scGPS - Single Cell Global fate Potential of Subpopulations

[quanaibn]

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

• Repository: https://github.com/IMB-Computational-Genomics-Lab/scGPS

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[quanaibn]

Hi Marcel,

Thanks very much!

We're aiming to submit a manuscript based on the scGPS package by mid-July. We can continue to work on it after we have received your feedback.

Best wishes,

Quan

On Tue, Jun 4, 2019 at 5:13 AM Marcel Ramos notifications@github.com wrote:

Hi Quan, @quanaibn https://github.com/quanaibn Apologies for the delay. I was traveling last week. I will respond to your questions. Briefly, you can go over the 5 minute limit without problems. I will have another look at your package soon.

Best, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1042?email_source=notifications&email_token=AB6U7UEMLIQNP64R2GWJ72LPYVUOVA5CNFSM4G5RC4CKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW2M2NY#issuecomment-498388279, or mute the thread https://github.com/notifications/unsubscribe-auth/AB6U7UCQ2EEMII74EWIM7EDPYVUOVANCNFSM4G5RC4CA .

[LiNk-NY]

Hi Quan, @quanaibn

Please clean up the package. There are a lot of files that should not be there even if you're using pkgdown (including _pkgdown.yml, logo, scGPS.md, etc.). You should build your pkgdown website independently of the GitHub repository.

• Avoid using 1:x sequence generation. It is not robust. Please see: http://bioconductor.org/developers/package-guidelines/#rcode
• I think your users would appreciate an argument such as verbose = FALSE at the main function level.

Best, Marcel

[quanaibn]

Thanks Marcel,

We are revising the package to address your comments. We will try to submit the revised package by the middle of next week.

Best regards,

Quan

On Wed, Jun 5, 2019 at 1:24 AM Marcel Ramos notifications@github.com wrote:

Hi Quan, @quanaibn https://github.com/quanaibn

Please clean up the package. There are a lot of files that should not be there even if you're using pkgdown (including _pkgdown.yml, logo, scGPS.md, etc.). You should build your pkgdown website independently of the GitHub repository.

• Avoid using 1:x sequence generation. It is not robust. Please see: http://bioconductor.org/developers/package-guidelines/#rcode
• I think your users would appreciate an argument such as verbose = FALSE at the main function level.

Best, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1042?email_source=notifications&email_token=AB6U7UCCCDKXLCAJVG7TSS3PY2CKVA5CNFSM4G5RC4CKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW45XWY#issuecomment-498719707, or mute the thread https://github.com/notifications/unsubscribe-auth/AB6U7UCR5OIOCZAUJ2ID3XTPY2CKVANCNFSM4G5RC4CA .

[bioc-issue-bot]

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

e5c63fe vectorise, verbose, rename 1e52bd1 version bump

[bioc-issue-bot]

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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]

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

5839ac5 Update headings cdd1ff4 version bump

[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: "skipped, 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.

[bioc-issue-bot]

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

1520cdb version bump

[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: "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]

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

39a9667 version bump, server check

[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.

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

Please see the build report for more details.

[quanaibn]

Dear Marcel,

We have done with all revision of the package to address your comments.

In addition, we also created a github html user's instruction file, in here: https://imb-computational-genomics-lab.github.io/scGPS/articles/vignette.html

I hope you could have time to finalise our package soon.

Many thanks,

Quan

[bioc-issue-bot]

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

b08d641 merged for loops 117aa7f fixed broken link 8703ffd version bump

[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.

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

Please see the build report for more details.

[bioc-issue-bot]

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

15ece0c simplified function 60c83e6 version bump

[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.

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

Please see the build report for more details.

[LiNk-NY]

Hi Quan, @quanaibn Thank you for making those changes. It looks good! Your package has been accepted. Thank you for your contribution. Best, Marcel

[bioc-issue-bot]

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!

[quanaibn]

Hi Marcel, Fantastic! Thanks very much for your very valuable comments and help and we hope to contribute more packages in the future. Best wishes, Quan

[mtmorgan]

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

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See further instructions at

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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("scGPS"). The package 'landing page' will be created at

https://bioconductor.org/packages/scGPS

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.