[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

Fri Oct 25 09:08:56 CEST 2024

Hi Oleksii,

Actually "/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found"
was *the* reason to introduce conda (to install GNU compilers 14.x (gcc,
gxx together with libstdcxx)).
But then it appeared that adding ~/miniforge3/lib to LD_LIBRARY_PATH breaks
dnf/yum ...
Now I reworked the way miniforge3/lib is exposed to the builder and it
should be OK again!
Thanks for reporting it!

Martin

On Thu, Oct 24, 2024 at 7:20 PM Oleksii Nikolaienko <
oleksii.nikolaienko using gmail.com> wrote:

> 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]]
>>>>> >
>>>>> > _______________________________________________
>>>>> > Bioc-devel using r-project.org mailing list
>>>>> >
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>>>>>
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>>>>

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