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Invalid pointer after unlink! #28

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andyferris opened this issue Sep 13, 2017 · 4 comments
Closed

Invalid pointer after unlink! #28

andyferris opened this issue Sep 13, 2017 · 4 comments

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@andyferris
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I'm trying to load an .xml file, mutate the xml document in memory, and save it to disk again. However, I get errors whenever I use unlink! to remove a subset of elements from my xml. Perhaps I'm misusing unlink! or I'm not allowed to mutate xml files that I've loaded - any help appreciated.

Minimal example. Create a file called tmp2.xml with content

<?xml version="1.0" encoding="UTF-8"?>
<Response bayid="597658" srid="32755">
    <Zones>
        <Zone id="260662925" typeid="52" spanid="12830086">
        </Zone>
        <Zone id="260662926" typeid="53" spanid="12830086">
        </Zone>
    </Zones>
</Response>

(this is a simplified and much reduced version of some data I have)

Then I run Julia v0.6 and get an pointer error from something calling free. To be clear, in my real example with more complex data, the error happens before exiting Julia - and is possibly happening during some Julia garbage collection event - but in the example below the "tmp3.xml" file is written successfully before the error happens. Speculatively, I'm wondering if unlink! free's some resources which are still referenced somewhere, and a finalizer or destructor or something then attempts to free it again later.

julia> using EzXML

julia> function f(in, out)
           xmldoc = readxml(in)
           nodes = find(xmldoc, "Response/Zones/Zone")
           unlink!.(nodes)
           open(out, "w") do io
               write(io, string(xmldoc))
           end
       end
f (generic function with 1 method)

julia> f("tmp2.xml","tmp3.xml")
121

julia> exit()
*** Error in `julia': free(): invalid pointer: 0x0000000002c5f237 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fdbe347b7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7fdbe348437a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fdbe348853c]
/usr/lib/x86_64-linux-gnu/libxml2.so.2(xmlFreeNodeList+0x232)[0x7fdbd50e8fd2]
/usr/lib/x86_64-linux-gnu/libxml2.so.2(xmlFreeNode+0x7c)[0x7fdbd50e92fc]
[0x7fdbc1de2aa2]
[0x7fdbc1de2ae3]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_apply_generic+0x467)[0x7fdbe3e33077]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x7f60e)[0x7fdbe3e7660e]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x7f8c7)[0x7fdbe3e768c7]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x83aee)[0x7fdbe3e7aaee]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_atexit_hook+0x1eb)[0x7fdbe3e4ab1b]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_exit+0x17)[0x7fdbe3e61c37]
/home/ferris/julia-0.6/usr/lib/julia/sys.so(+0x47bf1c)[0x7fdbde2e5f1c]
/home/ferris/julia-0.6/usr/lib/julia/sys.so(+0x47bf29)[0x7fdbde2e5f29]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_apply_generic+0x467)[0x7fdbe3e33077]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x5090e)[0x7fdbe3e4790e]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x4f90a)[0x7fdbe3e4690a]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x50844)[0x7fdbe3e47844]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x67c4b)[0x7fdbe3e5ec4b]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_toplevel_eval_in+0x126)[0x7fdbe3e41476]
/home/ferris/julia-0.6/usr/lib/julia/sys.so(+0x2716da)[0x7fdbde0db6da]
/home/ferris/julia-0.6/usr/lib/julia/sys.so(+0x2716f0)[0x7fdbde0db6f0]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_apply_generic+0x467)[0x7fdbe3e33077]
/home/ferris/julia-0.6/usr/lib/julia/sys.so(+0x2df643)[0x7fdbde149643]
/home/ferris/julia-0.6/usr/lib/julia/sys.so(+0x2df860)[0x7fdbde149860]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_apply_generic+0x467)[0x7fdbe3e33077]
[0x7fdbc1dd8036]
[0x7fdbc1dd82b0]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(jl_apply_generic+0x467)[0x7fdbe3e33077]
/home/ferris/julia-0.6/usr/bin/../lib/libjulia.so.0.6(+0x55f20)[0x7fdbe3e4cf20]
======= Memory map: ========
00400000-00403000 r-xp 00000000 fc:05 10120118                           /home/ferris/julia-0.6/usr/bin/julia
00602000-00603000 r--p 00002000 fc:05 10120118                           /home/ferris/julia-0.6/usr/bin/julia
00603000-00604000 rw-p 00003000 fc:05 10120118                           /home/ferris/julia-0.6/usr/bin/julia
00c6a000-02daa000 rw-p 00000000 00:00 0                                  [heap]
7fdbb8000000-7fdbb8021000 rw-p 00000000 00:00 0 
7fdbb8021000-7fdbbc000000 ---p 00000000 00:00 0 
7fdbbc01b000-7fdbbd8d1000 r-xp 00000000 fc:05 12853709                   /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7fdbbd8d1000-7fdbbdad0000 ---p 018b6000 fc:05 12853709                   /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7fdbbdad0000-7fdbbdad1000 r--p 018b5000 fc:05 12853709                   /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7fdbbdad1000-7fdbbdad2000 rw-p 018b6000 fc:05 12853709                   /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7fdbbdad2000-7fdbc1ad6000 rw-p 00000000 00:00 0 
7fdbc1ad6000-7fdbc1bd6000 r--s 00100000 00:05 2443422                    /memfd:julia-codegen (deleted)
7fdbc1bd6000-7fdbc1dd6000 r--s 00000000 00:05 2443422                    /memfd:julia-codegen (deleted)
7fdbc1dd6000-7fdbc1ed6000 r-xs 00000000 00:05 2443422                    /memfd:julia-codegen (deleted)
7fdbc1ed6000-7fdbc5ed6000 rw-p 00000000 00:00 0 
7fdbc5ed6000-7fdbc5ed7000 r-xp 00000000 fc:05 10120869                   /home/ferris/julia-0.6/usr/lib/libsuitesparse_wrapper.so
7fdbc5ed7000-7fdbc60d6000 ---p 00001000 fc:05 10120869                   /home/ferris/julia-0.6/usr/lib/libsuitesparse_wrapper.so
7fdbc60d6000-7fdbc60d7000 r--p 00000000 fc:05 10120869                   /home/ferris/julia-0.6/usr/lib/libsuitesparse_wrapper.so
7fdbc60d7000-7fdbc60d8000 rw-p 00001000 fc:05 10120869                   /home/ferris/julia-0.6/usr/lib/libsuitesparse_wrapper.so
7fdbc60d8000-7fdbc60da000 r-xp 00000000 fc:05 10120859                   /home/ferris/julia-0.6/usr/lib/libsuitesparseconfig.so
7fdbc60da000-7fdbc62d9000 ---p 00002000 fc:05 10120859                   /home/ferris/julia-0.6/usr/lib/libsuitesparseconfig.so
7fdbc62d9000-7fdbc62da000 r--p 00001000 fc:05 10120859                   /home/ferris/julia-0.6/usr/lib/libsuitesparseconfig.so
7fdbc62da000-7fdbc62db000 rw-p 00002000 fc:05 10120859                   /home/ferris/julia-0.6/usr/lib/libsuitesparseconfig.so
7fdbc62db000-7fdbc62e6000 r-xp 00000000 fc:05 10120863                   /home/ferris/julia-0.6/usr/lib/libccolamd.so
7fdbc62e6000-7fdbc64e6000 ---p 0000b000 fc:05 10120863                   /home/ferris/julia-0.6/usr/lib/libccolamd.so
7fdbc64e6000-7fdbc64e7000 r--p 0000b000 fc:05 10120863                   /home/ferris/julia-0.6/usr/lib/libccolamd.so
7fdbc64e7000-7fdbc64e8000 rw-p 0000c000 fc:05 10120863                   /home/ferris/julia-0.6/usr/lib/libccolamd.so
7fdbc64e8000-7fdbc64f2000 r-xp 00000000 fc:05 10120862                   /home/ferris/julia-0.6/usr/lib/libcamd.so
7fdbc64f2000-7fdbc66f2000 ---p 0000a000 fc:05 10120862                   /home/ferris/julia-0.6/usr/lib/libcamd.so
7fdbc66f2000-7fdbc66f3000 r--p 0000a000 fc:05 10120862                   /home/ferris/julia-0.6/usr/lib/libcamd.so
7fdbc66f3000-7fdbc66f4000 rw-p 0000b000 fc:05 10120862                   /home/ferris/julia-0.6/usr/lib/libcamd.so
7fdbc66f4000-7fdbc66fd000 r-xp 00000000 fc:05 10120860                   /home/ferris/julia-0.6/usr/lib/libamd.so
7fdbc66fd000-7fdbc68fc000 ---p 00009000 fc:05 10120860                   /home/ferris/julia-0.6/usr/lib/libamd.so
7fdbc68fc000-7fdbc68fd000 r--p 00008000 fc:05 10120860                   /home/ferris/julia-0.6/usr/lib/libamd.so
7fdbc68fd000-7fdbc68fe000 rw-p 00009000 fc:05 10120860                   /home/ferris/julia-0.6/usr/lib/libamd.so
7fdbc68fe000-7fdbc6905000 r-xp 00000000 fc:05 10120861                   /home/ferris/julia-0.6/usr/lib/libcolamd.so
7fdbc6905000-7fdbc6b04000 ---p 00007000 fc:05 10120861                   /home/ferris/julia-0.6/usr/lib/libcolamd.so
7fdbc6b04000-7fdbc6b05000 r--p 00006000 fc:05 10120861                   /home/ferris/julia-0.6/usr/lib/libcolamd.so
7fdbc6b05000-7fdbc6b06000 rw-p 00007000 fc:05 10120861                   /home/ferris/julia-0.6/usr/lib/libcolamd.so
7fdbc6b06000-7fdbc6c05000 r-xp 00000000 fc:05 10120865                   /home/ferris/julia-0.6/usr/lib/libcholmod.so
7fdbc6c05000-7fdbc6e05000 ---p 000ff000 fc:05 10120865                   /home/ferris/julia-0.6/usr/lib/libcholmod.so
7fdbc6e05000-7fdbc6e06000 r--p 000ff000 fc:05 10120865                   /home/ferris/julia-0.6/usr/lib/libcholmod.so
7fdbc6e06000-7fdbc6e07000 rw-p 00100000 fc:05 10120865                   /home/ferris/julia-0.6/usr/lib/libcholmod.so
7fdbc6e07000-7fdbc6e36000 r-xp 00000000 fc:05 10119158                   /home/ferris/julia-0.6/usr/lib/libssh2.so.1.0.1
7fdbc6e36000-7fdbc7036000 ---p 0002f000 fc:05 10119158                   /home/ferris/julia-0.6/usr/lib/libssh2.so.1.0.1
7fdbc7036000-7fdbc7037000 r--p 0002f000 fc:05 10119158                   /home/ferris/julia-0.6/usr/lib/libssh2.so.1.0.1
7fdbc7037000-7fdbc7038000 rw-p 00030000 fc:05 10119158                   /home/ferris/julia-0.6/usr/lib/libssh2.so.1.0.1
7fdbc7038000-7fdbc7086000 r-xp 00000000 fc:05 10118670                   /home/ferris/julia-0.6/usr/lib/libmbedcrypto.so.2.3.0
7fdbc7086000-7fdbc7285000 ---p 0004e000 fc:05 10118670                   /home/ferris/julia-0.6/usr/lib/libmbedcrypto.so.2.3.0
7fdbc7285000-7fdbc7288000 r--p 0004d000 fc:05 10118670                   /home/ferris/julia-0.6/usr/lib/libmbedcrypto.so.2.3.0
7fdbc7288000-7fdbc7289000 rw-p 00050000 fc:05 10118670                   /home/ferris/julia-0.6/usr/lib/libmbedcrypto.so.2.3.0
7fdbc7289000-7fdbc728c000 rw-p 00000000 00:00 0 
7fdbc728c000-7fdbc729e000 r-xp 00000000 fc:05 10118669                   /home/ferris/julia-0.6/usr/lib/libmbedx509.so.2.3.0
7fdbc729e000-7fdbc749e000 ---p 00012000 fc:05 10118669                   /home/ferris/julia-0.6/usr/lib/libmbedx509.so.2.3.0
7fdbc749e000-7fdbc749f000 r--p 00012000 fc:05 10118669                   /home/ferris/julia-0.6/usr/lib/libmbedx509.so.2.3.0
7fdbc749f000-7fdbc74a0000 rw-p 00013000 fc:05 10118669                   /home/ferris/julia-0.6/usr/lib/libmbedx509.so.2.3.0
7fdbc74a0000-7fdbc74c5000 r-xp 00000000 fc:05 10118677                   /home/ferris/julia-0.6/usr/lib/libmbedtls.so.2.3.0
7fdbc74c5000-7fdbc76c4000 ---p 00025000 fc:05 10118677                   /home/ferris/julia-0.6/usr/lib/libmbedtls.so.2.3.0
7fdbc76c4000-7fdbc76c6000 r--p 00024000 fc:05 10118677                   /home/ferris/julia-0.6/usr/lib/libmbedtls.so.2.3.0
7fdbc76c6000-7fdbc76c7000 rw-p 00026000 fc:05 10118677                   /home/ferris/julia-0.6/usr/lib/libmbedtls.so.2.3.0
7fdbc76c7000-7fdbc7729000 r-xp 00000000 fc:05 10119568                   /home/ferris/julia-0.6/usr/lib/libcurl.so.4.4.0
7fdbc7729000-7fdbc7928000 ---p 00062000 fc:05 10119568                   /home/ferris/julia-0.6/usr/lib/libcurl.so.4.4.0
7fdbc7928000-7fdbc792a000 r--p 00061000 fc:05 10119568                   /home/ferris/julia-0.6/usr/lib/libcurl.so.4.4.0
7fdbc792a000-7fdbc792b000 rw-p 00063000 fc:05 10119568                   /home/ferris/julia-0.6/usr/lib/libcurl.so.4.4.0
7fdbc792b000-7fdbc7a38000 r-xp 00000000 fc:05 10117458                   /home/ferris/julia-0.6/usr/lib/libgit2.so.0.25.1
7fdbc7a38000-7fdbc7c38000 ---p 0010d000 fc:05 10117458                   /home/ferris/julia-0.6/usr/lib/libgit2.so.0.25.1
7fdbc7c38000-7fdbc7c39000 r--p 0010d000 fc:05 10117458                   /home/ferris/julia-0.6/usr/lib/libgit2.so.0.25.1
7fdbc7c39000-7fdbc7c3c000 rw-p 0010e000 fc:05 10117458                   /home/ferris/julia-0.6/usr/lib/libgit2.so.0.25.1
7fdbc7c3c000-7fdbc9c3c000 rw-p 00000000 00:00 0 
7fdbc9c3c000-7fdbc9c3d000 ---p 00000000 00:00 0 
7fdbc9c3d000-7fdbca43d000 rw-p 00000000 00:00 0 
7fdbca43d000-7fdbcc43d000 rw-p 00000000 00:00 0 
7fdbcc43d000-7fdbcc43e000 ---p 00000000 00:00 0 
7fdbcc43e000-7fdbccc3e000 rw-p 00000000 00:00 0 
7fdbccc3e000-7fdbccc3f000 ---p 00000000 00:00 0 
7fdbccc3f000-7fdbcd43f000 rw-p 00000000 00:00 0 
7fdbcd43f000-7fdbd343f000 rw-p 00000000 00:00 0 
7fdbd343f000-7fdbd3440000 ---p 00000000 00:00 0 
7fdbd3440000-7fdbd3c40000 rw-p 00000000 00:00 0 
7fdbd4ad2000-7fdbd4af3000 r-xp 00000000 fc:05 9441741                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fdbd4af3000-7fdbd4cf2000 ---p 00021000 fc:05 9441741                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fdbd4cf2000-7fdbd4cf3000 r--p 00020000 fc:05 9441741                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fdbd4cf3000-7fdbd4cf4000 rw-p 00021000 fc:05 9441741                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fdbd4cf4000-7fdbd4e73000 r-xp 00000000 fc:05 12853750                   /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7fdbd4e73000-7fdbd5073000 ---p 0017f000 fc:05 12853750                   /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7fdbd5073000-7fdbd5083000 r--p 0017f000 fc:05 12853750                   /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7fdbd5083000-7fdbd5084000 rw-p 0018f000 fc:05 12853750                   /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7fdbd5084000-7fdbd5088000 rw-p 00000000 00:00 0 
7fdbd5088000-7fdbd5239000 r-xp 00000000 fc:05 12858710                   /usr/lib/x86_64-linux-gnu/libxml2.so.2.9.3
7fdbd5239000-7fdbd5438000 ---p 001b1000 fc:05 12858710                   /usr/lib/x86_64-linux-gnu/libxml2.so.2.9.3
7fdbd5438000-7fdbd5440000 r--p 001b0000 fc:05 12858710                   /usr/lib/x86_64-linux-gnu/libxml2.so.2.9.3
7fdbd5440000-7fdbd5442000 rw-p 001b8000 fc:05 12858710                   /usr/lib/x86_64-linux-gnu/libxml2.so.2.9.3
7fdbd5442000-7fdbd5443000 rw-p 00000000 00:00 0 
7fdbd5443000-7fdbd5481000 r-xp 00000000 fc:05 12850392                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fdbd5481000-7fdbd5680000 ---p 0003e000 fc:05 12850392                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fdbd5680000-7fdbd5681000 r--p 0003d000 fc:05 12850392                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fdbd5681000-7fdbd5682000 rw-p 0003e000 fc:05 12850392                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fdbd5682000-7fdbd57ab000 r-xp 00000000 fc:05 12849959                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fdbd57ab000-7fdbd59aa000 ---p 00129000 fc:05 12849959                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fdbd59aa000-7fdbd59ab000 r--p 00128000 fc:05 12849959                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fdbd59ab000-7fdbd59ad000 rw-p 00129000 fc:05 12849959                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fdbd59cd000-7fdbd7c8b000 r-xp 00000000 fc:05 10120848                   /home/ferris/julia-0.6/usr/lib/libopenblas64_.so
7fdbd7c8b000-7fdbd7e8a000 ---p 022be000 fc:05 10120848                   /home/ferris/julia-0.6/usr/lib/libopenblas64_.so
7fdbd7e8a000-7fdbd7e90000 r--p 022bd000 fc:05 10120848                   /home/ferris/julia-0.6/usr/lib/libopenblas64_.so
7fdbd7e90000-7fdbd7eaa000 rw-p 022c3000 fc:05 10120848                   /home/ferris/julia-0.6/usr/lib/libopenblas64_.so
7fdbd7eaa000-7fdbd7f0a000 rw-p 00000000 00:00 0 
7fdbd7f0a000-7fdbd7f0d000 r-xp 00000000 fc:05 10118665                   /home/ferris/julia-0.6/usr/lib/libdSFMT.so
7fdbd7f0d000-7fdbd810c000 ---p 00003000 fc:05 10118665                   /home/ferris/julia-0.6/usr/lib/libdSFMT.so
7fdbd810c000-7fdbd810d000 r--p 00002000 fc:05 10118665                   /home/ferris/julia-0.6/usr/lib/libdSFMT.so
7fdbd810d000-7fdbd810e000 rw-p 00003000 fc:05 10118665                   /home/ferris/julia-0.6/usr/lib/libdSFMT.so
7fdbd810e000-7fdbd816f000 r-xp 00000000 fc:05 10119187                   /home/ferris/julia-0.6/usr/lib/libmpfr.so.4.1.5
7fdbd816f000-7fdbd836e000 ---p 00061000 fc:05 10119187                   /home/ferris/julia-0.6/usr/lib/libmpfr.so.4.1.5
7fdbd836e000-7fdbd8370000 r--p 00060000 fc:05 10119187                   /home/ferris/julia-0.6/usr/lib/libmpfr.so.4.1.5
7fdbd8370000-7fdbd8371000 rw-p 00062000 fc:05 10119187                   /home/ferris/julia-0.6/usr/lib/libmpfr.so.4.1.5
7fdbd8371000-7fdbd83e6000 r-xp 00000000 fc:05 10118951                   /home/ferris/julia-0.6/usr/lib/libgmp.so.10.3.2
7fdbd83e6000-7fdbd85e5000 ---p 00075000 fc:05 10118951                   /home/ferris/julia-0.6/usr/lib/libgmp.so.10.3.2
7fdbd85e5000-7fdbd85e6000 r--p 00074000 fc:05 10118951                   /home/ferris/julia-0.6/usr/lib/libgmp.so.10.3.2
7fdbd85e6000-7fdbd85e7000 rw-p 00075000 fc:05 10118951                   /home/ferris/julia-0.6/usr/lib/libgmp.so.10.3.2
7fdbd85e7000-7fdbd86e7000 rw-p 00000000 00:00 0 
7fdbd86e7000-7fdbd8767000 r-xp 00000000 fc:05 10118933                   /home/ferris/julia-0.6/usr/lib/libpcre2-8.so.0.5.0
7fdbd8767000-7fdbd8966000 ---p 00080000 fc:05 10118933                   /home/ferris/julia-0.6/usr/lib/libpcre2-8.so.0.5.0
7fdbd8966000-7fdbd8967000 r--p 0007f000 fc:05 10118933                   /home/ferris/julia-0.6/usr/lib/libpcre2-8.so.0.5.0
7fdbd8967000-7fdbd8968000 rw-p 00080000 fc:05 10118933                   /home/ferris/julia-0.6/usr/lib/libpcre2-8.so.0.5.0
7fdbd8968000-7fdbd9665000 rw-p 00000000 00:00 0 
7fdbd9665000-7fdbdd669000 rw-p 00000000 00:00 0 
7fdbdd669000-7fdbdd66a000 ---p 00000000 00:00 0 
7fdbdd66a000-7fdbdde6a000 rw-p 00000000 00:00 0 
7fdbdde6a000-7fdbdfda4000 r-xp 00000000 fc:05 10120254                   /home/ferris/julia-0.6/usr/lib/julia/sys.so
7fdbdfda4000-7fdbdffa4000 ---p 01f3a000 fc:05 10120254                   /home/ferris/julia-0.6/usr/lib/julia/sys.so
7fdbdffa4000-7fdbdfffe000 r--p 01f3a000 fc:05 10120254                   /home/ferris/julia-0.6/usr/lib/julia/sys.so
7fdbdfffe000-7fdbdffff000 rw-p 01f94000 fc:05 10120254                   /home/ferris/julia-0.6/usr/lib/julia/sys.so
7fdbdffff000-7fdbe0027000 rw-p 00000000 00:00 0 
7fdbe0027000-7fdbe0028000 ---p 00000000 00:00 0 
7fdbe0028000-7fdbe0828000 rw-p 00000000 00:00 0 
7fdbe0828000-7fdbe0b00000 r--p 00000000 fc:05 12845269                   /usr/lib/locale/locale-archive
7fdbe0b00000-7fdbe0b19000 r-xp 00000000 fc:05 9437571                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fdbe0b19000-7fdbe0d18000 ---p 00019000 fc:05 9437571                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fdbe0d18000-7fdbe0d19000 r--p 00018000 fc:05 9437571                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fdbe0d19000-7fdbe0d1a000 rw-p 00019000 fc:05 9437571                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fdbe0d1a000-7fdbe0d30000 r-xp 00000000 fc:05 9441712                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fdbe0d30000-7fdbe0f2f000 ---p 00016000 fc:05 9441712                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fdbe0f2f000-7fdbe0f30000 rw-p 00015000 fc:05 9441712                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fdbe0f30000-7fdbe1038000 r-xp 00000000 fc:05 9447363                    /lib/x86_64-linux-gnu/libm-2.23.so
7fdbe1038000-7fdbe1237000 ---p 00108000 fc:05 9447363                    /lib/x86_64-linux-gnu/libm-2.23.so
7fdbe1237000-7fdbe1238000 r--p 00107000 fc:05 9447363                    /lib/x86_64-linux-gnu/libm-2.23.so
7fdbe1238000-7fdbe1239000 rw-p 00108000 fc:05 9447363                    /lib/x86_64-linux-gnu/libm-2.23.so
7fdbe1239000-7fdbe13ab000 r-xp 00000000 fc:05 12845454                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fdbe13ab000-7fdbe15ab000 ---p 00172000 fc:05 12845454                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fdbe15ab000-7fdbe15b5000 r--p 00172000 fc:05 12845454                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fdbe15b5000-7fdbe15b7000 rw-p 0017c000 fc:05 12845454                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fdbe15b7000-7fdbe15bb000 rw-p 00000000 00:00 0 
7fdbe15bb000-7fdbe307a000 r-xp 00000000 fc:05 10117732                   /home/ferris/julia-0.6/usr/lib/libLLVM-3.9.so
7fdbe307a000-7fdbe3279000 ---p 01abf000 fc:05 10117732                   /home/ferris/julia-0.6/usr/lib/libLLVM-3.9.so
7fdbe3279000-7fdbe33c4000 r--p 01abe000 fc:05 10117732                   /home/ferris/julia-0.6/usr/lib/libLLVM-3.9.so
7fdbe33c4000-7fdbe33da000 rw-p 01c09000 fc:05 10117732                   /home/ferris/julia-0.6/usr/lib/libLLVM-3.9.so
7fdbe33da000-7fdbe3404000 rw-p 00000000 00:00 0 
7fdbe3404000-7fdbe35c4000 r-xp 00000000 fc:05 9447368                    /lib/x86_64-linux-gnu/libc-2.23.so
7fdbe35c4000-7fdbe37c4000 ---p 001c0000 fc:05 9447368                    /lib/x86_64-linux-gnu/libc-2.23.so
7fdbe37c4000-7fdbe37c8000 r--p 001c0000 fc:05 9447368                    /lib/x86_64-linux-gnu/libc-2.23.so
7fdbe37c8000-7fdbe37ca000 rw-p 001c4000 fc:05 9447368                    /lib/x86_64-linux-gnu/libc-2.23.so
7fdbe37ca000-7fdbe37ce000 rw-p 00000000 00:00 0 
7fdbe37ce000-7fdbe37e6000 r-xp 00000000 fc:05 9447351                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fdbe37e6000-7fdbe39e5000 ---p 00018000 fc:05 9447351                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fdbe39e5000-7fdbe39e6000 r--p 00017000 fc:05 9447351                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fdbe39e6000-7fdbe39e7000 rw-p 00018000 fc:05 9447351                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fdbe39e7000-7fdbe39eb000 rw-p 00000000 00:00 0 
7fdbe39eb000-7fdbe39f2000 r-xp 00000000 fc:05 9447354                    /lib/x86_64-linux-gnu/librt-2.23.so
7fdbe39f2000-7fdbe3bf1000 ---p 00007000 fc:05 9447354                    /lib/x86_64-linux-gnu/librt-2.23.so
7fdbe3bf1000-7fdbe3bf2000 r--p 00006000 fc:05 9447354                    /lib/x86_64-linux-gnu/librt-2.23.so
7fdbe3bf2000-7fdbe3bf3000 rw-p 00007000 fc:05 9447354                    /lib/x86_64-linux-gnu/librt-2.23.so
7fdbe3bf3000-7fdbe3bf6000 r-xp 00000000 fc:05 9447357                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fdbe3bf6000-7fdbe3df5000 ---p 00003000 fc:05 9447357                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fdbe3df5000-7fdbe3df6000 r--p 00002000 fc:05 9447357                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fdbe3df6000-7fdbe3df7000 rw-p 00003000 fc:05 9447357                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fdbe3df7000-7fdbe3fca000 r-xp 00000000 fc:05 10117689                   /home/ferris/julia-0.6/usr/lib/libjulia.so.0.6.0
7fdbe3fca000-7fdbe41ca000 ---p 001d3000 fc:05 10117689                   /home/ferris/julia-0.6/usr/lib/libjulia.so.0.6.0
7fdbe41ca000-7fdbe41cd000 r--p 001d3000 fc:05 10117689                   /home/ferris/julia-0.6/usr/lib/libjulia.so.0.6.0
7fdbe41cd000-7fdbe420e000 rw-p 001d6000 fc:05 10117689                   /home/ferris/julia-0.6/usr/lib/libjulia.so.0.6.0
7fdbe420e000-7fdbe44fb000 rw-p 00000000 00:00 0 
7fdbe44fb000-7fdbe4521000 r-xp 00000000 fc:05 9447346                    /lib/x86_64-linux-gnu/ld-2.23.so
7fdbe4540000-7fdbe46fe000 rw-p 00000000 00:00 0 
7fdbe4709000-7fdbe470a000 rw-p 00000000 00:00 0 
7fdbe470a000-7fdbe471a000 rwxp 00000000 00:00 0 
7fdbe471a000-7fdbe471b000 r--p 00000000 fc:05 927527                     /usr/share/locale-langpack/en_AU/LC_MESSAGES/libc.mo
7fdbe471b000-7fdbe471e000 r--p 00000000 00:00 0 
7fdbe471e000-7fdbe4720000 rw-p 00000000 00:00 0 
7fdbe4720000-7fdbe4721000 r--p 00025000 fc:05 9447346                    /lib/x86_64-linux-gnu/ld-2.23.so
7fdbe4721000-7fdbe4722000 rw-p 00026000 fc:05 9447346                    /lib/x86_64-linux-gnu/ld-2.23.so
7fdbe4722000-7fdbe4723000 rw-p 00000000 00:00 0 
7ffe93b60000-7ffe93d30000 rw-p 00000000 00:00 0                          [stack]
7ffe93d7c000-7ffe93d7e000 r--p 00000000 00:00 0                          [vvar]
7ffe93d7e000-7ffe93d80000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

signal (6): Aborted
while loading no file, in expression starting on line 0
raise at /build/glibc-bfm8X4/glibc-2.23/signal/../sysdeps/unix/sysv/linux/raise.c:54
abort at /build/glibc-bfm8X4/glibc-2.23/stdlib/abort.c:89
__libc_message at /build/glibc-bfm8X4/glibc-2.23/libio/../sysdeps/posix/libc_fatal.c:175
malloc_printerr at /build/glibc-bfm8X4/glibc-2.23/malloc/malloc.c:5006 [inlined]
_int_free at /build/glibc-bfm8X4/glibc-2.23/malloc/malloc.c:3867
__libc_free at /build/glibc-bfm8X4/glibc-2.23/malloc/malloc.c:2968
xmlFreeNodeList at /usr/lib/x86_64-linux-gnu/libxml2.so.2 (unknown line)
xmlFreeNode at /usr/lib/x86_64-linux-gnu/libxml2.so.2 (unknown line)
finalize_node at /home/ferris/.julia/v0.6/EzXML/src/node.jl:323
unknown function (ip: 0x7fdbc1de2ae2)
jl_call_fptr_internal at /home/ferris/julia-0.6/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /home/ferris/julia-0.6/src/julia_internal.h:358 [inlined]
jl_apply_generic at /home/ferris/julia-0.6/src/gf.c:1933
jl_apply at /home/ferris/julia-0.6/src/julia.h:1424 [inlined]
run_finalizer at /home/ferris/julia-0.6/src/gc.c:111
jl_gc_run_finalizers_in_list at /home/ferris/julia-0.6/src/gc.c:200
run_finalizers at /home/ferris/julia-0.6/src/gc.c:234 [inlined]
jl_gc_run_all_finalizers at /home/ferris/julia-0.6/src/gc.c:276
jl_atexit_hook at /home/ferris/julia-0.6/src/init.c:265
jl_exit at /home/ferris/julia-0.6/src/jl_uv.c:551
exit at ./initdefs.jl:22
unknown function (ip: 0x7fdbde2e5f28)
jl_call_fptr_internal at /home/ferris/julia-0.6/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /home/ferris/julia-0.6/src/julia_internal.h:358 [inlined]
jl_apply_generic at /home/ferris/julia-0.6/src/gf.c:1933
do_call at /home/ferris/julia-0.6/src/interpreter.c:75
eval at /home/ferris/julia-0.6/src/interpreter.c:242
jl_interpret_toplevel_expr at /home/ferris/julia-0.6/src/interpreter.c:34
jl_toplevel_eval_flex at /home/ferris/julia-0.6/src/toplevel.c:577
jl_toplevel_eval_in at /home/ferris/julia-0.6/src/builtins.c:496
eval at ./boot.jl:235
unknown function (ip: 0x7fdbde0db6ef)
jl_call_fptr_internal at /home/ferris/julia-0.6/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /home/ferris/julia-0.6/src/julia_internal.h:358 [inlined]
jl_apply_generic at /home/ferris/julia-0.6/src/gf.c:1933
eval_user_input at ./REPL.jl:66
unknown function (ip: 0x7fdbde14985f)
jl_call_fptr_internal at /home/ferris/julia-0.6/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /home/ferris/julia-0.6/src/julia_internal.h:358 [inlined]
jl_apply_generic at /home/ferris/julia-0.6/src/gf.c:1933
macro expansion at ./REPL.jl:97 [inlined]
#1 at ./event.jl:73
unknown function (ip: 0x7fdbc1dd82af)
jl_call_fptr_internal at /home/ferris/julia-0.6/src/julia_internal.h:339 [inlined]
jl_call_method_internal at /home/ferris/julia-0.6/src/julia_internal.h:358 [inlined]
jl_apply_generic at /home/ferris/julia-0.6/src/gf.c:1933
jl_apply at /home/ferris/julia-0.6/src/julia.h:1424 [inlined]
start_task at /home/ferris/julia-0.6/src/task.c:267
unknown function (ip: 0xffffffffffffffff)
Allocations: 1574356 (Pool: 1573174; Big: 1182); GC: 0
Aborted (core dumped)
@bicycle1885
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Thank you for reporting. I think this is a bug of ExXML.jl and may have found the reason. So, I'll fix that soon.

Below is a note for myself.

function unlink!(node::Node)
    @show unsafe_load(convert(Ptr{_Element}, node.ptr)).name
    ccall(
        (:xmlUnlinkNode, libxml2),
        Void,
        (Ptr{Void},),
        node.ptr)
    update_owners!(node, node)
    # Unlinking must remove documents as well because
    # a node can free resources its document owns.
    unset_documents!(node)
    return node
end

bug.jl

using EzXML

# This results in SIGABRT.
xmldoc = readxml("X.xml")
nodes = find(xmldoc, "X")
unlink!(nodes[1])

X.xml

<?xml version="1.0" encoding="UTF-8"?>
<X/>

~/.j/v/EzXML ((v0.5.0)|✚1…) $ julia bug.jl
unsafe_load(convert(Ptr{_Element}, node.ptr)).name = Cstring(0x00007f8bea1b7057)
julia(38822,0x7fffc20e13c0) malloc: *** error for object 0x7f8bea1b7057: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug

signal (6): Abort trap: 6
while loading no file, in expression starting on line 0
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 984957 (Pool: 983841; Big: 1116); GC: 0
fish: 'julia bug.jl' terminated by signal SIGABRT (Abort)

Loading an XML document from a file fills the .name field to each node to indicate the file name. So, I need to remove the .name fields under the node.

@andyferris
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Thanks for the quick response!

bicycle1885 added a commit that referenced this issue Sep 13, 2017
@bicycle1885
do not reuse the context dictionary (fix #28)
ae877a2
@bicycle1885
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Try v0.5.1 once it is registered in METADATA (or check out the tag).

@andyferris
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Awesome, thanks!

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@bicycle1885 @andyferris