trvinh 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/BIONF/PhyloProfile

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

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bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

07e715a not loading svMisc::package

bioc-issue-bot commented 5 years ago

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trvinh commented 5 years ago

Dear @nturaga and @mtmorgan , thanks to @lshep I have moved the data from experiment data from github to AWS S3 and created an Experiment data package for them (https://github.com/BIONF/PhyloProfileData). I have revised the PhyloProfile package according to Martin's comments. I think it is ready for the next review now. Best, Vinh

bioc-issue-bot commented 5 years ago

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

f0b0d36 version bump

bioc-issue-bot commented 5 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: "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.

lshep commented 5 years ago

Hang tight the ABNORMAL is on our end. We will manually kick off a build for you when it is fixed. You should have a report within the next 10 min

lshep commented 5 years ago

Everything should be back to normal, we are manually kicking off a build of your data package first to have it build on all three builders, and then we will manually kick off a build of your software package. Once those post feel free to do version bumps as normal.

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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

1f78172 version bump

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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

451e036 added ggdendro to DESCRIPTION and NAMESPACE

bioc-issue-bot commented 5 years ago

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trvinh commented 5 years ago

Dear @nturaga and @lshep , just want to drop a quick note, that the package is ready for the next round of review :) Best, Vinh

nturaga commented 5 years ago

Ok. I will review in the next few days

On Tue, Jun 11, 2019 at 9:43 AM Vinh Tran notifications@github.com wrote:

Dear @nturaga https://github.com/nturaga and @lshep https://github.com/lshep , just want to drop a quick note, that the package is ready for the next round of review :) Best, Vinh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1039?email_source=notifications&email_token=AAU6QS5RQG75LYN3SOIDBATPZ6TZPA5CNFSM4G4TU7CKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXNFHVI#issuecomment-500847573, or mute the thread https://github.com/notifications/unsubscribe-auth/AAU6QSZ2ZWQH2LMJFTUA2QDPZ6TZPANCNFSM4G4TU7CA .

trvinh commented 5 years ago

Many thanks in advance @nturaga ! :-)

trvinh commented 5 years ago

@nturaga Hi Nitesh, I don't want to bother you but I just want to ask how is the status of the review :-P

nturaga commented 5 years ago

PhyloProfile review

R CMD build

ok

R CMD INSTALL

ok

DESCRIPTION

Ok

NAMESPACE

ok

NEWS

Make sure the NEWS file is parsable by utils::news()

vignette

ok

man

ok

R

One major issue is your package introduces a lot of dependencies, which i'm not conviced you need.

Packages like stringr, have been used in core functions, very sparsely, and can easily be replaced by base R functions, just as easily.

The same applies to plyr as well. You can use

It appears that there no consistency in the data manipulation.

Imports:
    ape, bioDist, BiocStyle, Biostrings, Cairo, colourpicker, data.table,
    dendextend, devtools, dplyr, DT, energy, ExperimentHub, IRanges,
    GenomeInfoDbData, ggdendro, ggplot2, gplots, GO.db, grDevices, grid,
    gridExtra, gtable, knitr, pbapply, praise, RColorBrewer, reshape2,
    rmarkdown, scales, shiny, shinyBS, shinycssloaders, shinyjs, stats, stringr,
    svMisc, tidyr, testthat, tree, utils, OmaDB, plyr, xml2, zoo

Do you need all these packages? Remember, the more number of imports you have, the harder your package becomes to install and successfully run since you are dependent on all these to be installed on your users machine

Validating arguments, instead of use stop, and provide a useful error message. This is more valuable to the user than, just returning whenever something is not correct.
```
if (is.null(profiles)) return()
```
use,
```
if(is.null(profiles)) 
    stop("'profiles' is NULL, provide the correct value")
```
Make these changes everywhere. You seem to want to use "return" as the only way to exit from a function, this is not the case.
Remove commented out code.
Try not to have multiline functions declared within other functions. They get harder to debug as time passes. eg: generatePlot() is a lot of code to be embedded in another function varDistTaxPlot(). Keep them seperate, do this all across your code base.
This one NOTE is of value and makes sense to follow,
Checking function lengths.

    * NOTE: Recommended function length <= 50 lines.
      There are 23 functions > 50 lines.
      The longest 5 functions are:
        heatmapPlotting() (R/createProfilePlot.R, line 174): 191 lines
        filterProfileData() (R/parsePhyloProfile.R, line 702): 168
      lines
        estimateGeneAge() (R/estimateGeneAge.R, line 37): 150 lines
        varDistTaxPlot() (R/compareTaxaGroups.R, line 329): 139 lines
        createArchiPlot() (R/createDomainPlot.R, line 37): 133 lines

trvinh commented 5 years ago

@nturaga Hi Nitesh, the 2-weeks deadline is almost over but I want to leave a short note here, so that you know that I am still working on the revision :-) I will let you know when everything is ready for the next review. Best, Vinh

nturaga commented 5 years ago

Perfect. Keep working. No issues.

On Sat, Jul 20, 2019, 6:30 PM Vinh Tran notifications@github.com wrote:

@nturaga https://github.com/nturaga Hi Nitesh, the 2-weeks deadline is almost over but I want to leave a short note here, so that you know that I am still working on the revision :-) I will let you know when everything is ready for the next review. Best, Vinh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1039?email_source=notifications&email_token=AAU6QS4EB7LBH5UZTJXBZN3QAM4R5A5CNFSM4G4TU7CKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2NRTXI#issuecomment-513481181, or mute the thread https://github.com/notifications/unsubscribe-auth/AAU6QS3UZDPHNRLMNVXJGGTQAM4R5ANCNFSM4G4TU7CA .

nturaga commented 5 years ago

Hi @trvinh

Just leaving a message hoping you are still working on the package. If it takes more time, it is really best to close the issue and reopen the issue. The builder still works and you can keep updating your version number for a "closed" issue as well.

This will help us better gauge the number of active packages we have to review as reviewers. If it takes longer please close the issue and reopen.

Best,

Nitesh

trvinh commented 5 years ago

Hi @nturaga, The package is still alive and active :-) I am just on vacation right now. Next week I will push some changes to build a new version. I hope that it will be ok not to close this issue. Best, Vinh

bioc-issue-bot commented 4 years ago

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

286baee version bump

bioc-issue-bot commented 4 years ago

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

f2c3b22 Bioc revision2 - cont. (#102) * removed commented...

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

f24aac6 reduced function lengths - cont (#104)

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trvinh commented 4 years ago

@nturaga Hi Nitesh, I have revised the package based on your comments. I reduced the number of required packages stated in the DESCRIPTION file, as well as the length of several functions. However there are still 6 long functions which I cannot solve (it is not possible to split into multiple smaller functions). The NEWS file works with news() function in R terminal but not in RStudio, I read that it was RStudio‘s issue. I think it is ready for the next review. I am waiting for the new comments :-) Best, Vinh

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!

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/trvinh.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("PhyloProfile"). The package 'landing page' will be created at

https://bioconductor.org/packages/PhyloProfile

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/trvinh.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("PhyloProfileData"). The package 'landing page' will be created at

https://bioconductor.org/packages/PhyloProfileData

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

PhyloProfile #1039

PhyloProfile review

R CMD build

R CMD INSTALL

DESCRIPTION

NAMESPACE

NEWS

vignette

man

R