Hi Nitesh,
I think I have successfully updated the NuPoP package through github. Please
see the output below.
But since this is the first time to use github for update Bioconductor package,
I would very appreciate if you
could take a look. Or if there is anything else I need to do, please also
No worries at all. Thank you for letting me know.
Laurent
From: Pages, Herve
Sent: 28 May 2019 22:24
To: Laurent Gatto; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] index of Bioc repository unavailable
Hi Laurent,
This is temporary. We're in the p
Hi Laurent,
This is temporary. We're in the process of creating the 3.10 annotation
repo by "forking" the 3.9 annotation repo. As part of this process, we
run a script that generates the PACKAGES index for the new 3.10
annotation repo. The process will take a few more hours before it
completes.
Travis recently started to fail for Bioc devel (see [0] and [1] for another
possibly related report), which seems to related to a warning in
BiocManager::available():
> BiocManager::version()
[1] ‘3.10’
> str(BiocManager::available())
Warning: unable to access index for repository
https://bioco
No idea Jiping. I'm not sure I have any suggestions regarding that problem.
> On May 28, 2019, at 2:55 PM, Jiping Wang wrote:
>
> It's interesting that if I logged in this computer by different account, ssh
> -T git g...@bioconductor.org does return a list of packages.
> So there might be so
Hi,
I restarted my computer, it works fine now. that's very strange. Thanks for
help!
Best,
jiping
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It's interesting that if I logged in this computer by different account, ssh -T
git g...@bioconductor.org does return a list of packages.
So there might be some settings under my current user account on my computer.
What could it be? Do you have an suggestions?
On 5/28/19, 12:47 PM, "Turaga, Ni
Hi Nitesh,
Thanks for help. I am confused about " It seems you authenticate to GitHub
using HTTP protocol, so most likely you enter a password."
When I do ssh to github, I received he authentication. Does it mean I am not
using HTTP? I thought I am using SSH here. I didn't enter password ei
I see, I based my assumption that you access Github via HTTP protocol as per
your remotes.
bash-3.2$ git remote -v
origin https://github.com/jipingw/NuPoP (fetch)
origin https://github.com/jipingw/NuPoP (push)
upstreamg...@git.bioconductor.org:packages/NuPoP (fetch)
upstreamg...
At this point, I'd suggest two things,
1. Create a new key, and try to use that new key by adding it in your
BiocCredentials account.
2. Use a different computer? It might be something else entirely which we are
missing.
I've double checked everything on Bioconductor's end of things, and it
On 5/28/19 07:57, Pariksheet Nanda wrote:
> Hi Hervé,
>
> Indeed, an IRanges with 2^31 elements is 17.1 GB.
> The reason I was interested in IRanges, was GRanges are needed to create
> the BSgenome::BSgenomeViews.
> More broadly, my use case is chopping up a large genome into a fixed
> kmer size
Hi Turaga,
I noticed there are two packages under my name (see below). But I should only
have access to NuPoP. The other package was from a different contributor who
has same initial as me (J. Wang, for Jing Wang). I don't whether that's the
issue. The second key you listed below is my key.
> Kasper Daniel Hansen
> on Fri, 24 May 2019 10:31:31 -0400 writes:
> [ This is a crazy bug where you have to increase optimization. ]
> I some to add here. I am involved in at least two packages which requires
> overriding the optimization switch to downgrade optimization
Ok, now that we know that there remotes have been set up right, I'd like to
also make sure that the private keys you are using correspond to the public
keys we have on file.
cat */j.wang*
ssh-rsa
B3NzaC1yc2EDAQABAAACAQDEqshGh957
Hi Hervé,
Indeed, an IRanges with 2^31 elements is 17.1 GB.
The reason I was interested in IRanges, was GRanges are needed to create
the BSgenome::BSgenomeViews.
More broadly, my use case is chopping up a large genome into a fixed kmer
size so that repetitive "unmappable" regions can be removed.
h
bash-3.2$ssh -T g...@git.bioconductor.org
g...@git.bioconductor.org: Permission denied (publickey).
bash-3.2$ git remote -v
origin https://github.com/jipingw/NuPoP (fetch)
origin https://github.com/jipingw/NuPoP (push)
upstreamg...@git.bioconductor.org:packages/NuPoP (fetch)
upstream
Hi,
Can I see the output of your (inside your package repository, to check if you
have correctly set up your remotes)?
git remote -v
http://bioconductor.org/developers/how-to/git/faq/ #14 is very important for me
to help your trouble short.
Best,
Nitesh
This email message may co
Hi,
Please activate your account in the BiocCredentials app. You can use your new
email to activate it and add SSH keys da...@bccrc.ca.
Once you activate, and add SSH keys, you should have access to your package.
Best,
Nitesh
This email message may contain legally privileged and/or confide
Hi Shuyu,
The first SSH key you added in your BiocCredentials account is not a valid SSH
key. The rest of your 3 keys seem to be valid, please try to use one of those.
1. Based on your logs, from `ssh -Tv g...@git.bioconductor.org` you are not
using the keys which you have submitted.
2. I wo
Hi Pariksheet,
On 5/25/19 12:49, Pariksheet Nanda wrote:
Hello,
R 3.0 added support for long vectors, but it's not yet possible to use them
with IRanges. Without long vector support it's not possible to construct
an IRanges object with more than 2^31 elements:
ir <- IRanges(start = 1:(2^31
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