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CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
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Segfault when loading rcdk #37

Closed eduardszoecs closed 7 years ago

eduardszoecs commented 7 years ago

Using r-devel version I get a segfault when loading rcdk. See also the CRAN checks.

sessionInfo()
R Under development (unstable) (2016-11-14 r71659)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] clisymbols_1.0.0 prompt_1.0.0     gitty_1.0.0     

loaded via a namespace (and not attached):
[1] compiler_3.4.0 parr_3.3.0     whisker_0.3-2  crayon_1.3.2   memuse_3.0-1

Note, that there are no problems under current R:

❯ library(rcdk)
Loading required package: fingerprint

❯ sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=de_DE.UTF-8           LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=de_DE.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=de_DE.UTF-8          LC_NAME=de_DE.UTF-8          
 [9] LC_ADDRESS=de_DE.UTF-8        LC_TELEPHONE=de_DE.UTF-8     
[11] LC_MEASUREMENT=de_DE.UTF-8    LC_IDENTIFICATION=de_DE.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] rcdk_3.3.6        fingerprint_3.5.4 clisymbols_1.0.0  prompt_1.0.0     
[5] gitty_1.0.0      

loaded via a namespace (and not attached):
 [1] parr_3.3.0      parallel_3.3.2  whisker_0.3-2   crayon_1.3.2   
 [5] rcdklibs_1.5.13 memuse_3.0-1    iterators_1.0.8 itertools_0.1-3
 [9] rJava_0.9-8     png_0.1-7

I don't see this, when running on Travis-CI, which runs R-devel on Ubuntu 12.04 LTS. Maybe it something with my installation... Investigating... Maybe a different jdk version openjdk version "1.8.0_111" vs oraclejdk8

Nope. Segfault also with oracle.

eduardszoecs commented 7 years ago

Running r-dev as sudo works...

eduardszoecs commented 7 years ago

Problems arises from .jinit used in .onLoad. Checking rJava now. .jinit seems to work?!

eduardszoecs commented 7 years ago

Maybe it's a problem with my R-devel...

rajarshi commented 7 years ago

I don't have an extra machine available to test out r-devel, but it sounds like a combination of a local java issue and an r-devel issue. Have you tried rerunning sudo R CMD javareconf and reinstalling rJava and see if that resolved the problem?

eduardszoecs commented 7 years ago

Maybe it also related to my local R-dev installation (and the related java) .

I don't see this problem on travis-ci (which runs r-dev on an older ubuntu). Will further investigate...

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Am 25. November 2016 19:39:33 schrieb Rajarshi Guha notifications@github.com:

I don't have an extra machine available to test out r-devel, but it sounds like a combination of a local java issue and an r-devel issue. Have you tried rerunning sudo R CMD javareconf and reinstalling rJava and see if that resolved the problem?

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/rajarshi/cdkr/issues/37#issuecomment-263009530