Bioconductor / Contributions

Contribute Packages to Bioconductor
135 stars 33 forks source link

gdrplatform release [sixth package: gDR] #3004

Closed gladkia closed 1 year ago

gladkia commented 1 year 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 questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 1 year ago

Hi @gladkia

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:

Type: Package
Package: gDR
Title: Umbrella package for R packages in the gDR suite
Version: 0.99.0
Date: 2023-03-23
Authors@R: c(
    person("Support", "gDR", , "gdr-support-d@gene.com", role = "cre",
 comment = c(ORCID = "0009-0006-9310-1135")),
    person("Allison", "Vuong", , "vuong.allison@gene.com", role = "aut"),
    person("Bartosz", "Czech", role = "aut"),
    person("Arkadiusz", "Gladki", role = "aut"),
    person("Marc", "Hafner", role = "aut"),
    person("Dariusz", "Scigocki", role = "aut"),
    person("Sergiu", "Mocanu", role = "aut")
  )
Description: Package is a part of the gDR suite. It provides info about processing functions 
    and utilities from individual gDR packages. The vignette walks through 
    the full processing pipeline for drug response analyses that the gDR suite offers.
License: file LICENSE
Depends:
    R (>= 4.2),
    gDRcore (>= 0.99.0),
    gDRimport (>= 0.99.0),
    gDRutils (>= 0.99.0)
Suggests:
    BumpyMatrix,
    futile.logger,
    gDRstyle (>= 0.99.0),
    gDRtestData (>= 0.99.0),
    kableExtra,
    knitr,
    markdown,
    purrr,
    rmarkdown,
    SummarizedExperiment,
    testthat,
    yaml
VignetteBuilder: 
    knitr
biocViews: Software, DataImport
ByteCompile: TRUE
DeploySubPath: gDR
Encoding: UTF-8
LazyLoad: yes
RoxygenNote: 7.2.3
SwitchrLibrary: gDR
vjcitn commented 1 year ago
--- re-building ‘gDR.Rmd’ using knitr
Quitting from lines 95-98 (gDR.Rmd) 
Error: processing vignette 'gDR.Rmd' failed with diagnostics:
'length = 3840' in coercion to 'logical(1)'
--- failed re-building ‘gDR.Rmd’
gladkia commented 1 year ago

@vjcitn thanks - we will merge the bugfix soon (https://github.com/gdrplatform/gDRcore/pull/62).

gladkia commented 1 year ago

@vjcitn fixed.

gladkia commented 1 year ago

Hi @vjcitn and @lshep,

I would like to push the latest changes to git@git.bioconductor.org:packages/gDR.git but I'm getting:

gladkia@gladkia-UHMD6M /tmp % git clone git@git.bioconductor.org:packages/gDR.git        
Cloning into 'gDR'...
FATAL: R any packages/gDR gladkia 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.

I see the same issue for other packages, submitted as candidates for the 3.17 release, on which gDR depends (gDRcore, gDRutils, gDRimport, gDRtestData). How to solve it?

Thanks in advance for your help!

Best, Arek

vjcitn commented 1 year ago

I don't think we are using git.bioconductor.org yet ... the package is not far enough along. we are working from your github. And finding

* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘gDRinternalData’
* 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 ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'gDRcore-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_mae_to_raw_data
> ### Title: Transform mae into raw data
> ### Aliases: convert_mae_to_raw_data
> 
> ### ** Examples
> 
> mae <- get_synthetic_data("finalMAE_small.RDS")
Error in get_synthetic_data("finalMAE_small.RDS") : 
  could not find function "get_synthetic_data"
Execution halted

Please sync all your packages to a consistent state in your github and ensure that they will pass check.

vjcitn commented 1 year ago

building gDR fails

* checking for file 'gDR/DESCRIPTION' ... OK
* preparing 'gDR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gDR.Rmd’ using knitr
Quitting from lines 113-121 (gDR.Rmd) 
Error: processing vignette 'gDR.Rmd' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘gDR.Rmd’

SUMMARY: processing the following file failed:
  ‘gDR.Rmd’
 sessionInfo()
R Under development (unstable) (2023-03-18 r84003)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /home/stvjc/R-43dev-dist/lib/R/lib/libRblas.so 
LAPACK: /home/stvjc/R-43dev-dist/lib/R/lib/libRlapack.so;  LAPACK version 3.11.0

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       

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
[1] gDR_0.99.3       gDRutils_0.99.4  gDRimport_0.99.3 gDRcore_0.99.3  
[5] rmarkdown_2.21  

loaded via a namespace (and not attached):
 [1] Matrix_1.5-4                compiler_4.3.0             
 [3] SummarizedExperiment_1.29.1 Biobase_2.59.0             
 [5] GenomicRanges_1.51.4        bitops_1.0-7               
 [7] IRanges_2.33.1              fastmap_1.1.1              
 [9] lattice_0.21-8              XVector_0.39.0             
[11] GenomeInfoDb_1.35.16        knitr_1.42                 
[13] BiocGenerics_0.45.3         backports_1.4.1            
[15] DelayedArray_0.25.0         checkmate_2.1.0            
[17] tibble_3.2.1                MatrixGenerics_1.11.1      
[19] GenomeInfoDbData_1.2.10     pillar_1.9.0               
[21] rlang_1.1.0                 utf8_1.2.3                 
[23] xfun_0.38                   cli_3.6.1                  
[25] magrittr_2.0.3              zlibbioc_1.45.0            
[27] grid_4.3.0                  digest_0.6.31              
[29] lifecycle_1.0.3             S4Vectors_0.37.5           
[31] vctrs_0.6.1                 startup_0.20.0             
[33] evaluate_0.20               glue_1.6.2                 
[35] data.table_1.14.8           stats4_4.3.0               
[37] RCurl_1.98-1.12             fansi_1.0.4                
[39] matrixStats_0.63.0          tools_4.3.0                
[41] pkgconfig_2.0.3             htmltools_0.5.5  
vjcitn commented 1 year ago

I am going to pass the pre-check so that the build system reports are directly addressible by you. I would not begin reviewing until you get to a WARNINGS state.

gladkia commented 1 year ago

@vjcitn, thanks! Can you please give me some hints on how to trigger the build system reports?

gladkia commented 1 year ago

@vjcitn, FYI, the error in the gDR vignette has just been fixed.

bioc-issue-bot commented 1 year 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 1 year 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/gDR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

vjcitn commented 1 year ago
td <- get_test_data()
td$m_file
[1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/manifest.xlsx”

td$t_files
[1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_7daytreated.xlsx” [2] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_Untreated.xlsx”

This is quite unpleasant, in the vignette. You should define an object class that manages the paths, with methods that can use them. You don't have to use S4 but it is recommended.

gladkia commented 1 year ago
td <- get_test_data()
td$m_file
[1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/manifest.xlsx”

td$t_files
[1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_7daytreated.xlsx” [2] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_Untreated.xlsx”

This is quite unpleasant, in the vignette. You should define an object class that manages the paths, with methods that can use them. You don't have to use S4 but it is recommended.

Hi, We've just merged the PRs with the suggested solution (https://github.com/gdrplatform/gDR/pull/28, https://github.com/gdrplatform/gDRcore/pull/75 and https://github.com/gdrplatform/gDRimport/pull/42).

gladkia commented 1 year ago

Hi, @vjcitn and @lshep Thanks in advance for the feedback regarding the current status.

vjcitn commented 1 year ago

are you bumping version numbers to get new builds?

gladkia commented 1 year ago

Hi,

No just to assure all dependencies are up-to-date.

Best, Arek

On Thu, Apr 20, 2023 at 5:42 PM Vince Carey @.***> wrote:

are you bumping version numbers to get new builds?

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3004#issuecomment-1516555585, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJ2CMZO5DRMY7KTR4EQ56VTXCFKOFANCNFSM6AAAAAAWOKVZ24 . You are receiving this because you were mentioned.Message ID: @.***>

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 22a5ffd2df729e13a8ca9ce0fd9c837e121579aa

bioc-issue-bot commented 1 year 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/gDR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c03ef3bdc5cb7bc644217a0d7fc4fe62ded1352a

bioc-issue-bot commented 1 year 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/gDR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

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.

lshep commented 1 year ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/gladkia.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

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("gDR"). The package 'landing page' will be created at

https://bioconductor.org/packages/gDR

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.