[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

[Oleksii Nikolaienko]

Hi Martin,
could you please also install libz-dev or zlib1g-dev (not sure which one is
needed)?  -
https://bioconductor.org/checkResults/devel/bioc-LATEST/epialleleR/kunpeng2-install.html

Best,
Oleksii

On Wed, 23 Oct 2024 at 08:33, Martin Grigorov <martin.grigorov using gmail.com>
wrote:

> Hi,
>
> The problem was missing rustc and cargo on kunpeng2:
> =====================================================
> /bin/sh: line 2: rustc: command not found
> Rust version:
> /bin/sh: line 3: cargo: command not found
> Cargo version:
> /bin/sh: line 11: cargo: command not found
> make: *** [Makevars:25:
>
> /home/biocbuild/tmp/RtmpT7Ahcq/R.INSTALL28b5195beb22/clarabel/src/rust/target/release/libclarabel.a]
> Error 127
> ERROR: compilation failed for package ‘clarabel’
> * removing ‘/home/biocbuild/R/R-4.4.1/site-library/clarabel’
> ERROR: dependency ‘clarabel’ is not available for package ‘CVXR’
> * removing ‘/home/biocbuild/R/R-4.4.1/site-library/CVXR’
> =====================================================
>
> I have installed them and now all is fine:
>
> biocbuild using kunpeng2 ~/git> R CMD build ANCOMBC
>
>                                                       (base)
> * checking for file ‘ANCOMBC/DESCRIPTION’ ... OK
> * preparing ‘ANCOMBC’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to process help pages
> Loading required namespace: ANCOMBC
> * saving partial Rd database
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files and shell scripts
> * checking for empty or unneeded directories
> * looking to see if a ‘data/datalist’ file should be added
> * building ‘ANCOMBC_2.7.1.tar.gz’
>
> Regards,
> Martin
>
>
> On Tue, Oct 22, 2024 at 9:38 PM Kern, Lori via Bioc-devel <
> bioc-devel using r-project.org> wrote:
>
> > Thank you for reaching out.  The ERROR will not affect your package being
> > released in 3.20.  We will investigate why CVXR is not available on that
> > platform.
> >
> > Cheers,
> >
> >
> >
> > Lori Shepherd - Kern
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Huang
> > Lin (Frederick) <huanglinfrederick using gmail.com>
> > Sent: Tuesday, October 22, 2024 2:28 PM
> > To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> > Subject: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform
> >
> > Dear BioC Team,
> >
> > I recently submitted a change to the devel branch for the ANCOMBC
> package:
> >
> >
> https://secure-web.cisco.com/1mLHqucygNoVYQpL98cfWLJcc4ukFxfVEK1vO3vWKlsZT9SSd6975Fe56mS2AulHLyW0Cuo05ZZrklydxCocZm1WmRE8dQUB6TV7cwcpj565q6Cq6pN7X3z1zoP400iBKDsqU9u9OnINotXj3qVYFsvhU-hAkZG8LqbQd3yRS0DBCFAqDmRKp9D0BllxGmc8GSZ4hkKM4UhrThBjBrlVhxflD6cclkThD3mlhzqcjC-e7novu6wIngsUj5nQfrdoFqInH53w_Nuxi7J6t51Q1mvpHpjOJFwk_3v5HCEXu5yE4ww-rjiu19Sg_cMIgYzgSvVzh_R4fBO5grhbyXhQqDA/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.20%2Fbioc-LATEST%2FANCOMBC%2Fnebbiolo2-buildsrc.html
> >
> > However, it showed an error on the kunpeng2 platform. Upon checking the
> raw
> > results, it appears that the error is due to the missing dependency
> ‘CVXR’
> > package.
> >
> > Since this package is maintained by others, I wanted to seek your advice
> on
> > this issue. Will this cause any problems for the release of ANCOMBC on
> > Bioconductor 3.20?
> >
> > Best regards,
> >
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> >
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