Fatal JRE error

Tim ts+ml at rcmd.org
Tue May 27 06:05:48 EDT 2014


 Hi Gilbert,

 thanks for your interest in this and your time.

 On Tue, 27 May 2014 00:22:41 -0400, Benjamin Gilbert 
 <bgilbert at cs.cmu.edu> wrote:
> On 05/26/2014 01:11 PM, Tim wrote:
>>   src/.libs/libopenslide.so: undefined reference to 
>> `opj_set_event_mgr'
>>   src/.libs/libopenslide.so: undefined reference to `opj_cio_open'
>>   src/.libs/libopenslide.so: undefined reference to `opj_cio_close'
>>   src/.libs/libopenslide.so: undefined reference to
>>   `opj_destroy_decompress'
> [...]
> You appear to be building against OpenJPEG 2.x, which is not yet
> supported by OpenSlide.  The configure script should only accept
> OpenJPEG 1.x, so that shouldn't be happening.  What was the exact
> configure command line you used?  Could you run "make V=1" and report
> what it says?

 The configure command I used was only './configure'. For the 
 GIT-version, I executed 'autoreconf -i' before that.

 Here is the full output of 'make V=1' (all of the following is for the 
 GIT version):


 -------------------------- output of 'make V=1' (stdout + stderr, GIT) 
 --------------------
 make  all-am
 make[1]: Entering directory `/home/ts/builds/openslide-git'
 /bin/sh ./libtool  --tag=CC   --mode=link gcc -std=gnu99 -Wall -Wextra 
 -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations 
 -Wnested-externs  -fvisibility=hidden -DG_DISABLE_SINGLE_INCLUDES 
 -DGLIB_VERSION_MIN_REQUIRED=GLIB_VERSION_2_26 
 -DGLIB_VERSION_MAX_ALLOWED=GLIB_VERSION_MIN_REQUIRED -fno-common -g -O2  
 -o tools/openslide-show-properties 
 tools/tools_openslide_show_properties-openslide-tools-common.o 
 tools/tools_openslide_show_properties-openslide-show-properties.o 
 src/libopenslide.la -pthread -lgthread-2.0 -lgio-2.0 -lgobject-2.0 
 -lglib-2.0   -ljpeg -lm
 libtool: link: gcc -std=gnu99 -Wall -Wextra -Wstrict-prototypes 
 -Wmissing-prototypes -Wmissing-declarations -Wnested-externs 
 -fvisibility=hidden -DG_DISABLE_SINGLE_INCLUDES 
 -DGLIB_VERSION_MIN_REQUIRED=GLIB_VERSION_2_26 
 -DGLIB_VERSION_MAX_ALLOWED=GLIB_VERSION_MIN_REQUIRED -fno-common -g -O2 
 -o tools/.libs/openslide-show-properties 
 tools/tools_openslide_show_properties-openslide-tools-common.o 
 tools/tools_openslide_show_properties-openslide-show-properties.o 
 -pthread  src/.libs/libopenslide.so -L/lib64 -lcairo -lsqlite3 
 /usr/lib64/libxml2.so -ldl -llzma -lopenjpeg -ltiff -lpng12 
 -lgdk_pixbuf-2.0 -lz -lgthread-2.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 
 -ljpeg -lm -pthread -Wl,-rpath -Wl,/usr/lib64
 src/.libs/libopenslide.so: undefined reference to `opj_set_event_mgr'
 src/.libs/libopenslide.so: undefined reference to `opj_cio_open'
 src/.libs/libopenslide.so: undefined reference to `opj_cio_close'
 src/.libs/libopenslide.so: undefined reference to 
 `opj_destroy_decompress'
 collect2: error: ld returned 1 exit status
 make[1]: *** [tools/openslide-show-properties] Error 1
 make[1]: Leaving directory `/home/ts/builds/openslide-git'
 make: *** [all] Error 2
 --------------------------------------------- end of output  
 ---------------------------------


 I also had a look at the installed openjpeg packages on the box (the 
 'i' at the start of each line means 'installed'):

 --------------------------------------------------------------------
 root at artio # zypper se openjpeg
 Loading repository data...
 Reading installed packages...
 S | Name                     | Summary                                  
                | Type
 --+--------------------------+----------------------------------------------------------+-----------
 i | libopenjpeg1             | An open-source JPEG 2000 codec           
                | package
   | libopenjpeg1-32bit       | An open-source JPEG 2000 codec           
                | package
 i | libopenjpeg2_0           | The OpenJPEG library is an open-source 
 JPEG 2000 library | package
   | libopenjpeg2_0-debuginfo | Debug information for package 
 libopenjpeg2_0             | package
 i | openjpeg                 | An open-source JPEG 2000 codec           
                | package
 i | openjpeg-devel           | Development files for the OpenJPEG 
 library               | package
   | openjpeg-devel-32bit     | Development files for the OpenJPEG 
 library               | package
   | openjpeg2                | The OpenJPEG library is an open-source 
 JPEG 2000 library | srcpackage
 i | openjpeg2-devel          | Development files for openjpeg2          
                | package
 --------------------------------------------------------------------

 Since you said that openjpeg2 is not supported yet, I uninstalled 
 openjpeg2-devel and then, once more, ran 'autoreconf -i', followed by 
 './configure' and 'make V=1'. Here is the make output after removing 
 openjpeg2-devel:


 ----------------- output of 'make V=1' after uninstalling 
 openjpeg2-devel (stdout + stderr, GIT) --------------------
 make  all-am
 make[1]: Entering directory `/home/ts/builds/openslide-git'
 /bin/sh ./libtool  --tag=CC   --mode=link gcc -std=gnu99 -Wall -Wextra 
 -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations 
 -Wnested-externs  -fvisibility=hidden -DG_DISABLE_SINGLE_INCLUDES 
 -DGLIB_VERSION_MIN_REQUIRED=GLIB_VERSION_2_26 
 -DGLIB_VERSION_MAX_ALLOWED=GLIB_VERSION_MIN_REQUIRED -fno-common -g -O2  
 -o tools/openslide-show-properties 
 tools/tools_openslide_show_properties-openslide-tools-common.o 
 tools/tools_openslide_show_properties-openslide-show-properties.o 
 src/libopenslide.la -pthread -lgthread-2.0 -lgio-2.0 -lgobject-2.0 
 -lglib-2.0   -ljpeg -lm
 libtool: link: gcc -std=gnu99 -Wall -Wextra -Wstrict-prototypes 
 -Wmissing-prototypes -Wmissing-declarations -Wnested-externs 
 -fvisibility=hidden -DG_DISABLE_SINGLE_INCLUDES 
 -DGLIB_VERSION_MIN_REQUIRED=GLIB_VERSION_2_26 
 -DGLIB_VERSION_MAX_ALLOWED=GLIB_VERSION_MIN_REQUIRED -fno-common -g -O2 
 -o tools/.libs/openslide-show-properties 
 tools/tools_openslide_show_properties-openslide-tools-common.o 
 tools/tools_openslide_show_properties-openslide-show-properties.o 
 -pthread  src/.libs/libopenslide.so -L/lib64 -lcairo -lsqlite3 
 /usr/lib64/libxml2.so -ldl -llzma -lopenjpeg -ltiff -lpng12 
 -lgdk_pixbuf-2.0 -lz -lgthread-2.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 
 -ljpeg -lm -pthread -Wl,-rpath -Wl,/usr/lib64
 /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: 
 cannot find -lopenjpeg
 collect2: error: ld returned 1 exit status
 make[1]: *** [tools/openslide-show-properties] Error 1
 make[1]: Leaving directory `/home/ts/builds/openslide-git'
 make: *** [all] Error 2
 --------------------------------------------- end of output  
 ---------------------------------

 Since it cannot find libopenjpeg now (even though openjpeg-devel is 
 marked as installed), I think that it used openjpeg2 before and cannot 
 find the older version it needs for some reason. Strange. Any ideas? Can 
 I point it to the openjpeg-devel somehow?


 Greetings,

-- 
 Tim


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