[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

[Oleksii Nikolaienko]

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
>>> >
>>> >
>>> https://secure-web.cisco.com/1_PXUY54xMcyvZd-axtsGrsQIplTfY0lVue__l7qO7-luvgzGuniKIsiUSSi8IY181DNyD5-2auTbnMRe72kfIfwAMeLoYjHVFTIiYaB_5vn6kfTETYLRCWloTL9Rukze7_khHKVu7XK_I_J5Mq0GyVUuqu9DzwZp7LfxS1QcE4WsViKTdO8lnkNf3kgy04NzRYkfu5fuEggGVuSS2Q75UX8ILLADwFKLtampqpMWlQKt6e26oi_pRD08JSLJ0NcABrSz9tzLW4a5jC-awuByjl71Jj9CjV50wtq0fmSXlxXqYHblouixuLGrw_LXtcyJJhgGH2g9xoceNvTo-6kawg/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>>> >
>>> >
>>> >
>>> > This email message may contain legally privileged and/or confidential
>>> > information.  If you are not the intended recipient(s), or the
>>> employee or
>>> > agent responsible for the delivery of this message to the intended
>>> > recipient(s), you are hereby notified that any disclosure, copying,
>>> > distribution, or use of this email message is prohibited.  If you have
>>> > received this message in error, please notify the sender immediately by
>>> > e-mail and delete this email message from your computer. Thank you.
>>> >         [[alternative HTML version deleted]]
>>> >
>>> > _______________________________________________
>>> > Bioc-devel using r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>

	[[alternative HTML version deleted]]