[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform
Oleksii Nikolaienko
o|ek@||@n|ko|@|enko @end|ng |rom gm@||@com
Fri Oct 25 10:35:37 CEST 2024
Thanks, Martin!
Oleksii
On Fri, 25 Oct 2024 at 09:09, Martin Grigorov <martin.grigorov using gmail.com>
wrote:
> 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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