[Bioc-devel] still issues with ggplot2/ggproto in Mac OS X, stable
rdiaz02 at gmail.com
Wed Nov 23 10:06:19 CET 2016
Thanks for the detailed analysis.
On Wed, 23-11-2016, at 00:41, Hervé Pagès <hpages at 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
> Content type 'unknown' length 802187 bytes (783 KB)
> downloaded 783 KB
> The downloaded binary packages are in
> > 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:
> 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:
> 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.
> 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:
> 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
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).
> 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.
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
Email: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
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