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