I am not sure if the _intention_ is that bioc-devel installs r-devel. But note that this is a change in the last 48h. Monday, the right thing was to use r-stable. Some switch has to be flipped and it may not have happened yet.
What would be nice is clear documentation as to whether bioc-devel implies switching to r-devel every 6 months, or if the travis people wants users (us) to make the switch by changing .travis.yml. Kasper On Thu, Oct 20, 2016 at 1:50 PM, Kevin RUE <kevinru...@gmail.com> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
