[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

[Oleksii Nikolaienko]

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 using gmail.com> wrote:

> Thanks very much!
>
> Oleksii
>
> On Wed, 23 Oct 2024 at 10:52, Martin Grigorov <martin.grigorov using gmail.com>
> wrote:
>
>> Hi Oleksii,
>>
>> On Wed, Oct 23, 2024 at 9:47 AM Oleksii Nikolaienko <
>> oleksii.nikolaienko using 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 using 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 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,
>>>> >
>>>> >         [[alternative HTML version deleted]]
>>>> >
>>>> > _______________________________________________
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