libxml2 fails upgrade (_rk_glob undefined in link stage)

[poftwaresatent@…]

Problem history

1. tried to install xffm w/ macports v<1.5
2. received link error along the lines of:
   link error... cannot prebind... _rk_glob and _rk_globfree not found
3. checked macports.org and saw that v1.5 was released
4. decided to selfupdate and upgrade installed to see if fix exists
5. upgrade stalled on libxml2 w/ same link error
6. tried to clean --all and re-install libxml2 but problem persists

Further symptoms

cannot 'sudo su -' anymore, fails with error:

dyld: su can't open library: /opt/local/lib/libcom_err.1.dylib  (No such file or directory, errno = 2)
Trace/BPT trap

luckily I still have root access in another console...

Error Log

captured with 'port -d upgrade libxml2 2>&1' after a 'port clean --all libxml2'

Summary

make[2]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macpor
ts_sources_rsync.macports.org_release_ports_textproc_libxml2/work/libxml2-2.6.28
'

[...]

if gcc -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./include  -D_REENTRANT    -I/o
pt/local/include -I/opt/local/include  -O2 -pedantic -W -Wformat -Wunused -Wimpl
icit -Wreturn-type -Wswitch -Wcomment -Wtrigraphs -Wformat -Wchar-subscripts -Wu
ninitialized -Wparentheses -Wshadow -Wpointer-arith -Wcast-align -Wwrite-strings
 -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wnested-externs -W
inline -Wredundant-decls -MT runtest.o -MD -MP -MF ".deps/runtest.Tpo" -c -o run
test.o runtest.c; \
        then mv -f ".deps/runtest.Tpo" ".deps/runtest.Po"; else rm -f ".deps/run
test.Tpo"; exit 1; fi
runtest.c: In function `xpathDocTest':
runtest.c:2416: warning: comparison between signed and unsigned
runtest.c: In function `xptrDocTest':
runtest.c:2464: warning: comparison between signed and unsigned
runtest.c: In function `schemasTest':
runtest.c:3018: warning: comparison between signed and unsigned
runtest.c: In function `rngTest':
runtest.c:3180: warning: comparison between signed and unsigned
runtest.c: In function `rngStreamTest':
runtest.c:3268: warning: comparison between signed and unsigned
runtest.c: In function `launchTests':
runtest.c:4285: warning: comparison between signed and unsigned
/usr/include/stdio.h: At top level:
runtest.c:3840: warning: `catalog' defined but not used
runtest.c:3841: warning: `testfiles' defined but not used
runtest.c:3863: warning: `thread_specific_data' defined but not used
/bin/sh ./libtool --tag=CC --mode=link gcc  -O2 -pedantic -W -Wformat -Wunused -
Wimplicit -Wreturn-type -Wswitch -Wcomment -Wtrigraphs -Wformat -Wchar-subscript
s -Wuninitialized -Wparentheses -Wshadow -Wpointer-arith -Wcast-align -Wwrite-st
rings -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wnested-exter
ns -Winline -Wredundant-decls  -L/opt/local/lib -o runtest  runtest.o ./libxml2.
la -lpthread -lz -L/opt/local/lib -liconv -lm  
gcc -O2 -pedantic -W -Wformat -Wunused -Wimplicit -Wreturn-type -Wswitch -Wcomme
nt -Wtrigraphs -Wformat -Wchar-subscripts -Wuninitialized -Wparentheses -Wshadow
 -Wpointer-arith -Wcast-align -Wwrite-strings -Waggregate-return -Wstrict-protot
ypes -Wmissing-prototypes -Wnested-externs -Winline -Wredundant-decls -o .libs/r
untest runtest.o  -L/opt/local/lib ./.libs/libxml2.dylib -lpthread -lz /opt/loca
l/lib/libiconv.dylib -lm 
ld: warning prebinding disabled because dependent library: /opt/local/lib/libxml
2.2.dylib is not prebound
ld: Undefined symbols:
_rk_glob
_rk_globfree
make[2]: *** [runtest] Error 1

[...]

gcc -O2 -pedantic -W -Wformat -Wunused -Wimplicit -Wreturn-type -Wswitch -Wcomme
nt -Wtrigraphs -Wformat -Wchar-subscripts -Wuninitialized -Wparentheses -Wshadow
 -Wpointer-arith -Wcast-align -Wwrite-strings -Waggregate-return -Wstrict-protot
ypes -Wmissing-prototypes -Wnested-externs -Winline -Wredundant-decls -o .libs/r
untest runtest.o  -L/opt/local/lib ./.libs/libxml2.dylib -lpthread -lz /opt/loca
l/lib/libiconv.dylib -lm 
ld: warning prebinding disabled because dependent library: /opt/local/lib/libxml
2.2.dylib is not prebound
ld: Undefined symbols:
_rk_glob
_rk_globfree
make[2]: *** [runtest] Error 1
make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macport
s_sources_rsync.macports.org_release_ports_textproc_libxml2/work/libxml2-2.6.28'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macport
s_sources_rsync.macports.org_release_ports_textproc_libxml2/work/libxml2-2.6.28'
make: *** [all] Error 2

Warning: the following items did not execute (for libxml2): org.macports.destroo
t org.macports.build
DEBUG: invalid command name "registry"
    while executing
"registry get $key "locale""
Error: Unable to upgrade port: 1

Full Log

attachment:macports-libxml2-config.log​

attachment:macports-libxml2-upgrade-error.log​

[ryandesign (Ryan Carsten Schmidt)]

I don't know about your undefined rk_glob symbols, but there have been reports of libcom_err problems ​all over the mailing list so check those messages. It seems to relate to the heimdal port.

[blb@…]

Is this still an issue, libxml2 has seen numerous changes since?

[poftwaresatent@…]

Sorry, I haven't tried in a really long time. I guess you can close this ticket, in case I run into it again I'll just refile.

[(none)]

Milestone Port Bugs deleted