netDx - Githubissues

shraddhapai commented 5 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/BaderLab/netDx.examples

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

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bioc-issue-bot commented 4 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: "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.

bioc-issue-bot commented 4 years ago

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

a7c0bf2 changing R dep to 3.4 as per bioc instructions

bioc-issue-bot commented 4 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: "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.

bioc-issue-bot commented 4 years ago

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

5bc1b96 Update DESCRIPTION

bioc-issue-bot commented 4 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: "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.

LiNk-NY commented 4 years ago

Hi Shraddha, @shraddhapai

I hope you are well.

Please make sure that you are using a temporary directory / file when using write.table.
outDir should be set to tempdir() by default.
Try to avoid using system2 (especially with rm) calls when there are native R functions available (unlink). In this case, using a temporary directory avoids the use of deleting folders for the user.

See: https://github.com/BaderLab/netDx/blob/5bc1b9640752726c0cf820175c88c726cb05e0b0/R/buildPredictor.R#L529

There are also some unresolved notes here:

* checking R code for possible problems ... [21s/21s] NOTE
pruneNets: warning in write.table(dat[idx, ], file = sprintf("%s/%s",
  newDir, f), sep = "\t", col = FALSE, row = FALSE, quote = FALSE):
  partial argument match of 'row' to 'row.names'
pruneNets: warning in write.table(dat[idx, ], file = sprintf("%s/%s",
  newDir, f), sep = "\t", col = FALSE, row = FALSE, quote = FALSE):
  partial argument match of 'col' to 'col.names'
buildPredictor: no visible binding for global variable TT_STATUS
compareShortestPath: no visible binding for global variable intType
compareShortestPath: no visible binding for global variable dijk
getPatientPredictions: no visible binding for global variable
  pctCorrect
makePSN_NamedMatrix: no visible binding for global variable curSet
makePSN_RangeSets: no visible binding for global variable spos
Undefined global functions or variables:
  TT_STATUS curSet dijk intType pctCorrect spos
* checking Rd files ... NOTE
prepare_Rd: featScores.Rd:11-13: Dropping empty section \source
prepare_Rd: featScores.Rd:14-15: Dropping empty section \references

Best regards, Marcel

LiNk-NY commented 4 years ago

Hi Shraddha, @shraddhapai I appreciate your diligence in getting the package ready for acceptance. Please provide any updates. You are almost there. :smile: Best, Marcel

shraddhapai commented 4 years ago

Hi Marcel, Happy New Year! Yes, I will plough on shortly. Just getting caught up with the to-do list after the holidays. Appreciate the time you're taking on the feedback.

Best Shraddha

On Mon, Jan 6, 2020 at 7:20 PM Marcel Ramos notifications@github.com wrote:

Hi Shraddha, @shraddhapai https://github.com/shraddhapai I appreciate your diligence in getting the package ready for acceptance. Please provide any updates. You are almost there. 😄 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/1149?email_source=notifications&email_token=ABZHUATW56KYFRXPFOI5XN3Q4PDC7A5CNFSM4HYMJN42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIHHUYA#issuecomment-571374176, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZHUAXOA27CBI5NO77QJ7LQ4PDC7ANCNFSM4HYMJN4Q .

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Shraddha Pai, PhD http://shraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto

LiNk-NY commented 4 years ago

Hi Shraddha, @shraddhapai Happy New Year! I hope you're doing well. Please update us on the status of the package. Thank you. -Marcel

shraddhapai commented 4 years ago

Hi Marcel, Thanks for checking in. Barring any other issues I will have the changes in by next week. Best,Shraddha

On Wed, Jan 22, 2020 at 1:01 PM Marcel Ramos notifications@github.com wrote:

Hi Shraddha, Happy New Year! I hope you're doing well. Please update us on the status of the package. Thank you. -Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1149?email_source=notifications&email_token=ABZHUAX35CBIIEFYBJP3PVDQ7CCWPA5CNFSM4HYMJN42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJUQ6ZA#issuecomment-577310564, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZHUAXXYFJM5MWBZ2LAQVDQ7CCWPANCNFSM4HYMJN4Q .

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Shraddha Pai, PhD http://shraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto

bioc-issue-bot commented 4 years ago

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

389a805 clear notes 981e69e address no visible binding errors 940e3bd Merge branch 'master' of https://github.com/BaderL...

shraddhapai commented 4 years ago

Hi Marcel, I resolved the issues listed in your message from December and increased the version number, triggering a build. However, I haven't yet gotten a build report, despite it having started several hours ago. Just letting you know incase there is something more I need to do that I am unaware of (in terms of getting the build to complete). Thanks,Shraddha

On Mon, Jan 27, 2020 at 12:36 PM bioc-issue-bot notifications@github.com wrote:

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

389a805 https://github.com/BaderLab/netDx/commit/389a8058393964de6133302b054d767e5c1b60d7 clear notes 981e69e https://github.com/BaderLab/netDx/commit/981e69e9dcdde14a869933c877f97729d6b1e6f1 address no visible binding errors 940e3bd https://github.com/BaderLab/netDx/commit/940e3bd8f340a6fbfbb69203646c167327877481 Merge branch 'master' of https://github.com/BaderL...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1149?email_source=notifications&email_token=ABZHUASQZVB3HFOMIIQ2KULQ74LTFA5CNFSM4HYMJN42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKAMGEA#issuecomment-578863888, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZHUATTC72QLBHK72HF5VDQ74LTFANCNFSM4HYMJN4Q .

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Shraddha Pai, PhD http://shraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto

lshep commented 4 years ago

Sorry. On our end. You should receive a report shortly.

bioc-issue-bot commented 4 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: "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.

bioc-issue-bot commented 4 years ago

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

bf4b04e need to build with R3.6

bioc-issue-bot commented 4 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: "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.

LiNk-NY commented 4 years ago

Hi Shraddha, @shraddhapai I had another look at your package. It's looking much better! Thank you for your contribution and sticking with it. Best regards, Marcel

bioc-issue-bot commented 4 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!

shraddhapai commented 4 years ago

Hurray! :) Now this makes my day. Thanks for all your guidance. When will the package be available for the community to download on BioConductor?

Also, I have more functionality I'd like to add in anticipation of a software update we're planning to publish. What is the process for the review process for that?

Thank you, Shraddha

On Thu, Feb 6, 2020 at 5:20 PM bioc-issue-bot notifications@github.com wrote:

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!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1149?email_source=notifications&email_token=ABZHUAXFJGSZG75CZDAQDA3RBSEMPA5CNFSM4HYMJN42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELBACCQ#issuecomment-583139594, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZHUAW5U5TPKBYECQED5JTRBSEMPANCNFSM4HYMJN4Q .

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Shraddha Pai, PhD http://shraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto

LiNk-NY commented 4 years ago

@shraddhapai Once it gets added to the manifest (soon after the issue is closed). You can continue to add functionality up until the release. This means you can make changes once it is in the devel branch. Don't forget to build and check changes before uploading.

Best, Marcel

shraddhapai commented 4 years ago

Hi, OK got it - thank you! Best,Shraddha

On Thu, Feb 6, 2020 at 9:08 PM Marcel Ramos notifications@github.com wrote:

Once it gets added to the manifest (soon after the issue is closed). You can continue to add functionality up until the release. This means you can make changes once it is in the devel branch. Don't forget to build and check changes before uploading.

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/1149?email_source=notifications&email_token=ABZHUAQQPWP6S23CFOMDEDLRBS7B5A5CNFSM4HYMJN42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELBPBDY#issuecomment-583200911, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZHUASYMVZUKW673LP2MEDRBS7B5ANCNFSM4HYMJN4Q .

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Shraddha Pai, PhD http://shraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto

mtmorgan commented 4 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/shraddhapai.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 BiocManager::install("netDx.examples"). The package 'landing page' will be created at

https://bioconductor.org/packages/netDx.examples

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.

mtmorgan commented 4 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/shraddhapai.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 BiocManager::install("netDx"). The package 'landing page' will be created at

https://bioconductor.org/packages/netDx

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

netDx #1149

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