crupR submission

[akbariomgba]

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the package you wish to submit to Bioconductor

• Repository: https://github.com/akbariomgba/crupR

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[bioc-issue-bot]

Hi @akbariomgba

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: crupR
Type: Package
Title: an R package to predict condition-specific enhancers from ChIP-seq data
Version: 0.99.0
Authors@R: c(
   person("Persia", "Akbari Omgba", email = "omgba@molgen.mpg.de", role = c("cre")),
   person("Verena", "Laupert", email = "verena.laupert@bayer.com", role = c("aut")),
   person("Martin", "Vingron", email = "vingron@molgen.ppg.com", role = c("aut")))
Description: An R package offers a workflow to predict condition-specific enhancers from ChIP-seq data.
    The prediction of regulatory units is done in four main Steps:
    Step 1 is the normalization of the ChIP-seq counts.
    Step 2 is the actual prediction of active enhancers bin-wise on the whole genome.
    Step 3 is the condition-specific clustering of the putative active enhancers.
    Step 4 is the search for possible target genes of the condition-specific clusters using RNA-seq counts.
License: GPL-3
Encoding: UTF-8
LazyData: false
Imports: 
    BSgenome.Mmusculus.UCSC.mm10,
    BSgenome.Mmusculus.UCSC.mm9,
    BSgenome.Hsapiens.UCSC.hg19,
    BSgenome.Hsapiens.UCSC.hg38,
    bamsignals,
    Rsamtools,
    GenomicRanges,
    preprocessCore,
    randomForest,
    rtracklayer,
    GenomeInfoDb,
    S4Vectors,
    parallel,
    ggplot2,
    matrixStats,
    dplyr,
    IRanges,
    GenomicAlignments,
    GenomicFeatures,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    TxDb.Mmusculus.UCSC.mm9.knownGene,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    BSgenome,
    reshape2,
    magrittr,
    stats,
    utils,
    grDevices
Depends:
    R (>= 4.2.0)
Suggests: testthat, BiocStyle, knitr, rmarkdown
biocViews:
    DifferentialPeakCalling,
    GeneTarget,
    FunctionalPrediction,
    HistoneModification,
    PeakDetection
BiocType: Software
URL: https://github.com/akbariomgba/crupR
RoxygenNote: 7.2.3
VignetteBuilder: knitr

[lshep]

I currently cannot build the package

R CMD build crupR 
* checking for file 'crupR/DESCRIPTION' ... OK
* preparing 'crupR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘crupR-vignette.Rmd’ using rmarkdown

Quitting from lines  at lines 167-168 [unnamed-chunk-11] (crupR-vignette.Rmd)
Error: processing vignette 'crupR-vignette.Rmd' failed with diagnostics:
object 'C_pKS2' not found
--- failed re-building ‘crupR-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘crupR-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

[akbariomgba]

Hello,
When I am trying to build the package it runs w/o any errors, so I have trouble finding the bug. Could you please provide your session info or other information about your environment such that I can replicate it?

[lshep]

R CMD build crupR 
* checking for file 'crupR/DESCRIPTION' ... OK
* preparing 'crupR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘crupR-vignette.Rmd’ using rmarkdown

Quitting from lines 167-168 [unnamed-chunk-11] (crupR-vignette.Rmd)
Error: processing vignette 'crupR-vignette.Rmd' failed with diagnostics:
object 'C_pKS2' not found
--- failed re-building ‘crupR-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘crupR-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

My sessionInfo()

Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.0 Patched (2024-04-30
  r86503)
> sessionInfo()
R version 4.4.0 Patched (2024-04-30 r86503)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /home/lorikern/R-Installs/bin/R-4-4-branch/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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] praise_1.0.0        BiocManager_1.30.23

loaded via a namespace (and not attached):
[1] compiler_4.4.0

[akbariomgba]

Thank you for the session info. I was able to reproduce the bug and fixed it. The repo has been updated.

I apologize for the inconvenience.

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the
pre-review process. A build report will be posted shortly. Please
fix any ERROR and WARNING in the build report before a reviewer is
assigned or provide a justification on why you feel the ERROR or
WARNING should be granted an exception.

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): crupR_0.99.0.tar.gz

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

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.