Hi, I have been trying to add extra R packages as suggested. However, with the following:
easyblock = 'Bundle' name = 'R' version = '3.5.1' versionsuffix='-zedat_extras' rver = '3.5.1' homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" toolchain = {'name': 'foss', 'version': '2018b'} # these are extensions for R exts_defaultclass = 'RPackage' exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', '3.5.1'), ] name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages ], 'source_tmpl': name_tmpl, } # !! order of packages is important !! # packages updated on 22nd January 2019 exts_list = [ ('StanHeaders', '2.18.1', ext_options), ('inline', '0.3.15', ext_options), ('rstan', '2.17.2', ext_options), ] moduleclass = 'lang' I get the error: == FAILED: Installation ended unsuccessfully (build directory: /trinity/shared/easybuild/build/R/3.5.1/foss-2018b-zedat_extras): build failed (first 300 chars): Sanity check failed: no (non-empty) directory found at 'bin' in /trinity/shared/easybuild/software/R/3.5.1-foss-2018b-zedat_extras no (non-empty) directory found at 'lib' or 'lib64' in /trinity/shared/easybuild/software/R/3.5.1-foss-2018b-zedat_extras extensions sanity check failed for 3 extensions: If I remove the explicit sanity checks with sanity_check_paths = { 'files': [], 'dirs': [], } I get == FAILED: Installation ended unsuccessfully (build directory: /trinity/shared/easybuild/build/R/3.5.1/foss-2018b-zedat_extras): build failed (first 300 chars): Sanity check failed: extensions sanity check failed for 3 extensions: StanHeaders, inline, rstan failing sanity check for 'StanHeaders' extension: command "R -q --no-save" (stdin: "library(StanHeaders)") failed; output: > library(StanHeaders) Error in library(StanHeaders) : there is no package calle The problem seems to be that the packages are installed successfully under /trinity/shared/easybuild/software/R/3.5.1-foss-2018b-zedat_extras but because this directory is not in the library path, the default R sanity check of loading the packages fails. What I am missing? Cheers, Loris "Dey, John F" <[email protected]> writes: > To customize R to your site create a separate EasyConfig using easyblock = > 'Bundle' and exts_defaultclass = 'RPackage'. Depend the "Published" R from > the > official EasyBuild/EasyConfig repo. Create a new exts_list with packages local > to your site that are not in the base R easyconfig. You will also be able to > add BioConductor packages to your new custom build of R. > > Please look at an example; I add the suffix "fh1" for Fred Hutch". > https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/R-3.5.1-foss-2018b-fh1.eb > > > > John Dey > > On 1/18/19, 4:05 AM, "[email protected] on behalf of Loris > Bennett" <[email protected] on behalf of > [email protected]> wrote: > > Hi, > > I'm installing R and see that a whole bunch of R packages are also > being installed via exts_list. However, if I need additional packages, > do I just make a copy of the original easyconfig and just add to > exts_list? Or is there some way of having a list of only the additional > packages which could somehow be included by the current and all future > standard R easyconfigs? > > Cheers, > > Loris > > -- > Dr. Loris Bennett (Mr.) > ZEDAT, Freie Universität Berlin Email [email protected] > > -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email [email protected]
