Hi Shraddha, It looks like Michael has fixed this on GitHub: https://github.com/lawremi/rtracklayer/commit/86407bbef2d02455053b7b7c96afe9c5ce6949e7
but the fix hasn't been pushed to Bioconductor devel. In the meantime, you can install the GH version with BiocManager::install("lawremi/rtracklayer") Best regards, Marcel On 2/15/24 4:09 PM, Shraddha Pai wrote: Hello BioC community, Running BiocManager::install(c("rtracklayer”)) returns an error message (see below). I’m running this inside a Docker of bioc level version that I just ran today. A quick Google search on the handlers.c error turned up no obvious solutions. Anyone else run into this/have a solution? I was able to install “GenomicRanges” so it’s not like the package install process isn’t working in this setup. My setup: docker run \ -e PASSWORD=bioc \ -p 8787:8787 \ -v /Users/spai/software:/home/rstudio/software \ bioconductor/bioconductor_docker:devel And I’m running Rstudio via localhost:8787 in my browser. sessionInfo() output below as well. Thank you, Shraddha -- handlers.c: In function ‘R_warnHandler’: handlers.c:10:11: error: format not a string literal and no format arguments [-Werror=format-security] 10 | warning(warn_buf); | ^~~~~~~~ cc1: some warnings being treated as errors make: *** [/usr/local/lib/R/etc/Makeconf:191: handlers.o] Error 1 ERROR: compilation failed for package ‘rtracklayer’ * removing ‘/usr/local/lib/R/site-library/rtracklayer’ The downloaded source packages are in ‘/tmp/Rtmp23htnS/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/local/lib/R/library packages: survival Warning message: In install.packages(...) : installation of package ‘rtracklayer’ had non-zero exit status sessionInfo() R Under development (unstable) (2024-02-07 r85873) Platform: aarch64-unknown-linux-gnu Running under: Ubuntu 22.04.3 LTS Matrix products: default BLAS: /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/aarch64-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 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 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Etc/UTC tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] BiocManager_1.30.22 compiler_4.4.0 tools_4.4.0 -- Shraddha Pai, PhD Principal Investigator Adaptive Oncology Assistant Professor Department of Medical Biophysics University of Toronto shraddha....@oicr.on.ca<mailto:shraddha....@oicr.on.ca><mailto:shraddha....@oicr.on.ca><mailto:shraddha....@oicr.on.ca> Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news<https://twitter.com/oicr_news><https://twitter.com/oicr_news> | www.oicr.on.ca<http://www.oicr.on.ca><http://www.oicr.on.ca/><http://www.oicr.on.ca/> Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Marcel Ramos Pérez Roswell Park Comprehensive Cancer Center Dept. of Biostatistics and Bioinformatics Elm & Carlton Streets Buffalo, New York, 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel