[Bioc-devel] git push to devel versions

Hi all, The new release of Bioconductor is coming soon and I would like to be sure that I am doing the right things with Git. I am a bit confused with the Git commands to use in order to update the devel versions of my packages Prostar and DAPAR and DAPARdata (which is an experimentData packa

Re: [Bioc-devel] EXTERNAL: change maintainer of a package

Sorry for the oversight; I responded to the mail at packages@ just now. Martin On 10/10/2017 02:44 PM, Christoph Bernau wrote: Hi, I would like to appoint a new maintainer for my package and could not find any documentation on this topic. I was told to send an email mentioning both new and old

Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

On 10/10/2017 01:56 PM, greg gloor wrote: I too am having problems with this. I checked to make sure I had an ssh public key on github, I submitted my svn id (gloor.g) and re-submitted the form last Friday. Today I did the following, and am still not able to access the upstream repository: se

Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

Hi Nitesh: Thank you for sending these along. All of our public keys match the three keys you sent to me, and we were able to sync from my Desktop computer; access from our two VMs failed, suggesting that it’s an issue on that side of things. Thanks again for your help. I’ll let you know if we

Re: [Bioc-devel] EXTERNAL: Re: Git permission denied (publickey)

On 2017-10-10 22:48:43, martin.mor...@roswellpark.org wrote: > On 10/10/2017 04:43 PM, Sebastian Gibb wrote: > > Dear Biocondcutor admins, > > > > I am the maintainer of the cleaver package (and a co-maintainer of MSnbase, > > Pbase, synapter). As many other user mentioned here I got the same > >

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Done. Do you see it? On Tue, Oct 10, 2017 at 1:37 PM Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > I believe you have the wrong form. > https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5YyQm5UD4pcs1dhEs > (this is the correct link). > > http://master.bioconductor.org/develope

Re: [Bioc-devel] EXTERNAL: Re: Git permission denied (publickey)

On 10/10/2017 04:43 PM, Sebastian Gibb wrote: Dear Biocondcutor admins, I am the maintainer of the cleaver package (and a co-maintainer of MSnbase, Pbase, synapter). As many other user mentioned here I got the same "permission denied (publickey)" error message. I already submit my mail address,

Re: [Bioc-devel] EXTERNAL: Bioconductor support for explicit SSE vectorization

On 10/10/2017 04:33 PM, Benjamin Callahan wrote: Hi, In the BioC 3.6 release of the dada2 package, I've added sections of C code that are explicitly vectorized using Intel SSE2 intrinsics. I've finally got the package building on all three platforms, but to get WIndows/MinGW building, I've had to

Re: [Bioc-devel] Git permission denied (publickey)

Dear Biocondcutor admins, I am the maintainer of the cleaver package (and a co-maintainer of MSnbase, Pbase, synapter). As many other user mentioned here I got the same "permission denied (publickey)" error message. I already submit my mail address, svn username and github id via the google form.

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

I believe you have the wrong form. https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5YyQm5UD4pcs1dhEs (this is the correct link). http://master.bioconductor.org/developers/how-to/git/faq/ (point #3) Best, Nitesh > On Oct 10, 2017, at 4:30 PM, Vladislav Petyuk wrote: > > Here

[Bioc-devel] Bioconductor support for explicit SSE vectorization

Hi, In the BioC 3.6 release of the dada2 package, I've added sections of C code that are explicitly vectorized using Intel SSE2 intrinsics. I've finally got the package building on all three platforms, but to get WIndows/MinGW building, I've had to add the -msse2 to the PKG_CXXFLAGS (etc) which is

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Here is the link I was using. https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform On Tue, Oct 10, 2017 at 1:28 PM Vladislav Petyuk wrote: > done > > On Tue, Oct 10, 2017 at 1:24 PM Turaga, Nitesh < > nitesh.tur...@roswellpark.org> wrote: > >> Pleas

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

done On Tue, Oct 10, 2017 at 1:24 PM Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Please resubmit. > > > > On Oct 10, 2017, at 4:24 PM, Turaga, Nitesh > wrote: > > > > We do not have a submission with that email. > > > > Nitesh > > > >> On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Please resubmit. > On Oct 10, 2017, at 4:24 PM, Turaga, Nitesh > wrote: > > We do not have a submission with that email. > > Nitesh > >> On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk wrote: >> >> pet...@gmail.com >> >> On Tue, Oct 10, 2017 at 1:08 PM Turaga, Nitesh >> wrote: >> Hi, >>

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

We do not have a submission with that email. Nitesh > On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk wrote: > > pet...@gmail.com > > On Tue, Oct 10, 2017 at 1:08 PM Turaga, Nitesh > wrote: > Hi, > > What is the email you submitted with? So that I can check your submission. > > Nitesh > >

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Hi, What is the email you submitted with? So that I can check your submission. Nitesh > On Oct 10, 2017, at 3:57 PM, Van Twisk, Daniel > wrote: > > > > > > From: Vladislav Petyuk > Sent: Tuesday, October 10, 2017 2:56 PM > To: Van Twisk, Daniel > Subject

[Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

From: Vladislav Petyuk Sent: Tuesday, October 10, 2017 2:56 PM To: Van Twisk, Daniel Subject: EXTERNAL: Re: MSnID failing on release and devel I submitted my SSH RSA key back on Friday evening. made sure that I have upstream in .git/config [remote "upstream"

Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

You have to resubmit your key to the google form. > On Oct 10, 2017, at 2:35 PM, greg gloor wrote: > > Thanks. Could the key be changed to this, which is the output from: > > more .ssh/id_rsa.pub > > B3NzaC1yc2EDAQABAAACAQDlWXPvutaf4Po3VuJAU+zKMvW9DtC56KiJVG9h0ZHqSkXY5K0wy8g/zYMvho

[Bioc-devel] change maintainer of a package

Hi, I would like to appoint a new maintainer for my package and could not find any documentation on this topic. I was told to send an email mentioning both new and old maintainer to packa...@bioconductor.org However, I did not

Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

Hi We have a key on file for you. Your public key is ssh-rsa B3NzaC1yc2EDAQABAAABAQCxSTknqlL1IAExkqVS4+ZpvRIq2IGWzamjcTE//PANbZ9wQg09FuB+qDDhC1/AMQUd/1YWW8s7iC1lfnLt6Qp9Jbt0v2EuY2or/RwF36efIu2P/AERsUHqlgJRZc+qW583kNXRaHo2tCfUOW0ikrjAHnFh4SeZzfDXtJ/6JipBFju6vLwW+dIz/lPYwIM50oOApPqoae00

[Bioc-devel] error: Could not fetch upstream

I too am having problems with this. I checked to make sure I had an ssh public key on github, I submitted my svn id (gloor.g) and re-submitted the form last Friday. Today I did the following, and am still not able to access the upstream repository: settings: origin https://github.com/ggloor/AL

Re: [Bioc-devel] clarification of the BiocParallel vignette for SnowParam() usage

On 10/10/2017 04:56 AM, Aaron Lun wrote: Dear list; Currently the vignette for the BiocParallel package states that the functions to be executed should contain the necessary library() calls if bplapply is used with SnowParam(). Now, I use bplapply in several of my packages with internal help

Re: [Bioc-devel] EXTERNAL: can not fetch git upstream repository

On 10/10/2017 12:06 PM, Yu Kong wrote: Dear Bioc-devel group, Sorry for the disrupt here, I got the same errors many people had these days. I can not fetch remote upstream repository using github. I've already submitted my git ID through google form. Is there anything that I missed? Thanks a lot

[Bioc-devel] can not fetch git upstream repository

Dear Bioc-devel group, Sorry for the disrupt here, I got the same errors many people had these days. I can not fetch remote upstream repository using github. I've already submitted my git ID through google form. Is there anything that I missed? Thanks a lot for your help! Thanks, Yu Here are the

[Bioc-devel] Git related or ssh queries to bioc-devel

Hi Maintainers, I have been getting a lot of emails addressed to me directly regarding SSH or Git related issues. Please send these emails to bioc-devel, which gives the question a larger audience and potentially a faster reply from someone else. Another perk, other people who have the same qu

Re: [Bioc-devel] rcellminer Bioconductor package

Thanks, Fathi On 10/10/17, 10:25 AM, "Turaga, Nitesh" wrote: You should have access if you have submitted the new key. We suggest your link your GitHub ID. And add keys to your Github, and we can get them from there. If you have submitted your GitHub ID once to the google form, y

Re: [Bioc-devel] rcellminer Bioconductor package

You should have access if you have submitted the new key. We suggest your link your GitHub ID. And add keys to your Github, and we can get them from there. If you have submitted your GitHub ID once to the google form, you won’t have to resubmit. Best, Nitesh > On Oct 7, 2017, at 9:04 AM, E

Re: [Bioc-devel] EXTERNAL: Re: Enabling SSH keys

Your keys are already in our system, please make sure you are using the correct private key for access to the package. Did you try to access the system? Or are you just waiting for a response. There is no response provided by that google form. ssh-rsa B3NzaC1yc2EDAQABAAABAQDSTjBIKs2

Re: [Bioc-devel] EXTERNAL: Can't push to git

Hi I see that you have submitted your key multiple times. But missed one key component to get access to your package, i.e your previous SVN-ID given to your by bioconductor. You are supposed to submit your SVN ID in the google form, without with your keys will not get access. Best, Nitesh

Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

You have the following public key’s in the Bioconductor system, are you sure you are using the correct private keys. ssh-rsa B3NzaC1yc2EDAQABAAACAQC6JEwwW5rBwmwQ2YQNF5S6mdMxmyT3B95m770JpNmaTInDCX89oeUJNUketMmTptJOmKfQUDxVmqcDovVQs0HlT2DOcP0fN8qH+yUf7rDFceyP6suB1IVz+UXFzVVy+RSJCkwl7DfBvx

Re: [Bioc-devel] Bad SSH key submissions

Please resubmit your key if you have lost private key. Nitesh > On Oct 9, 2017, at 5:30 PM, Juan David Henao Sanchez > wrote: > > Dear Nitesh > > The command is: > > git clone g...@git.bioconductor.org:packages/coexnet.git > > and the message of error is: > > Clonar en «coexnet»... > Perm

[Bioc-devel] Can't push to git

Hi all, I am unable to push to git with the 'tjh48' ID following the instructions on https://www.bioconductor.org/developers/how-to/git/. I have submitted my public key through the google form and tried to link my git account, which also has my keys, but to no avail. Any solutions? Best wish

[Bioc-devel] Git permission denied (publickey)

Hello, A few days ago I submitted my GitHub id andreamrau (since GitHub knows my SSH key) and my SVN id (a.rau) using the Git/SVN transition form, and I still seem to be having difficulty accessing my packages coseq and HTSFilter. I see the following message when I try to git clone one of my pac

Re: [Bioc-devel] clarification of the BiocParallel vignette for SnowParam() usage

Dear list; Currently the vignette for the BiocParallel package states that the functions to be executed should contain the necessary library() calls if bplapply is used with SnowParam(). Now, I use bplapply in several of my packages with internal helper/wrapper functions, and that piece of adv