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PhenoGeneRanker #1576

Closed JakeP627 closed 3 years ago

JakeP627 commented 4 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 4 years ago

Hi @JakeP627

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: PhenoGeneRanker
Type: Package
Title: PhenoGeneRanker: A gene and phenotype prioritization tool
Version: 0.99.0
Authors@R: c(person("Cagatay", "Dursun", email="cagataydursun@gmail.com", role=c("aut")), 
  person("Serdar", "Bozdag", email="serdar.bozdag@marquette.edu", role="aut"),
 person("Jake", "Petrie", email="jacob.m.petrie@marquette.edu", role = "cre"))
Description: This package is a gene/phenotype prioritization tool that utilizes 
    multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene
    and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking
    using random stratified sampling of genes/phenotypes based on their connectivity degree 
    in the network.
License: Creative Commons Attribution 4.0 International License
Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel
Suggests: knitr, rmarkdown
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.1.1
biocViews:  BiomedicalInformatics, GenePrediction, GraphAndNetwork,
    Network, NetworkInference, Pathways, Software, SystemsBiology
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". 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/PhenoGeneRanker 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: 50a2d0f4f3ee29b579baad6d912dc7eb6cbdc941

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/PhenoGeneRanker 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: d9890f72b114667a48f78f916b82ed36fec8d9ff

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/PhenoGeneRanker 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: da45fc28fb68a596035ac13f2017f104adf57aac

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

hpages commented 4 years ago

Hi @JakeP627,

Thanks for your submission. Note that there are no examples that I can run in the man pages or in the vignette so I can't review the package. This is software so it's important that for the review process we can try your functions and make sure that they work as advertised. Without running examples, we can't do that. Please provide runnable examples. Note that this is a requirement per our guidelines. Thanks!

Best, H.

hpages commented 4 years ago

Hi @JakeP627, are you planning to follow up with this submission? Thanks

serdarbozdag commented 3 years ago

Hi @hpages

We will follow up with this submission as soon as possible. We encountered some other potential issues and fixing these at the moment. Thanks!

lshep commented 3 years ago

Is there an update on this package? We like to see responses and updates in a 3-4 weeks; This issue has seen no updates since September. If you need more time to work on the issue we can temporarily close until you are ready to continue with the review.

serdarbozdag commented 3 years ago

Thanks for reaching out. We have our update almost ready. We will submit the updated version this week.

Serdar

On Nov 17, 2020, at 8:20 AM, lshep notifications@github.com wrote:



Is there an update on this package? We like to see responses and updates in a 3-4 weeks; This issue has seen no updates since September. If you need more time to work on the issue we can temporarily close until you are ready to continue with the review.

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serdarbozdag commented 3 years ago

Is there an update on this package? We like to see responses and updates in a 3-4 weeks; This issue has seen no updates since September. If you need more time to work on the issue we can temporarily close until you are ready to continue with the review.

Hello, we would like to submit a new version, but the initial maintainer is no longer in the project so we need to change the maintainer. I just sent an email to bioc-devel@r-project.org bioc-devel@r-project.org to request to associate @cdursun as the maintainer. Is there anything you could help with this? thanks

lshep commented 3 years ago

@serdarbozdag @cdursun has been updated in our system as maintainer. Please make sure to make the appropriate change in the DESCRIPTION of the package as well when you push changes. @cdursun you will have to activate your Bioconductor Git Credentials account using your email cagataydursun@gmail.com . I will be sending your temporary password to that email momentarily.

lshep commented 3 years ago

The Git Credentials account can be found here: https://git.bioconductor.org/BiocCredentials Please choose account activation to active account.

serdarbozdag commented 3 years ago

Great, thanks.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2cd4f8e686ee99ba258a7736c0d379051a633009

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/PhenoGeneRanker 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: 7a58355dd48387825a671c9a381fc93538dc35c5

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/PhenoGeneRanker 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: 468d05c3c7530a6501c980bdc971c0ae3dd771db

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/PhenoGeneRanker 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: 43792a6dd0025059ca1c4558d4d83c1b91e6f9d1

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/PhenoGeneRanker 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: fe812ebdd5a52e2818b64b47e58df8ff059807ed

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/PhenoGeneRanker 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: 5a30b8fc780fa8ab8825fc1bb3ee3801819fc594

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/PhenoGeneRanker 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: 5639475e833a6ed248a32715f754b18b4812b197

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/PhenoGeneRanker 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: 2bdb71faf444ad9251736a7ef62605e68e95f153

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/PhenoGeneRanker 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: e161cefeedc57c74b016a4d79cdc1572d1542a03

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

hpages commented 3 years ago

Hi @serdarbozdag, is the package ready for review? Thanks. H.

serdarbozdag commented 3 years ago

Yes, the latest submission we had a couple of weeks ago is ready for your review. Let me know if you need us to submit it again.

Thanks Serdar

On Dec 10, 2020, at 11:29 PM, Hervé Pagès notifications@github.com wrote:



Hi @serdarbozdaghttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_serdarbozdag&d=DwMCaQ&c=S1d2Gs1Y1NQV8Lx35_Qi5FnTH2uYWyh_OhOS94IqYCo&r=hA-XTKcE0pHLi8qKA6Dq1o8P8ckUkKd0p5cTStqyOwY&m=G7gKc7w9562OwjNlbOVKJIYkj8F21sadPvJdjBBJlUM&s=iKfstkt1V_FgKRPf-PtGr4GNas1PbY3Qy7y6vvLsxZs&e=, is the package ready for review? Thanks. H.

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hpages commented 3 years ago

Hi @serdarbozdag ,

I'll take a look at the package ASAP. Sorry for the delay.

H.

serdarbozdag commented 3 years ago

Thanks. We are looking forward to hearing your comments. We will be submitting the revised version of our paper very soon. If the bioconductor package is approved, we would be able to put the link to the manuscript.

Best,

Serdar

hpages commented 3 years ago

Hi @serdarbozdag ,

I get 1 ERROR and 1 WARNING when I run R CMD check on the package:

hpages@spectre:~$ R CMD check PhenoGeneRanker_0.99.6.tar.gz 
* using log directory ‘/home/hpages/pkgreviews/PhenoGeneRanker.review/PhenoGeneRanker.Rcheck’
* using R Under development (unstable) (2020-11-18 r79449)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘PhenoGeneRanker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenoGeneRanker’ version ‘0.99.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PhenoGeneRanker’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
Warning: parse error in file 'lines':
40: unexpected ','
43: ranksWithPval <- RandomWalkRestart(CreateWalkMatrix('myFile.txt'),c('gene1'), 
44:        c(), TRUE, 12, 0.7, 0.6, tau =(1,
                                           ^
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PhenoGeneRanker-Ex.R’ failed
The error most likely occurred in:

> ### Name: CreateWalkMatrix
> ### Title: Create Walk Matrix
> ### Aliases: CreateWalkMatrix
> 
> ### ** Examples
> 
> CreateWalkMatrix('myInput.txt')
Warning in file(file, "rt") :
  cannot open file 'myInput.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: CreateWalkMatrix -> ReadSettings -> read.table -> file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘PhenoGeneRanker.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/hpages/pkgreviews/PhenoGeneRanker.review/PhenoGeneRanker.Rcheck/00check.log’
for details.

I'm on Ubuntu 20.10 (see my sessionInfo() below).

Hopefully you can reproduce and address. Make sure you are using R 4.1 + BioC 3.13, and that all your packages are up-to-date (you can check this with BiocManager::valid()).

Thanks, H.

sessionInfo():

> library(BiocManager)
Bioconductor version 3.13 (BiocManager 1.30.10), ?BiocManager::install for help
> BiocManager::valid()
[1] TRUE
> library(PhenoGeneRanker)
> sessionInfo()
R Under development (unstable) (2020-11-18 r79449)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.10

Matrix products: default
BLAS:   /home/hpages/R/R-4.1.r79449/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.1.r79449/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.10    PhenoGeneRanker_0.99.6

loaded via a namespace (and not attached):
 [1] igraph_1.2.6      magrittr_2.0.1    tidyselect_1.1.0  doParallel_1.0.16
 [5] lattice_0.20-41   R6_2.5.0          rlang_0.4.10      foreach_1.5.1    
 [9] dplyr_1.0.3       tools_4.1.0       parallel_4.1.0    grid_4.1.0       
[13] DBI_1.1.1         iterators_1.0.13  ellipsis_0.3.1    assertthat_0.2.1 
[17] tibble_3.0.5      lifecycle_0.2.0   crayon_1.3.4      Matrix_1.3-2     
[21] purrr_0.3.4       vctrs_0.3.6       codetools_0.2-18  glue_1.4.2       
[25] compiler_4.1.0    pillar_1.4.7      generics_0.1.0    pkgconfig_2.0.3
cdursun commented 3 years ago

Hi @hpages, I am the author and maintainer for the package. When you address only @serdarbozdag I don't get any email. We have just seen your comment, I will check the problem soon. Thanks, Cagatay

cdursun commented 3 years ago

Hi @hpages, The version for PhenoGeneRanker should be 0.99.13. Could you please check it again? Thanks, Cagatay

hpages commented 3 years ago

@cdursun You didn't submit the package and you never commented in this issue so I'm not sure how I was supposed to know that I needed to address you. I will do it from now.

Ok so it seems that last time I checked the package I picked up the wrong version, sorry for that. I'm cloning the package repo again, but now from https://git.bioconductor.org/packages/PhenoGeneRanker instead of https://github.com/bozdaglab/PhenoGeneRanker, and I'm indeed seeing version 0.99.13.

Checking this version of the package now...

hpages commented 3 years ago

@cdursun PhenoGeneRanker 0.99.13 passes R CMD check and R CMD BiocCheck cleanly. Only one minor thing before we can add the package to Bioconductor: the description of the inputFileName argument in the man page for CreateWalkMatrix() seems truncated:

inputFileName: The name of the text file that contains the names of

Please address. Note that a complete description of this argument would also require describing the format of the input file, which is something you already do with great details in the vignette, so you could point to the vignette for that in order to avoid repetition.

Thanks

cdursun commented 3 years ago

Thank you for your feedback @hpages, we will address it soon.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 360da0720501b0acf3266caf69da4abd5d681b47

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/PhenoGeneRanker 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: e59b275f3e932551f4f58ea23a58b2423382f131

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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