date:20190114

[Rd] Error: corrupted double-linked list

2019-01-14 Thread Glen MacLachlan

Hello,

Not sure if this is the right list of if this is a gdal/sf issue so I
apologize but recently I've been seeing errors that crash R/3.5.1 and throw
a double-linked list error (see below). Has anyone else come across this
issue and if so is there a fix?



> rwhole <- st_transform(rwhole,st_crs(ele.map))
*** Error in `/usr/local/lib64/R/bin/exec/R': corrupted double-linked list:
0x82787a00 ***
=== Backtrace: =
/lib64/libc.so.6(+0x80aef)[0x7f774ceceaef]
/lib64/libc.so.6(+0x8137e)[0x7f774cecf37e]
/usr/local/lib/libproj.so.13(pj_dealloc+0xe)[0x7f773f13ddee]
/usr/local/lib/libgdal.so.20(_ZN10OGRProj4CTD1Ev+0x77)[0x7f773f75a2f7]
/usr/local/lib/libgdal.so.20(_ZN10OGRProj4CTD0Ev+0x9)[0x7f773f75a3f9]
/usr/local/lib64/R
/library/sf/libs/sf.so(_Z13CPL_transformN4Rcpp6VectorILi19ENS_15PreserveStorageEEENS0_ILi16ES1_EE+0x1e2)[0x7f7738566582]
/usr/local/lib64/R
/library/sf/libs/sf.so(_sf_CPL_transform+0x72)[0x7f7738556472]
/usr/local/lib64/R/lib/libR.so(+0xf58ed)[0x7f774d97f8ed]
/usr/local/lib64/R/lib/libR.so(+0x131b36)[0x7f774d9bbb36]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x1416c6)[0x7f774d9cb6c6]
/usr/local/lib64/R/lib/libR.so(+0x13d89c)[0x7f774d9c789c]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(+0x17f7b4)[0x7f774da097b4]
/usr/local/lib64/R/lib/libR.so(+0x17fba7)[0x7f774da09ba7]
/usr/local/lib64/R/lib/libR.so(+0x17ff93)[0x7f774da09f93]
/usr/local/lib64/R/lib/libR.so(+0x130109)[0x7f774d9ba109]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(+0x17f7b4)[0x7f774da097b4]
/usr/local/lib64/R/lib/libR.so(+0x17fc28)[0x7f774da09c28]
/usr/local/lib64/R/lib/libR.so(+0x17ff93)[0x7f774da09f93]
/usr/local/lib64/R/lib/libR.so(+0x130109)[0x7f774d9ba109]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x7f774d9caf2c]
/usr/local/lib64/R/lib/libR.so(+0x144e76)[0x7f774d9cee76]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x55d)[0x7f774d9cb18d]
/usr/local/lib64/R/lib/libR.so(+0x14655b)[0x7f774d9d055b]
/usr/local/lib64/R/lib/libR.so(+0x131b36)[0x7f774d9bbb36]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x1416c6)[0x7f774d9cb6c6]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x800)[0x7f774d9cb430]
/usr/local/lib64/R/lib/libR.so(+0x146841)[0x7f774d9d0841]
/usr/local/lib64/R/lib/libR.so(+0x17d7f9)[0x7f774da077f9]
/usr/local/lib64/R/lib/libR.so(+0x130109)[0x7f774d9ba109]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
/usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
/usr/local/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x7f774d9caf2c]
/usr/local/lib64/R/lib/libR.so(Rf_ReplIteration+0x232)[0x7f774d9fada2]
/usr/local/lib64/R/lib/libR.so(+0x171191)[0x7f774d9fb191]
/usr/local/lib64/R/lib/libR.so(run_Rmainloop+0x4f)[0x7f774d9fb22f]
/usr/local/lib64/R/bin/exec/R(main+0x1b)[0x40075b]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f774ce70445]
/usr/local/lib64/R/bin/exec/R[0x40078b]
=== Memory map: 
0040-00401000 r-xp  07:01 70665
/usr/local/lib64/R/bin/exec/R
0060-00601000 r--p  07:01 70665
/usr/local/lib64/R/bin/exec/R
00601000-00602000 rw-p 1000 07:01 70665
/usr/local/lib64/R/bin/exec/R
019c6000-a7898000 rw-p  00:00 0
[heap]
7f773853-7f77385ae000 r-xp  07:01 68
 /usr/local/lib64/R/library/sf/libs/sf.so
7f77385ae000-7f77387ad000 ---p 0007e000 07:01 68
 /usr/local/lib64/R/library/sf/libs/sf.so
7f77387ad000-7f77387af000 r--p 0007d000 07:01 68
 /usr/local/lib64/R/library/sf/libs/sf.so
7f77387af000-7f77387b1000 rw-p 0007f000 07:01 68
 /usr/local/lib64/R/library/sf/libs/sf.so
7f77387b1000-7f77387b3000 rw-p  00:00 0
7f77387b3000-7f77387cd000 r-xp  07:01 139267
 /usr/local/lib/libudunits2.so.0.1.0
7f77387cd000-7f77389cc000 ---p 0001a000 07:01 139267
 /usr/loca

Re: [Rd] Error: corrupted double-linked list

2019-01-14 Thread Iñaki Ucar

On Mon, 14 Jan 2019 at 10:58, Glen MacLachlan  wrote:
>
> Hello,
>
> Not sure if this is the right list of if this is a gdal/sf issue so I
> apologize but recently I've been seeing errors that crash R/3.5.1 and throw
> a double-linked list error (see below). Has anyone else come across this
> issue and if so is there a fix?

R-sig-geo is probably a better place for this. Also, a reproducible
example and/or the output from valgrind would be helpful.

Iñaki

>
>
>
> > rwhole <- st_transform(rwhole,st_crs(ele.map))
> *** Error in `/usr/local/lib64/R/bin/exec/R': corrupted double-linked list:
> 0x82787a00 ***
> === Backtrace: =
> /lib64/libc.so.6(+0x80aef)[0x7f774ceceaef]
> /lib64/libc.so.6(+0x8137e)[0x7f774cecf37e]
> /usr/local/lib/libproj.so.13(pj_dealloc+0xe)[0x7f773f13ddee]
> /usr/local/lib/libgdal.so.20(_ZN10OGRProj4CTD1Ev+0x77)[0x7f773f75a2f7]
> /usr/local/lib/libgdal.so.20(_ZN10OGRProj4CTD0Ev+0x9)[0x7f773f75a3f9]
> /usr/local/lib64/R
> /library/sf/libs/sf.so(_Z13CPL_transformN4Rcpp6VectorILi19ENS_15PreserveStorageEEENS0_ILi16ES1_EE+0x1e2)[0x7f7738566582]
> /usr/local/lib64/R
> /library/sf/libs/sf.so(_sf_CPL_transform+0x72)[0x7f7738556472]
> /usr/local/lib64/R/lib/libR.so(+0xf58ed)[0x7f774d97f8ed]
> /usr/local/lib64/R/lib/libR.so(+0x131b36)[0x7f774d9bbb36]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x1416c6)[0x7f774d9cb6c6]
> /usr/local/lib64/R/lib/libR.so(+0x13d89c)[0x7f774d9c789c]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(+0x17f7b4)[0x7f774da097b4]
> /usr/local/lib64/R/lib/libR.so(+0x17fba7)[0x7f774da09ba7]
> /usr/local/lib64/R/lib/libR.so(+0x17ff93)[0x7f774da09f93]
> /usr/local/lib64/R/lib/libR.so(+0x130109)[0x7f774d9ba109]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(+0x17f7b4)[0x7f774da097b4]
> /usr/local/lib64/R/lib/libR.so(+0x17fc28)[0x7f774da09c28]
> /usr/local/lib64/R/lib/libR.so(+0x17ff93)[0x7f774da09f93]
> /usr/local/lib64/R/lib/libR.so(+0x130109)[0x7f774d9ba109]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x7f774d9caf2c]
> /usr/local/lib64/R/lib/libR.so(+0x144e76)[0x7f774d9cee76]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x55d)[0x7f774d9cb18d]
> /usr/local/lib64/R/lib/libR.so(+0x14655b)[0x7f774d9d055b]
> /usr/local/lib64/R/lib/libR.so(+0x131b36)[0x7f774d9bbb36]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x1416c6)[0x7f774d9cb6c6]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x800)[0x7f774d9cb430]
> /usr/local/lib64/R/lib/libR.so(+0x146841)[0x7f774d9d0841]
> /usr/local/lib64/R/lib/libR.so(+0x17d7f9)[0x7f774da077f9]
> /usr/local/lib64/R/lib/libR.so(+0x130109)[0x7f774d9ba109]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(+0x136e17)[0x7f774d9c0e17]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x348)[0x7f774d9caf78]
> /usr/local/lib64/R/lib/libR.so(+0x14256b)[0x7f774d9cc56b]
> /usr/local/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x7f774d9caf2c]
> /usr/local/lib64/R/lib/libR.so(Rf_ReplIteration+0x232)[0x7f774d9fada2]
> /usr/local/lib64/R/lib/libR.so(+0x171191)[0x7f774d9fb191]
> /usr/local/lib64/R/lib/libR.so(run_Rmainloop+0x4f)[0x7f774d9fb22f]
> /usr/local/lib64/R/bin/exec/R(main+0x1b)[0x40075b]
> /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f774ce70445]
> /usr/local/lib64/R/bin/exec/R[0x40078b]
> === Memory map: 
> 0040-00401000 r-xp  07:01 70665
> /usr/local/lib64/R/bin/exec/R
> 0060-00601000 r--p  07:01 70665
> /usr/local/lib64/R/bin/exec/R
> 00601000-00602000 rw-p 1000 07:01 70665
> /usr/local/lib64/R/bin/exec/R
> 019c6000-a7898000 rw-p  00:00 0
> [heap]
> 7f773853-7f77385ae000 r-xp  07:01 68
>  /usr/local/lib64/R/library/sf/libs/sf.so
> 7f77385ae000-7f77387ad000 ---p 0007e000 07:01 68
>  /usr/local/lib64/R/library/sf/libs/sf.so
> 7f77387ad000-7f7

[Rd] Error: corrupted double-linked list

Re: [Rd] Error: corrupted double-linked list

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