[R-pkg-devel] Package from in imports bioconductor is not compiling on R-devel

Wed May 11 07:04:04 CEST 2022

This is the package DESCRIPTION after installing the current version from the Bioc repo:

> packageDescription("SNPRelate")
Package: SNPRelate
Type: Package
Title: Parallel Computing Toolset for Relatedness and Principal Component Analysis
        of SNP Data
Version: 1.28.0
Date: 2021-10-19
Depends: R (>= 2.15), gdsfmt (>= 1.8.3)
LinkingTo: gdsfmt
Imports: methods
Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics
Enhances: SeqArray (>= 1.12.0)
Authors using R: c(person("Xiuwen", "Zheng", role=c("aut", "cre", "cph"),
        email="zhengx using u.washington.edu", comment=c(ORCID="0000-0002-1390-0708")),
        person("Stephanie", "Gogarten", role="ctb", email="sdmorris using uw.edu"),
        person("Cathy", "Laurie", role="ctb", email="cclaurie using uw.edu"),
        person("Bruce", "Weir", role=c("ctb", "ths"), email="bsweir using uw.edu",
        comment=c(ORCID="0000-0002-4883-1247")))
Description: Genome-wide association studies (GWAS) are widely used to investigate
        the genetic basis of diseases and traits, but they pose many
        computational challenges. We developed an R package SNPRelate to provide
        a binary format for single-nucleotide polymorphism (SNP) data in GWAS
        utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS
        format offers the efficient operations specifically designed for integers
        with two bits, since a SNP could occupy only two bits.  SNPRelate is also
        designed to accelerate two key computations on SNP data using parallel
        computing for multi-core symmetric multiprocessing computer
        architectures: Principal Component Analysis (PCA) and relatedness
        analysis using Identity-By-Descent measures. The SNP GDS format is also
        used by the GWASTools package with the support of S4 classes and generic
        functions. The extended GDS format is implemented in the SeqArray package
        to support the storage of single nucleotide variations (SNVs),
        insertion/deletion polymorphism (indel) and structural variation calls in
        whole-genome and whole-exome variant data.
License: GPL-3
VignetteBuilder: knitr
URL: http://github.com/zhengxwen/SNPRelate
BugReports: http://github.com/zhengxwen/SNPRelate/issues
biocViews: Infrastructure, Genetics, StatisticalMethod, PrincipalComponent
git_url: https://git.bioconductor.org/packages/SNPRelate
git_branch: RELEASE_3_14
git_last_commit: 8fcd837
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
NeedsCompilation: yes
Packaged: 2021-10-27 03:33:37 UTC; biocbuild
Author: Xiuwen Zheng [aut, cre, cph] (<https://orcid.org/0000-0002-1390-0708>),
        Stephanie Gogarten [ctb], Cathy Laurie [ctb], Bruce Weir [ctb, ths]
        (<https://orcid.org/0000-0002-4883-1247>)
Maintainer: Xiuwen Zheng <zhengx using u.washington.edu>
Built: R 4.1.1; x86_64-apple-darwin17.0; 2021-10-27 17:11:51 UTC; unix

-- File: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/SNPRelate/Meta/package.rds
—
David. 

Sent from my iPhone

> On May 10, 2022, at 9:47 PM, David Winsemius <dwinsemius using comcast.net> wrote:
> 
> You can download the source from the package archives. It can then be installed from a terminal console and the logs should tell you the problem. 
> 
> — 
> David. 
> 
> Sent from my iPhone
> 
>> On May 10, 2022, at 9:19 PM, Bernd.Gruber <Bernd.Gruber using canberra.edu.au> wrote:
>> 
>> Hi,
>> 
>> 
>> I just got an email from Brian Ripley, which informed me that one of my dependencies in imports (SNPRelate) cannot be installed in R-devel and that I should check the check pages on CRAN or contact the maintainer.
>> 
>> 
>> 
>> AsS SNPRelate is actually a Bioconductor package (has been removed from CRAN in 2014) I do not know which check pages I am supposed to check.
>> 
>> 
>> 
>> I definitely will contact the maintainer, but to understand why it is not compiling is there a way to find out, so I can direct the maintainer to the problem more efficiently?
>> 
>> 
>> 
>> Thanks, Bernd
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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