Re: [Bioc-devel] Warning for Matrix during R CMD Check

Likely you or one of your dependent packages makes use of Matrix without using import() in the NAMESPACE file. Email formatting makes it hard to tell exactly what is going on; make sure you are sending email in plain text, and that the build / check steps are done at the command line rather

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

On 08/21/2017 05:30 PM, Stephanie M. Gogarten wrote: I was actually thinking of SeqVarTools, since I have local commits that I'm not ready to push yet. GENESIS and GWASdata could be put on the "do not regenerate" list also - they have no unknown users, and I'd rather not go through all the

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

I was actually thinking of SeqVarTools, since I have local commits that I'm not ready to push yet. GENESIS and GWASdata could be put on the "do not regenerate" list also - they have no unknown users, and I'd rather not go through all the steps again if I don't have to. thanks, Stephanie On

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

Hi Martin, Can you check DEGreport? I have made commits already but is not in your list. I am off the office, so cannot check anything until tomorrow. Thanks sent not from my computer > On Aug 21, 2017, at 16:23, Martin Morgan > wrote: > >> On 08/21/2017

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

On 08/21/2017 03:17 PM, Stephanie M. Gogarten wrote: If we followed the steps here: https://www.bioconductor.org/developers/how-to/git/maintain-github-bioc/ How much, if any, of this will need to be redone after the repositories are regenerated? In particular, if I don't have an unknown user,

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

If we followed the steps here: https://www.bioconductor.org/developers/how-to/git/maintain-github-bioc/ How much, if any, of this will need to be redone after the repositories are regenerated? In particular, if I don't have an unknown user, will the regenerated commits be equal to the previous

Re: [Bioc-devel] Search on www.bioconductor.org fails

I've restarted the service and the search is fixed (for the time being). The website search is powered by solr. We continue to have problems with this service (or it's child processes) dying unexpectedly. An initial look at the logs is not very informative and I haven't had a chance to dig into

Re: [Bioc-devel] git / svn transition: ssh keys

Thanks, Nitesh! Best regards, Julie On 8/21/17, 12:38 PM, "Turaga, Nitesh" wrote: Hi, Your key is not in the system yet. It currently runs on a 24 hour cycle till we perfect the system. In the meantime if you would like read-only

Re: [Bioc-devel] git / svn transition: ssh keys

Hi, Your key is not in the system yet. It currently runs on a 24 hour cycle till we perfect the system. In the meantime if you would like read-only access you can use HTTPS. ``` git clone https://git.bioconductor.org/packages/CRISPRseek ``` Best, Nitesh > On Aug 21, 2017, at 11:25 AM,

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

Hi git transitioners -- We'd like to regenerate git repositories from svn. This is because some svn user ids were mapped to 'unknown' git users, so that contributors would not be credited accurately. This will invalidate any local clones made from git.bioconductor.org. Our plan is to

Re: [Bioc-devel] Search on www.bioconductor.org fails

Thanks for the report. I'll look into it. Valerie On 08/21/2017 08:07 AM, Kevin RUE wrote: Hi, I got the same issue yesterday if that can help track down the origin; it wasn't just today. I thought it was a transient glitch and didn't report it immediately. I hadn't checked today yet. Best

Re: [Bioc-devel] Git transition is happening August 16th.

Hi Matthew, > On Aug 20, 2017, at 10:26 PM, Matthew Myint > wrote: > > Hi, thanks for the transition! Its nice to work from git without the need to > use svn. > > Anyway, I have a couple of questions regarding the usage of git > > 1) When syncing my own GitHub

Re: [Bioc-devel] git / svn transition: ssh keys

Dear Nitesh, I submitted my ssh keys. However, I cannot download my packages from github. Could you please help? Thanks! # juliezhumac2017:Trunk ZHUJ$ git clone g...@git.bioconductor.org:packages/CRISPRseek Cloning into 'CRISPRseek'... Permission denied (publickey). fatal: Could not read

Re: [Bioc-devel] Search on www.bioconductor.org fails

Hi, I got the same issue yesterday if that can help track down the origin; it wasn't just today. I thought it was a transient glitch and didn't report it immediately. I hadn't checked today yet. Best Kevin On Mon, Aug 21, 2017 at 3:58 PM, Laurent Gatto wrote: > > Dear

[Bioc-devel] Search on www.bioconductor.org fails

Dear Bioconductor admins, When using the search box on www.bioconductor.org, I systematically get the following error A timeout or invalid search term resulted in an error. Best wishes, Laurent -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/

Re: [Bioc-devel] Generate valid SSH keys for the bioc-git server!

The GitHub ID and the associated key was added to the bios-git server on August 18th. You’d need to use that specific public key to access the server. Best, Nitesh > On Aug 21, 2017, at 9:35 AM, Turaga, Nitesh > wrote: > > Hi Dario, > > Did you upload a new

Re: [Bioc-devel] Generate valid SSH keys for the bioc-git server!

Hi Dario, Did you upload a new key? I’m attaching the thread you need to follow up on. This was sent out specifically in response to the key you submitted. Best, Nitesh —— —— —— Thanks! It works now. Kylie ~~~ Kylie Ariel Bemis Future

Re: [Bioc-devel] Odd version in release

Ok, I'll do that. Thanks *Bernat Gel Moreno* Bioinformatician Hereditary Cancer Program Program of Predictive and Personalized Medicine of Cancer (PMPPC) Germans Trias i Pujol Research Institute (IGTP) Campus Can Ruti Carretera de Can Ruti, Camí de les Escoles s/n 08916 Badalona, Barcelona,

Re: [Bioc-devel] Odd version in release

On 08/21/2017 09:22 AM, Bernat Gel wrote: Hi, It seems like a couple of months ago I fixed a bug in release version of karyoploteR and pushed a DESCRIPTION with the wrong version number, going from 1.0.1 to 1.1.6 (the one in devel at the moment). So now both devel and release are in 1.1.*

[Bioc-devel] Odd version in release

Hi, It seems like a couple of months ago I fixed a bug in release version of karyoploteR and pushed a DESCRIPTION with the wrong version number, going from 1.0.1 to 1.1.6 (the one in devel at the moment). So now both devel and release are in 1.1.* Should I do something to get release back

Re: [Bioc-devel] Generate valid SSH keys for the bioc-git server!

Good day, I filled out the form on Thursday, but can't fetch the repository. $ git fetch upstream Permission denied (publickey). fatal: Could not read from remote repository. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia