R 3.6.3 on Ubuntu Focal points to a non-existant sed

[florisvdh]

When installing R 3.6.3 for Ubuntu Focal using https://docs.rstudio.com/resources/install-r/#download-and-install-r, it appears that /opt/R/3.6.3/lib/R/bin/R at line 120 has:

## some systems have a more portable sed, e.g. /usr/xpg4/bin/sed on Solaris,
## so make sure that is used.
SED=/usr/bin/sed
export SED

However sed is in /bin, not /usr/bin, and the path had to be changed into the following, in order to let e.g. bookdown::render_book() do its job.

## some systems have a more portable sed, e.g. /usr/xpg4/bin/sed on Solaris,
## so make sure that is used.
SED=/bin/sed
export SED

[florisvdh]

I must add that I'm on Linux Mint 20 (derived from Ubuntu 20.04), so not 100% sure the path to sed in Mint equals that of Ubuntu, but I'd expect so (Mint uses the Ubuntu repo).

[glin]

Hi, the SED variable is auto-configured by R, and not something we've set. sed does seem to be at /usr/bin/sed on Ubuntu Focal:

$ docker run -it --rm ubuntu:focal

root@d0461c08a686:/# which sed
/usr/bin/sed

/bin/sed also exists, but it's a symlink to /usr/bin/sed:

root@d0461c08a686:/# readlink -f /bin/sed
/usr/bin/sed

I'm not familiar with Linux Mint 20, but I think recent versions of Ubuntu now have /bin/ as a symlink to /usr/bin (ref). Could you put a symlink to /bin/sed at /usr/bin/sed?

[florisvdh]

Hi @glin , thanks for the help. Indeed, in the meantime I had solved it with a symlink from /usr/bin/sed to /bin/sed. BTW, renv likewise complained about tar not being in /usr/bin (same solution applied). May be Mint-specific indeed, don't know for sure.

I think this issue can be closed.

[florisvdh]

@glin I have been thinking further about this, regarding the R build.

After all, my regular R install from CRAN (from https://cloud.r-project.org) runs perfectly on Mint (also with renv), and it is the 'official' Ubuntu build (I use deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/). In the output of less $(which R), we can read:

## some systems have a more portable sed, e.g. /usr/xpg4/bin/sed on Solaris,
## so make sure that is used.
SED=/bin/sed
export SED

So for some reason this is different from the build from RStudio - and clearly the above one is Mint-proof 😉 - so that may be worth considering. Note, I did not compile R, I just installed the binary packages (r-base, r-base-dev) from named repo.

Thanks for referring to the message on Disco Dingo. This seems quite a deep change, I didn't know about, and it seems the Mint developers may not have followed this. I may look further at it (live Ubuntu desktop, Mint devs) when I find some time.

As a final note: I said I changed the path to sed in /opt/R/3.6.3/lib/R/bin/R, but eventually I also added an extra symlink to sed because the compilation of the fs package, in the R 3.6.3 builld, apparently also looked for /usr/bin/sed - which by default is not there in Mint. I don't understand why it looked there (as I had changed the path in to sed in /opt/R/3.6.3/lib/R/bin/R), given the fact that fs does not complain when compiling under regular CRAN R on my machine. So I think it also will have to do with the specific R build (which I use in a project with renv, by running env RSTUDIO_WHICH_R=/opt/R/3.6.3/bin/R rstudio projectname.Rproj &).

[florisvdh]

FYI, this is followed up at Linux Mint: linuxmint/linuxmint#294