Oops, I misread this, and can reproduce. You can clone the current source out of github in the container and install it there.
docker run -ti bioconductor/bioconductor_docker:devel bash 3 git clone https://github.com/bioconductor/S4Arrays 4 R CMD INSTALL S4Arrays On Fri, Jan 12, 2024 at 9:51 AM Vincent Carey <st...@channing.harvard.edu> wrote: > 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. 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