ASCETIC

[danro9685]

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• Repository: https://github.com/danro9685/ASCETIC

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[bioc-issue-bot]

Hi @danro9685

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: ASCETIC
Version: 0.99.2
Date: 2022-10-03
Title: ASCETIC
Authors@R: c(
    person("Daniele", "Ramazzotti", role=c("cre","aut"),email="[email protected]",
      comment = c(ORCID = "0000-0002-6087-2666")),
    person("Luca", "De Sano", role=c("aut"), email="[email protected]",
      comment = c(ORCID = "0000-0002-9618-3774")))
Maintainer: Luca De Sano <[email protected]>
Depends:
    R (>= 4.1.0)
Imports:
    bnlearn,
    Rcpp
Suggests:
    BiocStyle,
    testthat,
    knitr
Name:
    An R package for the inference of statistically significant temporal patterns involving alternations in driver genes from cancer genomics data
Description:
    Cancer development is a stochastic process involving large populations of cells. Random genetic and epigenetic alterations commonly occurring in any cell can occasionally be beneficial to neoplastic ones, thus defining clones characterized by a functional selective advantage. During clonal evolution, certain clones can be positively selected for increased proliferation and survival ability, outgrowing competing cells and this can eventually lead to invasion and metastasis. Throughout such a multi-step stochastic process, cancer cells can acquire over time a set of biological capabilities that sometimes are referred to as hallmarks. Not all variants are involved in their acquisition, but only a relative small subset of them – i.e., the drivers –, while most mutations present in the cancer clones do not increase their fitness – i.e., the passengers.
    ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal patterns involving alternations in driver genes from cancer genomics data.
Encoding: UTF-8
License: file LICENSE
URL: https://github.com/danro9685/ASCETIC
BugReports: https://github.com/danro9685/ASCETIC
biocViews: BiomedicalInformatics, 
 SomaticMutation
RoxygenNote: 7.2.1
LinkingTo: Rcpp
NeedsCompilation: yes
VignetteBuilder: knitr

[vjcitn]

Thanks for this submission. I think it needs some work. First, there is no definition of "agony" readily visible in the documents. Second, no Bioconductor data structures are used, and the main structure I saw had patients as rows and mutations as columns. It might be relevant to look at curatedTCGAData structures to see how cancer mutational data are structured for use in Bioconductor ... and there are other packages that could be relevant. It is important for the submission to include some indication of why and how the software fits in the Bioconductor ecosystem. Let us know your thoughts.

[danro9685]

Dear @vjcitn,

Thanks for your quick feedback. We will include a definition of agony, sorry for missing this. And, we will have a look at curatedTCGAData and other potentially interesting packages within Bioconductor. We will get back to you soon.

Thank you, Daniele

[danro9685]

Dear @vjcitn,

We have updated the documentation as suggested. Moreover, we have looked at the curatedTCGAData package, but we could not retrieve information on cancer cell fractions data from it, which are required for our tool.

Please let us know if you have additional pre-review suggestions.

Thanks, Daniele

[luca-dex]

Dear @vjcitn I'm the maintainer of the package. I already added the bioconductor remotes to our package and we're trying to push some changes but, at the moment, ASCETIC is not among the packages to which I access on git.bioconductor.org so my SSH key is not accepted.

$ git fetch --all
Fetching origin
Fetching upstream
FATAL: R any packages/ASCETIC l.desano DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: could not fetch upstream

Could you please help us in sorting out this issue?

Thanks

[lshep]

push access has not been granted yet as this package is still in the pre-check stage. Once the package passes pre-checks it will be added to git.bioconductor.org. At this stage updating the github and pinging @vjcitn is sufficient

[luca-dex]

thanks @lshep for the clarification

[luca-dex]

Hi @vjcitn and @lshep

We would like to know if there anything we should do for this package or if everything is fine.

Thanks

[luca-dex]

Hi @vjcitn and @lshep I still cannot push on this repository, so we cannot trigger new build. Could you please let us know how we can proceed?

I have the repo configured properly in BiocCredentials and I'm able to trigger push on other repository buy this one is not accepting my credentials.

Best,

[lshep]

again -- @vjcitn has not processed it passed pre-checks so you would not have access on git.bioconductor.org

[luca-dex]

thanks for the clarification @lshep is there anything we can do at this stage to speed up the process, in order to avoid to pass the deadline of Wednesday?

Best,

[vjcitn]

I just compiled the vignette. I see

## Warning in check.data(x): variable 2 has levels that are not observed in the
## data.
## Warning in check.data(x): variable 3 has levels that are not observed in the
## data.
## Warning in check.data(x): variable 10 has levels that are not observed in the
## data.
## Warning in check.data(x): variable 13 has levels that are not observed in the
## data.
## Warning in check.data(x): variable 17 has levels that are not observed in the
## data.
## Warning in check.data(x): variable 18 has levels that are not observed in the
## data.
## Warning in check.data(x): variable 20 has levels that are not observed in the
## data.
## Warning in check.data(x): variable 27 has levels that are not observed in the
## data.

We refer to the manual for a detailed description of each parameter and to the ASCETIC manuscript for details on the method.

You have similar content in .rnw and .Rmd. Please fix the warnings and simplify the vignette layout before review can begin.

[danro9685]

Dear @vjcitn, This warning is generated during the likelihood fit part of the inference by ASCETIC when input data, which are expected to be binary (two levels, 0 and 1), show only one level. This is something that can happen, i.e., the user sometimes can have data of this type, and it is not an error (the warning needs to be shown in these cases). We can easily remove it, but I was wondering if you still wants us to do it, being this a common workflow for the user? Please let us know so that we can proceed accordingly. Thanks, Daniele and @luca-dex

[danro9685]

Dear @vjcitn, Just to be sure, I have fixed the input data to remove the warnings, as you have asked. All the best, Daniele

[luca-dex]

Dear @vjcitn , considering that the deadline for new packages to be included in bioc 3.16 has passed, we would like to know what should we do and if there still possibility to include our package in the release.

Please, let us know

Best,

[vjcitn]

I'd suggest that you improve the package to meet guidelines/reviewer/pre-reviewer advice and get it added to Bioc 3.17. There is no rush, you can distribute via github, tell people it is in 3.17 once it passes review, etc. Sorry for delays but there are so many tasks in connection with getting to a release that some submissions that come in close to release time just don't make it in.

[luca-dex]

Thanks @vjcitn

we will follow your suggestion.

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[bioc-issue-bot]

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 [email protected]:packages/ASCETIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[DarioS]

The issues identified by Vincent still apply. In addition,

• The package needs conform to Bioconductor coding style. camelCase instead of snake_case. Don't use = for variable assignment but <-. Use spaces around assignment operators and after commas. In most cases, don't use for loops but vapply or lapply.
• Phyogenetic trees can be input. But the software doesn't make use of Bioconductor package treeio infrastructure.
• Return values are a basic list. The package should define a class with accessor functions to store results in.
• Vignette provides no biological interpretation of the results. What is the user supposed to discover in the results?
• man folder has 30 Rd files but vignette demonstrates only 5 functions. Please make it more comprehensive.

[lshep]

@luca-dex may we expect updates to the package soon?

[danro9685]

Dear @lshep, Sorry for the radio silence from our side, we have been pretty full in this period. But me and @luca-dex plan to fix this soon. Thanks!

[danro9685]

Dear @lshep,

Just a quick update on this. The maintainer of the package (@luca-dex) has been traveling with very limited Internet access since last month and will be back on January 21st .

I am working to address the issues for the review, but it will take a little bit more time given that @luca-dex is not available for two more weeks.

I apologize for the inconvenience. We will try to finalize this soon.

Thanks, Daniele

[DarioS]

No rush. It is currently summer holidays in Australia with most researchers returning to work next week.

[bioc-issue-bot]

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.

[danro9685]

Dear @DarioS,

Me and @luca-dex are working at all the suggestions you have provided and plan to push the updated version of the ASCETIC package within next week. So, I would ask you if possibile to reopen this issue.

Thanks, Daniele & Luca

[luca-dex]

Dear @DarioS and @lshep, during past weeks we worked on improving the packages following the feedback we received and we think we addressed the issues that were blocking the release of the package. We also revised the documentation of the package and we did a cleanup of the C code that is not more integrated in the package.

We kindly ask you to reopen the issue, if possible.

Thanks a lot for your understanding

Luca & Daniele

[bioc-issue-bot]

Dear @danro9685 ,

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.

[luca-dex]

Dear @lshep , I have remotes correctly set up, but when I try to push a version bump but I got the following error:

$ git push upstream devel
FATAL: W any packages/ASCETIC l.desano DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Am I missing something? It was working before

[luca-dex]

Just to add that ASCETIC is not in the list of pachages to which I have access on BiocCredentials anymore:

'[email protected]' has access to the following packages: TRONCO OncoScore SIMLR SparseSignatures RESOLVE