Hi again, I applied your YAML config in my latest commit <https://github.com/kevinrue/TVTB/blob/master/.travis.yml> But in my (ongoing) Travis build <https://travis-ci.org/kevinrue/TVTB/builds/169301723>, I can already see that it has installed the wrong R version (3.1.1, not devel), see line 370 <https://travis-ci.org/kevinrue/TVTB/builds/169301723#L370>
$ curl -Lo /tmp/R-3.3.1.xz https://s3.amazonaws.com/rstudio-travis/R-3.3.1.xz As opposed to the configuration I posted earlier that states: r: devel which did install R-devel (line 370 <https://travis-ci.org/kevinrue/TVTB/builds/169258984#L370> of the previous build): $curl -Lo /tmp/R-devel.xz https://s3.amazonaws.com/rstudio-travis/R-devel.xz I honestly don't know how YAML instructions work on Travis, but maybe some action must be taken before "bioc-devel" becomes synonym to "R-devel" ? Thanks for your help. Kevin On Thu, Oct 20, 2016 at 4:49 PM, Lukas Weber <lukmwe...@gmail.com> wrote: > Hi Kevin, > > I have been using the following setup in my .travis.yml file. Travis CI > should automatically use the correct version of R for the Bioconductor > version specified in the "r: bioc-devel" line (you can replace this with > "r: bioc-release" to use the release version). There is some more > information here: https://docs.travis-ci.com/user/languages/r/ (see the > Bioconductor section). > > language: r > r: bioc-devel > sudo: false > cache: packages > r_github_packages: > - jimhester/covr > after_success: > - Rscript -e 'covr::codecov()' > > The additional "covr" lines are for checking unit test code coverage with > codecov. > > Lukas > > > On Thu, Oct 20, 2016 at 4:51 PM, Kevin RUE <kevinru...@gmail.com> wrote: > >> Actually, nevermind, I think I solved the issue of R-devel with the >> following YAML instructions: >> >> language: r >> r: devel >> >> before_install: >> - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R >> ");tryCatch(useDevel(devel = TRUE), error = function(err){message(err)})' >> - if [[ "$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