[Bioc-devel] bioconductor_docker:RELEASE_3_12 is available

Hello Developers, The Bioconductor docker images have been updated to reflect the latest release. For more details on how to use the docker image, http://bioconductor.org/help/docker/ . `bioconductor/bioconductor_docker:RELEASE_3_12` is the new image (Bioc 3.12 and R version 4.0.3).

Re: [Bioc-devel] Bioconductor Git Credentials

:29 PM Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: Hi, 1. You can use the password reset link https://git.bioconductor.org/BiocCredentials/password_reset/<https://secure-web.cisco.com/1E

Re: [Bioc-devel] Bioconductor version 3.12 branching today

, 2020, at 9:35 AM, Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: Dear Bioconductor developers, As announced earlier, the commits have now been blocked. We will follow up with an email once push access is restored. Best, Nitesh On Oct 27, 2020, at 8:56 AM, Tu

Re: [Bioc-devel] Bioconductor version 3.12 branching today

Dear Bioconductor developers, As announced earlier, the commits have now been blocked. We will follow up with an email once push access is restored. Best, Nitesh On Oct 27, 2020, at 8:56 AM, Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: Dear Bioconductor developers,

[Bioc-devel] Bioconductor version 3.12 branching today

Dear Bioconductor developers, Today we'll be creating the Bioconductor 3.12 branch (RELEASE_3_12) starting at 9:30am EST. All push access to git.bioconductor.org will be blocked for a few hours starting at 9:30AM. We'll post back when push access is restored and

Re: [Bioc-devel] Bioconductor Git Credentials

Hi, 1. You can use the password reset link https://git.bioconductor.org/BiocCredentials/password_reset/ and add a new SSH key to your account which is also on your new machine. 2. You cannot update the RELEASE_3_11 branch anymore. The Bioc 3.12 release happens in a couple of days. Check the

Re: [Bioc-devel] IgGeneUsage Bioconductor package

n 20.10.20 6:22 PM, Turaga, Nitesh wrote: Hi Simo, I need more details about “rstan” and the configuration. I’m trying to figure it out. Nitesh On Oct 20, 2020, at 12:20 PM, Simo Kitanovski mailto:simo.kitanov...@uni-due.de>> wrote: Dear Nitesh, as mentioned in my previous email

Re: [Bioc-devel] IgGeneUsage Bioconductor package

Simo On 13.10.20 4:58 PM, Turaga, Nitesh wrote: Hi Simo, Can you tell me how you configured rstan on your windows machine? Either way, don’t worry about the release version on Windows, there seems to be a version which has propagated through. But the issue persists in devel, which you’ll need

Re: [Bioc-devel] Update CARNIVAL maintainer

Hi Enio and Olgo, I’ve taken care of this. Olga, you should have access to the package as soon as you add your SSH keys to your git.bioconductor.org/BiocCredentials account. You’ll get a private email from me about your account information.

Re: [Bioc-devel] Access g...@git.bioconductor.org:packages/Spectra.git

You have access now Laurent. Best regards, Nitesh On Oct 16, 2020, at 7:32 AM, Laurent Gatto mailto:laurent.ga...@uclouvain.be>> wrote: Dear Nitesh, Could you please grant me write access to g...@git.bioconductor.org:packages/Spectra.git. Johannes, who is

[Bioc-devel] Bioconductor Release Announcement: RELEASE_3_11 branch frozen

Dear Maintainers, Following up on my last email, the RELEASE_3_11 branch has now been frozen on the Bioconductor git repository. You will no longer be able to make any changes on the RELEASE_3_11 branch of your package. Please keep in mind that we are on schedule for our release as given in

[Bioc-devel] Bioconductor Release Announcement: RELEASE_3_11 branch freeze

Dear Maintainers, Please keep in mind that we are on schedule for our release as given in http://bioconductor.org/developers/release-schedule/. Today (Oct 13th 2020) at 1:30pm EDT, I will freeze the commits to the RELEASE_3_11 branch in Bioconductor. So, commits should be made for any bug

Re: [Bioc-devel] Reset BioCredentials

owever, I don't have access to the repo for the 3rd package GeneAnswers. Could you please help me on that? Thanks, Lei On Tue, Sep 29, 2020 at 7:39 AM Turaga, Nitesh < nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>> wrote: Hi Lei, Thanks for notifying us. I’ve

Re: [Bioc-devel] Reset BioCredentials

Hi Lei, Thanks for notifying us. I’ve changed your email. Please activate your account again with the new email. Your SSH keys should still be valid. https://git.bioconductor.org/BiocCredentials/account_activation/ You should also change the email address in the “Maintainer” field of the

Re: [Bioc-devel] MPFE Bioconductor package

:55 AM To: Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> Cc: Stone, Matt mailto:mst...@fredhutch.org>>; bioc-devel mailto:bioc-devel@r-project.org>>; Jiefei Wang mailto:szwj...@gmail.com>> Subject: Re: [Bioc-devel] MPFE Bioconductor package Hi guys, It seems to be work

Re: [Bioc-devel] MPFE Bioconductor package

, I highly encourage you to email the bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> mailing list where other people can help you more readily. Best, Nitesh From: Conrad Burden Date: Wednesday, September 16, 2020 at 10:16 PM To: "Turaga, Nitesh" Subject: Re: MPFE Bioc

Re: [Bioc-devel] fetch upstream of an existing package

Please follow http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ . Notice that the branch name is RELEASE_3_11 (case sensitive). Nitesh From: Irene Zeng Date: Thursday, September 10, 2020 at 5:33 AM To: "Turaga, Nitesh" , "Shepherd, Lori" Cc:

Re: [Bioc-devel] fetch upstream of an existing package

r Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Irene Zeng mailto:i.z...@auckland.ac.nz>> Sent: Sunday, September 6, 2020 5:08 AM To: Shepherd, Lori mailto:lori.sheph...@roswellpark.org>>; T

Re: [Bioc-devel] fetch upstream of an existing package

or.org<http://git.bioconductor.org/>:packages/sparsenetgls.git 2fef8fa..b8f64e4 master -> master " Do you know what the error messages tell us? Appreciate your guidance. Irene From: Irene Zeng Sent: Sunday, 6 September 2020 4:33 p.m. To: Shepherd, Lori

[Bioc-devel] Fwd: fetch upstream of an existing package

inerData and rcellminerData new versions (Elloumi, Fathi (NIH/NCI) [C]) -- Message: 1 Date: Tue, 25 Aug 2020 00:01:37 + From: "Elloumi, Fathi (NIH/NCI) [C]" mailto:fathi.ello...@nih.gov>> To: =?utf-8?B?SGVydsOpIFBhZ8Oocw==?=

Re: [Bioc-devel] About rcellminerData and rcellminerData new versions

branch and 'upstream/RELEASE_3_11' have diverged, and have 1 and 21 different commits each, respectively. (use "git pull" to merge the remote branch into yours) Should I do now: git push -f upstream RELEASE_3_11 (with option -f) ? Fathi From: "Turaga, Nitesh" mailto:nitesh.tur

Re: [Bioc-devel] About rcellminerData and rcellminerData new versions

Hi Fathi, You can try those steps. Let me know if it works. Nitesh On Aug 25, 2020, at 9:28 AM, Elloumi, Fathi (NIH/NCI) [C] mailto:fathi.ello...@nih.gov>> wrote: Dear Martin, I have attached my commit log for my local branch RELEASE_3_11 for package rcellminerData. To undo the changes and

[Bioc-devel] bioconductor_docker updates

Hello Bioconductor Community, A quick update about the latest developments on the Bioconductor Docker images. We have updated the ‘devel’ image to inherit from the latest ‘rocker/rstudio:4.0.2’ image. This means that the `bioconductor/Bioconductor_docker:devel` image, which is now available

Re: [Bioc-devel] Maintenance on new package contributions and git hooks

Hello Bioconductor developers, The maintenance is complete. Please watch for another email with details on the changes. Best regards, Nitesh On Jul 1, 2020, at 10:34 AM, Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: Hello Bioconductor developers, The new package contri

[Bioc-devel] Maintenance on new package contributions and git hooks

Hello Bioconductor developers, The new package contribution is undergoing some maintenance and changes this week starting now. Along with this, we are testing our git hooks and making some changes in them as well. The maintenance will impact our RSS feeds on our website, which gives you the

Re: [Bioc-devel] New maintainer request for GAPGOM package

Hi, I’ve added Rezvan to the package. A private email will be sent to Rezvan for his BiocCredentials account. Once SSH keys are added, package access will be granted. Best, Nitesh On Jun 25, 2020, at 9:40 AM, Casper van Mourik mailto:cp1...@hotmail.com>> wrote: Dear Bioconductor, I wish

Re: [Bioc-devel] Problem with pushing package to Bioconductor

Try adding a new SSH key and retrying again. Best, Nitesh > On Apr 20, 2020, at 12:29 PM, Cao, Quy wrote: > > Dear all, > > I made some updates for my package PERFect on GitHub but I have some trouble > pushing it to Bioconductor. Here is what I have done: > > > 1. I have activated my

Re: [Bioc-devel] Unable to access Bioconductor git repo

Hi Peter, The account was using peter.humb...@csiro.org. I've changed it to the gmail address. Please activate your account again, and try to add SSH keys. You'll gain access. https://git.bioconductor.org/BiocCredentials/account_activation/ Best, Nitesh > On Apr 18, 2020, at 7:26 PM, Peter

Re: [Bioc-devel] Transfer Maintainership of a Package ClusterJudge

Hi Adrian, You have to first activate your BiocCredentials account https://git.bioconductor.org/BiocCredentials/. Once you activate your account, you should be able to log in and add some SSH keys. You'll be given access to the system once you add your SSH keys. Also, please change the

Re: [Bioc-devel] credentials/authors for MTseeker, biscuiteer, and data packages corresponding to each

> Once I have access, I'll go ahead and update the Maintainer field with my > name and that email address. > > Thanks, > Jacob > From: Turaga, Nitesh > Sent: Thursday, April 16, 2020 9:09 AM > To: Tim Triche, Jr. > Cc: Morrison, Jacob ; bioc-devel > > Subject:

Re: [Bioc-devel] credentials/authors for MTseeker, biscuiteer, and data packages corresponding to each

Once Jacob is given access, he should change the Maintainer field on the package DESCRIPTION for biscuiteer and biscuiteerData as well. Nitesh > On Apr 16, 2020, at 9:03 AM, Turaga, Nitesh > wrote: > > Hi Tim and Jacob, > > So, as I understand it, (in the ideal world)

Re: [Bioc-devel] credentials/authors for MTseeker, biscuiteer, and data packages corresponding to each

Hi Tim and Jacob, So, as I understand it, (in the ideal world) 1) Tim would maintain --> MTseekerData and MTseekerData 2) Jacob would maintain --> biscuiteer and biscuiteerData There are 2 aspects you need to understand here, 1) access 2) emails - Access, the access to the packages was given

Re: [Bioc-devel] Access issues to package fcoex

w and I will add. > > I am not super savvy with git too, and I already apologize for any basic > mistakes. > I am sorry for the trouble and thank you very much for your time and help. > > Tiago > > Tiago Lubiana, > MSc in Bioinformatics, University of São Paulo > Co

[Bioc-devel] RELEASE_3_10 branch has been frozen

Dear Maintainers, As a follow up to yesterday's email, the RELEASE_3_10 branch of Bioconductor has been frozen. You will not be able to push your commits to this branch anymore for any reason. Thank you for your contributions to the RELEASE_3_10. Best regards, Nitesh Turaga This email

Re: [Bioc-devel] Git credentials issue - ExiMiR R package maintenance

Hi, This is the first time you are trying to login, please try to activate your account, https://git.bioconductor.org/BiocCredentials/account_activation/ Best, Nitesh > On Apr 13, 2020, at 4:07 PM, Gubian, Sylvain wrote: > > Dear Bioconductor Core Team, > > I am maintaining ExiMiR R

[Bioc-devel] RELEASE_3_10 branch freeze tomorrow at 3pm EDT

Dear Maintainers, Please keep in mind that we are on schedule for our release as given in http://bioconductor.org/developers/release-schedule/. Tomorrow (April 14th 2020) at 3pm EDT, I will freeze the commits to the RELEASE_3_10 branch in Bioconductor. So, commits should be made for any bug

Re: [Bioc-devel] Access issues to package fcoex

We need more information, http://bioconductor.org/developers/how-to/git/faq/ #13 and #14 in the FAQ are relevant to you. Nitesh > On Apr 9, 2020, at 12:39 PM, Tiago Lubiana Alves > wrote: > > Hello all, > > I have recently made a few change to a package that I mantain, but I seem > to be

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Hi, Please add another SSH key in BiocCredentials and it'll give you access. Feel free to remove any key in that list which you think is not needed. There cannot be keys which are concatenated, it will not work that way. Let me know if there is problem. Best, Nitesh > On Apr 7, 2020, at

[Bioc-devel] Weekly update of "bioconductor_docker:devel" docker image

Hello Community, A brief update on the "bioconductor/bioconductor_docker:devel" image which is produced by the Bioconductor team. The image will now be updated "weekly" on Friday evening around 6pm EST. This means that the image will have the latest version of R-devel by the week, and pushed

Re: [Bioc-devel] Unable to update maintainer email address

Hi, I've updated your email address to the one you are emailing from now. pierre.neuv...@math.cnrs.fr. Please "activate" you BiocCredentials account first and add SSH keys. Once you do that you'll be able to change the email on the description file.

Re: [Bioc-devel] Problems with Biocredentials

e try again, and see that you have access to all your packages. Best, Nitesh > On Apr 1, 2020, at 9:04 AM, Turaga, Nitesh > wrote: > > Hi, > > Did you add your Github username to your BiocCredentials account? > > If you add your Github username to your BiocCredentials

Re: [Bioc-devel] Problems with Biocredentials

Hi, Did you add your Github username to your BiocCredentials account? If you add your Github username to your BiocCredentials account, it will import the SSH keys you add on your Github account. Best, Nitesh > On Mar 31, 2020, at 11:46 PM, Saskia Freytag wrote: > > Hi, > > I have added

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

tive message > git push > git push upstream master > > > Lori Shepherd > Bioconductor Core Team > Roswell Park Comprehensive Cancer Center > Department of Biostatistics & Bioinformatics > Elm & Carlton Streets > Buffalo, New York 14263 > From: Bioc-devel

Re: [Bioc-devel] 'MACSQuantifyR' Bioconductor package

Please read the instructions on this document carefully, and follow the steps. If in doubt, do NOT push but check your `git log`, and make sure everything is as expected. https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ Best, Nitesh > On Mar 30, 2020, at 8:09 AM,

Re: [Bioc-devel] BiocCredentials email issue

Hi, I've reset your email to mdwilker...@outlook.com Please activate your BiocCredentials account to gain access to your account. https://git.bioconductor.org/BiocCredentials/account_activation/ Best. Nitesh On 3/28/20, 11:52 AM, "Bioc-devel on behalf of Matt Wilkerson" wrote: Hello

Re: [Bioc-devel] Re phospphonormalizer package

I changed your email address, please try again now with sohrab.sar...@blueprintgenetics.com. On 3/28/20, 12:02 PM, "Bioc-devel on behalf of Sohrab Saraei" wrote: I have been trying to log in to my bioconductor account for sometime now, but unfortunately no luck. I trie to reset my

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

TPS option. Might there > be something wrong with my GitHub settings? > > Cheers, > > On Fri, 27 Mar 2020 at 17:18, Turaga, Nitesh > wrote: > Can you access any git repository via the SSH protocol? > > Not via HTTPS. > > So you'll have to check if you can do some

[Bioc-devel] Fwd: Trying to access the source repository of a bioconductor package (Developer Access)

rch 27, 2020 at 12:25:42 PM EDT To: "Turaga, Nitesh" mailto:nitesh.tur...@roswellpark.org>> Hi, Ahh apparently I cannot. I tried to clone a random repo (PHONEMeS) locally through the command you provided, and then got the following: Cloning into 'PHONEMeS'... Permission denied (pu

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

> > IdentityFile ~/.ssh/id_rsa_bioconductor > User git > > The public key of id_rsa_bioc is already added on my profile in > BiocCredentials and also on my GitHub account. > > As always any help is very much appreciated. > > Cheers, > Enio > &

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

e "permission denied (public key)" error. > > How can I check for my git set up? > > Sorry again, but quiet new on this. > > Cheers, > > On Fri, 27 Mar 2020 at 13:38, Turaga, Nitesh > wrote: > Try adding another key. If that doesn't work, show us your git

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

Try adding another key. If that doesn't work, show us your git set up. http://bioconductor.org/developers/how-to/git/faq/ #13 and #14 Best, Nitesh On 3/27/20, 6:15 AM, "Bioc-devel on behalf of Enio Gjerga" wrote: Hello, I am Enio Gjerga and I am the maintainer of the

Re: [Bioc-devel] Problem updating Bioconductor package

Hi, Take a look at #13 and #14 on the frequently asked questions, http://bioconductor.org/developers/how-to/git/faq/ Best, Nitesh > On Mar 24, 2020, at 5:24 PM, Hong Zheng wrote: > > Hi, > > We followed the instruction >

Re: [Bioc-devel] Help needed on BioC Git credential for package maintainer

Hi I've created the account for you. I'll send you your login details in a private email. Nitesh > On Mar 24, 2020, at 12:20 PM, Huang, Lei [CRI] > wrote: > > Dear Bioconductor team, > > I am one of the maintainers of BioC packages Lumi >

Re: [Bioc-devel] Problems with BiocCredentials

Hi Saskia, The email it is registered to is freyta...@wehi.edu.au. So, you'll first have to "activate" your account before you can do anything else. https://git.bioconductor.org/BiocCredentials/account_activation/ Once you activate your account, please add your SSH keys. You will then be able

Re: [Bioc-devel] Change associated email/github

gt; > -R > > On Wed, Mar 18, 2020 at 10:56 AM Russell Bainer wrote: > Oh, great- I think I am in and have updated my profile credentials. Thanks so > much for all of the n00b question help. > > Stay safe > > -R > > On Wed, Mar 18, 2020 at 10:50 AM Turaga, Ni

Re: [Bioc-devel] Change associated email/github

have access to the registered email address, and I'm > afraid that I registered long enough ago that I don't have the password that > I used. > > > On Tue, Mar 17, 2020 at 2:05 PM Turaga, Nitesh > wrote: > Hi, > > There are a couple of things you'd have to do, > > 1. In

Re: [Bioc-devel] Fw: Bioconductor package SIM

You'll have to activate your account first, https://git.bioconductor.org/BiocCredentials/account_activation/ > On Mar 17, 2020, at 5:11 PM, ni41435_ca wrote: > > The SIM package is registered to mboetze...@hotmail.com. > > You can change the email on BiocCredentials app yourself. > >

Re: [Bioc-devel] Fw: Bioconductor package SIM

The SIM package is registered to mboetze...@hotmail.com. You can change the email on BiocCredentials app yourself. Best, Nitesh > On Mar 17, 2020, at 11:52 AM, r.mene...@nki.nl wrote: > > l.s. > > > I cannot seem to be able to activate my account on the bioconductor git. I > get a message

Re: [Bioc-devel] Change associated email/github

Hi, There are a couple of things you'd have to do, 1. In the BiocCredentials app, you'd have to change your email address registered. And update your SSH keys if needed, add your personal Github ID as well. 2. In the DESCRIPTION file of the package, you'd have to change your email address to

Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

You cannot merge your master branch into the RELEASE_3_10 branch. The version number will not match, and all the devel changes will go into the release. Instead, 1) git checkout RELEASE_3_10 2) Make the changes again in the RELEASE_3_10 branch. 3) git add 4) git commit -m

Re: [Bioc-devel] XINA additional maintainers

oftware > > We were advised to contact your email to add Lang to XINA related issues > > ~s > >> On Mar 12, 2020, at 1:42 PM, Turaga, Nitesh >> wrote: >> >> External Email - Use Caution >> >> Hi >> >> It seems t

Re: [Bioc-devel] XINA additional maintainers

Hi It seems that "langholee" is already the username on the package maintainer list. I'm not entirely sure what your request is? Do you need to change the email address on your BiocCredentials account? Best, Nitesh > On Mar 10, 2020, at 10:31 AM, Singh, Sasha A.,Ph.D. > wrote: > > Hi

Re: [Bioc-devel] commit access to the Bioconductor Git repository of multtest package

urgent). > > Thanks, > Katie > > >> On Mar 11, 2020, at 1:33 PM, Turaga, Nitesh >> wrote: >> >> Hi >> >> I can give you commit access, but have you explored fixing the bug on the >> GitHub repository and then having Katie sync it with

Re: [Bioc-devel] commit access to the Bioconductor Git repository of multtest package

Hi I can give you commit access, but have you explored fixing the bug on the GitHub repository and then having Katie sync it with Bioconductor? If you still feel that having access to the Bioconductor git repo is the best option, I'll go ahead and give you access. Best, Nitesh > On Mar

Re: [Bioc-devel] Bioconductor Release 3.11 Schedule

Hello Bioconductor developers, As per the release schedule, I wanted to add that Bioconductor is now taking submission of Docker images as well. Please note that the same deadlines apply for the docker images and packages. Relevant links for Docker image submissions are: 1. General Docker

[Bioc-devel] Fwd: how to get write permission of my R Bioconductor package to Bioconductor github

> Hi Weiliang, > > You would need to activate your BiocCredentials account and SSH keys to gain > access to the package. > https://git.bioconductor.org/BiocCredentials/account_activation/ > > The email listed on the BiocCredentials page is weiliang@gmail.com . > > Best, > > Nitesh >

Re: [Bioc-devel] how to get write permission of my R Bioconductor package to Bioconductor github

Hi Weiliang, You would need to activate your BiocCredentials account and SSH keys to gain access to the package. https://git.bioconductor.org/BiocCredentials/account_activation/ The email listed on the BiocCredentials page is weiliang@gmail.com . Best, Nitesh > On Mar 4, 2020, at 7:19

Re: [Bioc-devel] Reverting on the 'master' branch

option I'll reconsider our > options. > > Kind regards, > Roel Janssen > > > On Mon, 2020-03-02 at 19:13 +, Turaga, Nitesh wrote: >> I suggest you go forward with the version numbering. >> >> 1.99.0 --> 1.99.1 >> >> At the next relea

Re: [Bioc-devel] Reverting on the 'master' branch

ind regards, > Roel Janssen > > > On Mon, 2020-03-02 at 17:40 +, Turaga, Nitesh wrote: >> Hi Roel, >> >> You cannot revert on the Git Bioconductor repo. >> >> What is your package name? >> >>> On Mar 2, 2020, at 10:51 AM, Roe

Re: [Bioc-devel] Reverting on the 'master' branch

Hi Roel, You cannot revert on the Git Bioconductor repo. What is your package name? > On Mar 2, 2020, at 10:51 AM, Roel Janssen wrote: > > Dear Bioconductor developers, > > I'd like to revert the changes I made on the development branch > ("master" in Git), but a pre-receive hook that

Re: [Bioc-devel] issue: maintainer of a Bioconductor package

Hi, We allow only one maintainer per package. Please take a look at the instructions at this link, http://bioconductor.org/developers/package-guidelines/#description. Both you and your colleague can remain an authors but you should remove one of the names as maintainer. For this reason you

Re: [Bioc-devel] Duplicated commits in BioC git repository

Hi, If you send me your GitHub repo where you have the cleaned repo. I will compare it to the repo on the bioconductor git server. I'll do a quick check and sync them once I think they are correctly done. Thank you for taking time to read the documentation and fixing the duplicate commits.

Re: [Bioc-devel] Account activation problems

It is registered to antti.honk...@tkk.fi. I have changed you email address and now you can go through the activation process again. Once you activate it, you'd need to add your SSH keys to gain access to the package. Best regards, Nitesh > On Feb 27, 2020, at 2:12 PM, Antti Honkela

[Bioc-devel] Fwd: Changing the maintanor of IMMAN package

w one is https://github.com/Minoo-ASTY. Thanks a lot for your assistance. Minoo On Wed, Feb 19, 2020 at 5:23 PM Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: Hi, The remote is wrong. You need to have to do something similar to #6 http://bioconductor.org/developers/how-t

Re: [Bioc-devel] Integrating python into an R package

Take a look at BiocSklearn. Nitesh > On Feb 18, 2020, at 8:11 AM, Zhang, David wrote: > > Dear all, > > I’m a bioinformatics PhD student at UCL who’s recently been trying to develop > an R package that has some python dependencies. Specifically, areas of my > current pipeline are written

Re: [Bioc-devel] Changing the maintanor of IMMAN package

Hi, The error you are showing in your feed is currently saying, you are NOT in a repository which is hosted by github. Also, your remotes should be the set to look like Step #2 (http://bioconductor.org/developers/how-to/git/push-to-github-bioc/). If that is set up, your GitHub name should

Re: [Bioc-devel] Permission denied (publickey)

Hi Daniel, Could you try adding a new public key? Because everything on our end is fine. Best Nitesh > On Feb 11, 2020, at 1:09 PM, Danrley Fernandes wrote: > > Hi, > I'm the developer of the package rSWeeP, and I'm trying to clone my > package's repository on Bioconductor, so I can commit

Re: [Bioc-devel] Account Activation Issue

It is registered to, "c...@fgz.eth.ch". Would you like me to change the address? Best, Nitesh On 2/6/20, 5:18 AM, "Bioc-devel on behalf of Opitz Lennart" wrote: Dear BC-Devel-Team, I am the maintainer of the package ‘NextLink' and I tried to activate the relevant GIT accounts

Re: [Bioc-devel] activation of account

Hi, The email registered on the BiocCredentials app is different. It is, m.futsc...@biologie.hu-berlin.de. All your packages are registered under the same email. Nitesh > On Jan 30, 2020, at 7:25 PM, Mattthias Erwin Futschik > wrote: > > Hello, > I am the maintainer of the package Mfuzz,

Re: [Bioc-devel] Problems on BiocCredentials account_activation

Hi, I've activated your account from my end and set a temp password. I'll send you a private email with the temp password. Please make sure to change your password after that. Best, Nitesh > On Jan 28, 2020, at 1:43 PM, Danrley Fernandes wrote: > > Hi, > I'm the developer of the package

Re: [Bioc-devel] Still unable to access git bioconductor credentials

Hi I've just activated the account for you and set a temp password. I'll send that to you privately. You should then be able to access your account, add SSH keys if needed and then access your package. Nitesh > On Jan 29, 2020, at 9:41 AM, Richard Virgen-Slane > wrote: > > Hi All, > >

Re: [Bioc-devel] trouble with BiocCredentials account_activation

Hi Zach, I can confirm that your email address is the same "zixuanshao.z...@gmail.com". Can you please check the spam folder? Or try again to activate maybe? Best, Nitesh > On Jan 25, 2020, at 8:13 PM, Zach Shao wrote: > > Hello, > > I'm the developer of the package ERSSA. > I'm trying

Re: [Bioc-devel] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: Bioconductor package sagenhaft

I've changed your email address. Please activate your account and access your git repository. You'd need to activate and add your SSH credentials to the BiocCredentials account. https://git.bioconductor.org/BiocCredentials/account_activation/ Nitesh > On Jan 24, 2020, at 10:19 AM, Tim

Re: [Bioc-devel] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: Bioconductor package sagenhaft

Your email listed is beissba...@wehi.edu.au Best, Nitesh > On Jan 24, 2020, at 8:04 AM, Tim Beissbarth > wrote: > >> Firstly you will probably have to log into the git credentials app to load >> a ssh key >> https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ >> >

Re: [Bioc-devel] Help git package maintaining

push and fix it for you this one time. > On Jan 22, 2020, at 10:33 AM, Raphael Bonnet > wrote: > > It shows fatal: 'RELEASE_3_10' branch already exist > > > Le 22/01/2020 à 16:28, Turaga, Nitesh a écrit : >> Ok, try this instead >> >> git check

Re: [Bioc-devel] Help git package maintaining

> odd y after creation of RELEASE_3_10 branch > |/ > * a724b95 (HEAD, upstream/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to > even y prior to creation of RELEASE_3_10 branch > > > > Best , > > Raphael > > Le 22/01/2020 à 16:16, Turaga, Nitesh a écrit

Re: [Bioc-devel] Help git package maintaining

Hi Rafael, Please try the following git checkout origin/RELEASE_3_10 git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd This is the cleanest way to achieve what you need. Please also keep in mind to back up your entire folder in another directory should something

Re: [Bioc-devel] Error: Bioconductor Git Credentials

The email registered is rvs.bioto...@gmail.com. You have to first activate it before you can access it, as you have never signed in before. https://git.bioconductor.org/BiocCredentials/account_activation/ Please check your spam email as well. > On Jan 21, 2020, at 2:41 PM, Richard

[Bioc-devel] New bioconductor_docker image officially released

Hello developers, The new "bioconductor/bioconductor_docker" image is officially released. The link to access it on Dockerhub is: https://hub.docker.com/repository/docker/bioconductor/bioconductor_docker. The source code in on GitHub at: https://github.com/bioconductor/bioconductor_docker.

[Bioc-devel] Bioconductor Image deprecation 2 day notice for bioc_docker and bioconductor_full

Dear Bioconductor developers, ​ This is the 2 day notice before the formal deprecation of the images listed below in favor of the latest ​ "bioconductor/bioconductor_docker" image. My previous email for anyone who might have missed the update​ about the direction the Bioconductor team is taking

Re: [Bioc-devel] DeMixT issue

Hi Peng, I was looking through your version bumps, and it looks a little off-track I have to say. The version bumps you should have in your repository should be following the order(from the commit below) should be 1.3.0 --> 1.3.1 --> 1.3.2 and so on. commit

Re: [Bioc-devel] Bug fix issue package MACSquantifyR

wrote: >> >> Hi, >> >> Thank you for your response, >> >> here it is, >> >> https://github.com/Peyronlab/MACSQuantifyR >> >> Best, >> >> Raphaël >> >> Le 15/01/2020 à 15:56, Turaga, Nitesh a écrit : >>

[Bioc-devel] Deprecation of bioc_docker and bioconductor_full containers

Dear Bioconductor developers, There are new set of Bioconductor docker images under the name bioconductor/bioconductor_docker. These are located at https://github.com/Bioconductor/bioconductor_docker. The new set of images will have a `devel` image and a `RELEASE_3_10` / `latest` image. With

Re: [Bioc-devel] Problem in activating the Account for Bioconductor Git Credentials

Hi Paola, It seems your email is registered to pa...@idsia.ch on the Bioconductor Git repository. I've changed it on my end. You should be able to activate your account https://git.bioconductor.org/BiocCredentials/account_activation/ with the new email address. Once

Re: [Bioc-devel] resetting git.bioconductor password

It seems you've never activated your account before trying to reset your password. https://git.bioconductor.org/BiocCredentials/account_activation/ > On Dec 31, 2019, at 2:14 PM, Giorgio Melloni > wrote: > > Dear Bioc-devel, > > I want to reset both support.bioconductor and git.bioconductor

Re: [Bioc-devel] How to move package from workflow to software

review today. Happy holidays, Nitesh > On Dec 9, 2019, at 10:31 AM, Turaga, Nitesh > wrote: > > Hi Julien, > > After re-considering how this package should go forward. Please submit your > package to the https://github.com/Bioconductor/Contributions. This will put &

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

Hi Ludwig, Thank you for volunteering to take over as maintainer for PathNet and PathNetData. You should now have access to both packages as the maintainer. They should show up on the build machine tomorrow. You should port your fix(s) to the build machine for the PathNet package when you

Re: [Bioc-devel] Question regarding pruning release of large files

Hi Saskia, Mike is correct, you cannot force push to the Bioconductor git repo. If you point me to the GitHub location, and you are confident that you want your repo overwritten, let me know I'll force push it for you. Best, Nitesh > On Dec 19, 2019, at 8:49 AM, Mike Smith wrote: > > Hi

Re: [Bioc-devel] Bioconductor phenoTest

Hi, Please try again, I've updated your email address it was listed to a irb-barcelona account previously. Best, Nitesh > Dear Lori, > > Thank you for your message. I was about to work on the corrections for the > package. > > The system changed a bit since last time I used it. It seems

Re: [Bioc-devel] Add collaborator

You have been added and given permissions Pedro. Please check for a private email with credentials. -- Nitesh Turaga Senior Programmer Analyst Bioconductor core team Roswell Park From: Bioc-devel on behalf of Turaga, Nitesh Sent: Wednesday, December 11, 2019

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