[Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R
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 <kevinrue67 at 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-martinez13 at 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-bounces at r-project.org> on behalf of Martin Morgan <martin.morgan at roswellpark.org> Sent: 20 October 2016 10:28:34 To: Michael Lawrence; bioc-devel at 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 at 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.michael at 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.michael at gene.com> Sent: 19 October 2016 23:02:17 To: Rodriguez Martinez, Andrea Cc: bioc-devel at 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-martinez13 at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel