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Rcwl #980

Closed hubentu closed 5 years ago

hubentu commented 5 years ago

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

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bioc-issue-bot commented 5 years ago

Hi @hubentu

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: Rcwl
Title: Wrap Command Tools and Pipelines Using CWL
Version: 0.99.8
Authors@R: person("Qiang", "Hu", email = "qiang.hu@roswellpark.org", role = c("aut", "cre"))
Description: The package can be a simple and user-friendly way to manage command line tools and build data analysis pipelines in R using Common Workflow Language (CWL).
Depends: R (>= 3.6), yaml, methods, S4Vectors, batchtools, DiagrammeR, reticulate
Imports: utils, stats, BiocParallel
License: GPL
Encoding: UTF-8
LazyData: true
Suggests: testthat,
    knitr,
    rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.1.1
biocViews: Software, WorkflowStep
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, UNSUPPORTED, 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: "WARNINGS, skipped, UNSUPPORTED, 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 5 years ago

@hpages @lshep This package requires the python module(s) cwltool.

bioc-issue-bot commented 5 years ago

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

fd99d3b add SystemRequirements

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, UNSUPPORTED, 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.

lshep commented 5 years ago

So as a general comment - We feel like you shouldn't be changing or writing to a users system in the vignette or examples/tests. You should include instructions of what the user needs to do to set up to use the package and run the code assuming that this set up has been done (ie. there should be no system install or upgrades for the user )

bioc-issue-bot commented 5 years ago

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

e86c8ba remove scripts to install cwltool

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, UNSUPPORTED, 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.

hubentu commented 5 years ago

Hi @lshep , I have removed the scripts to install the cwltool and give an installation URL instead. Thanks!

lshep commented 5 years ago

Thank you. Please see initial review below.




General

Readme

vignette

> readLines(tres$output)
[1] "WARNING: ignoring environment value of R_HOME"
[2] "[1] 4 2 1 9 5"                                

> readLines(r7$output)
[1] "WARNING: ignoring environment value of R_HOME"
[2] "[1]  6  9 10  1  3"                           
[https://www.commonwl.org/v1.0/CommandLineTool.html#CWLType]()

R

doesn't need separate statements
cat("class:", class(object), "\n",
    "cwlClass:", cwlClass(object), "\n",
    "cwlVersion:", cwlVersion(object), "\n")

- [ ] There is WARNING in the build report about library/require call
- [ ] There is a NOTE about sapply vs vapply that should be updated
- [ ] For what its worth there is an ifelse function that could be a cleaner syntax for single input 
 It takes the for ifelse(test_expression, x, y) 
i.e 
   if(cwlClass(cwl) == "Workflow"){
        ilist <- c(id = names(inputList)[i], inputList[[i]])
    }else{
        ilist <- inputList[[i]]
    }
Could be written as

ilist <- ifelse((cwlClass(cwl) == "Workflow"), c(id = names(inputList)[i], inputList[[i]]), inputList[[i]])


Totally optional but I'm generally in favor of concise code. 

- [ ] There are occassionally comment out code chunks that should be removed. 

# Man 
- [ ] I would expand the package documentation maybe have a seealso link to main
package function

<br>
<br>
<br>

When the above have been addressed please kick off a new build with a version bump and comment back here with response/how the code has been updated.  

Thank you and I look forward to getting your package accepted into Bioconductor
~Lori
hubentu commented 5 years ago

Hi @lshep ,

Readme

 Installation instructions added.

vignette

  1. user_guide.Rmd has been renamed to Rcwl.Rmd.
  2. All outputs have been defined to tempdir() by outdir option.
  3. I could not repeat your warning from readLines outputs. The warning was not shown when I run check in the bioconductor/devel_core2 container. It might be caused by the R environment set in Renviron via google.
  4. The links were fixed.
  5. Real Bioinformatics pipelines and examples are packaged in another package RcwlPipelines. A new section of Resources was added to give more details about how this package could be used in practice.

R

  1. The show methods updated with shorter cat statements.
  2. The internal function runFun is used to assign Rcwl functions and inputs to each computing nodes in cluster server via the BiocParallel, so library(Rcwl) is used in this function.
  3. sapply was changed to vapply.
  4. I prefer shorter if and else. Thanks..
  5. Commented codes were cleaned.

Man

seealso links added to main package man.

Thanks, Qiang

bioc-issue-bot commented 5 years ago

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

3b58fd8 bump version

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, UNSUPPORTED, 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:

40fe7aa change noDocker to docker 40a2d6e Add cwlShiny; arguments works for workflow 987de9e Add cwlShiny

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:

3198f76 Fix warning for cwlShiny a1a9aa0 bump version

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, UNSUPPORTED, 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.

lshep commented 5 years ago

Sorry for the delay - I'm looking at the package and should have a review within the next day or two.

bioc-issue-bot commented 5 years ago

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

90f7140 Add cwltool version check

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, UNSUPPORTED, 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.

lshep commented 5 years ago

I still would also add the Bioconductor installation instructions to the README.md

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Rcwl")

But otherwise looks good.

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.

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  2. Submit your SSH key to Bioconductor

See further instructions at

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for working with this repository. See especially

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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

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

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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.