Re: [Bioc-devel] error pushing changes

Hi Marta, There are a few issues with your repository. Let’s take a look at your commit history. t/hipathia (RELEASE_3_8)❯❯❯ git log —oneline d93efc9 (HEAD -> RELEASE_3_8, origin/RELEASE_3_8) Fixing bug in Wilcoxon test bd245a5 fixing version number

Re: [Bioc-devel] regutools: request to add more git push access

Hi Leo, I've added you and Alejandro to the regutools package. Carmina and Emiliano, please confirm the email addresses you'll be using. I can add you both as well, and create BiocCredentials accounts for you. Nitesh On 4/26/2020 11:42 PM, Leonardo Collado Torres wrote: Hi Nitesh, Could

Re: [Bioc-devel] regutools: request to add more git push access

. 2020 a las 5:59, Nitesh Turaga (mailto:nturaga.b...@gmail.com>>) escribió: Hi Leo, I've added you and Alejandro to the regutools package. Carmina and Emiliano, please confirm the email addresses you'll be using. I can add you both as well, and create BiocCredentials

Re: [Bioc-devel] Fwd: About rcellminer package

Hi Fathi, You should update the version to 2.11.1, if you want a new build for your package. Developers should only change the version number in the "z" coordinate of the "x.y.z" versioning system. Best, Nitesh Hi Nitesh, My name is Fathi Elloumi one of the maintainer of package

[Bioc-devel] Fwd: Creating Bioconductor 3.11 branch on April 27th - 1:30PM EDT

urther notice so we can create the RELEASE_3_11 branch for all packages (software, data experiment and workflow). The process will take about 2.5 - 3 hours once commits are stopped. Best regards, Nitesh Turaga Bioconductor Core Team -- Forwarded message - From: Nitesh Turaga Dat

[Bioc-devel] All commits to Bioconductor git repository frozen

Dear Maintainers, As per my email about an hour ago, I've frozen the commits to Bioconductor git repository at 1:30pm EDT. Once we create the release 3.11 branch, I will re-enable access. The process will take about 2.5 - 3 hours. Best, Nitesh

[Bioc-devel] Creating Bioconductor 3.11 branch on April 27th - 1:30PM EDT

packages (software, data experiment and workflow). The process will take about 2.5 - 3 hours once commits are stopped. Best regards, Nitesh Turaga Bioconductor Core Team ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo

[Bioc-devel] Bioconductor git repository commits have resumed

Dear Maintainers, The commits to the Bioconductor repository have been resumed. The new branch RELEASE_3_11 has been created for all packages. All maintainers should have access to the "master" (devel branch) and the RELEASE_3_11 branch of their packages. Best regards, Nit

Re: [Bioc-devel] Package CNVPanelizer needs my attention

Hi, First, it seems that your question was stripped because it was in HTML and the mailing list doesn't support that. (Martin can chime in if any additional details are needed here) Second, for people wondering, this is the question, " Dear Martin, thanks for your reply, The CNVpanelizer

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

Hi, Right now, both you and Tim are on the package as people with access to the package on the Bioconductor git repository. I would refrain from setting up a generic email. Mostly because, it doesn�t come with the same amount of accountability as a user�s email address. Nitesh From:

Re: [Bioc-devel] write access to the package

Hi Hamed, It seems you had two usernames for whatever reason, I've corrected the issue. You should see access to both your packages now. Best, Nitesh -- Bioconductor Core Team On 5/1/2020 11:06 AM, Hamed Haseli wrote: Hi Lori, we have recently submitted OpenStats package to Bioconductor

Re: [Bioc-devel] How to change version number in release

Hi, You have to reset your commits before you can update your package again. Please do something in the order of, 1) git reset --soft 2) Edit your DESCRIPTION file to fix the version number. 3) git add DESCRIPTION 4) git commit -m "Version bump" 5) git push origin master 6) git push

Re: [Bioc-devel] Fw: Change mantainer

Please see forwarded message. On Thu, Apr 30, 2020 at 11:55 AM Nitesh Turaga wrote: > Hi Hector, > > I've updated your email address on the BiocCredentials account. Please > activate your account once again after this change with your new email > address. All the settings

Re: [Bioc-devel] Fw: Change mantainer

Hi Hector, I've updated your email address on the BiocCredentials account. Please activate your account once again after this change with your new email address. All the settings should be saved as they were before. As soon as you activate your account you should have access to your packages.

[Bioc-devel] EnMCB issues in version numbers

Hi, Please hold off on making any further changes on your package for the time being. It seems that there is an issue when you committed with the merge conflicts. I will reset your package, and you should make the changes again, with the correct version number. Please wait for a while so

Re: [Bioc-devel] Could not read from remote repository

Best regards, Yingxin On 5/5/20, 1:11 am, "Nitesh Turaga" wrote: You must be using the wrong SSH key most likely. If you have R W access it means the key exists but when you try to "fetch" via git, it's using the wrong key. You can set up your conf

Re: [Bioc-devel] Could not read from remote repository

You must be using the wrong SSH key most likely. If you have R W access it means the key exists but when you try to "fetch" via git, it's using the wrong key. You can set up your config file if you identify which SSH key is correct. Your git remote is malformed(formatting), if you resend it

[Bioc-devel] Do not push with merge conflicts to Bioconductor git repo.

Dear Developers, Every time there is a release for Bioconductor we (the core team), face an issue where developers end up pushing code with the "merge conflicts". One of the reasons why we get the issue "Bad description" file in the build report is because of a merge which has gone bad and

Re: [Bioc-devel] Could not read from remote repository

nk you for your suggestion! However it still doesn’t work (same error). > > Best regards, > Yingxin > > From: "Chengyang.Ji12" > Date: Tuesday, 5 May 2020 at 11:44 am > To: Yingxin Lin , Nitesh Turaga > , "bioc-devel@r-project.org" > > Subject: RE:

Re: [Bioc-devel] Docker images for RELEASE_3_11 and devel on R-4.0.0

iology and Neuroscience Goethe University Frankfurt Biologicum, Room 3.209 Phone +49 (0)69/798-42118 On 8. May 2020, at 00:43, Nitesh Turaga <mailto:nturaga.b...@gmail.com>> wrote: Dear Maintainers, The latest set of docker images on R-4.0.0 are now available on docker hub.

Re: [Bioc-devel] No credentials for reconsi

Hi, This is because you are not a maintainer on the package. You are an author. I’ve now added you to have access to the package. Best, Nitesh > On May 18, 2020, at 2:54 AM, Stijn Hawinkel wrote: > > Dear Bioc-devel, > > > Our reconsi package was accepted a few months ago, but I still

[Bioc-devel] Docker images for RELEASE_3_11 and devel on R-4.0.0

e produced now, build almost all the packages in Bioconductor. RStudio is also available as in previous versions. Best regards, Nitesh Turaga Bioconductor Core Team ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Error when pushing to RELEASE_3_11

gt; am not sure why this is failing now. > > Any suggestions? > > THANKS! > David > > > > On Thu, May 21, 2020 at 10:40 AM Nitesh Turaga <mailto:nturaga.b...@gmail.com>> wrote: > Hi, > > Just try again, you shouldn’t see this issue. > > Nitesh >

Re: [Bioc-devel] Error when pushing to RELEASE_3_11

Hi, Just try again, you shouldn’t see this issue. Nitesh > On May 21, 2020, at 1:37 PM, David Jimenez-Morales > wrote: > > Hello everybody, > > I am getting the following error when pushing upstream to the RELEASE > branch: > > --> git push upstream RELEASE_3_11 > Enumerating objects: 23,

Re: [Bioc-devel] Maintenance of MetaNeighbor package

Hi Stephan, First, I’d like you to cc Dr. Jesse Gillis and also Manthan so we know that everyone is in agreement. I can help you with the permissions on the Bioconductor repo. Before you get permissions you will only be able to fetch using the HTTP protocol, i.e git remote set-url

Re: [Bioc-devel] Hotfix rejected by git

Hi Mikhail, The RSS issue should be fixed now. Best regards, Nitesh > On Sep 8, 2020, at 7:45 AM, Shepherd, Lori > wrote: > > Yes I can see the updates 1.17.1 on the master branch on > git.bioconductor.org . We are looking into the > RSS git ERROR. > > We

Re: [Bioc-devel] maintainer access to scater

Hi Aaron, Alan should be able to access the package now. Please change the the DESCRIPTION file of the package to reflect the change in maintainer. Nitesh > On Sep 7, 2020, at 1:40 PM, Aaron Lun > wrote: > > For record-keeping purposes: > > We are transitioning maintainership of scater

Re: [Bioc-devel] Maintenance of MetaNeighbor package

he MetaNeighbor package. Nitesh nicely offered to help me > > with the task, but would like to make sure that everyone agrees first. Can > > you please briefly confirm the change by answering this email? > > > > > > Thanks everyone, > > > > >

Re: [Bioc-devel] Pushing to Bioconductor repo gives errors

The RSS feed issue has been taken care of. The bug fix was issued today at 10 AM Eastern standard time. This should not be showing up on your push to the git server anymore. Best, Nitesh > On Sep 7, 2020, at 8:44 AM, Nitesh Turaga wrote: > > Your push went through. This is a differ

Re: [Bioc-devel] Pushing to Bioconductor repo gives errors

Your push went through. This is a different issue. I’ll look into it tomorrow. Thanks, Nitesh > On Sep 6, 2020, at 12:44 PM, Alina Selega wrote: > > Sorry, looks like the error got mangled. I pasted it in this gist: > https://gist.github.com/alinaselega/f5c4f724309211cc4a5bedd2a05bfd1e > >

Re: [Bioc-devel] BiocCredentials

Hi Katherine, I’ve changed your email to your “gmail”. Please “activate” your account first. Once you do that you’ll have access to your package. Also check if you still have the SSH keys. Best Nitesh > On Oct 6, 2020, at 3:15 AM, Katherine Icay wrote: > > Hi, > > I can't log into

Re: [Bioc-devel] Add Bioconductor Maintainer Questions

Hi Melanie, I’m happy to give you access. But I need confirmation from one of the authors to give you access. Since Elana is on leave, can Thomas Sherman respond? Best, Nitesh > On Oct 14, 2020, at 2:59 PM, Melanie Loth wrote: > > Hello, > > I need to get access to the CoGAPS package on

Re: [Bioc-devel] Add Bioconductor Maintainer Questions

e Melanie. > > Sent from my iPhone > >> On Oct 14, 2020, at 3:45 PM, Nitesh Turaga wrote: >> >>  Hi Melanie, >> >> I’m happy to give you access. But I need confirmation from one of the >> authors to give you access. >> >> Since Elana i

Re: [Bioc-devel] Issue when fetching upstream

, yet I made a bump version (from 0.99.13 to 0.99.14) ... > Should I wait a little longer? > cheers, > Hélène > > Le mar. 6 oct. 2020 à 17:18, Nitesh Turaga <mailto:nturaga.b...@gmail.com>> a écrit : > Hi, > > Easiest solution is to upload a new key. I’ve c

Re: [Bioc-devel] Issue when fetching upstream

Hi, Easiest solution is to upload a new key. I’ve checked our system and everything is correct, and you seem to be doing things right on your end as well. The most likely problem is, when you “fetch” the wrong key is being used. Best, Nitesh > On Oct 6, 2020, at 11:15 AM, Hélène Borges

Re: [Bioc-devel] Lost access to my package "AffiXcan", and gained W permissions to empty repo "AffiXan"

Hi Alessandro, This package seems to have been added with the wrong name in our BiocCredentials system. It is fixed now. Please check it on your end. Best, Nitesh > On Oct 11, 2020, at 9:08 AM, Alessandro Lussana via Bioc-devel > wrote: > > Hi, > > Unexpectedly I found to have lost

Re: [Bioc-devel] Disabled email address - clustComp package

Hi Aurora, I’ve updated your email address to the new one which you included. You should now be able to activate your BiocCredentials account with the new email. Once you add SSH keys to your account you’ll gain access to your package. Best, Nitesh > On Oct 15, 2020, at 11:30 AM, ESTER

Re: [Bioc-devel] Co-maintainer for SpectralTAD and TADCompare

Hi Mikhail, You should have access to your packages now. Best, Nitesh > On Oct 19, 2020, at 3:13 PM, Mikhail Dozmorov > wrote: > > Hello, > Would it be possible to add me as a co-maintainer to two packages? > https://bioconductor.org/packages/SpectralTAD/ >

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

Hi, It is an enhancement. Only bug fixes should go into RELEASE_3_11. The devel branch is the “master” branch in git, there is no RELEASE_3_12 yet. We will create it in the next release. Push your changes to the “master” branch. Address your emails to bioc-devel@r-project.org

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

wrote: > > Thanks Nitesh for you prompt response. > > Dear Bioconductor team, > > Could please help reset the two packages rcellminer and rcellminerData to a > previous commit done on April the 27th (I think version 2.10.0). > > Thanks, > > Fathi > > From

Re: [Bioc-devel] Few questions of maintaining a new bioconductor package

ter if I had the email all lower case on submission? > > The package is still in the devel stage, could this be the issue? > > Best, > > Krutik > From: Nitesh Turaga > Sent: 24 September 2020 13:37 > To: Krutik Patel (PGR) > Cc: bioc-devel@r-project.org >

Re: [Bioc-devel] DMCHMM package new release

Hi Farhad, It seems you should follow this http://bioconductor.org/developers/how-to/git/resolve-conflicts/ . Another tip, if you have to locate files with conflicts is git diff --name-only --diff-filter=U I took a

Re: [Bioc-devel] Few questions of maintaining a new bioconductor package

> contact bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> for help. > > Would it have been better if I had the email all lower case on submission? > > The package is still in the devel stage, could this be the issue? > > Best, > > Krutik > From

Re: [Bioc-devel] Few questions of maintaining a new bioconductor package

Everything on our end seems to be fine. You have to first activate your account, and it might be case sensitive "k.pat...@newcastle.ac.uk ” Try that. Nitesh > On Sep 19, 2020, at 4:46 AM, Krutik Patel (PGR) > wrote: > > Thank you for your advice Nitesh

Re: [Bioc-devel] An issue about submitting my SSH key to Bioconductor

Hi You have to activate your account. I believe the problem is because our system got your email in a case-sensitive manner “xiaowen.c...@jax.org ”, but it should be all lowercase. Please try again, I’ve corrected it. Best, Nitesh > On Sep 25, 2020, at 4:10

Re: [Bioc-devel] Issue with connecting to 'git.bioconductor.org' during git fetch --all

Most people don’t use passphrase for SSH keys on Bioconductor. But it seems like you do have one or your permissions for the SSH key pair you have are wrong. 1. If you have a passphrase and forgot it, just make a new SSH key and add it to your BiocCredentials account. 2. If it’s a

Re: [Bioc-devel] Git pack file greater than 5MB

git repository. Nitesh > On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson > wrote: > > Doesn't a git rewrite break all existing clones, forks out there? I'm happy > to be corrected, if this is not the case. > > /Henrik > > On Thu, Oct 1, 2020, 08:16 Nitesh Turaga <

Re: [Bioc-devel] Git pack file greater than 5MB

Hi, The BiocCheck will complain on the build system about the > 5MB package size. The rewrite of the history with BFG cleaner (https://rtyley.github.io/bfg-repo-cleaner/ ) is not as severe as you think it is to be honest. It is just removing these

Re: [Bioc-devel] Granting package access to other developers

Hi Jason This has been resolved. Aaron should have access Nitesh > On Sep 15, 2020, at 10:30 PM, Jason Ji wrote: > > Dear Bioconductor maintainers, > > I am the developer and maintainer of the TSCAN package > (https://bioconductor.org/packages/release/bioc/html/TSCAN.html). I wonder >

Re: [Bioc-devel] [External] Re: Package Submission Limbo

Hi Benjamin and Chris, I’ll have the review out today. Best regards, Nitesh > On May 30, 2020, at 8:32 PM, Haibe-Kains, Benjamin > wrote: > > Thanks Martin, your prompt reply is mostly appreciated. Any chance that > RadioGx and ToxicoGx will be reviewed before July? This would be really

Re: [Bioc-devel] git push permission denied

Hi, This is because you don’t have access to FRASER package. Only Ines Scheller seems to have access to it. I’ve made the change and you should have access to it now. Best, Nitesh > On Jun 2, 2020, at 12:34 AM, Christian Mertes wrote: > > Dear Bioc team, > > I tried to push an update

Re: [Bioc-devel] Few questions of maintaining a new bioconductor package

Hi, You will not have to do anything once your package is accepted. http://bioconductor.org/developers/package-submission/ . Almost all your queries are answered in this help page. 1. To trigger a new build, include a version bump in

Re: [Bioc-devel] immunoClust e-mail contact will change

Hi You can contact me after your email changes, if you need help, but you can do it yourself. One thing you can do yourself is, change the email on 1. BiocCredentials and then 2. The package DESCRIPTION file, in that order. Best, Nitesh > On Jul 13, 2020, at 7:31 AM, Sörensen, Till Antoni

Re: [Bioc-devel] MultiAssayExperiment not found in docker devel image

Hi Joesph, 1. The RELEASE_3_11 and devel images do not have any installed packages. You are free to install the packages within these images. Please read the help http://bioconductor.org/help/docker/ . The goal behind these images is to provide an image

Re: [Bioc-devel] MultiAssayExperiment not found in docker devel image

rsion or the > stable release version? > > Thanks, > > Joe > > On Mon, Aug 3, 2020 at 8:11 AM Nitesh Turaga wrote: >> >> Hi Joesph, >> >> 1. The RELEASE_3_11 and devel images do not have any installed packages. You >> are free to

Re: [Bioc-devel] bioconductor_docker updates

g fix >> with regards to the igraph package’s missing dependency. >> >> docker inspect --format '{{ index .Config.Labels.version}}' >> bioconductor/bioconductor_docker:RELEASE_3_11 >> >> >> If you have any further questions, please reply to this thread.

Re: [Bioc-devel] bioconductor_docker updates

> Nitesh! Is there a place to start discussing how to implement tests for these > images, or is that premature? > > Sean > > > On Tue, Aug 4, 2020 at 6:33 AM Nitesh Turaga <mailto:nturaga.b...@gmail.com>> wrote: > Hi Levi, > > Within the RStudio termina

Re: [Bioc-devel] bioconductor_docker updates

.14" Best, Nitesh > On Aug 4, 2020, at 6:33 AM, Nitesh Turaga wrote: > > Hi Levi, > > Within the RStudio terminal console you can check the contents of the file > `/etc/environment`. This should show you a version number > > $ cat /etc/environment > ‘BI

Re: [Bioc-devel] Changing Package Maintainer

Hi Chris, The email benjamin.haibe.ka...@utoronto.ca is registered to you Chris Eeles. You should be added to the packages now for access. However the “maintainer” field in the description file needs to be changed by you. Best, Nitesh > On Jul 6,

Re: [Bioc-devel] Changing Package Maintainer

ing back to me. So in the future to change maintainers I can > simply update the DESCRIPTION? > > I wasn’t sure based on the issues we had with the credentials account and > didn’t want to assume. > > Best, > Chris > > From: Nitesh Turaga mailto:nturaga.b...@gmail.com>&

Re: [Bioc-devel] rename a package

Hi Estefi, It would help us inform you better if you tell us 1. Is the package in Bioconductor already? 2. Name of the package/issue number in the contributions. Best, Nitesh > On Jul 13, 2020, at 3:41 AM, Estefania Mancini wrote: > > Hi all, > > Can someone share with me a guideline /

Re: [Bioc-devel] rename a package

> My package is in Bioconductor since 2016 and its name is ASpli > (http://bioconductor.org/packages/release/bioc/html/ASpli.html) > > I was wondering how to rename it just in case we need it. > > thanks a lot, > > Estefi > ________ >

Re: [Bioc-devel] Bioconductor credentials issue

Hi Chris, This is a very strange problem which I haven’t come across before. But let me say this though, the fact that this email "benjamin.haibe.ka...@utoronto.ca ” is connected to your username, Github ID and has your SSH keys is not correct. I

Re: [Bioc-devel] Lost bioconductor email

Hi Jurrian, The email listed on your account is jurriandekan...@gmail.com . It is the same email you are using now. You have never activated your BiocCredentials account. You should first https://git.bioconductor.org/BiocCredentials/account_activation/

Re: [Bioc-devel] Bioconductor credentials issue

; are: > consensusOV > CoreGx > genefu > PharmacoGx > predictionnet > RadioGx > survcomp > ToxicoGx > Xeva > > If you think duplicated account public keys may be the cause, could you > reinitialize my credentials account without any SSH keys and I will ad

Re: [Bioc-devel] Maintainer transfer

Hi Jakob, It seems your didn’t get the BiocCredentials email from me. But you have an account with the email "jakob.wir...@embl.de ”. It is associated with the SIAMCAT package. Once you add your SSH keys you should be able to access the package. Try again to

Re: [Bioc-devel] git push access to MsCoreUtils repository

You should have access now. I’m cc-ing Laurent and Johannes who are authors on the package as well. Best, Nitesh > On Jun 24, 2020, at 6:42 AM, Sebastian Gibb via Bioc-devel > wrote: > > Dear Bioconductor team, > > we (Laurent Gatto, Johannes Rainer, both CC) are maintainers of the >

Re: [Bioc-devel] git fetch and push issues to TreeAndLeaf

Hi, It seems you need to take a look at our documentation https://bioconductor.org/developers/how-to/git/. There is a "New Package Workflow" which you need to read and follow. That should set you up and get you going. Best, Nitesh On 6/24/2020 2:52 PM, Milena Andreuzo wrote: Dear

Re: [Bioc-devel] Bioconductor credentials issue

And you cannot see the packages listed under your account even now? Can you add a new SSH key if that is the case? Best, Nitesh > On Jun 19, 2020, at 6:59 PM, Chris Eeles > wrote: > > Hi Nitesh, > > I had to reset the password but yes I can. > > Best, >

Re: [Bioc-devel] Bioconductor credentials issue

stopher.ee...@outlook.com > <mailto:christopher.ee...@outlook.com> does not work and I cannot reset the > password (I don’t get an email). > > Best, > Chris > > From: Nitesh Turaga mailto:nturaga.b...@gmail.com>> > Sent: June 20, 2020 10:36 AM > To: Chris

Re: [Bioc-devel] bioconductor singularity images

ver on an HPC over ssh. Sincerely, Poorani Subramanian, Ph.D. Computational Biology Specialist, BCBB Science Support Contractor, MSC, Inc. Office: 240.747.7378 | Mobile: 301.875.8573 bioinformatics @NIAID <https://bioinformatics.niaid.nih.gov/services> *From: *Nitesh Turaga *Date: *Monda

Re: [Bioc-devel] bioconductor singularity images

Please check https://singularity-hub.org/collections/3955 <https://singularity-hub.org/collections/3955> > On Jun 15, 2020, at 11:09 AM, Nitesh Turaga wrote: > > Yes we do. > > You should see it in about 1 hour. It should have been available. My > bootstrap file to

Re: [Bioc-devel] bioconductor singularity images

Yes we do. You should see it in about 1 hour. It should have been available. My bootstrap file to convert the docker image to singularity had an extra newline character which prevented the build. Thanks for spotting this. I’ve made the fix. Best, Nitesh > On Jun 15, 2020, at 10:56 AM,

Re: [Bioc-devel] SSH Issues

share these credentials with Chris in a private email. Both Chris and Benjamin will have maintainer access to the packages in question. Best, Nitesh > On Jun 3, 2020, at 1:27 PM, Nitesh Turaga wrote: > > Hi Chris, > > Thanks for that list. I’ll give you and Benjamin a

Re: [Bioc-devel] Submitting SSH key

Hi Alemu, You need to do this only if you want to maintain the package. If you don’t want to maintain the package, you don’t have to do this. Best, Nitesh > On Jun 9, 2020, at 4:00 AM, Alemu Takele Assefa > wrote: > > a [[alternative HTML version deleted]]

Re: [Bioc-devel] SSH Issues

redentials for PharmacoGx and CoreGx are > managed under? If not how can I manage access to these repos? > > Thanks for your support. > > Best, > Chris > > From: Nitesh Turaga > Sent: June 3, 2020 11:05 AM > To: Chris Eeles > Cc: Bioc-devel@r-project.org > Subj

Re: [Bioc-devel] SSH Issues

consensusOV > CoreGx > > Benjamin’s GitHub username is bhaibeka, if I just change the username back > will that work? > > Sorry for an inconvenience. > > Best, > Chris > > From: Nitesh Turaga mailto:nturaga.b...@gmail.com>> > Sent: June 3, 202

Re: [Bioc-devel] SSH Issues

Hi Chris, http://bioconductor.org/developers/how-to/git/faq/ Take a look at #13 and #14. I’ll be able to better help you with more information. Best, Nitesh > On Jun 3, 2020, at 10:49 AM, Chris Eeles > wrote: > > Hello Bioconductor

Re: [Bioc-devel] UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 234445: ordinal not in range(128)

Hi, Just to keep the mailing list informed. This has been solved. Please push again. Nitesh > On May 18, 2020, at 11:20 AM, Jakob Theorell > wrote: > > Dear all, > I guess this is related to some to me unknown failure on my side to avoid > merge conflicts, but I now get the above error when

[Bioc-devel] Fwd: safe: Bioc build error in release and devel

Hi, This is just following up that this issue has been resolved. Best, Nitesh > Begin forwarded message: > > From: Ludwig Geistlinger > Subject: Re: safe: Bioc build error in release and devel > Date: June 10, 2020 at 5:30:45 PM EDT > To: Nitesh Turaga > Cc: "Sh

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

Hi Aditya, http://bioconductor.org/developers/how-to/git/faq/ #14 would give me more information on how to help you with this issue. Best, Nitesh > On Jun 11, 2020, at 12:15 PM, Bhagwat, Aditya > wrote: > > Dear Bioc Core, > > Thank

Re: [Bioc-devel] No access to dorothea package

Hi Christian Can you try to upload a new SSH key to your BiocCredentials account? It is likely that the SSH private key you are using doesn’t “match” the public key we have on record for your account. The easiest way to solve this, you upload a new key to BiocCredentials and try again.

Re: [Bioc-devel] Triggering a new build

There was no version bump. To trigger a build you have bump the version. Best, Nitesh > On Jul 16, 2020, at 10:37 AM, Spiro Stilianoudakis > wrote: > > Hello Bioconductor, > > I submitted a new package titled preciseTAD, for review. There were errors > in the build results. I have

Re: [Bioc-devel] Triggering a new build

Since you are able to push, please issue a version bump 0.99.1 on your package DESCRIPTION file. Only then we can confirm if something is broken. Nitesh > On Jul 16, 2020, at 10:47 AM, Shepherd, Lori > wrote: > > Thank you for your inquiry. We have experienced some issues adding >

Re: [Bioc-devel] Bioconductor Package Submission - Removing git pack objects

Hi, Please make sure the bare repository is updated with the “removed” artifacts of the .pack files. From what I understand, the .pack files should also be removed by the BFG cleaner. Try and follow this https://stackoverflow.com/questions/11050265/remove-large-pack-file-created-by-git

Re: [Bioc-devel] credential not recognized when git clone my packages

Hi Julie, Lori is correct, it seems you've never activated your account on BiocCredentials which is linked to julie@umassmed.edu. Please activate your account, add new SSH keys and you will gain access to your package. Best, Nitesh On 1/11/21, 2:51 AM, "Bioc-devel on behalf of Kern,

Re: [Bioc-devel] Illegal Version Bump after accidentally pushing Version Bump to 1.1.1

Hi, Which package are you talking about? Best, Nitesh > On Dec 7, 2020, at 4:32 AM, wrote: > > I was hoping to update my Bioconductor package, which I now know should have > been a version bump from 1.0.0 to 1.0.1. However, I have by mistake version > bumped to 1.1.1 meaning that the

Re: [Bioc-devel] (no subject)

Hi, Your packages are associated with kathleen.kl...@ladydavis.ca. I've changed it to your mcgill address now. Please try to activate it. Best, Nitesh On Mon, Dec 21, 2020 at 3:58 AM Kathleen Klein < kathleen.kl...@mail.mcgill.ca> wrote: > Good morning, > I am trying to activate my account on

Re: [Bioc-devel] can not activate account

Hi, I'll take a look at why this is happening and get back to you. Nitesh On Tue, Dec 15, 2020 at 10:21 PM 曹洋 wrote: > Dear > > Thanks for your attention. > > I'm currently maintain a bioconductor package GeneExpressionSignature. I > want to maintain github repository for

Re: [Bioc-devel] can not activate account

Hi, The email registered for this account is "amms.yang@gmail.com". This is the reason you have not been able to activate your account. I have changed the email to the one listed on the package. Please try to activate again. Best, Nitesh On Wed, Dec 16, 2020 at 7:51 AM Nit

Re: [Bioc-devel] git credential problem

Hi Qian, You should have access to the package using qian@roswellpark.org . You should be able to login to your BiocCredentials account and check if you have access. Everything on our end looks fine. You should change the DESCRIPTION in your package to

Re: [Bioc-devel] change of e-mail address

Hi, I don’t think we can help you change email on the bioc-devel mailing list. Please check password retrieval steps or just resubscribe with your new email. https://stat.ethz.ch/mailman/listinfo/bioc-devel Activate your account in

Re: [Bioc-devel] Access denied to lpNet package

Hi Lars, I’ve resolved your issue. You should have access now. Best regards, Nitesh > On Oct 20, 2020, at 5:21 AM, Prof.Dr. Lars Kaderali > wrote: > > Dear Bioconductor team, > > I changed institution and my old email address @tu-dresden.de no longer > exists. The packages RNAither and

Re: [Bioc-devel] Unable to install "msdata" package in current BioC 3.13 docker

Hi Johannes, I’ll take a look at this and get back to you. Best, Nitesh > On Nov 5, 2020, at 7:21 AM, Rainer Johannes wrote: > > Dear all, > > I'm unable to install the "msdata" package for the current BioC 3.13 release. > I keep getting the following error: > >>

Re: [Bioc-devel] cannot reproduce the build error with InTAD package

Hi Konstantin, It seems this is a new issue. Please give the devel build machine one more cycle and we'll see if the issue persists. Did you try to build it using the command in the build machine log (although I doubt it'll change the end result of successfully building on the

Re: [Bioc-devel] Version change when major redesign

Hi Enora, Bioconductor follows the following rules when it comes to version numbering. http://bioconductor.org/developers/how-to/version-numbering/ Remember, In your version number x.y.z, y should be odd in devel branch, and such major changes need to happen only in the devel branch. For

Re: [Bioc-devel] activate BiocCredentials account issue

Hi, This is because your account shows it is not activated. Please try to activate your account https://git.bioconductor.org/BiocCredentials/account_activation before trying to log in. Best, Nitesh On 1/9/21, 5:58 AM, "Bioc-devel on behalf of Yuzhou Chang" wrote: Thank you for the

Re: [Bioc-devel] Change of package mantainer/manager

Hi Carles, We would need your colleagues email address so we can make BiocCredentials account. The BiocCredentials account allows for SSH key maintenance. Once the maintenance access is given, your colleague would have to change the DESCRIPTION file where the names of the maintainer is

Re: [Bioc-devel] Change of package mantainer/manager

posome and omicRexposome. Best, Nitesh From: Carles Hernández Date: Thursday, January 21, 2021 at 7:44 AM To: Nitesh Turaga Cc: bioc-devel , Xavier Escribà Montagut Subject: Re: [Bioc-devel] Change of package mantainer/manager Dear Nitesh and colleagues, I humbly ask for the transference to

Re: [Bioc-devel] Error by commiting changes to Release_3_12

Best, Nitesh From: "Kern, Lori" Date: Monday, January 4, 2021 at 3:26 AM To: Nitesh Turaga , Khadija El Amrani Subject: Fw: Error by commiting changes to Release_3_12 Nitesh, This does not appear to have gone through on bioc-devel mailing list. Could you please assist. Lori Shephe

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