Out of curiosity, why do they install two instances of R in a Docker container? On a traditional physical tin server, sure, you can't avoid that sort of thing, but why in Docker? I didn't see a rationale for it on the Rocker wiki or website.
Greg On Mon, 11 Aug 2025 at 16:05, Ott Toomet <otoo...@gmail.com> wrote: > Thanks. > > I thought this was the issue, and even manually deleted /usr/bin/R and > /usr/bin/Rscript, but the problem persisted. But now I am thinking that > /usr/bin/R may not be the relevant executables, the development version may > pull up something directly from /usr/lib/R/bin instead (the devel is > installed in /usr/local/lib/R ). > > Will try! > > Ott > > On Sun, Aug 10, 2025 at 9:57 PM Tim Taylor < > tim.tay...@hiddenelephants.co.uk> > wrote: > > > You may be hitting the following issue in tinytest: > > https://github.com/markvanderloo/tinytest/issues/135 > > > > There is a linked PR you could try that hopefully fixes the problem: > > https://github.com/markvanderloo/tinytest/pull/134 > > > > Tim > > > > On 11 Aug 2025, at 05:39, Ott Toomet <otoo...@gmail.com> wrote: > > > > Hey everyone who is more familiar with R-devel and docker. > > > > I am trying to test the new version of my package (maxLik) on R-devel, > > using the docker container. I am using rocker/r-devel as the base. Note > > that R-devel is called "RD" in the image. I am copying in my package > > sources and a few scripts, and run "RD CMD build" and "RD CMD check". > > However, the latter fails with complaints about missing packages that are > > installed and accessible when I run RD from command line. > > > > Here are a few results: > > > > * After a successful build inside the container, I run check: > > root@f4024e015396:/# RD CMD check --as-cran maxLik_1.6-3.tar.gz > > * using log directory ‘//maxLik.Rcheck’ > > * using R Under development (unstable) (2025-08-11 r88561) > > * using platform: x86_64-pc-linux-gnu > > * R was compiled by > > gcc (Debian 14.2.0-19) 14.2.0 > > GNU Fortran (Debian 14.2.0-19) 14.2.0 > > * running under: Debian GNU/Linux trixie/sid > > * using session charset: UTF-8 > > * using option ‘--as-cran’ > > * checking for file ‘maxLik/DESCRIPTION’ ... OK > > * this is package ‘maxLik’ version ‘1.6-3’ > > * checking CRAN incoming feasibility ... [6s/35s] OK > > * checking package namespace information ... OK > > * checking package dependencies ... OK > > * checking if this is a source package ... OK > > * checking if there is a namespace ... OK > > * checking for executable files ... OK > > * checking for hidden files and directories ... OK > > * checking for portable file names ... OK > > * checking for sufficient/correct file permissions ... OK > > * checking serialization versions ... OK > > * checking whether package ‘maxLik’ can be installed ... ERROR > > Installation failed. > > See ‘//maxLik.Rcheck/00install.out’ for details. > > * DONE > > > > Status: 1 ERROR > > See > > ‘//maxLik.Rcheck/00check.log’ > > for details. > > > > * Take a look at the log: > > > > root@f4024e015396:/# cat maxLik.Rcheck/00install.out > > * installing *source* package ‘maxLik’ ... > > ** this is package ‘maxLik’ version ‘1.6-3’ > > ** using staged installation > > ** R > > ** inst > > ** byte-compile and prepare package for lazy loading > > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = > vI[[i]]) > > : > > there is no package called ‘lattice’ > > Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> > > doWithOneRestart > > Execution halted > > ERROR: lazy loading failed for package ‘maxLik’ > > * removing ‘/maxLik.Rcheck/maxLik’ > > > > Apparently 'lattice' is missing??? > > > > * But it is there and I can load it with no errors: > > > > root@f4024e015396:/# RDscript -e "packageVersion('lattice')" > > [1] ‘0.22.7’ > > root@f4024e015396:/# RDscript -e "library(lattice)" > > > > Formerly I got similar missing package messages for other packages, I > have > > also tried to manually overwrote the R_LIB_USR environment variable (that > > resulted in another error a bit further down in the line), and to install > > my own package into different locations. So far everything seems to lead > > to the same problem. > > > > Note that it works if I run it inside the container using the stable R > ("R" > > instead of "RD"). Currently it is based on r88561 (2025-08-11) version > of > > R-devel as you can see above. > > > > For reference, here is the Dockerfile: > > > > # -*- dockerfile-mode -*- > > FROM rocker/r-devel > > RUN apt-get install -y texlive-science > > ENV INSIDE_DOCKER=true > > COPY packages.R . # install script for necessary packages > > RUN RDscript packages.R # install dependencies/suggestions etc > > COPY pkg ./pkg # copy the maxlik package source > > COPY build-check . # building/checking script > > CMD ["bash"] > > > > > > Any ideas? > > > > Ott > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
