Hi Oleksii, Actually "/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found" was *the* reason to introduce conda (to install GNU compilers 14.x (gcc, gxx together with libstdcxx)). But then it appeared that adding ~/miniforge3/lib to LD_LIBRARY_PATH breaks dnf/yum ... Now I reworked the way miniforge3/lib is exposed to the builder and it should be OK again! Thanks for reporting it!
Martin On Thu, Oct 24, 2024 at 7:20 PM Oleksii Nikolaienko < oleksii.nikolaie...@gmail.com> wrote: > 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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Thank you. >>>>> > [[alternative HTML version deleted]] >>>>> > >>>>> > _______________________________________________ >>>>> > Bioc-devel@r-project.org mailing list >>>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> > >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
