[R-sig-Geo] spgrass6 and R 2.9
Dylan Beaudette
debeaudette at ucdavis.edu
Fri Jun 5 22:04:21 CEST 2009
On Friday 05 June 2009, Roger Bivand wrote:
> On Fri, 5 Jun 2009, Dylan Beaudette wrote:
> > On Fri, Jun 5, 2009 at 1:55 AM, Roger Bivand<Roger.Bivand at nhh.no> wrote:
> >> On Thu, 4 Jun 2009, Dylan Beaudette wrote:
> >>> On Monday 01 June 2009, Roger Bivand wrote:
> >>>> On Mon, 1 Jun 2009, Dylan Beaudette wrote:
> >>>>> On Friday 29 May 2009, Torleif Markussen Lunde wrote:
> >>>>>> Hi
> >>>>>>
> >>>>>> First try updating glibc, and install spgrass6 again. If this does
> >>>>>> not work you could try
> >>>>>>
> >>>>>> export MALLOC_CHECK_=0
> >>>>>>
> >>>>>> before you start R. The error might be related to "somewhere
> >>>>>> something" is trying to free memory that has already been
> >>>>>> unallocated. I don't know
> >>>>>> the details here, but it could be worth a try?
> >>>>>>
> >>>>>> Best wishes
> >>>>>> Torleif
> >>>>>
> >>>>> 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 ?
> >>>>
> >>>> 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
> >>>
> >>> 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?
> >>
> >> 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
> >
> > 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.
Hi Roger thanks for the response.
> 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.
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
>
> > How exactly does the R -d gdb approach work?
>
> 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
>
> > 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 ***
> > -------------------------------------------------------------------------
> >--------------------------------------------
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
More information about the R-sig-Geo
mailing list