mcsurvdata - Githubissues

adricaba commented 6 years ago

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

Repository: https://github.com/adricaba/mcsurvdata

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

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bioc-issue-bot commented 6 years ago

Hi @adricaba

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: mcsurvdata
Type: Package
Version: 0.99.0
Date: 2018-07-20
Title: Meta cohort survival data
Author: Adria Caballe <adria.caballe@irbbarcelona.org>
Maintainer: Adria Caballe <adria.caballe@irbbarcelona.org>
Description: This package stores two merged expressionSet objects that contain
  the gene expression profile and clinical information of -a- six breast
  cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer
  data are employed in the vignette of the hrunbiased package for survival
  analysis of gene signatures.
VignetteBuilder: knitr
License: GPL (>=2)
NeedsCompilation: no
biocViews: Microarray, Preprocessing, Normalization, GeneExpression, Survival,
 ThirdPartyClient, DataImport, GUI
URL: https://github.com/adricaba/mcsurvdata
Depends: R (>= 3.5), ExperimentHub
Suggests: knitr
Imports: AnnotationHub, Biobase

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bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 6 years ago

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". 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.

mtmorgan commented 6 years ago

Usually experiment data packages have vignettes that describe the data, its origin and any pre-processing steps.

Is there any reason why your methodology is limited to microarrays, or is it likely to be used with more modern technologies (i.e., RNA-seq)? If the latter then SummarizedExperiment is much preferred as a representation. Also, consider providing the data in simple text-based format, and helper functions to input and assemble it into final objects; this helps protect your data package from 'bit rot' as the format of the R objects changes.

adricaba commented 6 years ago

Apologize for the error. I missed the vignettes folder which is now available in the github.

Thanks for the advice in using SummarizedExperiment instead of ExpressionSet. Our methodology (whose associated R package should be submitted soon) points out some issues in estimating gene signatures association with survival outcome, which can be critical when using microarray data. Right now we are not thinking about extending it for other methodologies though.

Best regards, Adria

On 08 Aug 2018, at 17:06, Martin Morgan notifications@github.com wrote:

Usually experiment data packages have vignettes that describe the data, its origin and any pre-processing steps.

Is there any reason why your methodology is limited to microarrays, or is it likely to be used with more modern technologies (i.e., RNA-seq)? If the latter then SummarizedExperiment https://bioconductor.org/packages/SummarizedExperiment is much preferred as a representation. Also, consider providing the data in simple text-based format, and helper functions to input and assemble it into final objects; this helps protect your data package from 'bit rot' as the format of the R objects changes.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/831#issuecomment-411438980, or mute the thread https://github.com/notifications/unsubscribe-auth/AnjzqgT9VgjxM3MC8RLLw9aHr7YzvIfWks5uOv5YgaJpZM4Vz44p.

Liubuntu commented 6 years ago

Hi @adricaba ,

If you already have the vignette available, please bump the version in DESCRIPTION so that it triggers an automatic building. When you get a new building report, try to fix all ERROR, or WARNING, and as much as the NOTE messages.

If you haven't already done so, please follow the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

Thanks for your contribution to Bioconductor, and let me know for any questions.

Cheers, Qian

Liubuntu commented 6 years ago

Hi @adricaba ,

Are you still actively maintaining your package? Like I said in the above comment, please add the vignette in the github repo and bump version, so that the ERROR could hopefully go.

We are having a general 2 week policy for processing the new package submission. We would expect the package maintain to be actively involved in the package review process (making modifications of your package according to the Bioconductor technical review, bumping versions, address other issues from building report), and we also expect the package maintainer to actively maintain their packages during each release (by fixing bugs, answering user's questions on support or mailing list) after the package is included into Bioconductor.

If there is no response at all within 2 weeks, we will close the issue for now. Feel free to reopen it whenever you think you would be more available for the process. Thanks, and let me know for any question.

Best, Qian

adricaba commented 6 years ago

Hi Qian,

If I am not wrong, I did that last week, but I am afraid I missed sending the confirmation email.

I hope it is all OK now.

Thanks, Adria

On 20 Aug 2018, at 21:30, Qian Liu notifications@github.com wrote:

Hi @adricaba https://github.com/adricaba ,

Are you still actively maintaining your package? Like I said in the above comment, please add the vignette in the github repo and bump version, so that the ERROR could hopefully go.

We are having a general 2 week policy for processing the new package submission. We would expect the package maintain to be actively involved in the package review process (making modifications of your package according to the Bioconductor technical review, bumping versions, address other issues from building report), and we also expect the package maintainer to actively maintain their packages during each release (by fixing bugs, answering user's questions on support or mailing list) after the package is included into Bioconductor.

If there is no response at all within 2 weeks, we will close the issue for now. Feel free to reopen it whenever you think you would be more available for the process. Thanks, and let me know for any question.

Best, Qian

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/831#issuecomment-414434795, or mute the thread https://github.com/notifications/unsubscribe-auth/Anjzqh1ff4-FVIpwX1hA7TANqWHlZRkJks5uSw47gaJpZM4Vz44p.

lshep commented 6 years ago

Please do a version bump in the package DESCRIPTION to kick off a new build. If the webhook was initialized correctly it will provide a new build report for review.

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

c183832 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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". 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.

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

d39fc8d Update DESCRIPTION

bioc-issue-bot commented 6 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

Liubuntu commented 6 years ago

The package is building successfully. A technical review will be given shortly. (within 2 weeks)

Liubuntu commented 6 years ago

Hi @adricaba ,

Thank you for the contribution to Bioconductor. Here is the technical review of your experiment data package. Please address the issues and comment back with any question or ready for a 2nd look. Thanks!

DESCRIPTION

Seems that you have some info for other authors in the documentation. You may want to use Authors@R to specificy in DESCRIPTION. e.g.,

Authors@R: c(person("Valerie", "Obenchain", role=c("aut", "cre"),
        email="maintainer@bioconductor.org"),
                    person("Martin", "Morgan", role="aut"),
                        person("First", "Last", role="ctb")

vignette

Add SessionInfo() as the section 3 before Reference.
Some typos, you may want to run a spell checker for the rest. L29, change "1.072" to "1,072"? L47, "samples processing" to "sample processing"? L53: "No samples were excluded" to "No sample was excluded"? ...

Cheers, Qian

Liubuntu commented 6 years ago

Hi @adricaba ,

I am reminding now (Usually we have 2 weeks notice) only because I will travel from next week with limited internet connection. It would be great if you can make updates soon. Since most of them are really just cosmetic, it would not be hard to address and the acceptance would be fast. Thanks!

Best, Qian

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

79beab0 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

lshep commented 6 years ago

Could you please also update the BiocViews listed in the DESCRIPTION to be from the ExperimentData subset of terms as this is an ExperimentData package.

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

f7b77e9 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

bioc-issue-bot commented 6 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

mtmorgan commented 6 years ago

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/adricaba.keys is not empty), then no further steps are required. Otherwise, do the following:

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 biocLite(\"mcsurvdata\"). The package 'landing page' will be created at

https://bioconductor.org/packages/mcsurvdata

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.

Bioconductor / Contributions

mcsurvdata #831

DESCRIPTION

vignette