[Bioc-devel] still issues with ggplot2/ggproto in Mac OS X, stable

[Ramon Diaz-Uriarte]

Hi Hervé,

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 
> '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: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es

http://ligarto.org/rdiaz