We have a project running in version 3.4.4 of R. When we build it, we are getting an error that BiocInstaller is not available (see below).
According to https://www.bioconductor.org/install/#Legacy, we should be able to use Bioconstructor packages by running
This is a project that isn't updated often, but it seems that it was working a few months ago and broke without anything changing on our end. Any ideas on what could be causing this or what we could try differently? We'd like to avoid upgrading our version of R if possible.
Code should be placed in three backticks as shown below
> source("https://bioconductor.org/biocLite.R") Warning: unable to access index for repository https://bioconductor.org/packages/3.6/bioc/src/contrib: Line starting '<!DOCTYPE HTML PUBLI ...' is malformed! 'biocLite.R' failed to install 'BiocInstaller', use 'install.packages("BiocInstaller", repos="https://bioconductor.org/packages/3.6/bioc")' or 'install.packages("BiocInstaller", repos="http://bioconductor.org/packages/3.6/bioc")' Warning message: package ‘BiocInstaller’ is not available (for R version 3.4.4) > sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so locale:  LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8  LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8  LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):  compiler_3.4.4 tools_3.4.4