Thanks both for the suggestions. I ended up piping the output to tail -n1 I've no idea how portable that is, but presumably similar to trying a grep/sed approach.
Cheers, Mike On Thu, 8 Apr 2021 at 15:48, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > You could also preprend your cat so it outputs something like > INCLUDE_DIR=.. > and then use grep and sed to trim it. Of course that can also end up being > brittle. > > On Wed, Apr 7, 2021 at 10:48 PM Henrik Bengtsson < > henrik.bengts...@gmail.com> wrote: > >> Correcting: the env var is R_LIBS_USER and nothing else. >> >> /Henrik >> >> On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson >> <henrik.bengts...@gmail.com> wrote: >> > >> > Can you go via a temporary file instead, i.e. output what you want to >> > grab to a temporary file and pull the info from that instead? >> > >> > Side tracking ... >> > >> > > I thought about using --vanilla but I use .Rprofile to set my library >> path, >> > > so ignoring that file completely defeats the point in my setup. >> > >> > I'm a proponent of customizing the library path via .Renviron instead >> > of via .Rprofile. In your case, you can have a line in ~/.Renviron >> > with: >> > >> > R_USER_LIBS=~/R/%p-library/%v-bioc_3.12 >> > >> > Alternatively, you can set it elsewhere, e.g. ~/.bashrc, in a Linux >> > environment module that is loaded, and so on. >> > >> > BTW, using Rscript --no-init-file ... would skip .Rprofile while still >> > parsing .Renviron. >> > >> > /Henrik >> > >> > On Wed, Apr 7, 2021 at 8:16 AM Mike Smith <grimbo...@gmail.com> wrote: >> > > >> > > I have the following line in the configure.ac for rhdf5filters, which >> > > returns the location of the HDF5 headers distributed with Rhdf5lib: >> > > >> > > RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e >> > > 'cat(system.file("include", package="Rhdf5lib"))'` >> > > >> > > For me the output is a path like >> > > /mnt/data/R-lib/4.0.3-bioc_3.12/Rhdf5lib/include, which gets >> inserted into >> > > the package Makevars file, and the package compilation works. >> > > >> > > However I've had multiple reports ( >> > > https://github.com/grimbough/rhdf5filters/issues/11) where this >> doesn't >> > > work, all of which seem to relate to messages printed when an >> Rprofile is >> > > loaded. They have well intentioned messages like below, which don't >> work >> > > so well when passed as compiler flags >> > > >> > > [1] "[BMRC] You have sourced the BMRC Rprofile provided at >> > > /apps/misc/R/bmrc-r-user-tools/Rprofile" >> > > [1] "[BMRC] Messages coming from this file (like this one) will be >> > > prefixed with [BMRC]" >> > > [1] "[BMRC] You are running R on host <rescomp3.hpc.in.bmrc.ox.ac.uk> >> > > with CPU <Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz>" >> > > [1] "[BMRC] While running on this host, local R packages will be >> > > sourced from and installed to >> > > /well/combat/users/ifl143/R/4.0/ivybridge" >> > > /gpfs3/well/combat/users/ifl143/R/4.0/ivybridge/Rhdf5lib/include >> > > >> > > I thought about using --vanilla but I use .Rprofile to set my library >> path, >> > > so ignoring that file completely defeats the point in my setup. Is >> anyone >> > > aware of either a more reliable way of getting the information I want >> > > (maybe suppressing messages, different mechanism entirely, etc)? >> > > Alternatively, is there anything definitive in WRE or the like that >> > > suggests printing messages Rprofile is a bad idea that I can pass on >> to the >> > > users? >> > > >> > > Cheers, >> > > Mike >> > > >> > > [[alternative HTML version deleted]] >> > > >> > > _______________________________________________ >> > > Bioc-devel@r-project.org mailing list >> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > -- > Best, > Kasper > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel