By the way, the reason why I am asking is that BiocCheck raised the following warning, after I upgraded my system to R-3.4 and Bioc-devel:
WARNING: Update R version dependency from 3.3 to 3.4 Now that I updated the R version dependency, everything is fine on my updated machine, but the Travis build fails because it doesn't have 3.4 installed. But I suppose that the BioC devel-build servers have R-3.4 installed, right? All the best, and sorry for the additional email, Kevin On Thu, Oct 20, 2016 at 3:07 PM, Kevin RUE <kevinru...@gmail.com> wrote: > Hi all, > > First of all, thanks for the question and answers, it helped me a lot on > my local machine. > > While we're on the topic, does anyone know when R-devel (R-3.4) will be > available on Travis CI ? Because it is running R-3.3.1, and therefore > produces the same error message when I instruct Travis to install packages > from the devel branch. > > I suppose this is something that I need to post on the Travis GitHub isse > tracker, right, considering the following message? > > R for Travis-CI is not officially supported, but is community maintained. > Please file any issues at https://github.com/travis-ci/travis-ci/issues > and mention @craigcitro, @hadley and @jimhester in the issue > Best, > Kevin > > On Thu, Oct 20, 2016 at 11:06 AM, Rodriguez Martinez, Andrea < > andrea.rodriguez-martine...@imperial.ac.uk> 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/packa >> ges/3.4/bioc/bin/macosx/mavericks/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 >> >> [[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
