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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