Hi Kevin, I have been using the following setup in my .travis.yml file. Travis CI should automatically use the correct version of R for the Bioconductor version specified in the "r: bioc-devel" line (you can replace this with "r: bioc-release" to use the release version). There is some more information here: https://docs.travis-ci.com/user/languages/r/ (see the Bioconductor section).
language: r r: bioc-devel sudo: false cache: packages r_github_packages: - jimhester/covr after_success: - Rscript -e 'covr::codecov()' The additional "covr" lines are for checking unit test code coverage with codecov. Lukas On Thu, Oct 20, 2016 at 4:51 PM, Kevin RUE <kevinru...@gmail.com> wrote: > Actually, nevermind, I think I solved the issue of R-devel with the > following YAML instructions: > > language: r > r: devel > > before_install: > - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R > ");tryCatch(useDevel(devel = TRUE), error = function(err){message(err)})' > - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tlmgr install bera > nowidow parnotes marginfix; fi > > Now the build <https://travis-ci.org/kevinrue/TVTB/builds/169246652> only > fails because S4Vectors is not available on the new devel branch, but I'm > sure that's going to resolve itself within the next couple of builds/days. > > All the best, > Kevin > > > Just for the record, prior to the recent BioC release, I had the following > (working) configuration. I have never been sure how elegant that was (I may > have combined some redundant bioc instructions): > > language: r > use_bioc: true > bioc_required: true > r: bioc-release > before_install: > - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R > ");tryCatch(useDevel(devel = TRUE), error = function(err){message(err)})' > - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tlmgr install bera > nowidow parnotes marginfix; fi > > > > On Thu, Oct 20, 2016 at 1:31 PM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > > > Sorry, can you try one more time? Thanks, Martin > > > > > > On 10/20/2016 06:06 AM, Rodriguez Martinez, Andrea wrote: > > > >> Thanks for your reply. > >> > >> > >> I have successfully removed BiocInstaller by hand, restart R, and then, > >> installed with: > >> > >> > >> source("https://bioconductor.org/biocLite.R") > >>> > >> Warning in install.packages : > >> URL > >> 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/maver > >> icks/contrib/3.4/PACKAGES.gz': > >> status was '404 Not Found' > >> Warning in install.packages : > >> URL > >> 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/maver > >> icks/contrib/3.4/PACKAGES': > >> status was '404 Not Found' > >> Warning in install.packages : > >> unable to access index for repository > >> https://bioconductor.org/packages/3.4/bioc/bin/macosx/maveri > >> cks/contrib/3.4: > >> cannot download all files > >> installing the source package ‘BiocInstaller’ > >> > >> trying URL > >> 'https://bioconductor.org/packages/3.4/bioc/src/contrib/Bioc > >> Installer_1.24.0.tar.gz' > >> Content type 'application/x-gzip' length 17756 bytes (17 KB) > >> ================================================== > >> downloaded 17 KB > >> > >> * installing *source* package ‘BiocInstaller’ ... > >> ** R > >> ** inst > >> ** preparing package for lazy loading > >> ** help > >> *** installing help indices > >> ** building package indices > >> ** testing if installed package can be loaded > >> Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help > >> Warning: Bioconductor version 3.4 is too old for R version 3.4.0; see > >> https://bioconductor.org/install/#troubleshoot-biocinstaller > >> * DONE (BiocInstaller) > >> > >> The downloaded source packages are in > >> ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn/T/ > >> RtmpRmVsc5/downloaded_packages’ > >> Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help > >> > >> BiocInstaller::useDevel() > >>> > >> Error: 'devel' version requires a more recent R > >> > > > > > >> > >> Thanks very much, > >> > >> Andrea > >> > >> > >> > >> ------------------------------------------------------------ > ------------ > >> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > >> Martin Morgan <martin.mor...@roswellpark.org> > >> *Sent:* 20 October 2016 10:28:34 > >> *To:* Michael Lawrence; bioc-devel@r-project.org > >> *Subject:* Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error: > >> > >> 'devel' version requires a more recent R > >> > >> On 10/20/2016 12:00 AM, Michael Lawrence wrote: > >> > >>> ---------- Forwarded message ---------- > >>> From: Rodriguez Martinez, Andrea <andrea.rodriguez-martinez13@i > >>> mperial.ac.uk> > >>> Date: Wed, Oct 19, 2016 at 3:33 PM > >>> Subject: Re: [Bioc-devel] BiocInstaller::useDevel() Error: 'devel' > >>> version requires a more recent R > >>> To: Michael Lawrence <lawrence.mich...@gene.com> > >>> > >>> > >>> Sorry again, > >>> > >>> I have just installed the R-devel version and now I get the following > >>> error: "Bioconductor does not yet support R version 3.4.0" > >>> > >> > >> Thank you, you installed BiocInstaller in R-devel (R-3.4) before > >> Bioconductor officially supported R-3.4, and need to manually remove and > >> re-install BiocInstaller. > >> > >> I have updated the online configure, so in a new session, try to load > >> the BiocInstaller package and you should now see > >> > >> Bioconductor version 3.4 is too old for R version 3.4.0; see > >> https://bioconductor.org/install/#troubleshoot-biocinstaller > >> > >> The instructions are to remove BiocInstaller by hand > >> > >> remove.packages("BiocInstaller") > >> remove.packages("BiocInstaller") # fails, if not then investigate > >> > >> and install again > >> > >> source("https://bioconductor.org/biocLite.R") > >> > >> Martin > >> > >> > >>> Thanks, > >>> > >>> Andrea > >>> > >>> ________________________________ > >>> From: Rodriguez Martinez, Andrea > >>> Sent: 19 October 2016 23:13:06 > >>> To: Michael Lawrence > >>> Subject: Re: [Bioc-devel] BiocInstaller::useDevel() Error: 'devel' > >>> version requires a more recent R > >>> > >>> > >>> Thanks! > >>> > >>> ________________________________ > >>> From: Michael Lawrence <lawrence.mich...@gene.com> > >>> Sent: 19 October 2016 23:02:17 > >>> To: Rodriguez Martinez, Andrea > >>> Cc: bioc-devel@r-project.org > >>> Subject: Re: [Bioc-devel] BiocInstaller::useDevel() Error: 'devel' > >>> version requires a more recent R > >>> > >>> Bioconductor 3.5 requires R-devel. > >>> > >>> On Wed, Oct 19, 2016 at 2:57 PM, Rodriguez Martinez, Andrea > >>> <andrea.rodriguez-martine...@imperial.ac.uk> wrote: > >>> > >>>> Hi, > >>>> > >>>> > >>>> I was just trying to use the devel branch, but I get this error > message > >>>> (using R.3.3.1) > >>>> > >>>> > >>>> BiocInstaller::useDevel() > >>>>> > >>>> > >>>> Error: 'devel' version requires a more recent R > >>>>> > >>>> > >>>> > >>>> Any help with this? > >>>> > >>>> Thanks very much in advance, > >>>> > >>>> Andrea > >>>> > >>>> [[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 > >>> > >>> > >> > >> This email message may contain legally privileged and/or...{{dropped:2}} > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > > > This email message may contain legally privileged and/or...{{dropped:2}} > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel