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

[Hervé Pagès]

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.

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.

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.

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.
>
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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Seattle, WA 98109-1024

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