I cannot reproduce this with a current pull of the devel container. BiocManager installation of S4Vectors succeeded. Please provide the version given in environment variable BIOCONDUCTOR_DOCKER_VERSION, I used 3.19.13
R Under development (unstable) (2024-01-03 r85769) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Etc/UTC tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] S4Vectors_0.41.3 BiocGenerics_0.49.1 loaded via a namespace (and not attached): [1] BiocManager_1.30.22 compiler_4.4.0 tools_4.4.0 On Fri, Jan 12, 2024 at 9:30 AM Sabanes Bove, Daniel via Bioc-devel < bioc-devel@r-project.org> wrote: > Hello, > > I am trying to reproduce a problem with the hermes package on BioC devel. > To this end, I installed docker, and loaded the RStudio session > from bioconductor_docker:devel. > Now the problem is that I cannot install the dependency S4Arrays because > the compilation fails with > > array_selection.c: In function ‘C_Lindex2Mindex’: > array_selection.c:352:17: error: format not a string literal and no > format arguments [-Werror=format-security] > 352 | error(errmsg_buf()); > | ^~~~~ > array_selection.c: In function ‘C_Mindex2Lindex’: > array_selection.c:416:17: error: format not a string literal and no > format arguments [-Werror=format-security] > 416 | error(errmsg_buf()); > | ^~~~~cc1: some warnings being treated as errors > > > Am I doing something wrong maybe? I expected that S4Arrays should > install just fine because > > https://bioconductor.org/checkResults/devel/bioc-LATEST/S4Arrays/ > > shows that its checks on BioC devel pass, and I assumed that the same > Docker image is used? > > > Thanks for your help, > > best regards > > Daniel > > > On Thu, Jan 11, 2024 at 8:55 PM Daniel Sabanes Bove < > daniel.sabanes_b...@roche.com> wrote: > > > Thanks a lot, > > we will look into this immediately. > > Best regards > > Daniel > > > > On Thu, Jan 11, 2024 at 5:37 PM CoreTeam Bioconductor < > > bioconductorcoret...@gmail.com> wrote: > > > >> Hello Package Maintainer, > >> > >> We would like to bring to your attention that your package is failing in > >> devel across all platforms. This is very problematic. Please investigate > >> the issues and fix the package to avoid deprecation. > >> > >> https://bioconductor.org/checkResults/devel/bioc-LATEST/ > >> < > https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow> > >> > >> If you have further questions or concerns please reach out on the > >> bioc-devel@r-project.org > >> > >> We appreciate your quick attention to this matter > >> > >> Cheers, > >> On behalf of the Bioconductor Core Team > >> > > > > > > -- > > *Dr. Daniel Sabanés Bové* > > Senior Principal Data Scientist > > > > F. Hoffmann-La Roche Ltd > > PD Data Sciences - Data Science Acceleration (DSX) > > B. 663 > > CH-4070 Basel > > Switzerland > > > > Discover our products at go.roche.com/statistical-engineering (internal > > page) and go.roche.com/statistical-engineering-presentation (public) > > www.roche.com > > > > *Confidentiality Note: *This message is intended only for the use of the > > named recipient(s) and may contain confidential and/or proprietary > > information. If you are not the intended recipient, please contact the > > sender and delete this message. Any unauthorized use of the information > > contained in this message is prohibited. > > > > > > > > > > -- > *Dr. Daniel Sabanés Bové* > Senior Principal Data Scientist > > F. Hoffmann-La Roche Ltd > PD Data Sciences - Data Science Acceleration (DSX) > B. 663 > CH-4070 Basel > Switzerland > > Discover our products at go.roche.com/statistical-engineering (internal > page) and go.roche.com/statistical-engineering-presentation (public) > www.roche.com > > *Confidentiality Note: *This message is intended only for the use of the > named recipient(s) and may contain confidential and/or proprietary > information. If you are not the intended recipient, please contact the > sender and delete this message. Any unauthorized use of the information > contained in this message is prohibited. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
