bamSliceR: Slicing and Tallied BAMs from GDC and local for Variants Analysis

[huangyizR]

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[bioc-issue-bot]

Hi @huangyizR

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: bamSliceR
Type: Package
Title: Slicing and Tallied BAMs from GDC and local for Variants Analysis
Version: 0.99.0
Authors@R: c( 
        person("Peter", "Huang", role=c("aut", "cre"), 
      email="[email protected]",
      comment=c(ORCID="0009-0004-5689-0193")),
        person("Lauren", "Harmon", role=c("ctb"),
      email="[email protected]",
      comment=c(ORCID="0000-0002-2248-060")), 
        person("Timothy", "Triche", role=c("ctb"),
      comment=c(ORCID="0000-0001-5665-946X")))
Description: A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories.
Depends: R (> 4.0), 
         gmapR,
         VariantAnnotation,
         GenomicRanges,
         plyranges,
         GenomicDataCommons, 
         Rsamtools,
         rtracklayer
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: DataImport, Sequencing
Suggests: 
    knitr,
    rmarkdown,
    pkgdown
Imports: 
    BiocParallel,
    biomaRt,
    Homo.sapiens,
    httr,
    jsonlite,
    stringr,
    BSgenome.Hsapiens.UCSC.hg38,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    VariantTools,
    data.table,
    maftools, 
    RColorBrewer,
    IRanges,
    S4Vectors,
    methods

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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.

On one or more platforms, the build results were: "skipped, ERROR".
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Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 61e4a81edc7f338778877e712dd7c7ddda978565

[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.

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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): bamSliceR_0.99.1.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
[email protected]:packages/bamSliceR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ee927c0acfb2f20eca5aa7d134ecbb024a5bcfe2

[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 24.04.1 LTS): bamSliceR_0.99.2.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
[email protected]:packages/bamSliceR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

You currently write a file, INPUT_VCF_FILE.vcf, to a users home directory by default. Please use tempdir() instead.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f1a0934ecc58e4af9e15457e60c123f4fb11f9e

[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 24.04.1 LTS): bamSliceR_0.99.3.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
[email protected]:packages/bamSliceR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

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