Closed arorarshi closed 3 months ago
Hi @arorarshi
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: survClust
Title: Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning
Version: 0.99.0
Date: 2022-08-04
Authors@R:
person("Arshi", "Arora", , "arshiaurora@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-4040-1787"))
Description: survClust is an outcome weighted integrative clustering algorithm used to classify multi-omic samples on their available time to event information.
VignetteBuilder: knitr
License: MIT + file LICENSE
Imports: Rcpp, MultiAssayExperiment, pdist, survival
LinkingTo: Rcpp
URL: https://github.com/arorarshi/survClust
BugReports: https://support.bioconductor.org/t/survClust
biocViews: Software, Clustering, Survival
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
LazyData: true
Depends:
R (>= 4.2.0)
Suggests:
testthat (>= 3.0.0)
Config/testthat/edition: 3
Thanks for this submission. The example data is in a form that does not reflect Bioconductor practice. You have a list of matrices or data frames. We use SummarizedExperiment and derived classes to couple the metadata to data to increase reliability. You should have a look at curatedTCGAData package to see how mutation and copynumber data can be represented in conventional ways for packages in the ecosystem. Let me know @vjcitn how you want to proceed.
Hi @vjcitn, thanks for the feedback. survClust needs complex processing of genomic data as input and can't work with raw TCGA data. I am happy to work on the interop issue - is it ok if I convert the input matrixes (used as an example data to illustrate survClust) as a mae object? Will that work? survClust takes mae objects as an input.
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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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi. Thanks for getting back to me. I am now going through the report and fixing the errors. Thanks!
Received a valid push on git.bioconductor.org; starting a build for commit id: e7a54b2bfac308fbb5ab073ac766a9d91e381ed4
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, skipped". 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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 713f76328e77a95bcb5d739ace88ac603d16de24
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hello @arorarshi - Checking in to see if you are making progress fixing the errors in the report. We generally like to see changes within 2-3 weeks to be sure the package is actively being worked on. Let me know if you are having any issues.
Best, Kayla
Hi @Kayla-Morrell, Thanks for following up. Yes, I am working on fixing these errors today. Thanks!
@arorarshi - A week has gone by since you said you were working on fixing the errors. If changes are not made in the next week I will be closing the issue due to inactivity.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: 7fd91141f18b55d543f56f782ad78c9e947874c1
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 4a822fd1d2a3d0102a746a0b9ed0a0c4949140b7
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 522bcf0976e660232861f78623af3a5bce04fa81
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @Kayla-Morrell - I have resolved most of the errors except the bioc-devel mailing list. I just subscribed to it but looks like it might need approval? Should I try to commit after the confirmation that I have been added to the list?
I don't see you registered. There is normally a confirmation email that gets sent to your email and sometimes it can be marked as spam. Could you please check your spam filter
Received a valid push on git.bioconductor.org; starting a build for commit id: 30ff91ff80f1048efe9fa596a0253ce31e0eddfa
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@arorarshi - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.
Suggests:
field. Please add 'gplots', 'htmltools', and
'BiocParallel'..
, which indicates S3 dispatch. Please change 'cv.survclust'.eval = FALSE
.if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("survClust")
dim
in the rowMeans
function
should be dims
.1:...
; use seq_len()
or seq_along()
instead.Best, Kayla
Dear Bioconductor team,I am starting my maternity leave starting today. I was able to work on most of these changes but will only be able to push them to Git when I am more settled. Will it be possible to request for more time to work on the package and get it ready for bioconductor submission? Any other hard deadlines that I should keep in mind?Thank you,Arshi On Feb 7, 2023, at 1:59 PM, Kayla-Morrell @.***> wrote: @arorarshi - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review. DESCRIPTION
REQUIRED: The LICENSE file should contain the full terms of the MIT license. I would remove the current LICENSE file and rename LICENSE.md as LICENSE. REQUIRED: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed. REQUIRED: Update R version dependency from 4.2.0 to 4.3.0. REQUIRED: There are packages used in vignette code that should be declared in the Suggests: field. Please add 'gplots', 'htmltools', and 'BiocParallel'.
NAMESPACE
REQUIRED: Exported functions should use camel case or underscoring and not include ., which indicates S3 dispatch. Please change 'cv.survclust'. SUGGESTION: Add the follwing to your NAMESPACE file and ensure that your DESCRIPTION Imports field contains these packages. importFrom("graphics", "axis", "boxplot", "par") importFrom("methods", "is") importFrom("stats", "cmdscale", "dist", "kmeans")
Vignette
SUGGESTION: Change the vignette file name to something pertaining to the package, such as 'survClust', 'survClust_vignette', or 'survClust_intro'. REQUIRED: All code blocks should be evaluated, except for installation code. If it is necessary please provide justification. REQUIRED: There should be an Installation section that demonstrates to the user how to download and load the package from Bioconductor. The code should look like the following and include eval = FALSE.
if(!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("survClust")
SUGGESTION: I would remove one '#' from each of the headers and subheadings. Right now the table of contents reads '0.1 Overview', '0.1.1 The tldr version', '0.2 Data and Pre-processing', etc. If you removed one '#' from each then they should become '1 Overview', '1.1 The tldr version', '2 Data and Pre-processing', etc.
Man pages
REQUIRED: There is no documenation for the exported function 'dist_wtbinary'. All exported functions must have a man page. REQUIRED: Add a runnable example to the 'get_spwss_stats' man page since this documents an exported function.
R code
REQUIRED: Line 35 in 'combineDist.R', dim in the rowMeans function should be dims. REQUIRED: Avoid 1:...; use seq_len() or seq_along() instead. SUGGESTION: For formating reasons, consider shorter lines. There are 214 lines that are > 80 characters long. SUGGESTION: For formating reasons, consider multiples of 4 spaces for line indents. There are 14 lines that are not.
Best, Kayla
—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>
@arorarshi - I'll close it for inactivity for now. When you are ready to make changes just comment on the issue and I'll reopen it for you. We will be releasing deadlines soon for the spring release but these are not hard deadlines. If you do not make the spring release your package will be eligible for the next fall release, so no rush on our end.
Best, Kayla
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
Thank you for your interest in Bioconductor.
Hi there, things are settling in after maternity leave, I am working on these changes and should be able to push soon. Should the issue be opened and then push the changes?
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
yes that way there is a new build report generated. Cheers
Dear @arorarshi ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
Received a valid push on git.bioconductor.org; starting a build for commit id: 35627ea1052562bd147733b20febc0ae4aa6aa8d
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): survClust_0.99.7.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2ebe0fe7d84fdf331dbd0f1f7696c102b39335b6
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): survClust_0.99.8.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/survClust
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@arorarshi - Thank you for making the necessary changes. I have reviewed everything and it all looks good. I'm more than happy to accept the package.
Best, Kayla
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
Thank you! This is excellent news. This is the outcome of the Bioconductor package mentorship program in 2022 :) I was finding my footing after maternity leave and would like to give a shout out to all the reviewers and my mentors @DarioS @nturaga
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