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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