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HicAggR
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/CuvierLab/HicAggR
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[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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Hi @CuvierLab
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:
Type: Package
Package: HicAggR
Title: Set of 3D genomic interaction analysis tools
Version: 0.99.0
Authors@R: c(
person("Nicolas", "Chanard", email = "[email protected]", role = "aut"),
person("David", "Depierre", email = "[email protected]", role = "aut"),
person("Pascal", "Martin", email = "[email protected]", role = "ctb"),
person("Stephane", "Schaak", email = "[email protected]", role = "ctb"),
person("Refka", "Askri", email = "[email protected]", role = "ctb"),
person("Robel", "tesfaye", email = "[email protected]", role = "ctb"),
person("Olivier", "Cuvier", email = "[email protected]", role = c("cre","ctb"))
)
Description:
This package provides a set of functions useful in the analysis
of 3D genomic interactions. It includes the import of
standard HiC data formats into R and HiC normalisation procedures.
The main objective of this package is to improve the visualization and
quantification of the analysis of HiC contacts through aggreagtion.
biocViews: Software, HiC, DataImport, DataRepresentation, Normalization, Visualization
License: MIT + file LICENSE
URL: https://cuvierlab.github.io/HicAggR/,
https://github.com/CuvierLab/HicAggR
Depends:
R (>= 4.1),
InteractionSet
Imports:
BiocGenerics,
BiocParallel,
dplyr,
GenomeInfoDb,
GenomicRanges,
ggplot2,
grDevices,
IRanges,
Matrix,
methods,
rhdf5,
rlang,
rtracklayer,
S4Vectors,
stats,
strawr,
tibble,
tidyr
Suggests:
covr,
kableExtra,
knitr,
rmarkdown,
testthat (>= 3.0.0)
VignetteBuilder:
knitr
Encoding: UTF-8
LazyDataCompression: xz
RoxygenNote: 7.2.3
Config/testthat/edition: 3
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: "WARNINGS". 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/HicAggR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
We apologize for the delay. I will look over the package in the next week and provide feedback
I'm having trouble building the package locally
lorikern@jbcj433:~/PkgReviews$ R CMD build HicAggR
* checking for file 'HicAggR/DESCRIPTION' ... OK
* preparing 'HicAggR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HicAggR.Rmd’ using rmarkdown
sh: 1: curl: not found
Quitting from lines 69-76 (HicAggR.Rmd)
Error: processing vignette 'HicAggR.Rmd' failed with diagnostics:
'curl' call had nonzero exit status
--- failed re-building ‘HicAggR.Rmd’
--- re-building ‘InDepth.Rmd’ using rmarkdown
sh: 1: curl: not found
Quitting from lines 80-83 (InDepth.Rmd)
Error: processing vignette 'InDepth.Rmd' failed with diagnostics:
'curl' call had nonzero exit status
--- failed re-building ‘InDepth.Rmd’
SUMMARY: processing the following files failed:
‘HicAggR.Rmd’ ‘InDepth.Rmd’
Error: Vignette re-building failed.
Execution halted
I was also wondering the size and nature of the files being downloaded. Is there a reason a smaller example set of these types of files could not be included with the package to show functionality of the package?
This is still occurring and there has been no response. Closing this issue for inactivity. If you would like to continue on development and inclusion into Bioconductor please request the issue be reopened.
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.
Hello,
We've addressed the issues on the build you've reported and we've performed some more modifications.
We've checked with R CMD and BiocCheck, so can you please reopen this issue.
Thanks
Dear @CuvierLab ,
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.
I'm having trouble to connect to git.bioconductor.org:packages/HicAggR with a Permission denied (publickey) error. I've added my ssh key to my github account and I can push to CuvierLab/HicAggR, but not the bioc repo.
The key should be added to the BiocCredentials account. Currently the only account that has push permissions is [email protected] that is now associated with CuvierLab as the original submitter and listed maintainer. Only keys at CuvierLab are automatically added for access. If you should also have permissions it might be beneficial to have a different BiocCredentials account but could we please have Oliver Cuvier confirm this.
Can he confirm that through mail (using that address mail) or does he have to do it through a github account?
He can leave a message here on the issue or he can reach out via email which ever is easier
Ok thanks. I believe this is the mail address [email protected] that he can address it to, am I right?
I've sent you an email with information on how to activate your BiocCredentials account
Received a valid push on git.bioconductor.org; starting a build for commit id: 1e84578451fd8200299934ad596cbfa6875b41d7
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". 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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): HicAggR_0.99.3.tar.gz
Links above 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/HicAggR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: f77227af2273e5484a84fc417bc8cbc5203256ef
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". 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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): HicAggR_0.99.4.tar.gz
Links above 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/HicAggR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@lshep I'm having an ERROR report with Subscribe to the Bioc-devel mailing list, I don't understand this because I'm already subscribed to the bioc-devel list...
It is the listed maintainers email that must be registered to the bioc-devel mailing list
person("Olivier", "Cuvier", email = "[email protected]", role = c("cre","ctb"))
That email is not registered
Received a valid push on git.bioconductor.org; starting a build for commit id: 753ff5b0fc6dc10bcd05ba15b7915f620743cd90
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): HicAggR_0.99.5.tar.gz
Links above 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/HicAggR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I apologize for the delay. Please see comments below:
vignette
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[ ] (Optional) It seems like HicAggR and InDepth are relatively the same but InDepth gives more descriptions. Is it worth having the two or should HicAggR be removed and InDepth be reanmed HicAggR as the main vignette? This would also cut down on run time since then only 1 vignette is compiled/executed.
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[ ] Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope.
-
[ ] Update installation instructions with Bioconductor.
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[ ] It might be worth using a BiocFileCache when downloading test data to ensure against spotting internet connection. That way if the test file has already been downloaded it can still run. Using the default cache would be fine rather than creating a custom in this case.
tests
- [ ] I see you run all your functions which is good, but is it actually testing against anything for correct values? It seems like all the functions are just run with no actual validation being done.
R functions
- [ ] Function arguments should have validity checking to ensure values going in are expected. Things like listing acceptable values and using match.args or checking for right class type is given.
Please push changes with a valid version bump and comment back here with what has been addressed above.
@lshep I made the necessary modifications as suggested and I made an R cmd check and my build is failing on windows due to failure to build one of my dependencies (rtracklayer 1.63.2). It built fine with version 1.62.0 on my previous checks. So I was thinking setting the dependency to rtracklayer to version 1.62.0 rather than the latest. This would require resetting the dependency once the issue is resolved at rtracklayer. What do you recommend?
I would recommend ignoring the failure on windows right now; if its failing from rtracklayer it should eventually clear up. Please push your changes to git.bioconductor.org with a valid version bump to trigger the new build report