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.nikolaie...@gmail.com> wrote: > Thanks very much! > > Oleksii > > On Wed, 23 Oct 2024 at 10:52, Martin Grigorov <martin.grigo...@gmail.com> > wrote: > >> Hi Oleksii, >> >> On Wed, Oct 23, 2024 at 9:47 AM Oleksii Nikolaienko < >> oleksii.nikolaie...@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@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.grigo...@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@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@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-boun...@r-project.org> on behalf of >>>> Huang >>>> > Lin (Frederick) <huanglinfreder...@gmail.com> >>>> > Sent: Tuesday, October 22, 2024 2:28 PM >>>> > To: bioc-devel@r-project.org <bioc-devel@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@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. 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