Thanks Lukas, I remember trying "r: bioc-devel" and having issues with it a while ago, but maybe I had an overall incorrect combination of YAML instructions, so I'll try again with your config and see if that works better. Things moving a lot during the release process, YAML files may just invalidate overnight, but only temporarily.
At the moment, I'm still just having the issue of S4Vectors not being available on the devel branch of BioC (apart from that, it seems my YAML now uses the correct version of R (devel); now, I just wonder if r: bioc-devel would get S4Vectors from the release branch if it's not available from the devel branch). As I wrote previously, I'm sure this is some minor issue that will disappear shortly (For S4Vectors. the R CMD check only fails for a unit test, which might prevent the package from being released on the devel branch, but that's another problem.) I'll play with my YAML file and find out how to make Travis happy again, before taking any risk pushing to Bioc, be it devel or release. In any case, thanks for your advice ! 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
