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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 source("https://bioconductor.org/biocLite.R").
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:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.4 tools_3.4.4
Yes, I get the same error:
I can get that to work using both the release R-4.2.0 version, as well as an old R-3.5.3. I don't have R-3.4.4 readily available but I imagine it would be the same.
Another alternative would be direct download
But really you shouldn't be using old versions like that and given that we don't support old stuff I really shouldn't be helping you to do so. Our general assumption is that anybody who wants to do this sort of thing is capable and willing to self-support, and otherwise should follow the recommendation of using the release version, which we do support.
James,
I really appreciate your quick response. It was very helpful to see that it worked on your end. It helped us narrow down the problem and we were able to fix it with a change to our build.
You're right about the risk of using old versions. There's politics involved in upgrading the version of R and I'm not sure we're able to do it yet.
Thank you!
I assume the politics have to do with the site-wide version of R? In over 20 years of using R, I have very rarely relied on an installation of R that wasn't under my control, and I have never had root or sudo privileges on any of the Linux boxes I use at work. IMO there is very little upside to sharing an R installation, and certainly no upside to bugging the sysadmin every six months for an upgrade. The three main ways I would circumvent using the site-wide install are: