[Bioc-devel] Error installing rtracklayer in BioC devel docker

[Ramos Perez, Marcel]

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

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Ontario Institute for Cancer Research
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--
Marcel Ramos Pérez
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics and Bioinformatics
Elm & Carlton Streets
Buffalo, New York, 14263


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