Re: [Bioc-devel] persistent build errors in bioconductor package
I see, when you say > experiencing. When I check the error online, it says: > > "001E# service=git-upload-pack > > 0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR' > FATAL: unknown git/gitolite command: 'packages/powerTCR' > 001E# service=git-upload-pack > > 0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'" you mean that you point your browser to https://git.bioconductor.org/packages/powerTCR I see that message too; it is currently not possible to navigate to package sources in this way on our system. It looks like the recent commits are powerTCR master$ git log -n 2 commit 6ba40e640fb779371cbe8b3a232f8b0b3d549d12 Author: LiNk-NY Date: Thu Sep 6 15:52:35 2018 + additional updates from BiocInstaller to BiocManager commit 8af9bbf7f788defc73021b0621efa29b5f2d2361 Merge: 97dadf9 f5e4d5f Author: Hillary Koch Date: Thu Sep 6 09:37:03 2018 -0400 merge upstream and from our 'build report' http://bioconductor.org/checkResults/devel/bioc-LATEST/ clicking on the 'ERROR' for your package, e.g., on Linux http://bioconductor.org/checkResults/devel/bioc-LATEST/powerTCR/malbec1-buildsrc.html the page reports Snapshot Date: 2018-09-11 16:46:14 -0400 (Tue, 11 Sep 2018) URL: https://git.bioconductor.org/packages/powerTCR Branch: master Last Commit: 6ba40e6 Last Changed Date: 2018-09-06 11:52:35 -0400 (Thu, 06 Sep 2018) so the checkout on the build machine is consistent (compare the 'Last Commit:' field with the hash on the commit in the repository) with the most recent commit. It looks like you've pushed changes, but they have not fixed the problem. In your vignettes directory you have /powerTCR/vignettes$ ls powerTCR_cachepowerTCR_files powerTCR.html powerTCR.tex powerTCR.fdb_latexmk powerTCR.flspowerTCR.Rmd but you should have only the powerTCR.Rmd file committed, the others should be removed. Note that the log shows a commit from the core team to address use of BiocManager (replacing BiocInstaller) so the right sequence of commands will be along the lines of git pull # update to current version git rm -r vignettes/powerTCR_cache vignettes/powerTCR_files powerTCR.html powerTCR.tex powerTCR.fdb_latexmk powerTCR.fls git commit after the git commit command, it can be helpful to change to a new directory and make a local clone of your powerTCR package to make sure it builds, e.g., cd /tmp git clone /path/to/original/powerTCR R CMD build powerTCR R CMD check powerTCR_1.1.3.tar.gz if that works out then change back to the original repository and git push. Martin On 09/12/2018 08:30 PM, Hillary Koch wrote: Hi again, I recently wrote about some build errors my bioconductor package is experiencing. When I check the error online, it says: "001E# service=git-upload-pack 0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR' FATAL: unknown git/gitolite command: 'packages/powerTCR' 001E# service=git-upload-pack 0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'" > I wrote about this a couple of days ago and received the response " Martin Morgan Sep 9, 2018, 12:47 PM (3 days ago) to me, bioc-devel I'd guess that your remote is incorrect; it should use ssh, and the separation between the host 'git.bioconductor.org' and repository path 'packages/powerTCR' should be a colon, e.g., powerTCR master$ git remote -v origin g...@git.bioconductor.org:packages/powerTCR (fetch) origin g...@git.bioconductor.org:packages/powerTCR (push) This could be corrected in various ways, one is git remote remove origin git remote add origin g...@git.bioconductor.org:packages/powerTCR" I have looked into all of this again - I have an SSH key associated with the package which BioConductor is aware of. When I check "git remote -v" in master I see exactly origin g...@git.bioconductor.org:packages/powerTCR (fetch) origin g...@git.bioconductor.org:packages/powerTCR (push) plus the fetch and push for the upstream branch which I created some time ago. I am not sure how to proceed here. Thanks in advance for the help! Hillary [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] persistent build errors in bioconductor package
Hi again, I recently wrote about some build errors my bioconductor package is experiencing. When I check the error online, it says: "001E# service=git-upload-pack 0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR' FATAL: unknown git/gitolite command: 'packages/powerTCR' 001E# service=git-upload-pack 0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'" I wrote about this a couple of days ago and received the response " Martin Morgan Sep 9, 2018, 12:47 PM (3 days ago) to me, bioc-devel I'd guess that your remote is incorrect; it should use ssh, and the separation between the host 'git.bioconductor.org' and repository path 'packages/powerTCR' should be a colon, e.g., powerTCR master$ git remote -v origin g...@git.bioconductor.org:packages/powerTCR (fetch) origin g...@git.bioconductor.org:packages/powerTCR (push) This could be corrected in various ways, one is git remote remove origin git remote add origin g...@git.bioconductor.org:packages/powerTCR" I have looked into all of this again - I have an SSH key associated with the package which BioConductor is aware of. When I check "git remote -v" in master I see exactly origin g...@git.bioconductor.org:packages/powerTCR (fetch) origin g...@git.bioconductor.org:packages/powerTCR (push) plus the fetch and push for the upstream branch which I created some time ago. I am not sure how to proceed here. Thanks in advance for the help! Hillary [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioc2019 planning committee
The location is driven primarily by willingness of local organizers to host; there is no current location set for BioC2020, so if you're interested... Martin On 09/12/2018 07:08 PM, Stephanie M. Gogarten wrote: Are there any plans to have another BioC on the west coast in the near future? thanks, Stephanie On 9/10/18 1:32 PM, Levi Waldron wrote: Hi all, I'm organizing a planning committee for Bioc2019 in New York City (at NYU and Rockefeller University), June 24-26. There is lots to be done including peer review of proposed talks, workshops, and posters, developing the programme, adapting the web site (e.g. see http://bioc2018.bioconductor.org/), seeking sponsorship, promoting the conference, and creating next year's workshop booklet (e.g. see https://bioconductor.github.io/BiocWorkshops/). If you like to take part, let me know, and I will include you in a kick-off planning meeting within the next couple weeks. Sincerely, Levi ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor Git Credentials
Hello, I recently had a package accepted but am unable to sign in to submit your SSH public key or github id to Bioconductor. I’m not sure if this is necessary to do since I submitted my app through GitHub in the first place but when I go to log in or create an account, I get the error message: "john.gagnon...@gmail.com is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel@r-project.org for help.” Any help would be greatly appreciated! Thanks, John ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioc2019 planning committee
Are there any plans to have another BioC on the west coast in the near future? thanks, Stephanie On 9/10/18 1:32 PM, Levi Waldron wrote: Hi all, I'm organizing a planning committee for Bioc2019 in New York City (at NYU and Rockefeller University), June 24-26. There is lots to be done including peer review of proposed talks, workshops, and posters, developing the programme, adapting the web site (e.g. see http://bioc2018.bioconductor.org/), seeking sponsorship, promoting the conference, and creating next year's workshop booklet (e.g. see https://bioconductor.github.io/BiocWorkshops/). If you like to take part, let me know, and I will include you in a kick-off planning meeting within the next couple weeks. Sincerely, Levi ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocManager updates / changes
Dear Bioc-devs,
We have successfully completed the migration from BiocInstaller to
BiocManager.
Together, we modified about 570 packages that were using old
BiocInstaller code.
Please ensure that your package(s) install / build / check without
errors and that all
dependencies are properly documented in the DESCRIPTION file.
If you have any issues with your package related to our BiocManager
commits. Feel
free to reach out to me.
Thank you all for your continued cooperation.
Best regards,
Marcel
--
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
On 08/31/2018 01:28 PM, Marcel Ramos wrote:
> Dear bioc-devs,
>
> Thank you to all maintainers who have made appropriate changes to their
> packages *in devel*.
>
> This is an ongoing effort to replace any outdated BiocInstaller,
> biocLite, etc.
> code from packages as we transition to `BiocManager` before the next
> release.
>
> You may have noticed a recent commit to your package. These commits are
> the result
> of a script to automatically replace a set number of lines of code with
> BiocManager code.
>
> These lines include `library(BiocInstaller)`,
> `source("https://bioconductor.org/biocLite.R;)`, and
> `biocLite("pkgname")`.
>
> All in all, we have changed about 314 packages from about 578 packages.
> There are still
> about 264 packages left with `BiocInstaller` and `biocLite` calls.
>
> Please DO ensure that:
>
> * The language around these new changes is in concordance with the
> actual code
>
> * You update your package to use BiocManager, if you haven't already
>
> * Your package is building and dependencies are accounted for
>
>
> For a list of outstanding packages please see:
> https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
>
> For example code see devel landing pages such as:
> http://bioconductor.org/packages/devel/bioc/html/RaggedExperiment.html
>
>
> Best regards,
> Marcel
>
> --
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
>
> On 07/13/2018 05:11 PM, Marcel Ramos wrote:
>> Dear bioc-devs,
>>
>> About 4 weeks ago, I notified maintainers to make changes to their
>> bioc-devel vignettes and package code to support the use of
>> `BiocManager`.
>>
>> There are a number of packages that haven't made the transition in
>> Bioc-devel.
>>
>> Please see this GitHub gist for a list of outstanding packages:
>>
>> https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
>>
>> Best regards,
>>
>> Marcel
>>
>> Bioconductor Core Team
>> Roswell Park Cancer Institute
>> Dept. of Biostatistics & Bioinformatics
>> Elm St. & Carlton St.
>> Buffalo, New York 14263
>>
>>
>> On 06/20/2018 12:23 PM, Marcel Ramos wrote:
>>> Dear bioc-devs,
>>>
>>>
>>> A month ago we notified you about our "next generation" changes to
>>> BiocInstaller.
>>>
>>> Thanks to all beta testers and those who provided feedback and
>>> suggestions for a new package name.
>>>
>>>
>>> I am pleased to inform you that BiocManager is now on CRAN:
>>> https://cran.r-project.org/web/packages/BiocManager/index.html
>>>
>>>
>>> As mentioned in our last email, you can now install BiocManager using:
>>>
>>> ```
>>> install.packages("BiocManager")
>>> BiocManager::install("YourPackageNameHere")
>>> ```
>>>
>>> Action Item:
>>>
>>> - Please modify the vignettes in your bioc-devel packages to
>>> reflect the use of BiocManager
>>>
>>>
>>> After the next couple of weeks or so, we will be identifying packages in
>>> bioc-devel (3.8) that still
>>> mention BiocInstaller / biocLite.
>>>
>>>
>>> Best regards,
>>> Marcel
>>>
>>> Bioconductor Core Team
>>> Roswell Park Cancer Institute
>>> Dept. of Biostatistics & Bioinformatics
>>> Elm & Carlton Streets
>>> Buffalo, New York 14263
>>>
>>>
>>> On 05/09/2018 06:11 PM, Martin Morgan wrote:
Developers --
A preliminary heads-up and request for comments.
Almost since project inception, we've used the commands
source("https://bioconductor.org/biocLite.R;)
biocLite(pkgs)
to install packages. This poses security risks (e.g., typos in the
url) and deviates from standard R package installation procedures.
We'd like to move to a different system where a base package, call it
'BiocManager', is installed from CRAN and used to install Bioconductor
packages
if (!"BiocManager" %in% rownames(installed.packages()))
install.packages("BiocManager")
BiocManager::install(pkgs)
This establishes a secure chain from user R session to Bioconductor
package installation. It is also more consistent with base R package
installation procedures.
BiocManager exposes four functions
- install() or update packages
- version() version of Bioconductor in use
Re: [Bioc-devel] Activating Account failed
Hi,
There was a bug in the code that added new accounts. The bug was fixed and your
account has been added. Please try again to activate and log in. I see that 2
SSH keys were automatically from your ipumin github account. Once you login
you'll be able to see these.
Valerie
On 09/12/2018 06:44 AM, $BM{IaL1(B wrote:
Hi,
ipu...@163.com is associated with a maintainer of the
primirTSS which has been
accepted(https://github.com/Bioconductor/Contributions/issues/817). But I can
not activate ipu...@163.com in
https://git.bioconductor.org/BiocCredentials/account_activation/, and "ssh -T
g...@git.bioconductor.org" shows
"g...@git.bioconductor.org: Permission denied
(publickey)."
How can I solve this problem? Than you for any suggestions.
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[Bioc-devel] Activation failure
Dear Mr. or Ms.
I am trying to submit my SSH key, since my package, XINA was accepted to
Bioconductor. However, I couldn't activate my ID and got the following
message.
langho...@gmail.com is not associated with a maintainer of a Bioconductor
package. Please check the spelling or contact bioc-devel@r-project.org for
help.
My package description for the maintainer is below.
Authors@R: c(person("Lang Ho", "Lee", email = "langho...@gmail.com", role
= c("aut", "cre")), person("Sasha", "Singh", email = "
sasi...@bwh.harvard.edu", role = c("aut")))
Maintainer: Lang Ho Lee and Sasha A. Singh <
sasi...@bwh.harvard.edu>
Could you help me to activate my account?
Thanks,
Lang
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[Bioc-devel] Activating Account failed
Hi, ipu...@163.com is associated with a maintainer of the primirTSS which has been accepted(https://github.com/Bioconductor/Contributions/issues/817). But I can not activate ipu...@163.com in https://git.bioconductor.org/BiocCredentials/account_activation/, and "ssh -T g...@git.bioconductor.org" shows "g...@git.bioconductor.org: Permission denied (publickey)." How can I solve this problem? Than you for any suggestions. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
