Henrik Bengtsson
2021-May-04 16:31 UTC
[Rd] Testing R build when using --without-recommended-packages?
I'm on Linux (Ubuntu 18.04). How do I check an R build when using --without-recommended-packages? 'make check' assumes 'recommended' packages are installed, so that fails without them available. DETAILS: When I build R from source without 'recommended' packages: curl -O https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz tar xvfz R-latest.tar.gz cd R-beta ./configure --enable-memory-profiling --enable-R-shlib --prefix="$PREFIX" make I cannot figure out how to validate the build. Following Section 'Installation' of 'R Installation and Administration', I run: make check results in: Testing examples for package ?stats? Error: testing 'stats' failed Execution halted This is because those tests assume 'MASS' is installed; $ cat /path/to/tests/Examples/stats-Ex.Rout.fail> utils::data(muscle, package = "MASS")Error in find.package(package, lib.loc, verbose = verbose) : there is no package called ?MASS? Calls: <Anonymous> -> find.package Execution halted BTW, isn't this a bug? Shouldn't this example run conditionally on 'MASS' being installed, because 'MASS' is a suggested package here; Package: stats Version: 4.1.0 ... Imports: utils, grDevices, graphics Suggests: MASS, Matrix, SuppDists, methods, stats4 /Henrik
Dirk Eddelbuettel
2021-May-04 17:16 UTC
[Rd] Testing R build when using --without-recommended-packages?
On 4 May 2021 at 09:31, Henrik Bengtsson wrote: | I'm on Linux (Ubuntu 18.04). How do I check an R build when using | --without-recommended-packages? 'make check' assumes 'recommended' | packages are installed, so that fails without them available. [...] | BTW, isn't this a bug? Shouldn't this example run conditionally on | 'MASS' being installed, because 'MASS' is a suggested package here; The 'R-admin' manual in Section 1.2 "Getting patched and development versions" ends on If downloading manually from CRAN, do ensure that you have the correct versions of the recommended packages: if the number in the file VERSION is ?x.y.z? you need to download the contents of ?https://CRAN.R-project.org/src/contrib/dir?, where dir is ?x.y.z/Recommended? for r-devel or x.y-patched/Recommended for r-patched, respectively, to directory src/library/Recommended in the sources you have unpacked. After downloading manually you need to execute tools/link-recommended from the top level of the sources to make the requisite links in src/library/Recommended. A suitable incantation from the top level of the R sources using wget might be (for the correct value of dir) wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \ https://CRAN.R-project.org/src/contrib/dir ./tools/link-recommended Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org