Please add package mirTarRnaSeq

Mercedeh66 commented 3 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/Mercedeh66/mirTarRnaSeq

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bioc-issue-bot commented 3 years ago

Hi @Mercedeh66

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: mirTarRnaSeq
Type: Package
Title: mirTarRnaSeq 
Version: 0.99.0
Authors@R: 
    c(person(given = "Mercedeh",
 family = "Movassagh",
 role = c("aut", "cre"),
 email = "mercedeh@ds.dfci.harvard.edu",
 comment = c(ORCID = "0000-0001-7690-0230")),
 person("Sarah","Morton", role="aut"),
 person("Rafael","Irizarry", role="aut"),
 person("Jeffrey", "Bailey", role= "aut"),
 person("Joseph N", "Paulson", email="paulson.joseph@gene.com", role="aut"))
Description: mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.
License: MIT
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
DeploySubPath: mirTarRnaSeq
biocViews: miRNA, Regression, Software, Sequencing, SmallRNA, TimeCourse, DifferentialExpression
RoxygenNote: 7.1.1
Suggests: BiocStyle, knitr, rmarkdown, R.cache
VignetteBuilder: knitr
Imports: 
    purrr,
    MASS,
    pscl,
    assertthat,
    caTools,
    dplyr,
    pheatmap,
    reshape2,
    corrplot,
    grDevices,
    graphics,
    stats,
    utils,
    data.table,
    R.utils

bioc-issue-bot commented 3 years ago

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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.

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bioc-issue-bot commented 3 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, WARNINGS, 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8f8d4897313e5cb95771d59e4074a68d837286b6

bioc-issue-bot commented 3 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, 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. 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9c35f2c048e4f8d8a1a54a7192186412a18bab4e

bioc-issue-bot commented 3 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, 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. 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mercedeh66 commented 3 years ago

@vjcitn hi I am getting a build error :

trying URL 'https://zenodo.org/record/4615670/files/Mouse_miRanda.txt.gz?download=1'
Content type 'application/octet-stream' length 2932105 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

Warning in readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) :
  invalid or incomplete compressed data
Quitting from lines 291-293 (mirTarRnaSeq.Rmd) 
Error: processing vignette 'mirTarRnaSeq.Rmd' failed with diagnostics:
error reading from the connection
--- failed re-building 'mirTarRnaSeq.Rmd'

It seems like a windows related error as I am not getting it on my computer, I would appreciate the advice.

Thanks a lot,

-M

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d1ed7f58c6b03da005e7d4f178ec5657a5e4b322

bioc-issue-bot commented 3 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, 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. 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b9444ed52da9f8a0e45dff8b1d65351aa3f292eb

bioc-issue-bot commented 3 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, 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. 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d6e346fe7342ca1fa1da7970e5a4140ea18cebb0

bioc-issue-bot commented 3 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, 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. 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 28aa4226d4ec6df7ac4f1eaa0d1e28356227dd17

bioc-issue-bot commented 3 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. 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mercedeh66 commented 3 years ago

@vjcitn Hi, I was able to resolve all warnings and errors except for the error on the windows machine. I am saving a tmp file but while reading it, it seems to be gone. Would you kindly check if this could be an issue with the build machine? Thanks a lot!

hpages commented 3 years ago

So I wonder what the ?download=1 part is for in the URLs you use in getInputSpecies() e.g.

https://zenodo.org/record/4615670/files/Mouse_miRanda.txt.gz?download=1

This seems to break the downloaded file on Windows (but surprisingly not on Unix).

For example, doing:

download.file("https://zenodo.org/record/4615670/files/Mouse_miRanda.txt.gz?download=1", "test.gz")

produces a test.gz file with size 2943594 (expected size is 2932105). Then trying to read the file with data.table::fread() or utils::read.table() fails with an "invalid or incomplete compressed data" error.

If I get rid of ?download=1, the download seems to work as expected on Windows.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1fd464b9183b61e4007285e2f01555ea31b1c460

bioc-issue-bot commented 3 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 17f82986fa41472987456556a48d578d98a75eb4

bioc-issue-bot commented 3 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mercedeh66 commented 3 years ago

@hpages Great point! Thanks for the guidance :).

vjcitn commented 3 years ago

I think we are almost done with this. There are a couple of issues.

First, your git repo is very large, even though the package tarball is small. Consider using the BFG to remove large files from git repo.

Second, BiocCheck has some recommendations

 [1] "Consider clarifying how 2 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within()."         
 [2] " Avoid sapply(); use vapply()"                                                                                                                                                     
 [3] " Avoid 1:...; use seq_len() or seq_along()"                                                                                                                                        
 [4] "Avoid '<<-' if possible (found in 1 files)"                                                                                                                                        
 [5] "Recommended function length <= 50 lines."                                                                                                                                          
 [6] "Consider adding runnable examples to the following man pages which document exported objects:"                                                                                     
 [7] "Usage of dontrun{} / donttest{} found in man page examples."                                                                                                                       
 [8] "Consider adding unit tests. We strongly encourage them. See\n  http://bioconductor.org/developers/how-to/unitTesting-guidelines/."                                                 
 [9] "Consider shorter lines; 332 lines (8%) are > 80 characters long."                                                                                                                  
[10] "Consider multiples of 4 spaces for line indents, 627 lines(15%) are not."

Third, the graphics could be improved by setting par(mar=c(4,3,3,2)) or something like that, to avoid all the white space in margins

Screenshot from 2021-03-25 11-06-46

Mercedeh66 commented 3 years ago

Hi, I made the final changes based on the notes provided by @vjcitn. I also shrunk my repository as requested using BFG but when I try to force push to bioc master I get the following error. I would appreciate the help.

# git push --force bioc master
Enumerating objects: 654, done.
Counting objects: 100% (654/654), done.
Delta compression using up to 4 threads
Compressing objects: 100% (220/220), done.
Writing objects: 100% (654/654), 9.58 MiB | 832.00 KiB/s, done.
Total 654 (delta 402), reused 642 (delta 395)
remote: Resolving deltas: 100% (402/402), done.
remote: FATAL: + refs/heads/master packages/mirTarRnaSeq Mercedeh66 DENIED by fallthru
remote: error: hook declined to update refs/heads/master
To git.bioconductor.org:packages/mirTarRnaSeq
 ! [remote rejected] master -> master (hook declined)
error: failed to push some refs to 'git@git.bioconductor.org:packages/mirTarRnaSeq'

vjcitn commented 3 years ago

@nturaga is this an ssh key issue?

nturaga commented 3 years ago

Hi @Mercedeh66

You cannot force push to the Bioconductor git server. This is not allowed with the hook we have in place.

I will have to assist you in making this change.

nturaga commented 3 years ago

@nturaga is this an ssh key issue?

Hi @vjcitn , this is not an SSH key issue. It is happening because the git repository on our server is out of sync and has diverged from the github repo. And we don't allow force pushes.

Mercedeh66 commented 3 years ago

@nturaga Thanks so much. Please let me know if you need anything from my side.

nturaga commented 3 years ago

@vjcitn This might be an issue on our end, or how we are processing packages. I'm investigating and will let you know.

nturaga commented 3 years ago

@Mercedeh66 Please try now and see?

I would suggest you git fetch --all again if it doesn't work. Or maybe just obliterate your local directory and try to clone and setup your git repo locally again.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 58d37aaf5fced89aed5f8615bfe3954c04f9748e

bioc-issue-bot commented 3 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/mirTarRnaSeq to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mercedeh66 commented 3 years ago

@nturaga Thanks for the help. It seems to work now. @vjcitn I tried to address most of the notes, hope it is good enough and thanks for the suggestions.

vjcitn commented 3 years ago

Looks good. Accepting.

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

vjcitn commented 3 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/Mercedeh66.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("mirTarRnaSeq"). The package 'landing page' will be created at

https://bioconductor.org/packages/mirTarRnaSeq

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

Please add package mirTarRnaSeq #1981