[Rd] Error: corrupted double-linked list

Mon Jan 14 15:32:08 CET 2019

On Mon, 14 Jan 2019 at 10:58, Glen MacLachlan <maclach using gwu.edu> 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:
> 0x0000000082787a00 ***
> ======= 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: ========
> 00400000-00401000 r-xp 00000000 07:01 70665
> /usr/local/lib64/R/bin/exec/R
> 00600000-00601000 r--p 00000000 07:01 70665
> /usr/local/lib64/R/bin/exec/R
> 00601000-00602000 rw-p 00001000 07:01 70665
> /usr/local/lib64/R/bin/exec/R
> 019c6000-a7898000 rw-p 00000000 00:00 0
> [heap]
> 7f7738530000-7f77385ae000 r-xp 00000000 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 00000000 00:00 0
> 7f77387b3000-7f77387cd000 r-xp 00000000 07:01 139267
>  /usr/local/lib/libudunits2.so.0.1.0
> 7f77387cd000-7f77389cc000 ---p 0001a000 07:01 139267
>  /usr/local/lib/libudunits2.so.0.1.0
> 7f77389cc000-7f77389cd000 r--p 00019000 07:01 139267
>  /usr/local/lib/libudunits2.so.0.1.0
> 7f77389cd000-7f77389ce000 rw-p 0001a000 07:01 139267
>  /usr/local/lib/libudunits2.so.0.1.0
> 7f77389ce000-7f77389e7000 r-xp 00000000 07:01 115212
>  /usr/local/lib64/R/library/units/libs/units.so
> 7f77389e7000-7f7738be7000 ---p 00019000 07:01 115212
>  /usr/local/lib64/R/library/units/libs/units.so
> 7f7738be7000-7f7738be8000 r--p 00019000 07:01 115212
>  /usr/local/lib64/R/library/units/libs/units.so
> 7f7738be8000-7f7738be9000 rw-p 0001a000 07:01 115212
>  /usr/local/lib64/R/library/units/libs/units.so
> 7f7738be9000-7f7738bfd000 r-xp 00000000 07:01 204
> /usr/local/lib64/R/library/tools/libs/tools.so
> 7f7738bfd000-7f7738dfd000 ---p 00014000 07:01 204
> /usr/local/lib64/R/library/tools/libs/tools.so
> 7f7738dfd000-7f7738dfe000 r--p 00014000 07:01 204
> /usr/local/lib64/R/library/tools/libs/tools.so
> 7f7738dfe000-7f7738dff000 rw-p 00015000 07:01 204
> /usr/local/lib64/R/library/tools/libs/tools.so
> 7f7738dff000-7f7738e00000 r-xp 00000000 07:01 107834
>  /usr/local/lib64/R/library/classInt/libs/classInt.so
> 7f7738e00000-7f7738fff000 ---p 00001000 07:01 107834
>  /usr/local/lib64/R/library/classInt/libs/classInt.so
> 7f7738fff000-7f7739000000 r--p 00000000 07:01 107834
>  /usr/local/lib64/R/library/classInt/libs/classInt.so
> 7f7739000000-7f7739001000 rw-p 00001000 07:01 107834
>  /usr/local/lib64/R/library/classInt/libs/classInt.so
> 7f7739001000-7f7739013000 r-xp 00000000 07:01 106999
>  /usr/local/lib64/R/library/e1071/libs/e1071.so
> 7f7739013000-7f7739213000 ---p 00012000 07:01 106999
>  /usr/local/lib64/R/library/e1071/libs/e1071.so
> 7f7739213000-7f7739214000 r--p 00012000 07:01 106999
>  /usr/local/lib64/R/library/e1071/libs/e1071.so
> 7f7739214000-7f7739215000 rw-p 00013000 07:01 106999
>  /usr/local/lib64/R/library/e1071/libs/e1071.so
> 7f7739215000-7f7739218000 r-xp 00000000 07:01 106908
>  /usr/local/lib64/R/library/class/libs/class.soAborted (core dumped)
>
> Best,
> Glen
>
> ==========================================
> Glen MacLachlan, PhD
> *Senior High Performance Computing Specialist  *
>
> *Adjunct Faculty, Data Sciences*
>
> Office of Technology Services
> The George Washington University
> Washington, DC 20052
>
> ==========================================
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Iñaki Úcar