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