[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

[Martin Grigorov]

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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