darth-donut 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/malhamdoosh/abseqR

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

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[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[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 commented 5 years ago

Hi @jiahfong

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: abseqR
Type: Package
Title: Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Version: 0.99.0
Authors@R: c(
    person("JiaHong", "Fong", email = "jiahfong@gmail.com", role = c("cre", "aut")),
    person("Monther", "Alhamdoosh", email = "m.hamdoosh@gmail.com", role = "aut"))
Description: AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets 
    generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users 
    of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and
    allows them to generate interactive HTML reports for the convenience of viewing and sharing with 
    other researchers. Additionally, abseqR extends abseqPy to compare multiple
    repertoire analyses and perform further downstream analysis on its output.
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: 
    ggplot2,
    RColorBrewer,
    circlize,
    reshape2,
    VennDiagram,
    plyr,
    flexdashboard,
    BiocParallel (>= 1.1.25),
    png,
    grid,
    gridExtra,
    rmarkdown,
    knitr,
    vegan,
    ggcorrplot,
    ggdendro,
    plotly,
    BiocStyle,
    stringr,
    utils,
    methods,
    grDevices,
    stats,
    tools,
    graphics
VignetteBuilder: knitr
RoxygenNote: 6.1.0
Collate: 
    'AbSeqCRep.R'
    'util.R'
    'distributions.R'
    'upstreamAnalysis.R'
    'productivityAnalysis.R'
    'primerAnalysis.R'
    'diversityAnalysis.R'
    'annotationAnalysis.R'
    'abundanceAnalysis.R'
    'plotter.R'
    'AbSeqRep.R'
    'abseqReport.R'
    'statistics.R'
    'pairwise.R'
SystemRequirements: pandoc (>= 1.19.2.1)
URL: https://github.com/malhamdoosh/abseqR
BugReports: https://github.com/malhamdoosh/abseqR/issues
biocViews: Sequencing,
    Visualization,
    ReportWriting,
    QualityControl,
    MultipleComparison

bioc-issue-bot commented 5 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 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: "skipped, 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 5 years ago

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

26db7c5 Remove example data's logfile 441e839 Replace T/F with TRUE/FALSE 252fd5f Remove restriction that sample must have a log fil... e7dc41c Version bump 0.99.1

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: "skipped, 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 5 years ago

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

f73bd72 Remove abseqR.Rproj 9e4d0f0 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: "skipped, 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.

darth-donut commented 5 years ago

It seems like the error from macOS is similar to this. I tried setting options(bphost="localhost") in both vignette and R source (before calling bplapply) but it gave the same error.

By default, abseqR uses BPPARAM <- BiocParallel::bpparam() if the user doesn't specify one. If I use SerialParam on macOS, the error goes away. I can mitigate this error by checking if the OS is mac and use Serial instead of bpparam but I was wondering if there's a better solution?

Your thoughts are much appreciated.

Regards, Harry.

bioc-issue-bot commented 5 years ago

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

95ea4a2 Fix race condition on file write in diversity anal... 1af90a7 Fix VJ-assoc and scatter plot resolution Reduce r... d006962 Version bump v0.99.3

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: "skipped, 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 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: "skipped, 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.

nturaga commented 5 years ago

Hi @jiahfong ,

Without passing the build report, I cannot review your package. Please make sure the build report is as clean as possible with no ERRORs, WARNINGs and NOTE messages (i'm particular about the efficient coding style NOTE messages).

Once you have made changes, bump the z in your version number (x.y.z). This will trigger a new build.

Best,

Nitesh

darth-donut commented 5 years ago

Hi @nturaga,

The build passes on all OSes except for macOS. It seems like the error from macOS is similar to this. I tried setting options(bphost="localhost") in both vignette (in the setup chunk) and R source (before calling bplapply) but it gave the same error.

By default, abseqR uses BiocParallel::bpparam() if the user doesn't specify one. If I use SerialParam or BiocParallel::MulticoreParam(1) on macOS, the error goes away. I can mitigate this error by checking if the OS is mac and use Serial instead of BiocParallel::bpparam() but I was wondering if there's a better solution?

Your thoughts are much appreciated.

Regards, Harry.

nturaga commented 5 years ago

Thats fine @jiahfong. I'll take a closer look at it, but that appears a decent solution.

bioc-issue-bot commented 5 years ago

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

e8a0db0 Update man pages b2afd00 Change vignette output format to PDF Use PDF to r... e6807b9 Version bump 0.99.4

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: "skipped, 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 5 years ago

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

a9a665a Vignette output back to HTML 03db7d0 Version bump 0.99.5

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.

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

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nturaga commented 5 years ago

abseqR review

DESCRIPTION

ok

NAMESPACE

ok

data

You can host the images folder in the man/figures folder instead. Check https://cran.r-project.org/web/packages/Rdpack/vignettes/Inserting_figures_and_evaluated_examples.pdf

inst

ok

man

ok

vignette

Good and informative vignette!

R

Accessors (simple functions that return components of your object) rather than direct slot access (using @) help to isolate the implementation of your class from its interface. Generally @ should only be used in an accessor, all other code should use the accessor. The accessor does not need to be exported from the class if the user has no need or business accessing parts of your data object. Plain-old-functions (rather than generic + method) are often sufficient for accessors; it’s often useful to employ (consistently) a lightweight name mangling scheme (e.g., starting the accessor method name with a 2 or 3 letter acronym for your package) to avoid name collisions between similarly named functions in other packages.

There is the use of @ in multiple locations in your codebase. Please fix them all.
Make sure all your paste functions are required within the message, stop and warning calls. Some of them don't require paste as the values being passed are not vectors, i.e there is no recycling of the operation.

General

The package is well written and documented.

One way to further improve this package is the author considers writing some unit tests, since it's such an extensive code base. This will make the package more robust.

bioc-issue-bot commented 5 years ago

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

d20ddbf Remove 'paste' calls in stop, warning, and message... aabdd81 Add accessors to common slots 279a1c1 Merge branch 'hotfix/code-style' into develop 62eed6b Add test cases for public functions Add new test ... 615b813 Update makefile 5b4b975 Fix warning message on missing trace 54dd5ad Test README rendering in github 2fe5b63 Update size 3e661b2 update size 989b433 Update README.md cef973a Update README ef2ba80 Update REAMDE b21ffbe rename gif cfe0676 Update README.md 39387a8 Remove static pngs 03a0f4c Merge branch 'feature/unit-test' into develop a0e03f4 Merge branch 'develop' 92fa8db 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: "ERROR, 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 5 years ago

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

a7207b7 Remove one test case to reduce R CMD CHECK time 6fc0c09 Try PDF vignette f7622dc Bump 0.99.7

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: "skipped, 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 5 years ago

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

31ed182 Vignette back to html 8668349 Bump 0.99.8

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: "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 5 years ago

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

e8575e1 Testing PDF vignette with normalizedPath in PNGS 8ef1efd Replace devtools install github with BiocManager 46ab6df Bump version 0.99.9

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.

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

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bioc-issue-bot commented 5 years ago

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

ebf4d3f Move images to man/figures instead 6aa1e17 Bump 0.99.10

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.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

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

357fbbd Add desc to man/figures/ b6df8c5 Bump 0.99.11

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.

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

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darth-donut commented 5 years ago

Hi @nturaga

Thank you very much for your suggestions, here are the fixes:

data

You can host the images folder in the man/figures folder instead

Done.

R

Accessors

Accessors (simple functions that return components of your object) rather than direct slot access (using @) help to isolate the implementation of your class from its interface. Generally @ should only be used in an accessor, all other code should use the accessor. The accessor does not need to be exported from the class if the user has no need or business accessing parts of your data object. Plain-old-functions (rather than generic + method) are often sufficient for accessors; it’s often useful to employ (consistently) a lightweight name mangling scheme (e.g., starting the accessor method name with a 2 or 3 letter acronym for your package) to avoid name collisions between similarly named functions in other packages.

All instances of @ were removed throughout the codebase and replaced with accessors.

Redundant `paste`

Make sure all your paste functions are required within the message, stop and warning calls. Some of them don't require paste as the values being passed are not vectors, i.e there is no recycling of the operation.

Redundant pastes were removed in all message, warning, and stop function calls.

Unit tests

One way to further improve this package is the author considers writing some unit tests, since it's such an extensive code base. This will make the package more robust.

We have added unit tests in abseqR, starting with all the publicly exported functions.

Best regards, Harry

bioc-issue-bot commented 5 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 5 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/jiahfong.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(\"abseqR\"). The package 'landing page' will be created at

https://bioconductor.org/packages/abseqR

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

abseqR #905

abseqR review

DESCRIPTION

NAMESPACE

data

inst

man

vignette

R

General

data

R

Accessors

Redundant `paste`

Unit tests

Bioconductor / Contributions

abseqR #905

abseqR review

DESCRIPTION

NAMESPACE

data

inst

man

vignette

R

General

data

R

Accessors

Redundant paste

Unit tests

Redundant `paste`