R SIG Debian - Jul 2018 - Segfault on ubuntu 18.04

Den 2018-07-06 kl. 17:51, skrev G?ran Brostr?m:
>
>
> Den 2018-07-06 kl. 17:43, skrev Henrik Bengtsson:
>> On Fri, Jul 6, 2018 at 8:18 AM G?ran Brostr?m <goran.brostrom at
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 G?ran 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.

G?ran
>
> G?ran
>
>>
>> /Henrik
>>
>>>
>>> G?ran
>>>
>>>> Dirk
>>>>
>>>
>>> _______________________________________________ R-SIG-Debian
>>> mailing list R-SIG-Debian at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

On 6 July 2018 at 21:52, G?ran Brostr?m wrote:
| 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.

We should also have r-cran-curl prebuilt for you.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On 2018-07-06 22:44, Dirk Eddelbuettel wrote:
> 
> On 6 July 2018 at 21:52, G?ran Brostr?m wrote:
> | 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.
> 
> We should also have r-cran-curl prebuilt for you.
$ sudo apt install r-cran-curl
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  r-cran-curl : Depends: r-api-3.4
E: Unable to correct problems, you have held broken packages.

G,
> 
> Dirk
>