[Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

[Martin Grigorov]

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]]