Thanks, Martin! Oleksii
On Fri, 25 Oct 2024 at 09:09, Martin Grigorov <martin.grigo...@gmail.com> wrote: > 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
