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spgrass6 and R 2.9

7 messages · Roger Bivand, Dylan Beaudette

Original
Dylan Beaudette
#
On Friday 29 May 2009, Torleif Markussen Lunde wrote:
Hi Torleif, thanks for the tips.

I just updated my libc, and tried the MALLOC_CHECK trick-- neither fixed the 
problem. Still get the same error... Very strange, as I did not encounter 
this problem on a very similar machine.

Could this have anything to do with configure arguments such as -march ?

Cheers,
Dylan

  
    

      
      
    

  


  


    

    

      
      

        


  

        

      Roger Bivand
    

    

      
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On Mon, 1 Jun 2009, Dylan Beaudette wrote:

        

            

      
      
      
    

        
You haven't told us what your underlying system is, or how you installed 
R. If you built R from source, did you run "make check"? Does the problem 
arise installing other packages? It most likely is something on your 
system, otherwise there would be lots of reports of the same.

Roger

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    
3 days later

    

      
      

        


  

        

      Dylan Beaudette
    

    

      
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On Monday 01 June 2009, Roger Bivand wrote:

            

      
      
      
    

        
Right. Should have been a little less hasty about posting to the list. R has 
been built from source, spgrass6 was accessed from CRAN via 
install.packages(). This problems has not occurred at anyother time while 
updating packages that were installed under R 2.7. 

1. make check (R 2.9.0): OK

2. sessionInfo()
R version 2.9.0 (2009-04-17) 
i686-pc-linux-gnu 

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

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

Is there any way that I can do a 'make check' type of operation with the 
latest spgrass6 from CRAN?

Note that trying to manually install the package, like this:
sudo R CMD INSTALL spgrass6_0.6-6.tar.gz

results in:
* Installing to library '/usr/local/lib/R/library'
* Installing *source* package 'spgrass6' ...
** R
** inst
** preparing package for lazy loading
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.7.0dev, released 2008/11/26
Path to GDAL shared files: /usr/local/share/gdal
Loaded PROJ.4 runtime: Rel. 4.6.0, 21 Dec 2007
Path to PROJ.4 shared files: (autodetected)
** help
*** installing help indices
 >>> Building/Updating help pages for package 'spgrass6'
     Formats: text html latex example 
  execGRASS                         text    html    latex   example
  gmeta6                            text    html    latex   example
  initGRASS                         text    html    latex   example
  readRAST6                         text    html    latex   example
  readVECT6                         text    html    latex   example
  spgrass6                          text    html    latex   example
** building package indices ...
* DONE (spgrass6)
*** glibc detected *** /usr/local/lib/R/bin/exec/R: double free or corruption 
(fasttop): 0x0857d880 ***

hope that is enough information.

Cheers,
Dylan

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
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On Thu, 4 Jun 2009, Dylan Beaudette wrote:

        

            

      
      
      
    

        
Yes, do R CMD check spgrass6_0.6-6.tar.gz. When building R, are you 
setting the architecture flags manually? Have you tried letting R sort 
things out for itself? Could you try R CMD check rgdal (from the source 
tarball)? Could you try:

R -d gbd

and then a traceback after install fails? Otherwise we are left with 
non-random cosmic rays as the explanation?

Roger

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dylan Beaudette
    

    

      
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On Fri, Jun 5, 2009 at 1:55 AM, Roger Bivand<Roger.Bivand at nhh.no> wrote:

            

      
      
      
    

        
Thanks Roger.

I usually set the march flag to -march=opteron ... and seem to recall
setting that as as system wide configure option, but cannot recall
what file that is in... I'll check. How exactly does the R -d gdb
approach work?

Thanks!
Dylan



Here is the check on spgrass6:

---------------------------------------------------------------------------------------------------------------------
R CMD check spgrass6_0.6-6.tar.gz
* checking for working pdflatex ... OK
* using log directory '/home/dylan/src/spgrass6.Rcheck'
* using R version 2.9.0 (2009-04-17)
* using session charset: ISO8859-1
* checking for file 'spgrass6/DESCRIPTION' ... OK
* this is package 'spgrass6' version '0.6-6'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'spgrass6' can be installed ...*** glibc
detected *** /usr/local/lib/R/bin/exec/R: double free or corruption
(fasttop): 0x09568348 ***
---------------------------------------------------------------------------------------------------------------------

Now rgdal:
---------------------------------------------------------------------------------------------------------------------
R CMD check rgdal_0.6-8.tar.gz
* checking for working pdflatex ... OK
* using log directory '/home/dylan/src/rgdal.Rcheck'
* using R version 2.9.0 (2009-04-17)
* using session charset: ISO8859-1
* checking for file 'rgdal/DESCRIPTION' ... OK
* this is package 'rgdal' version '0.6-8'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'rgdal' can be installed ...*** glibc
detected *** ./proj_conf_test: double free or corruption (fasttop):
0x08c5bec0 ***
======= Backtrace: =========
/lib/i686/cmov/libc.so.6[0xb75a31d4]
/lib/i686/cmov/libc.so.6(cfree+0x96)[0xb75a5186]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb6db3101]
/usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1d)[0xb6d907fd]
/usr/lib/libstdc++.so.6(_ZNSsD1Ev+0x4c)[0xb6d9221c]
/lib/i686/cmov/libc.so.6(__cxa_finalize+0xc1)[0xb7564c21]
/usr/local/lib/libgeos-3.1.0.so[0xb6b61734]
/usr/local/lib/libgeos-3.1.0.so[0xb6c5a200]
/lib/ld-linux.so.2[0xb7fbaa23]
/lib/i686/cmov/libc.so.6(exit+0x89)[0xb7564889]
./proj_conf_test[0x8048565]
/lib/i686/cmov/libc.so.6(__libc_start_main+0xe5)[0xb754a775]
./proj_conf_test[0x8048481]
======= Memory map: ========
08048000-08049000 r-xp 00000000 08:11 26624192
/home/dylan/src/rgdal.Rcheck/00_pkg_src/rgdal/proj_conf_test
08049000-0804a000 rw-p 00000000 08:11 26624192
/home/dylan/src/rgdal.Rcheck/00_pkg_src/rgdal/proj_conf_test
08c5b000-08c7c000 rw-p 08c5b000 00:00 0          [heap]
b5900000-b5921000 rw-p b5900000 00:00 0
b5921000-b5a00000 ---p b5921000 00:00 0
b5a3f000-b5a41000 rw-p b5a3f000 00:00 0
b5a41000-b6786000 r--p 00000000 08:11 3146351    /usr/lib/libicudata.so.40.1
b6786000-b6787000 rw-p 00d44000 08:11 3146351    /usr/lib/libicudata.so.40.1
b6787000-b6788000 rw-p b6787000 00:00 0
b6788000-b68ad000 r-xp 00000000 08:11 3151434    /usr/lib/libicuuc.so.40.1
b68ad000-b68b6000 rw-p 00124000 08:11 3151434    /usr/lib/libicuuc.so.40.1
b68b6000-b68b8000 rw-p b68b6000 00:00 0
b68b8000-b6a3c000 r-xp 00000000 08:11 3146355    /usr/lib/libicui18n.so.40.1
b6a3c000-b6a43000 rw-p 00184000 08:11 3146355    /usr/lib/libicui18n.so.40.1
b6a43000-b6c9e000 r-xp 00000000 08:11 3163289    /usr/local/lib/libgeos-3.1.0.so
b6c9e000-b6ca9000 rw-p 0025b000 08:11 3163289    /usr/local/lib/libgeos-3.1.0.so
b6ca9000-b6cd4000 r-xp 00000000 08:11 8437815    /lib/libgcc_s.so.1
b6cd4000-b6cd5000 rw-p 0002a000 08:11 8437815    /lib/libgcc_s.so.1
b6cd5000-b6cd6000 rw-p b6cd5000 00:00 0
b6cd6000-b6cfa000 r-xp 00000000 08:11 8437843    /lib/i686/cmov/libm-2.9.so
b6cfa000-b6cfb000 r--p 00023000 08:11 8437843    /lib/i686/cmov/libm-2.9.so
b6cfb000-b6cfc000 rw-p 00024000 08:11 8437843    /lib/i686/cmov/libm-2.9.so
b6cfc000-b6de1000 r-xp 00000000 08:11 3146421    /usr/lib/libstdc++.so.6.0.12
b6de1000-b6de5000 r--p 000e4000 08:11 3146421    /usr/lib/libstdc++.so.6.0.12
b6de5000-b6de6000 rw-p 000e8000 08:11 3146421    /usr/lib/libstdc++.so.6.0.12
b6de6000-b6ded000 rw-p b6de6000 00:00 0
b6ded000-b6e01000 r-xp 00000000 08:11 3146202    /usr/lib/libz.so.1.2.3.3
b6e01000-b6e02000 rw-p 00013000 08:11 3146202    /usr/lib/libz.so.1.2.3.3
b6e02000-b6e17000 r-xp 00000000 08:11 8437891    /lib/i686/cmov/libnsl-2.9.so
b6e17000-b6e18000 r--p 00014000 08:11 8437891    /lib/i686/cmov/libnsl-2.9.so
b6e18000-b6e19000 rw-p 00015000 08:11 8437891    /lib/i686/cmov/libnsl-2.9.so
b6e19000-b6e1b000 rw-p b6e19000 00:00 0
b6e1b000-b6e24000 r-xp 00000000 08:11 8437976    /lib/i686/cmov/libcrypt-2.9.so
b6e24000-b6e25000 r--p 00008000 08:11 8437976    /lib/i686/cmov/libcrypt-2.9.so
b6e25000-b6e26000 rw-p 00009000 08:11 8437976    /lib/i686/cmov/libcrypt-2.9.so
b6e26000-b6e4d000 rw-p b6e26000 00:00 0
b6e4d000-b6e62000 r-xp 00000000 08:11 8437975
/lib/i686/cmov/libpthread-2.9.so
b6e62000-b6e63000 r--p 00014000 08:11 8437975
/lib/i686/cmov/libpthread-2.9.so
b6e63000-b6e64000 rw-p 00015000 08:11 8437975
/lib/i686/cmov/libpthread-2.9.so
b6e64000-b6e67000 rw-p b6e64000 00:00 0
b6e67000-b700b000 r-xp 00000000 08:11 3154222
/usr/lib/libmysqlclient.so.15.0.0
b700b000-b704f000 rw-p 001a3000 08:11 3154222
/usr/lib/libmysqlclient.so.15.0.0
b704f000-b7050000 rw-p b704f000 00:00 0
b7050000-b7052000 r-xp 00000000 08:11 8437977    /lib/i686/cmov/libdl-2.9.so
b7052000-b7053000 r--p 00001000 08:11 8437977    /lib/i686/cmov/libdl-2.9.so
b7053000-b7054000 rw-p 00002000 08:11 8437977    /lib/i686/cmov/libdl-2.9.so
b7054000-b705b000 r-xp 00000000 08:11 8437904    /lib/i686/cmov/librt-2.9.so
b705b000-b705c000 r--p 00006000 08:11 8437904    /lib/i686/cmov/librt-2.9.so
b705c000-b705d000 rw-p 00007000 08:11 8437904    /lib/i686/cmov/librt-2.9.so
b705d000-b7079000 r-xp 00000000 08:11 3541773
/usr/local/pgsql/lib/libpq.so.5.1
b7079000-b707a000 rw-p 0001c000 08:11 3541773
/usr/local/pgsql/lib/libpq.so.5.1
b707a000-b7177000 r-xp 00000000 08:11 3151596    /usr/lib/libcfitsio.so.2.510
b7177000-b7179000 rw-p 000fc000 08:11 3151596    /usr/lib/libcfitsio.so.2.510
b7179000-b71ed000 rw-p b7179000 00:00 0
b71ed000-b721c000 r-xp 00000000 08:11 8274101    /usr/lib/libnetcdf.so.4.0.0
b721c000-b721d000 rw-p 0002f000 08:11 8274101    /usr/lib/libnetcdf.so.4.0.0
b721d000-b721f000 rw-p b721d000 00:00 0
b721f000-b7243000 r-xp 00000000 08:11 3146201    /usr/lib/libexpat.so.1.5.2
b7243000-b7245000 rw-p 00023000 08:11 3146201    /usr/lib/libexpat.so.1.5.2
b7245000-b72c6000 r-xp 00000000 08:11 3145848    /usr/lib/libsqlite3.so.0.8.6
b72c6000-b72c8000 rw-p 00081000 08:11 3145848    /usr/lib/libsqlite3.so.0.8.6
b72c8000-b750c000 r-xp 00000000 08:11 3162687    /usr/local/lib/libgeos-3.0.0.so
b750c000-b7516000 rw-p 00244000 08:11 3162687    /usr/local/lib/libgeos-3.0.0.so
b7516000-b7533000 r-xp 00000000 08:11 3163292
/usr/local/lib/libgeos_c.so.1.5.0
b7533000-b7534000 rw-p 0001c000 08:11 3163292
/usr/local/lib/libgeos_c.so.1.5.0
b7534000-b768e000 r-xp 00000000 08:11 8437821    /lib/i686/cmov/libc-2.9.so
b768e000-b7690000 r--p 0015a000 08:11 8437821    /lib/i686/cmov/libc-2.9.so
b7690000-b7691000 rw-p 0015c000 08:11 8437821    /lib/i686/cmov/libc-2.9.so
b7691000-b7695000 rw-p b7691000 00:00 0
b76b1000-b76ec000 r-xp 00000000 08:11 3162172    /usr/local/lib/libproj.so.0.5.4
b76ec000-b76ee000 rw-p 0003b000 08:11 3162172    /usr/local/lib/libproj.so.0.5.4
b76ee000-b7f0a000 r-xp 00000000 08:11 3162145
/usr/local/lib/libgdal.so.1.13.0
b7f0a000-b7fa4000 rw-p 0081c000 08:11 3162145
/usr/local/lib/libgdal.so.1.13.0
b7fa4000-b7fab000 rw-p b7fa4000 00:00 0
b7fab000-b7fac000 r-xp b7fab000 00:00 0          [vdso]
b7fac000-b7fc8000 r-xp 00000000 08:11 8437905    /lib/ld-2.9.so
b7fc8000-b7fc9000 r--p 0001b000 08:11 8437905    /lib/ld-2.9.so
b7fc9000-b7fca000 rw-p 0001c000 08:11 8437905    /lib/ld-2.9.so
bfbb5000-bfbca000 rw-p bffeb000 00:00 0          [stack]
*** glibc detected *** ./proj_conf_test: double free or corruption
(fasttop): 0x09e6aec0 ***
======= Backtrace: =========
/lib/i686/cmov/libc.so.6[0xb75641d4]
/lib/i686/cmov/libc.so.6(cfree+0x96)[0xb7566186]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb6d74101]
/usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1d)[0xb6d517fd]
/usr/lib/libstdc++.so.6(_ZNSsD1Ev+0x4c)[0xb6d5321c]
/lib/i686/cmov/libc.so.6(__cxa_finalize+0xc1)[0xb7525c21]
/usr/local/lib/libgeos-3.1.0.so[0xb6b22734]
/usr/local/lib/libgeos-3.1.0.so[0xb6c1b200]
/lib/ld-linux.so.2[0xb7f7ba23]
/lib/i686/cmov/libc.so.6(exit+0x89)[0xb7525889]
./proj_conf_test[0x8048565]
/lib/i686/cmov/libc.so.6(__libc_start_main+0xe5)[0xb750b775]
./proj_conf_test[0x8048481]
======= Memory map: ========
08048000-08049000 r-xp 00000000 08:11 26624192
/home/dylan/src/rgdal.Rcheck/00_pkg_src/rgdal/proj_conf_test
08049000-0804a000 rw-p 00000000 08:11 26624192
/home/dylan/src/rgdal.Rcheck/00_pkg_src/rgdal/proj_conf_test
09e6a000-09e8b000 rw-p 09e6a000 00:00 0          [heap]
b5800000-b5821000 rw-p b5800000 00:00 0
b5821000-b5900000 ---p b5821000 00:00 0
b5a00000-b5a02000 rw-p b5a00000 00:00 0
b5a02000-b6747000 r--p 00000000 08:11 3146351    /usr/lib/libicudata.so.40.1
b6747000-b6748000 rw-p 00d44000 08:11 3146351    /usr/lib/libicudata.so.40.1
b6748000-b6749000 rw-p b6748000 00:00 0
b6749000-b686e000 r-xp 00000000 08:11 3151434    /usr/lib/libicuuc.so.40.1
b686e000-b6877000 rw-p 00124000 08:11 3151434    /usr/lib/libicuuc.so.40.1
b6877000-b6879000 rw-p b6877000 00:00 0
b6879000-b69fd000 r-xp 00000000 08:11 3146355    /usr/lib/libicui18n.so.40.1
b69fd000-b6a04000 rw-p 00184000 08:11 3146355    /usr/lib/libicui18n.so.40.1
b6a04000-b6c5f000 r-xp 00000000 08:11 3163289    /usr/local/lib/libgeos-3.1.0.so
b6c5f000-b6c6a000 rw-p 0025b000 08:11 3163289    /usr/local/lib/libgeos-3.1.0.so
b6c6a000-b6c95000 r-xp 00000000 08:11 8437815    /lib/libgcc_s.so.1
b6c95000-b6c96000 rw-p 0002a000 08:11 8437815    /lib/libgcc_s.so.1
b6c96000-b6c97000 rw-p b6c96000 00:00 0
b6c97000-b6cbb000 r-xp 00000000 08:11 8437843    /lib/i686/cmov/libm-2.9.so
b6cbb000-b6cbc000 r--p 00023000 08:11 8437843    /lib/i686/cmov/libm-2.9.so
b6cbc000-b6cbd000 rw-p 00024000 08:11 8437843    /lib/i686/cmov/libm-2.9.so
b6cbd000-b6da2000 r-xp 00000000 08:11 3146421    /usr/lib/libstdc++.so.6.0.12
b6da2000-b6da6000 r--p 000e4000 08:11 3146421    /usr/lib/libstdc++.so.6.0.12
b6da6000-b6da7000 rw-p 000e8000 08:11 3146421    /usr/lib/libstdc++.so.6.0.12
b6da7000-b6dae000 rw-p b6da7000 00:00 0
b6dae000-b6dc2000 r-xp 00000000 08:11 3146202    /usr/lib/libz.so.1.2.3.3
b6dc2000-b6dc3000 rw-p 00013000 08:11 3146202    /usr/lib/libz.so.1.2.3.3
b6dc3000-b6dd8000 r-xp 00000000 08:11 8437891    /lib/i686/cmov/libnsl-2.9.so
b6dd8000-b6dd9000 r--p 00014000 08:11 8437891    /lib/i686/cmov/libnsl-2.9.so
b6dd9000-b6dda000 rw-p 00015000 08:11 8437891    /lib/i686/cmov/libnsl-2.9.so
b6dda000-b6ddc000 rw-p b6dda000 00:00 0
b6ddc000-b6de5000 r-xp 00000000 08:11 8437976    /lib/i686/cmov/libcrypt-2.9.so
b6de5000-b6de6000 r--p 00008000 08:11 8437976    /lib/i686/cmov/libcrypt-2.9.so
b6de6000-b6de7000 rw-p 00009000 08:11 8437976    /lib/i686/cmov/libcrypt-2.9.so
b6de7000-b6e0e000 rw-p b6de7000 00:00 0
b6e0e000-b6e23000 r-xp 00000000 08:11 8437975
/lib/i686/cmov/libpthread-2.9.so
b6e23000-b6e24000 r--p 00014000 08:11 8437975
/lib/i686/cmov/libpthread-2.9.so
b6e24000-b6e25000 rw-p 00015000 08:11 8437975
/lib/i686/cmov/libpthread-2.9.so
b6e25000-b6e28000 rw-p b6e25000 00:00 0
b6e28000-b6fcc000 r-xp 00000000 08:11 3154222
/usr/lib/libmysqlclient.so.15.0.0
b6fcc000-b7010000 rw-p 001a3000 08:11 3154222
/usr/lib/libmysqlclient.so.15.0.0
b7010000-b7011000 rw-p b7010000 00:00 0
b7011000-b7013000 r-xp 00000000 08:11 8437977    /lib/i686/cmov/libdl-2.9.so
b7013000-b7014000 r--p 00001000 08:11 8437977    /lib/i686/cmov/libdl-2.9.so
b7014000-b7015000 rw-p 00002000 08:11 8437977    /lib/i686/cmov/libdl-2.9.so
b7015000-b701c000 r-xp 00000000 08:11 8437904    /lib/i686/cmov/librt-2.9.so
b701c000-b701d000 r--p 00006000 08:11 8437904    /lib/i686/cmov/librt-2.9.so
b701d000-b701e000 rw-p 00007000 08:11 8437904    /lib/i686/cmov/librt-2.9.so
b701e000-b703a000 r-xp 00000000 08:11 3541773
/usr/local/pgsql/lib/libpq.so.5.1
b703a000-b703b000 rw-p 0001c000 08:11 3541773
/usr/local/pgsql/lib/libpq.so.5.1
b703b000-b7138000 r-xp 00000000 08:11 3151596    /usr/lib/libcfitsio.so.2.510
b7138000-b713a000 rw-p 000fc000 08:11 3151596    /usr/lib/libcfitsio.so.2.510
b713a000-b71ae000 rw-p b713a000 00:00 0
b71ae000-b71dd000 r-xp 00000000 08:11 8274101    /usr/lib/libnetcdf.so.4.0.0
b71dd000-b71de000 rw-p 0002f000 08:11 8274101    /usr/lib/libnetcdf.so.4.0.0
b71de000-b71e0000 rw-p b71de000 00:00 0
b71e0000-b7204000 r-xp 00000000 08:11 3146201    /usr/lib/libexpat.so.1.5.2
b7204000-b7206000 rw-p 00023000 08:11 3146201    /usr/lib/libexpat.so.1.5.2
b7206000-b7287000 r-xp 00000000 08:11 3145848    /usr/lib/libsqlite3.so.0.8.6
b7287000-b7289000 rw-p 00081000 08:11 3145848    /usr/lib/libsqlite3.so.0.8.6
b7289000-b74cd000 r-xp 00000000 08:11 3162687    /usr/local/lib/libgeos-3.0.0.so
b74cd000-b74d7000 rw-p 00244000 08:11 3162687    /usr/local/lib/libgeos-3.0.0.so
b74d7000-b74f4000 r-xp 00000000 08:11 3163292
/usr/local/lib/libgeos_c.so.1.5.0
b74f4000-b74f5000 rw-p 0001c000 08:11 3163292
/usr/local/lib/libgeos_c.so.1.5.0
b74f5000-b764f000 r-xp 00000000 08:11 8437821    /lib/i686/cmov/libc-2.9.so
b764f000-b7651000 r--p 0015a000 08:11 8437821    /lib/i686/cmov/libc-2.9.so
b7651000-b7652000 rw-p 0015c000 08:11 8437821    /lib/i686/cmov/libc-2.9.so
b7652000-b7656000 rw-p b7652000 00:00 0
b7672000-b76ad000 r-xp 00000000 08:11 3162172    /usr/local/lib/libproj.so.0.5.4
b76ad000-b76af000 rw-p 0003b000 08:11 3162172    /usr/local/lib/libproj.so.0.5.4
b76af000-b7ecb000 r-xp 00000000 08:11 3162145
/usr/local/lib/libgdal.so.1.13.0
b7ecb000-b7f65000 rw-p 0081c000 08:11 3162145
/usr/local/lib/libgdal.so.1.13.0
b7f65000-b7f6c000 rw-p b7f65000 00:00 0
b7f6c000-b7f6d000 r-xp b7f6c000 00:00 0          [vdso]
b7f6d000-b7f89000 r-xp 00000000 08:11 8437905    /lib/ld-2.9.so
b7f89000-b7f8a000 r--p 0001b000 08:11 8437905    /lib/ld-2.9.so
b7f8a000-b7f8b000 rw-p 0001c000 08:11 8437905    /lib/ld-2.9.so
bfa75000-bfa8a000 rw-p bffeb000 00:00 0          [stack]
 OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ...*** glibc detected ***
/usr/local/lib/R/bin/exec/R: double free or corruption (fasttop):
0x08dff5c0 ***

  
  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
      #
    

  


  

      
On Fri, 5 Jun 2009, Dylan Beaudette wrote:

        

            

      
      
      
    

        
Dylan,

Your post on R-help about problems with R and PostgreSQL may suggest a 
systemic problem, unless you are sure that your alias fix there is not 
system specific (try on another machine). Architectures ought to be found 
automatically.

            

      
      
      
    

        
Well, when you run it, you get the GDB interface, and type run to run R. 
Then do install.packages(), possibly from a local tarball, and use GDB 
commands to interrogate the crash.

I find it very hard to credit that this is not specific to your machine. 
Do you have an equivalent AMD (or Intel) x86 box you can try this on? It 
is very hard to help if nobody else can reproduce it (I run 2 x86 Intel 
Linux, 1 64-bit Intel Linux, with R built from source, and see nothing 
untoward in installing spgrass6. Did you try to run R CMD check on other 
packages?

Roger

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dylan Beaudette
    

    

      
      #
    

  


  

      
On Friday 05 June 2009, Roger Bivand wrote:

            

      
      
      
    

        
Hi Roger thanks for the response.

            

      
      
      
    

        
This is the strange part. I have 2 nearly identical setups: one is xeon-based 
the other is opteron-based, both running Debian unstable with R-2.9.0 
compiled from source. The post regarding PostgreSQL was actually related to 
problems on the xeon-based machine.

The opteron-based machine has a slightly newer set of packages:

opteron-machine:
gcc                                          4:4.3.3-8
libc6-i686                                   2.9-13

xeon-machine:
gcc                                    4:4.3.3-2
libc6-i686                             2.9-6


Another strange thing: I haven't had any other problems with the opteron-based 
machine, at least with respect to compiling related packages such as GRASS, 
GDAL, PROJ, PostGIS, PostgreSQL, etc.


I started R with the debugger like this:

# start R
sudo R -d /usr/bin/gdb

# start R from within gdb
(gdb) run

# install local copy of package:
install.packages('spgrass6_0.6-6.tar.gz')
inferring 'repos = NULL' from the file name
* Installing *source* package 'spgrass6' ...
** R
** inst

# run backtrace
(gdb) bt
#0  0xb7f86424 in __kernel_vsyscall ()
#1  0xb7d4ae73 in waitpid () from /lib/i686/cmov/libc.so.6
#2  0xb7ce6f6b in ?? () from /lib/i686/cmov/libc.so.6
#3  0x080e9423 in R_system ()
#4  0x081035c5 in do_system ()
#5  0x0806c2c7 in do_internal ()
#6  0x081999aa in Rf_eval ()
#7  0x0819b7a4 in do_begin ()
#8  0x081999aa in Rf_eval ()
#9  0x0819a130 in Rf_applyClosure ()
#10 0x08199c26 in Rf_eval ()
#11 0x0819c518 in Rf_evalList ()
#12 0x08199a94 in Rf_eval ()
#13 0x0819aaad in do_if ()
#14 0x081999aa in Rf_eval ()
#15 0x0819b7a4 in do_begin ()
#16 0x081999aa in Rf_eval ()
#17 0x0819b2c8 in do_for ()
#18 0x081999aa in Rf_eval ()
#19 0x0819b7a4 in do_begin ()
#20 0x081999aa in Rf_eval ()
#21 0x0819aaf5 in do_if ()
#22 0x081999aa in Rf_eval ()
#23 0x0819b7a4 in do_begin ()
#24 0x081999aa in Rf_eval ()
#25 0x0819a130 in Rf_applyClosure ()
#26 0x08199c26 in Rf_eval ()
#27 0x080593c3 in Rf_ReplIteration ()
#28 0x08059585 in R_ReplConsole ()
#29 0x0805a7bb in run_Rmainloop ()
#30 0x0805a7d2 in Rf_mainloop ()
#31 0x08058f95 in main ()
#32 0xb7cc2775 in __libc_start_main () from /lib/i686/cmov/libc.so.6
#33 0x08058ed1 in _start () at ../sysdeps/i386/elf/start.S:119


I don't really understand this output, but I wouldn't be surprised if it isn't 
something specific to this machine.

Any ideas?

Cheers,
Dylan