[R-sig-Debian] Segfault on ubuntu 18.04

[Göran Broström]

Den 2018-07-06 kl. 17:51, skrev Göran Broström:
>
>
> Den 2018-07-06 kl. 17:43, skrev Henrik Bengtsson:
>> On Fri, Jul 6, 2018 at 8:18 AM Göran Broström <goran.brostrom using umu.se>
>> wrote:
>>>
>>>
>>>
>>> Den 2018-07-06 kl. 16:28, skrev Dirk Eddelbuettel:
>>>>
>>>> On 6 July 2018 at 12:31, Enrico Schumann wrote: | Just as one
>>>> more datapoint: I cannot reproduce the segfault, with | R 3.5.1
>>>> on (L)Ubuntu 18.04. (I use the Ubuntu package, i.e. I did not |
>>>> build from source.)
>>>>
>>>> I have been a little too busy and have not yet upgraded to 18.04
>>>> so I can't attempt to replicate -- but it _looks_ just like a
>>>> garden variety binary mismatch.
>>>>
>>>> We _know_ R 3.5.* requires _all_ binary packages to be
>>>> reinstalled and it is easy to miss one.  So unless Göran shows us
>>>> a generally reproducible bug I will suspect that this is simply a
>>>> local deployment issue.
>>>
>>> I suspect that too, since the segfault does _not_ occur if run  R
>>> via RStudio. _But_, I have run 'update.packages(checkBuilt =
>>> TRUE)', and that should take care of reinstalling, right?
>>>
>>> Maybe it somehow is an issue with devtools::install_github.
>>
>> If you follow the error traceback (from the bottom of the stack to
>> the top), the most recent package involved is 'curl'.  It appears
>> that the segfault occurs when it is loaded.  You probably get the
>> same if you attempt:
>>
>> library(curl)
>
> Thanks for the suggestion, but that doesn't crash anything.
>
>> in a fresh R session.  If so, as Dirk suggests:
>>
>>> We _know_ R 3.5.* requires _all_ binary packages to be reinstalled
>>> and it is easy to miss one.
>>
>> make sure to reinstall 'curl'.  If that solves it, it's likely that
>> other packages have the same issue, so you probably want to start
>> from a clean slate and wipe your current package library, e.g.
>> unlink(.libPaths()[1], recursive = TRUE).
>
> Maybe I should do that anyway.

I did this and removed anything related to R and reinstalled. Then, in R,

 > install.packages("curl")

and got

Error: package or namespace load failed for 'curl' in dyn.load(file, 
DLLpath = DLLpath, ...):
  unable to load shared object 
'/usr/local/lib/R/site-library/curl/libs/curl.so':
   /usr/local/lib/R/site-library/curl/libs/curl.so: undefined symbol: 
curl_easy_escape
Error: loading failed

I have installed curl, libcurl4, libcurl4-openssl-dev.

Göran

>
> Göran
>
>>
>> /Henrik
>>
>>>
>>> Göran
>>>
>>>> Dirk
>>>>
>>>
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