands which I am using is calls to the ViennaRNA package (https://www.tbi.univie.ac.at/RNA/#) and calls to python which requires a specific pytho

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

On 08/22/2017 09:24 AM, Andrzej Oleś wrote: Hi Martin, I've just noticed that EBImage, which is on the list of packages not to be regenerated, is actually affected too (according to the output below). Therefore, I would like to ask to have it regenerated for the sake of clean commit history.

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Thanks for your patience. We updated the repositories below; if you cloned one of these repositories, you will need to DELETE your clone, and create a new clone. If you have added a remote and pulled from these repositories, you will need to redo the sync. See https://bioconductor.org/developer

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Hi Martin, I've just noticed that EBImage, which is on the list of packages not to be regenerated, is actually affected too (according to the output below). Therefore, I would like to ask to have it regenerated for the sake of clean commit history. Thanks, Andrzej [oles@localhost EBImage]$ git l

Re: [Bioc-devel] Trying to clone my repo but my key is not recognized.

Hi Martin, my bad, should have given you that info immediately. Thank you for the extensive info, turns out I registered only the key on my computer at home, not here at work. Your info helped me register the other key as well. Thank you again. Cheers Joris On Tue, Aug 22, 2017 at 12:45 PM, Mart

Re: [Bioc-devel] Trying to clone my repo but my key is not recognized.

On 08/22/2017 06:07 AM, Joris Meys wrote: As said, this is what I got after git fetch upstream As per instructions here: http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ (I did carry out the previous steps as well). I guess I'm looking for more information, for instance y

Re: [Bioc-devel] Trying to clone my repo but my key is not recognized.

As said, this is what I got after git fetch upstream As per instructions here: http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ (I did carry out the previous steps as well). Cheers Joris On Tue, Aug 22, 2017 at 11:24 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote

Re: [Bioc-devel] Trying to clone my repo but my key is not recognized.

On 08/22/2017 04:59 AM, Joris Meys wrote: Hi, I sent my public key as registered in my github account to you a while ago, but when I tried to clone my repository, I get the following error message after git fetch upstream: - The authenticity of host 'git.bioconductor.org (34.192.48.227)' c

[Bioc-devel] Trying to clone my repo but my key is not recognized.

Hi, I sent my public key as registered in my github account to you a while ago, but when I tried to clone my repository, I get the following error message after git fetch upstream: - The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be established. ECDSA key fingerprint i

[Bioc-devel] git and public keys

Hi, folks, I'm yet another lost soul whose public key doesn't seem to be providing access to the new git repository. svn username: g.brown packages: DiffBind, GreyListChIP I submitted my key (3rd try) Sunday, so the 24 hour cycle should not be a factor. So... some questions: 1) Do you suppor