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@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre", "cph"),
email="zhe...@u.washington.edu",
comment=c(ORCID="0000-0002-1390-0708")),
person("Stephanie", "Gogarten", role="ctb", email="sdmor...@uw.edu"),
person("Cathy", "Laurie", role="ctb", email="cclau...@uw.edu"),
person("Bruce", "Weir", role=c("ctb", "ths"), email="bsw...@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 <zhe...@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 <dwinsem...@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.gru...@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
>>
>>
>>
>>
>>
>>
>>
>> ==============================================================================
>> Dr Bernd Gruber )/_
>> _.--..---"-,--c_
>> Professor Ecological Modelling \|..' ._O__)_
>> Tel: (02) 6206 3804 ,=. _.+ _ \..--( /
>> Fax: (02) 6201 2328 \\.-''_.-' \ ( \_
>> Institute for Applied Ecology `''' `\__ /\
>> Faculty of Science and Technology ')
>> University of Canberra ACT 2601 AUSTRALIA
>> Email: bernd.gru...@canberra.edu.au<mailto:bernd.gru...@canberra.edu.au>
>> WWW:
>> bernd-gruber<https://researchprofiles.canberra.edu.au/en/persons/bernd-gruber>
>>
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