VarCon (guithub now with ssh key)

caggtaagtat commented 4 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/caggtaagtat/VarCon

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][2] instructions. My package is consistent with the Bioconductor [Package Guidelines][1].
[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.
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bioc-issue-bot commented 4 years ago

Hi @caggtaagtat

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: VarCon
Type: Package
Title: VarCon
Version: 0.99.0
Description: VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation with. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.
License: file LICENSE
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Imports: 
    methods,
    stats,
    seqinr,
    IRanges,
    shiny,
    shinycssloaders,
    shinyFiles,
    ggplot2
Depends: 
    Biostrings,
    BSgenome,
    GenomicRanges,
    R (>= 4.1)
Suggests: 
    testthat,
    knitr,
    rmarkdown
biocViews: FunctionalGenomics, AlternativeSplicing
RoxygenNote: 7.1.1
Authors@R: person("Johannes", "Ptok", role = c("aut", "cre"), email = "Johannes.Ptok@posteo.de")

bioc-issue-bot commented 4 years ago

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 commented 4 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, 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

caggtaagtat commented 4 years ago

Hi, when I try to push to bioconductor, I get the error: "error: src refspec master does not match any" and "error: failed to push some refs to 'git@git.bioconductor.org:packages/VarCon.git'" It tried the command: "git push upstream" and "git push upstream master" and my paths are:

git remote -v origin https://github.com/caggtaagtat/VarCon (fetch) origin https://github.com/caggtaagtat/VarCon (push) upstream git@git.bioconductor.org:packages/VarCon.git (fetch) upstream git@git.bioconductor.org:packages/VarCon.git (push)

All changes are commited and on guithub. I changed the version number in the DESCRIPTION file. Could this be related to something with the SSH key?

caggtaagtat commented 4 years ago

I reinitialized my git directory and now am able to push to guithub from console, but not to bioconductor:

git push upstream master "git@git.bioconductor.org: Permission denied (publickey). fatal: Could not read from remote repository.

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

mtmorgan commented 4 years ago

Does FAQ #1 at http://bioconductor.org/developers/how-to/git/faq/ provide any suggestions? It looks like the key you've uploaded to github at https://github.com/caggtaagtat.keys matches the key known to Bioconductor

caggtaagtat commented 4 years ago

I'm sorry, but I don't seem to be able to create an account there. it says: "johannes.ptok@posteo.de is not associated with a maintainer of a Bioconductor package.". Should I have an account there, although I am not an active maintainer already?

lshep commented 4 years ago

I can see your account and it is associated with that email. Your account doesn't seem to be activate yet. Have you tried this link: https://git.bioconductor.org/BiocCredentials/account_activation/

caggtaagtat commented 4 years ago

I tried activating it, but it says "johannes.ptok@posteo.de is not associated with a maintainer of a Bioconductor package.". Is there an alternative way to activate it?

nturaga commented 4 years ago

Hi @caggtaagtat

This is strange. Have you checked your spam? Please try to activate it again and if it doesn't work we'll take another look at it.

To reiterate Lori's point, everything on our end seems ok.

Best,

Nitesh

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b36a6d912d654fd603071a7f54b1bc123b3d6e88

caggtaagtat commented 4 years ago

Thank you all for the advice. Activating my account worked now and I was able to add my SSH key to my account.

bioc-issue-bot commented 4 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: "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.

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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8c1888f770a36c208e2923cb5d728bbfcc29432a

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 88d8747b97eb951d7d7367bc7a04558b831b9290

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d9a92acfe5d43f6bc7ab19dbcea11b013b2cf6d7

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mtmorgan commented 4 years ago

DESCRIPTION

Please provide a more informative Title:, like for a paper.
Standardize by using License: GPL-3.
Not sure why both seqinr and Biostrings are needed? Since this is a Bioconductor package, use Biostrings?

vignettes

VarCon.Rmd:17 it seems dangerous to ignoring all errors and warnings always.
VarCon.Rmd:161 it would be helpful to break this dense code chunk up into sentences that describe what is going to be done, and then one or two lines of R code that does what is said to be done, followed by a few lines describing what the output should be / why it is interesting before continuing to the next couple of lines.

R (comments are on specific lines, but apply generally)

calculateHZEIperNT.R:5 why not use Biostrings::DNAStringSet() to validate (and for subsequent manipualtion)?
calculateMaxEntScanScore.R:9 stop(paste0(...)) is generally redundant, since stop() applies paste0(...) internally
calculateMaxEntScanScore.R:32 use the following paradigm to set / restore the directory robustly, even if an error occurs
```
owd <- setwd(...)
on.exit(setwd(owd))
```
calculateMaxEntScanScore.R39 use message() (output to stderr) rather than cat() for informational messages
calculateMaxEntScanScore.R:48 calling this perl code seems unjustified and dangerous. For instance it seems that inst/extdata/score3.pl has
```
my $dir = "/bionet/geneyeo_essentials/MaxEntropy/webserver/splicemodels/";
```
and so assumes specific directory structure. It's remarkable that this does not cause problems when the pacakge is built and checked; are there examples or tests that exercise this functionality? Or perhaps the perl code is not used at all and should be removed? Is the perl code that is used necessary, or does it translate easily into R?

getSeqInfoFromVariation.R:9 increase readability by avoiding such nested calls, e.g.,

if(transcriptID %in% gene2transcript$gene_name){
    idx <- match(transcriptID, gene2transcript$gene_name)
    transcriptID <- gene2transcript$transcriptID[idx]
}

inst/

app.R:29 it seems like operations like this, on the data and unrelated to UI rendering / response, should be in the package, perhaps as non-exported helper functions, so that the code is subject to the checks that R CMD check provides.
app.R:62 the nested paste(paste(...)) doesn't look necessary; again, this code should be in the R/ directory

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5594dbc4a0ca13f1f9bf1b7ee668e43642bbd006

caggtaagtat commented 4 years ago

Thank you very much for the detailed review. I hope my corrections are sufficient. Four points of your review require some comments from my site:

1) calculateHZEIperNT.R:5 why not use Biostrings::DNAStringSet() to validate (and for subsequent manipualtion)? This would allow e.g. characters like "-" which in my case should lead to an error.

2) calculateMaxEntScanScore.R39 use message() (output to stderr) rather than cat() for informational messages The command in this line creates and manipulates a text file in the directory inst/extdata, since a text file is required as an input for the integrated perl script.

3) calculateMaxEntScanScore.R:48 calling this perl code seems unjustified and dangerous. For instance it seems that inst/extdata/score3.pl has I deleted the respective code segments, since it was not used

4) app.R:29 it seems like operations like this, on the data and unrelated to UI rendering / response, should be in the package There still was something wrong in the reactive data upload, so I updated the code accordingly. Now the data is uploaded using the path-input from the GUI.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9142641093b862272097be0390012473b237c301

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mtmorgan commented 4 years ago

Generally, you should not be creating files in the installed library (e.g., the inst/extdata directory) because the package might be installed by a user (e.g., system administrator) different from the user. For examples, use tempdir(), fl <- tempfile(); dir.create(fl) or similar. Enable users to specify their own directory with an argument, defaulting to one of the temporary locations just indicated.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0c4ddd44de216c14fb261e803422cf80aed46ec4

caggtaagtat commented 4 years ago

Thanks, I changed the code accordingly.

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d1bcc605f9bd0b05d4562f536a147fded454b568

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 99f44e040df67e6419309cc0ab70e8fc9c99d54c

bioc-issue-bot commented 4 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. 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/VarCon to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

mtmorgan commented 4 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/caggtaagtat.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("VarCon"). The package 'landing page' will be created at

https://bioconductor.org/packages/VarCon

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

VarCon (guithub now with ssh key) #1754