LinkHD-Bioconductor - Githubissues

lauzingaretti 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/lauzingaretti/LinkHD

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 5 years ago

Hi @lauzingaretti

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: LinkHD
Type: Package
Title: LinkHD: a versatile framework to explore and integrate heterogeneous data
Version: 1.0
Author: Laura M Zingaretti
Authors@R: as.person(c(
    "Laura M Zingaretti <m.lau.zingaretti@gmail.com> [aut, cre]"
  ))
Maintainer: Laura M Zingaretti <m.lau.zingaretti@gmail.com>
Depends:
    R(>= 3.3),
     methods,
    scales,
    ggplot2,
    dplyr,
    cluster,
    graphics, 
    ggpubr, 
    reshape,
    gridExtra,
    vegan,
    data.table,
    rio
Imports:
    methods,
    scales,
    ggplot2,
    dplyr,
    cluster,
    graphics, 
    ggpubr, 
    reshape,
    gridExtra,
    vegan,
    data.table,
    rio
Suggests:
    MASS (>= 7.3.0),
    knitr,
    rmarkdown
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{LinkHD:Multiple Heterogeneous (communities) Data Integration }
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
Description: Here we present Link-HD,
    an approach to integrate heterogeneous datasets, 
    as a generalization of STATIS-ACT
    (“Structuration des Tableaux A Trois Indices de la Statistique–Analyse Conjointe de Tableaux”),
    a family of methods to join and compare information
    from multiple subspaces. However, STATIS-ACT has some 
    drawbacks since it only allows continuous data and 
    it is unable to establish relationships  
    between samples and features. In order to tackle these 
    constraints, we incorporate multiple distance options 
    and a linear regression based Biplot model in order to stablish relationships between 
    observations and variable and perform variable selection. 
License: GPL-3
Encoding: UTF-8
Collate: 'Read_Data.R' 'DataProcessing.R' 'DistStatis-Class.R' 'LinkData.R' 'CompromisePlot.R' 'VarSelection.R'
    'GlobalPlot.R' 'CorrelationPlot.R' 'Selection-Class.R' 'Auxiliares.R' 'ComputeDistance.R' 'dAB.R' 'OTU2Taxa.R'
LazyData: true
NeedsCompilation: no
Roxygen: list(wrap=FALSE)
RoxygenNote: 6.0.1

lshep commented 5 years ago

You will receive a build report shortly. Please set up your webhook so that future version bumps on the package will trigger an automatic rebuild.

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.

lauzingaretti commented 5 years ago

A new version of LinkHD library (1.0.1) is now available.

lshep commented 5 years ago

Please see the link about about creating a webhook When version bumps are committed and pushed they should trigger a new build report. Please set up a webhook and push a new version.

lauzingaretti commented 5 years ago

Done.

lauzingaretti commented 5 years ago

Dear Bioconductor's I'm not sure if it was a problem with the deliver because I don't receive an automatic response to rebuild my package.

lshep commented 5 years ago

Are you sure you set the webhook up properly? Other issues are receiving posts so its not a system wide issue - Make sure you version bump, commit and push too.

lauzingaretti commented 5 years ago

Can I close this issue and restart the process?

El jue., 26 sept. 2019 13:51, lshep notifications@github.com escribió:

Are you sure you set the webhook up properly? Other issues are receiving posts so its not a system wide issue - Make sure you version bump, commit and push too.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1262?email_source=notifications&email_token=ACRX2ZMNMWZ63VQ4U6JKJRDQLSO3DA5CNFSM4IZ4HLU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7VJPSQ#issuecomment-535467978, or mute the thread https://github.com/notifications/unsubscribe-auth/ACRX2ZLDPCWLG2VON3BCMMDQLSO3DANCNFSM4IZ4HLUQ .

lshep commented 5 years ago

Please try again on this issue. Double check the webhook. Push a version bump up. We would prefer to try and figure this out and not have to do that as it will involve us doing work on our database to allow you to reopen an issue.

lauzingaretti commented 5 years ago

Ok, maybe I am confusing with the webhook process. I should add a new webhook or only to push using the first one? I have my master branch and I add a tag with 0.99.1 version. I fix a problem with the first version because it was 1.0.0... thanks!

El jue., 26 sept. 2019 14:01, lshep notifications@github.com escribió:

Please try again on this issue. Double check the webhook. Push a version bump up. We would prefer to try and figure this out and not have to do that as it will involve us doing work on our database to allow you to reopen an issue.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1262?email_source=notifications&email_token=ACRX2ZKCXCFCBDM4UCEIE7LQLSQBPA5CNFSM4IZ4HLU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7VKISA#issuecomment-535471176, or mute the thread https://github.com/notifications/unsubscribe-auth/ACRX2ZO5PUXCDLYTQIAAKNLQLSQBPANCNFSM4IZ4HLUQ .

lshep commented 5 years ago

I just tested with a different issue and everything seems to work find.
I would delete the webhook you set up and create a new one to make sure all the steps were followed correctly in Adding a Webhook. After that is done, please bump the version to 0.99.2 in the DESCRIPTION, add and commit the change in git, and push the changes to your github. That should hopefully trigger a new build. If it doesn't we will try and figure out a different solution.

bioc-issue-bot commented 5 years ago

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

66caef0 bump version after creating 0.99.2 branch bump ve...

lauzingaretti commented 5 years ago

thanks a lot @lshep. Maybe it was a problem with my old Webhook. Now it looks working!

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:

5ef2010 Add files via upload bump version after creating ...

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:

a6c9811 bump version after creating 0.99.5 branch

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:

def4b23 bump version after creating 0.99.6 branch

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:

0de12e1 bump version after creating 0.99.7 branch

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.

Please see the build report for more details.

bioc-issue-bot commented 5 years ago

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

9491b7c bump version after creating 0.99.8 branch

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.

Please see the build report for more details.

mtmorgan commented 5 years ago

DESCRIPTION

ok

NAMESAPCE

ok

vignettes

please format code chunks to more conventional form, e.g., via the formatR package. Please verify that the code is readable and complete, e.g., no lines that run off the edge of the page, in the vignette.

R (comments are on specific lines of code but apply throughout)

Please feel free to increase readability of your code by being more liberal inthe use of lines and spaces, e.g., Auxiliares.R:11.
```
else {
    idx <- is.finite(unlist(Data)) & Data > 0
    exp(mean(log(Data[idx])))
}
```
Please condsider using formatR or similar to ensure that your code adopts more standard formatting, including use of white space to improve constency and readability.
Auxiliares.R:90 since X is a matrix, all columns have the same type; use typeof(X) to test the type of X.
Auxiliares.R:109 it's not clear why you check for a data.frame when from the calculation it is clear that you require all columns to be numeric, i.e., a matrix...
Auxiliares.R:115 and throughout use vectorized calculations like rowSums() etc (including from the matrixStats package) for row and column summaries, rather than the apply() family.
Auxiliares.R:125 is this just df[is.na(df)] <- 0 ? but why replace NA values with 0?
Auxiliares.R:139 why isn't this code indented consistently? It's very hard to read.
Auxiliares.R:225: would it be better to use readline() here?
CompromisePlot.R:46 for generics with many arguments usually only one or two are actually used for dispatch (method selection). Indicate this using the signature= argument.
CompromisePlot.R:54 since this methdo is for 'DistStatis' objects, there is no need to test whehter x is of that class.
CompromisePlot.R:58 please define and use 'accessor' functions e.g. .compromise_coords <- function(x) x@Compromise.Coords rather than direct slot access. The accessor functions, even or perhaps especially within your pacakge. The accessor functions define the interface to your data object, allowing you to change the data structure (e.g., for more efficient internal represenation) without having to re-write code that uses your data object.

ComputeDistance.R:27 I think the code structure you are aiming for here is

if (...) {
    ...
} else if (..) {
    ...
}

or alternatively

Distance <- switch(
    tolower(Distance),
    scalarproduct = ..., 
    euclidean = ..
    ...
)

LinkData.R Consdier wrapping your markdown annotations, e.g., as

#' @description Integrating multiple Heterogeneous Datasets stored
#'     into a list. This function makes Statis using Distances
#'     options.  Statis is part of the PCA family and is based on
#'     singular value decomposition (SVD) and the generalized singular
#'     value decomposition (GSVD) of a matrix.  This methodology aims
#'     to analyze several data sets of variables that were collected
#'     on the same set of observations.  Originally, the comparisons
#'     were drawn from the compute of the scalar product between the
#'     different tables.  In our approach, the condition is relaxing
#'     allowing the incorporation of different distances.
#'@param Data should be a list of dataframes or ExpressionSet data
#'     with the same length of the number of tables to be integrate.
#'     In each dataframe, the Observations (common elements on Statis)
#'     should be in rows and the variables should be in columns. Data
#'     also might be a MultiAssayExperiment object from
#'     MultiAssayExperiment package, a software for multi-omics
#'     experiments integration in Bioconductor.

LinkData.R:88 Use the accessor functions provided by MultiAssayExperiment, rather than direct slot access.
LinkData.R:156 use seq_along() or seq_len() rather than 1:length(Data).
LinkData.R:254 This copy and append pattern (pit = c(); for (i in ...) pit[i] = ...) is inefficient and difficult to read; uselapply()orvapply()to manage memorypit <- vapply(seq_len(nrow(RV)), fucntion(i) ..., numeric(1))`
LinkData.R:350 instead of creating and then updating the DistStatis object, create the object once
```
new("DistStatis", RV = RV, Inertia.RV = Inertia.RV, ...)
```
VarSelection.R:138 use of which() is not necessary for subsetting; it makes the code more verbose than necessary.
dAB.R: 67 it's not usually necessary to use stop(paste0(...)); stop(...) usually accomplishes the same thing.

man

please pay attention to formatting of examples; as currently formatted they are difficult to read, spill outside the PDF version of the manuscript, and wrap around lines in a standard 80-column console view.

lauzingaretti commented 5 years ago

Martin, Many Thanks by your feedback! we are doing these changes and we will resubmit a revised version of our package coming soon. Best!

bioc-issue-bot commented 5 years ago

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

5bc93a0 bump version after creating 0.99.9 branch

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.

Please see the build report for more details.

lauzingaretti commented 5 years ago

Hi Martin, I have followed your recommendations and now the repo is updated with a revised version of LinkHD. Best regards

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/lauzingaretti.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("LinkHD"). The package 'landing page' will be created at

https://bioconductor.org/packages/LinkHD

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

LinkHD-Bioconductor #1262