Hi Hervé, Thanks for the detailed analysis.
On Wed, 23-11-2016, at 00:41, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Ramon, > > All packages (including ggrepel) were re-installed from scratch after we > updated R on the release build machines one week ago. However it seems > that re-installing ggrepel on Mac doesn't help. On morelia: > > > install.packages("ggrepel") > --- Please select a CRAN mirror for use in this session --- > HTTPS CRAN mirror > > 1: 0-Cloud [https] 2: Algeria [https] > 3: Australia (Melbourne) [https] 4: Australia (Perth) [https] > 5: Austria [https] 6: Belgium (Ghent) [https] > 7: Brazil (RJ) [https] 8: Brazil (SP 1) [https] > 9: Bulgaria [https] 10: Canada (MB) [https] > 11: Chile [https] 12: China (Beijing) [https] > 13: China (Hefei) [https] 14: China (Lanzhou) [https] > 15: Colombia (Cali) [https] 16: Czech Republic [https] > 17: Denmark [https] 18: France (Lyon 1) [https] > 19: France (Lyon 2) [https] 20: France (Marseille) [https] > 21: France (Montpellier) [https] 22: France (Paris 2) [https] > 23: Germany (Falkenstein) [https] 24: Germany (Münster) [https] > 25: Iceland [https] 26: India [https] > 27: Ireland [https] 28: Italy (Padua) [https] > 29: Japan (Tokyo) [https] 30: Malaysia [https] > 31: Mexico (Mexico City) [https] 32: New Zealand [https] > 33: Norway [https] 34: Philippines [https] > 35: Russia (Moscow) [https] 36: Serbia [https] > 37: Spain (A Coruña) [https] 38: Spain (Madrid) [https] > 39: Switzerland [https] 40: Taiwan (Chungli) [https] > 41: Turkey (Denizli) [https] 42: UK (Bristol) [https] > 43: UK (Cambridge) [https] 44: UK (London 1) [https] > 45: USA (CA 1) [https] 46: USA (IA) [https] > 47: USA (IN) [https] 48: USA (KS) [https] > 49: USA (MI 1) [https] 50: USA (TN) [https] > 51: USA (TX) [https] 52: USA (WA) [https] > 53: (HTTP mirrors) > > Selection: 52 > trying URL > 'https://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.3/ggrepel_0.6.3.tgz' > Content type 'unknown' length 802187 bytes (783 KB) > ================================================== > downloaded 783 KB > > > The downloaded binary packages are in > /var/folders/1c/_5ks0mjd3gvf_dq14g3thsr40000gn/T//RtmpMwsaS > /downloaded_packages > > library(ggrepel) > Loading required package: ggplot2 > > GeomTextRepel > Error: GeomTextRepel was built with an incompatible version of ggproto. > Please reinstall the package that provides this extension. > > So it looks like the Mac binary itself is broken. Note that the CRAN > check results for ggrepel are OK: > > http://cran.fhcrc.org/web/checks/check_results_ggrepel.html > > but that's because 'R CMD check' cannot detect a stale binary package > because it is run on the source package. > OK, I did not realize that. > The timestamp for ggrepel_0.6.3.tgz can be seen here: > > http://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.3/ > > It indicates that the binary was made on 21-Oct-2016 which predates the > latest change in ggplot2 (2016-11-11) that is supposedly the culprit. > Got it. > That means the ggrepel Mac binary would need to be re-generated. > Someone would need to contact the CRAN people about this with Cc the > ggrepel people. Probably the best solution is for the ggrepel people to > bump the version of their package otherwise people who already have the > old broken binary installed on their machine won't get the new binary > when doing update.packages(). > > Note that the Windows binary doesn't have this problem because it was > generated on 20-Nov-2016 i.e. after the change in ggplot2: > > http://cran.fhcrc.org/bin/windows/contrib/3.3/ > > Finally note that we could work around the problem on morelia by > re-installing ggrepel from source but that would just put a lid on > the problem: the end user would still see the problem on his/her > machine. I am writing the maintainer of ggrepel (I've CC'd you). I am attaching your full email, so he can see the full details, but I am suggesting explicitly bumping the version, since as you explain trying to get it regenerated in CRAN is only a partial solution (and trying to get CRAN to do that might be also more complicated). Thanks again, R. > > Cheers, > H. > > > On 11/22/2016 02:14 PM, Ramon Diaz-Uriarte wrote: >> Dear All, >> >> Sorry to return to this issue, but on Morelia (Mac OS X, stable), we are >> still seeing packages break during build with this message >> >> "GeomTextRepel was built with an incompatible version of ggproto. >> Please reinstall the package that provides this extension. >> Execution halted" >> >> >> that affects many (all?) packages that depend on ggrepel or other packages >> that depend on ggplot2/ggproto. >> >> Best, >> >> R. >> >> >> -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel