hjunwoo 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/hjunwoo/ccfindR

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bioc-issue-bot commented 6 years ago

Hi @hjunwoo

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: ccfindR
Version: 0.9-0
Date: 2018-03-015
Title: Cancer Clone Finder - R package
Authors@R: c(person('Jun','Woo',role='cre',email='jwoo@umn.edu'),
   person('Jinhua','Wang',role='aut',email='wangjh@umn.edu'))
Author: Jun Woo [aut,cre], Jinhua Wang [aut]
Maintainer: Jun Woo <jwoo@umn.edu>
Depends: R (>= 3.4.0),
Imports: stats,
         utils,
         methods,
         Matrix,
         Rtsne,
         graphics,
         grDevices,
         gtools,
         RColorBrewer, 
         ape
biocViews: Transcriptomics, 
 SingleCell, 
 Bayesian, 
 Clustering
Description: A collection of tools for cancer single cell RNA-seq analysis. 
    Cell clustering and feature gene selection analysis employ Maximum 
    likelihood and Bayesian Non-negative matrix factorization algorithm. 
    Input data set consists of RNA count matrix, gene, and cell bar code 
    annotations.  Analysis outputs are factor matrices for multiple ranks, 
    quality measures (maximum likelihood) or evidence (Bayesian) with 
    respect to rank.  The package includes utilities for downstream analyses, 
    including meta-gene identification, visualization, and construction of 
    rank-based trees for cell clusters.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-01-11 19:17:23 UTC; jun
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr

bioc-issue-bot commented 6 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.

mtmorgan commented 6 years ago

Please re-use the SingleCellExperiment representation (any matrix-like object can be used for the assays()) as the primary way to represent single cell count data to facilitate interoperability and use of your software.

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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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.

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LTLA commented 6 years ago

Just seconding @mtmorgan's suggestion. Switching to a SingleCellExperiment class should allow you to avoid having to write getters/setters for the counts, genes and cells slots. You can also store cell-based dimensionality reduction results (coeff?) in reducedDims slot of the SCE. For the other slots, you might have to subclass the SCE, but that's no more work than what you're already doing. (The other option would be to store matrices as metadata columns, which is also pretty cool.)

hjunwoo commented 6 years ago

Thanks @mtmorgan and @LTLA for suggestion. I switched to SingleCellExperiment as suggested. I did have to add extra slots for storing matrices because they have different dimensions and typically there are a lot of them. I considered using metadata slot but then I thought I do need it for real metadata. Hope it is better now.

mtmorgan commented 6 years ago

Thanks for your change; I think the version numbering must be 0.99.x (not 0.99-x), and that the next version number should be 0.99.2

hjunwoo commented 6 years ago

Thanks, I fixed the version number.

bioc-issue-bot commented 6 years ago

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

0708218 to force build

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

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a2b2fdb added cophenet hclust option to factorize

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bioc-issue-bot commented 6 years ago

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

912f15d version bump

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LiNk-NY commented 6 years ago

Hi Jun Woo, @hjunwoo Thank you for your submission.

Please see the package review below. Best regards, Marcel

ccfindR #675

DESCRIPTION

You should only include Authors@R. The Author and Maintainer fields are not needed.
No need to include a Packaged field.
Title shouldn't include R package. That is understood.

NAMESPACE

Looks good.

R

Avoid using 1:n sequence generation, use the more robust seq_len or seq_along.
Avoid using sapply in code
Separate the plot functionality from the filter_genes function
Remove any default arguments that are files from the read_10x and write_10x function definitions.
Fix typo in cell_map documentation
No need to convert logical to numerical index in most cases, i.e., which(ranks(object) == rank) can just be ranks(object) == rank
Show method repeats class name twice.
Avoid unnecessary calculations as much as possible: h <- t(x); apply(h, 1, f(x) {which(x == max(x))}) instead do: apply(x, 2, which.max).

Minor:

No need to use ;. You can include the code on another line and make it more readable.
Use logical evaluation once. For example: if (bayes) { do(this) } else { do(that) }
if (x != 0) is the same as if (x)

vignettes

remove extra files (.pdf, .R, etc.)
eval is TRUE by default

inst/extdata

You should put your example data files in this folder (e.g., barcodes.tsv)

NEWS

Update the NEWS file

bioc-issue-bot commented 6 years ago

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

c0dcf78 version bump

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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

15aa4eb version bump

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hjunwoo commented 6 years ago

Hi Marcel, @LiNk-NY

Thanks for reviewing our package and providing us inputs.
I revised the package to address the issues. Thanks again for your help.

Best regards, Jun

DESCRIPTION

The Author and Maintainer fields were removed.
Packaged field was removed.
Title was revised (no R package).

R

Sequence generations were changed to seq_len.
sapply was changed into either apply or vapply.
Plot functionality from filter_genes was split into a new function plot_genes.
File name arguments of read_10x and write_10x were removed.
Typo in cell_map documentation was fixed.
Now ranks(object) == rank is used whenever possible without index conversion.
Class showmethod was changed to display class name only once.
Redundant matrix manipulations were removed using which.max function.
Semicolon uses were replaced into multiple lines of code.
Multiple logicals were simplified, including if /else and if(x!).

Vignettes

Extra files were removed.
eval=TRUE were removed.

inst/extdata

Vignette data files were moved into inst/extdata.

NEWS

NEWS file was updated.

bioc-issue-bot commented 6 years ago

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

16b9ad3 packaged field edit

bioc-issue-bot commented 6 years ago

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LiNk-NY commented 6 years ago

Hi @hjunwoo,

Thank you for making those changes. It is looking better!

One thing about changing read_10x. What I meant was that you should remove the default arguments for count, genes and barcodes and not the arguments themselves.

I realize that these file names might be a standard way of saving the datasets? If so then, it would be better to just keep the arguments and their defaults as you had them originally.

As a note, it is always better to leave the arguments open to the user and add defaults if necessary rather than hard-coding the values inside the function (as it is now).

Best regards, Marcel

bioc-issue-bot commented 6 years ago

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

3947954 version bump

bioc-issue-bot commented 6 years ago

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Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, TIMEOUT". 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 6 years ago

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

1141f20 shorted vignette

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hjunwoo commented 6 years ago

Hi Marcel, @LiNk-NY

I was unsure about it too; indeed the file names I previously put as defaults are used as such almost always. It would help users if they don't have to type them in every time because read_10x is such a workhorse. I put the file name arguments back.

Thanks again for your help. Jun

bioc-issue-bot commented 6 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 6 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/hjunwoo.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

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nturaga commented 6 years ago

Please use the following link to Submit your SSH key to Bioconductor. The link listed in the previous message is deprecated.

Bioconductor / Contributions

ccfindR #675

ccfindR #675

DESCRIPTION

NAMESPACE

R

vignettes

inst/extdata

NEWS

DESCRIPTION

R

Vignettes

inst/extdata

NEWS