[R] Help installing devtools plus other packages in R terminal

[Ivan Krylov]

On Wed, 5 Oct 2022 20:02:02 +0000
"Rhon Calderon, Eric" <Eric.RhonCalderon using pennmedicine.upenn.edu> wrote:

> automake found. Running autoupdate and autogen.sh.
<...>
> + libtoolize --copy
> autogen.sh: line 43: libtoolize: command not found

Since you have automake installed, you also need libtool
<https://www.gnu.org/software/libtool/> installed in order to compile
this particular package from source. Depending on the HPC, there may be
a particular command to "activate" the installation already made by the
HPC administrator.

I guess you could also report this as a bug in devtools: they check for
automake but not libtool. If you can temporarily chmod -x automake, the
installation should succeed too, because then the package will not try
to regenerate its build system. I don't see why they even try to do
that, but maybe that's a workaround for some kind of compatibility
problem.

> CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh
> '/tmp/RtmpMjF6Ns/R.INSTALL4a3cb2204b0da/httpuv/src/libuv/missing'
> aclocal-1.16 -I m4
> /tmp/RtmpMjF6Ns/R.INSTALL4a3cb2204b0da/httpuv/src/libuv/missing: line
> 81: aclocal-1.16: command not found

Make sure your automake installation is working. I think the error is
caused by the previous error and may go away once you install libtool,
but I may be mistaken regarding that.

Do Bioconductor packages really depend on devtools? What do their
errors look like?

-- 
Best regards,
Ivan