[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

Hi Martin,
sorry to bother, but there's some other issue
<https://bioconductor.org/checkResults/devel/bioc-LATEST/epialleleR/kunpeng2-buildsrc.html>
now, possibly related to conda as well. Could you please have a look?

Best,
Oleksii



On Wed, 23 Oct 2024 at 11:14, Oleksii Nikolaienko <
oleksii.nikolaienko at gmail.com> wrote:

Thanks very much!

Oleksii

On Wed, 23 Oct 2024 at 10:52, Martin Grigorov <martin.grigorov at gmail.com>
wrote:

Hi Oleksii,

On Wed, Oct 23, 2024 at 9:47?AM Oleksii Nikolaienko <
oleksii.nikolaienko at gmail.com> wrote:

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

Done!

biocbuild at kunpeng2 ~/git> R CMD build epialleleR

                                                           (base)
* checking for file ?epialleleR/DESCRIPTION? ... OK
* preparing ?epialleleR?:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ?epialleleR_1.13.4.tar.gz?

I guess it got broken due to a recent introduction of using conda for
installing newer versions of dependencies than the ones in the OS repos.

Martin

Best,
Oleksii

On Wed, 23 Oct 2024 at 08:33, Martin Grigorov <
martin.grigorov at 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 at 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 at 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

Huang

Lin (Frederick) <huanglinfrederick at gmail.com>
Sent: Tuesday, October 22, 2024 2:28 PM
To: bioc-devel at r-project.org <bioc-devel at 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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