genomicInstability

[reef103]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/reef103/genomicInstability

Confirm the following by editing each check box to '[x]'

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• [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.

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[bioc-issue-bot]

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: "ABNORMAL". 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 git@git.bioconductor.org:packages/genomicInstability to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

I'll try to debug a little and try to kick off a new build. Please ignore the above build report.

[bioc-issue-bot]

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: "TIMEOUT, 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. 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 git@git.bioconductor.org:packages/genomicInstability to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[reef103]

Thanks @lshep , CHECK is still generating the same error when trying to install dependencies from ExperimentHub:

> dset <- eh[["EH5419"]]
Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0 (2021-05-18)
Installing package(s) 'GSE103322'
Error in UseMethod("conditionMessage") : 
  no applicable method for 'conditionMessage' applied to an object of class "character"
Calls: [[ ... tryCatchOne -> doTryCatch -> install.packages -> getDependencies
Execution halted

[lshep]

@nturaga I'm having trouble reproducing the ERROR as well both locally and manually on the builders. Please ignore the ERROR for now and review based on local builds/review. I'll have to spend more time trying to debug this on the builders but should not hold up the review process

[reef103]

Thanks !

[reef103]

@nturaga Any news about addressing the issue with ExperimentHub? Thanks !

[nturaga]

genomicInstability

build

• unable to build locally on mac

check

• unable to check, since there are no build products

NEWS

empty

DESCRIPTION

ok

NAMESPACE

ok

vignette

ok

R

• Please issue a new build report, to see if previously found issues on the builders are still there.

• Good use of assertions.

• Don't need to use which() in a few places, as it is just indexing a logical vector that can already be used as an index.

man

• Could be more elaborate

General

• Your GitHub repo, is not parallel to the Bioconductor git repo. Please make sure the same commits are present in both places.

GSE103322

• Everything ok on this additional package

@reef103, Your package looks in good shape. I'm not sure why it's not building/checking clean locally on my machine (mac). Please fix the errors, and I'll get back to you in a couple of days to see if it's on our end.

[nturaga]

Hi @reef103 May I get an update on your status? I believe you are very close to package acceptance.

Please issue a new build report and sync your Github repo.

[reef103]

Nitesh. I have submitted both packages and I’m waiting for BioC review. This has been very frustrating given the error in the vignette is related to ExperimentHub and there is nothing I can do from my side. Still waiting but this is delaying the submission of our manuscript at the point we are considering sending the package to an alternative repository. Please, let me know whether you can accelerate the process and fix the issue with ExperimentHub. Thanks

Mariano

On Aug 10, 2021, at 6:08 AM, Nitesh Turaga @.***> wrote:

 Hi @reef103 Can I get an update on your status?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[nturaga]

genomicInstability

build

• unable to build locally on mac

check

• unable to check, since there are no build products

NEWS

empty

DESCRIPTION

ok

NAMESPACE

ok

vignette

ok

R

• Please issue a new build report, to see if previously found issues on the builders are still there.
• Good use of assertions.
• Don't need to use which() in a few places, as it is just indexing a logical vector that can already be used as an index.

man

• Could be more elaborate

General

• Your GitHub repo, is not parallel to the Bioconductor git repo. Please make sure the same commits are present in both places.

GSE103322

• Everything ok on this additional package

@reef103, Your package looks in good shape. I'm not sure why it's not building/checking clean locally on my machine (mac). Please fix the errors, and I'll get back to you in a couple of days to see if it's on our end.

Hi @reef103 I'm not sure why you say you are waiting for a review when the review was posted on July 12th in this thread.

Either way, I've accepted your package since it's close to being done and you have a deadline for the manuscript. I would still appreciate it if you made the corrections suggested in the review.

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/reef103.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("genomicInstability"). The package 'landing page' will be created at

https://bioconductor.org/packages/genomicInstability

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/reef103.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("GSE103322"). The package 'landing page' will be created at

https://bioconductor.org/packages/GSE103322

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.