averissimo commented 6 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/sysbiomed/glmSparseNet

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

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[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.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 6 years ago

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

8bf0752 adds back a vignette for normal survival

bioc-issue-bot commented 6 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.

Please see the build report for more details.

bioc-issue-bot commented 6 years ago

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

a8b0949 adds all vignettes to see if it builds under 5 min...

bioc-issue-bot commented 6 years ago

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

7e911e2 a vignette was missing

bioc-issue-bot commented 6 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.

Please see the build report for more details.

bioc-issue-bot commented 6 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.

Please see the build report for more details.

averissimo commented 6 years ago

Hi Marcel ( @LiNk-NY ), here is the full response, point by point.

The feedback you gave was very helpful in greatly improving the package's implementation.

I hope I addressed all the technical concerns and look forward to your response.

glmSparseNet #849

DESCRIPTION

* Looks good overall.

* Why do you need `devtools` and `roxygen` in the `Suggests` field?

I don't and they have been removed, at one point I might had some problem in travis CI

NAMESPACE

* Avoid using `.` dot delimiters in function names such as
  `build.string.network` unless you're creating S3 methods. The Bioconductor
  convention is to use `camelCase`

Done! camelCase it is I also renamed non-exported functions to have '.' prefix

vignettes/

* It looks like you incorrectly reference `TCGAbiolinks` rather than
  `curatedTCGAData` in the vignettes

Corrected, nice eye!

* Your code can use helper functions in `TCGAutils` that allow you to separate
  assays by sample type code (referring to tumors, normals, etc.)

Converted code to use TCGAutils, very nice package that I did not know about

* "metastatic" samples (code 11) actually refer to 'Solid Tissue Normal', see
  `data(sampleTypes)` in `TCGAutils`

Copy/paste mistake thanks

* You should use functions like `TCGAbarcode`, `splitAssays`,
  `intersectColumns`, `as(X, "MatchedAssayExperiment")` etc.

Done that, I could not find an already implemented function that removed clinical cases that were not in a specific assay, so I kept my 'reduceByExperiment' function with slight improvements

* Your vignette code could probably be reduced to a few lines for the first
  part of the vignette (the 'data.show' chunk)

Yes!! although not for the survival case, that required additional processing

R/

* Don't create methods for regular classes such as `matrix`. Please create a
  regular function and have checks in place so that it only works for certain
  classes (in this case `matrix`)

Removed all methods from package as per your advice

* You don't need to create a generic if you're only going to set a method for
  a single class (see `degree.sparsebn`)

Done

* See bullet under `NAMESPACE` with regards to the dots `.` in functions

Done!!, see response in NAMESPACE

* Ensure that your code is readable by limiting line widths to less than 80
  columns

Done! Not a single one! also converted to 4 space indentation, with some exceptions such as function arguments definition so they are indented with first argument

exampleFun <- function(arg1,
                       arg2,
                       ...) {

Could not find if this is good practice, or should I continue to use 4 space for arg1 and ...

* Consider using the data structure as your first argument for functions like
  `degree.generic` and similar. You may also want to have a default function for
  the `fun` argument

added default fun argument, but not a structure

* Consider using `BiocParallel` for parallel computations

On my tests mclapply was faster than BiocParallel so I went with that one. I'll consider switching on a future version, especially if iterating over Bioc data structures

* Avoid using `seq(1, X)` use `seq_len(X)` for robustness

I believe all seq(1, X) was already converted to seq_len(X)

* Remove any code that is commented out or provide a working version of it.

* Consider including a script that generated the dataset documented in `data.R`

Done! data.R was moved to a publication-specific package that will not be submitted to Bioc

* You shouldn't have to create so many methods for the different class
  combinations, just create one regular function and have a filtering step
  that will account for the different inputs.

My basis for doing this was flawed and used the filtering step, thanks!

* Look into a replacement for `biocmaRt`. I'm not sure what package is
  recommended here.

Is there a problem for having biomaRt? I depend on this to get conversions between geneIds and geneNames

* You should only create methods for classes that you create and not external
  classes (e.g., `SummarizedExperiment` and `MultiAssayExperiment`)

Done!! removed all methods as they did not make sense

* If you need a function to work for a particular class, check class membership
  as part of the function

Done, see above

* Consider using `switch` for `calc.penalty` options rather than a series of
  calls

Done!

README.md

* Replace all `source` and `biocLite` calls with `BiocManager`. See the devel
  landing pages of any package on the Bioconductor website for examples or
  check the Bioc-devel mailing list.

Done!

averissimo commented 6 years ago

Note: I kept the cv.glmSparseNet, cv.glmHub, etc.. to keep up with the glmnet package's cross-validation function names that has the 'cv.' prefix

bioc-issue-bot commented 6 years ago

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

bb1a2e4 some functions had dot in their name

bioc-issue-bot commented 6 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.

Please see the build report for more details.

averissimo commented 6 years ago

There was 3 functions that I missed with dot in their name. Response above now fully applies

LiNk-NY commented 6 years ago

Hi André, @averissimo Thank you for making those changes. I will check your package shortly. -Marcel

LiNk-NY commented 6 years ago

Hi André, @averissimo

A few points to consider:

Only use cat for class show methods, otherwise use message or warning functions. See: http://bioconductor.org/developers/how-to/coding-style/
Use the proper extractor functions for MultiAssayExperiment such as sampleMap(multiassay)
Why not use MatchedAssayExperiment instead of reduceByExperiment? You can subset first and then convert to the class: as(multiassay[, , "experiment1"], "MatchedAssayExperiment")

Thanks.

bioc-issue-bot commented 6 years ago

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

41cd6e2 use MatchedExperimentAssay instead of own function...

bioc-issue-bot commented 6 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.

Please see the build report for more details.

bioc-issue-bot commented 6 years ago

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

e103162 error message in one call

bioc-issue-bot commented 6 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 6 years ago

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

8f6b071 reduce tests a bit as windows build is taking too ...

bioc-issue-bot commented 6 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 6 years ago

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

b2167c4 Revert "error message in one call" This reverts c...

bioc-issue-bot commented 6 years ago

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

0fc383c reverted wrong commit, message in one call and rev...

bioc-issue-bot commented 6 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 6 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 6 years ago

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

26d84a5 bumps version

bioc-issue-bot commented 6 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.

Please see the build report for more details.

averissimo commented 6 years ago

Hi Marcel ( @LiNk-NY )

I've implemented those changes.

cat, replaced with appropriate message/stop
sampleMap(..) code was removed in next bullet actions, so no action here
as(..., 'MatchedAssayExperiment') -- exactly what was necessary, sorry that you had to repeat yourself, I'm still familiarizing with Bioc data structures and auxiliary functions.

LiNk-NY commented 5 years ago

Hi André, @averissimo A couple of notes:

biomaRt has been unreliable in the past. If there are alternatives, I would certainly seek them out.
Indentation for functions with many arguments varies by author. I tend to prefer something like this if it doesn't fit in one line:
```
exampleFun <- 
function(arg1, arg2, ...)
{
}
```
but I will leave this up to you. Thanks.

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/averissimo.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 biocLite(\"glmSparseNet\"). The package 'landing page' will be created at

https://bioconductor.org/packages/glmSparseNet

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