Site2Target

[peymanzarrineh]

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• Repository: https://github.com/fls-bioinformatics-core/Site2Target

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[bioc-issue-bot]

Hi @peymanzarrineh

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: Site2Target
Type: Package
Title: An R package to associate peaks and target genes
Version: 0.99.0
Authors@R: person("Peyman Zarrineh", email="[email protected]", role=c("cre", "aut"), comment = c(ORCID = "0000-0003-4820-4101"))
Description: Statistics implemented for both peak-wise and gene-wise associations. In peak-wise associations, the p-value of the target genes of a given set of peaks are calculated. Negative binomial or Poisson distributions can be used for modeling the unweighted peaks targets and log-nromal can be used to model the weighted peaks. In gene-wise associations a table consisting of a set of genes, mapped to specific peaks, is generated using the given rules.
BugReports: https://github.com/fls-bioinformatics-core/Site2Target/issues
License: GPL-2
Encoding: UTF-8
LazyData: false
Imports: S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS, IRanges, GenomicRanges
biocViews: Annotation, ChIPSeq, Software, Epigenetics, GeneExpression, GeneTarget
RoxygenNote: 7.3.2
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr

[lshep]

When i try to R CMD build your package I'm getting the following ERROR

R CMD build Site2Target 
* checking for file 'Site2Target/DESCRIPTION' ... OK
* preparing 'Site2Target':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Site2Target.Rmd’ using rmarkdown
Could not find bibliography file: /Site2Target.bib
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'Site2Target.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘Site2Target.Rmd’

SUMMARY: processing the following file failed:
  ‘Site2Target.Rmd’

Error: Vignette re-building failed.
Execution halted

[peymanzarrineh]

Hello,

I got this error but I assumed it is about pandoc versioning. I could make .html file without any problem from .Rmd file. Do you know what is the problem?

Thank you,

[lshep]

I think you can just do bibliography: Site2Target.bib instead of bibliography: "`r file.path(system.file('vignettes', package = 'Site2Target'), 'Site2Target.bib')`". If that does not work I would ask on the [email protected]

[peymanzarrineh]

Thank you very much! that solved the problem. Now I don't get error or warning in check and BiocCheck. now my problem is that I cannot push a new version to the Bioconductor. I do:

git remote add origin https://github.com/fls-bioinformatics-core/Site2Target.git
git remote add upstream [email protected]:packages/Site2Target.git
git remote -v
git fetch --all

"error: Could not fetch upstream"

It seems " [email protected]:packages/Site2Target" does not exists. Should I make a new issue and start from beginning?

[lshep]

it is not yet on bioconductor. this is still in the preview stage. I will check your github repo for the updates soon