Contributions
Contributions copied to clipboard
Bioconductor
Ribostan
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/zslastman/Ribostan
Confirm the following by editing each check box to '[x]'
-
[x ] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
-
[ x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
-
[ x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
-
[ x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
-
[x ] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
-
[x ] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
-
[x ] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
- [x ] The 'devel' branch for new packages and features.
- [x ] The stable 'release' branch, made available every six months, for bug fixes.
- [x ] Bioconductor version control using Git (optionally via GitHub).
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.
Hi @zslastman
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: Ribostan
Title: Estimates Isoform Specific RPF Footprint Densities
Version: 0.99.0
Authors@R:
person(given = "Dermot",
family = "Harentt",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(github = "www.github.com/zslastman"))
Maintainers@R:
person(given = "Dermot",
family = "Harentt",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(github = "www.github.com/zslastman"))
Description: Ribostan is a simple package which contains functionality related
to ribosomal footprint data and quantitative analysis thereof. It includes
functions to align A/P sites by maximizing including in the CDS, to produce
plots of KL divergence in 'metacodon' plots, and to estimate Ribosomal Footprint
densities in an isoform aware manner. It also provides functions for quantifying
periodicity of open reading frames, and identifying translated uORFs.
License: `use_mit_license()`, `use_gpl3_license()` or friends to
pick a license
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: RiboSeq, Sequencing, QualityControl, DataImport, GenomeAnnotation,
Transcriptomics, Software, Coverage, RNASeq
Suggests:
here,
knitr,
rmarkdown,
BSgenome.Hsapiens.UCSC.hg38,
AnnotationHub,
BiocStyle,
Imports:
rtracklayer,
rstan,
Matrix,
ggplot2,
Rsamtools,
BiocGenerics,
Biostrings,
testthat,
GenomicFeatures,
GenomicAlignments,
GenomeInfoDb,
GenomicFiles,
GenomicRanges,
IRanges,
S4Vectors,
readr,
stringr,
dplyr,
multitaper,
tidyr,
magrittr,
ORFik,
broom,
tibble,
Depends:
R (>= 4.0.0)
see https://github.com/zslastman/RiboStan/issues/2 -- can't even build with current R/Bioc
Hi, sorry about that! I will be able to give this my focus again tuesday next week, will fix the licence issues and confirm it builds on my own machine, with the most recent bioc docker image.
On Tue, Dec 14, 2021, 2:39 PM Vince Carey @.***> wrote:
see zslastman/RiboStan#2 https://github.com/zslastman/RiboStan/issues/2 -- can't even build with current R/Bioc
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/2448#issuecomment-993553157, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJ3ENU6GX7ALJMVK7TMELLUQ5CJNANCNFSM5JWDHS7Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Hi! Sorry for the long delay. Changing jobs and address during the pandemic has taken up my time this past month. I'll be able to push again within two weeks.
@zslastman if you do not have time to work on the submission we can close the issue for inactivity and you can request it be opened again once your time allows.
Sorry for the delay guys, I'm available to work on the package again now.
https://github.com/zslastman/RiboStan/issues/2 is fixed
Can you let me know how to go about setting up a build environment that's identical to the one used by Bioconductor? My current understanding is that I want to load the most recent docker image and then run R CMD build, but I notice this doesn't work on e.g. the DESeq2 source code, (it fails because the vignette dependency rmarkdown isn't installed). So I must not have it right.
How to "set[...] up a build environment that's identical to the one used by Bioconductor" is pretty much an open question at this time. We are working on github action templates that should eventually accomplish this. You are welcome to discuss the issue further on bioc-devel mailing list, detailing your expectations and efforts. I am working on pre-checks for your package now.
Did you run R CMD check on your package source tarball before pushing? Do so with version bumps for every source code change. With
commit 8d233ee11231f88ef069693ba1cbc18c3c3446f3
Author: Dermot Harnett <[email protected]>
Date: Thu Feb 17 14:47:25 2022 -0500
GRlists not imported
I am getting
--- re-building ‘Ribostan.rmd’ using rmarkdown
Quitting from lines 71-76 (Ribostan.rmd)
Error: processing vignette 'Ribostan.rmd' failed with diagnostics:
length(tokeep) > 0 is not TRUE
--- failed re-building ‘Ribostan.rmd’
Even INSTALL is noisy
PC002284:SUBMISSIONS vincentcarey$ R CMD INSTALL Ribostan
1/11 packages newly attached/loaded, see sessionInfo() for details.
* installing to library '/Users/vincentcarey/R-dev-dist/lib/R/library'
* installing *source* package 'Ribostan' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
1/11 packages newly attached/loaded, see sessionInfo() for details.
Note: wrong number of arguments to 'sqrt'
Note: wrong number of arguments to '=='
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '=='
Note: wrong number of arguments to '=='
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '/'
** help
*** installing help indices
** building package indices
1/11 packages newly attached/loaded, see sessionInfo() for details.
** installing vignettes
** testing if installed package can be loaded from temporary location
1/11 packages newly attached/loaded, see sessionInfo() for details.
** testing if installed package can be loaded from final location
1/11 packages newly attached/loaded, see sessionInfo() for details.
** testing if installed package keeps a record of temporary installation path
* DONE (Ribostan)
Okay, thanks Vincent, and sorry no I wasn't running check on the tarball. I'd been using devtools::check, but will switch to tarball + R CLI.
What is the correct method of specifying dependencies and then building such that all dependencies are installed? Again I had been using devtools but I guess this isn't bioconductor koshure. Should I simply assume that all dependencies, including e.g. BiocStyle for the vignettes, are present on the system I"m building on?
Good questions. We endeavor to answer these on the developer guidelines so if those are not sufficiently clear please pose questions at bioc-devel. We have automated the derivation of dependencies on R packages so you can assume all packages from CRAN or Bioconductor that are imported or suggested or depended upon or enhancing are available. Packages outside these two regulated environments cannot be used at all. As for system dependencies like runtime libraries the SystemRequirements field in DESCRIPTION should be used. I don't think there's a standard syntax/vocabulary for those requirements yet. @lshep @jwokaty
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Ribostan to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@zslastman, Could you remove the ERRORs in the build report, I can start reviewing the package once that's complete
Yes, apologies, only get them myself when I installed on a fresh system.
Also removing the non-standard evaluation from the dplyr functions to clean up the build report.
@zslastman may we expect updates soon? We like to see progress within a 3-4 week time frame of leaving comments and feedback? If you have an updated version to clean up the ERRORs please remember to activate your GitCredentials account https://git.bioconductor.org/BiocCredentials and push the update to git.bioconductor.org with a valid version bump to trigger a new build as described http://contributions.bioconductor.org/git-version-control.html#new-package-workflow
Hi Ishep. Yes, sorry for the delay. I'll update by next weekend at the latest.
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
Thank you for your interest in Bioconductor.
Hi! Ownership of the repository for this package has been transferred to https://github.com/ohlerlab/RiboStan. We would like to resume the submission process. Is it possible to re-open this issue?
Should maintainer access still be @zslastman or does this need to be updated ? FWIW there is not Maintainer@R official field; Specifying "Cre" in Authors@R designates the maintainer.
You should update the maintainer, Gabe will take over.
On Wed, Nov 8, 2023 at 8:48 AM lshep @.***> wrote:
Should maintainer access still be @zslastman https://github.com/zslastman or does this need to be updated ? FWIW there is not @.*** official field; Specifying "Cre" in @.*** designates the maintainer.
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/2448#issuecomment-1801926800, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJ3ENXCG3GYBFMUJBUT5EDYDOET5AVCNFSM5JWDHS72U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBQGE4TENRYGAYA . You are receiving this because you were mentioned.Message ID: @.***>
@ggvillamil do you have a BiocCredentials account; it doesn't look like it? If not I can set one up for you. what would be the best email to use?
Dear @zslastman ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Hi @lshep. Thanks for the assistance! I don't have an account yet. My email address is [email protected].
We have updated the credentials on our side. I will be sending you an email for how to activate your BiocCredentials account to add ssh keys for access
@ggvillamil this should have been taken care of. You should push to git.bioconductor.org to trigger a build report to proceed.