help > Error bulding docs
Showing 1-11 of 11 posts
Mar 25, 2011 10:03 PM | Matthew Brett
Error bulding docs
Hi,
Thanks for the compilation fix - that works for me now. Again on Ubuntu 10.04, I am still getting another build error:
gives:
Again - thanks for any help...
Matthew
Thanks for the compilation fix - that works for me now. Again on Ubuntu 10.04, I am still getting another build error:
./configure --with-fop=/usr/bin/fop
--with-xalan-j=/usr/share/java
--with-docbook-xsl=/usr/share/xml/docbook/stylesheet/docbook-xsl
gives:
...
ln -s bxhabsorb afni2bxh
ln -s bxhabsorb afni2xcede
ln -s bxhabsorb analyze2bxh
ln -s bxhabsorb analyze2xcede
cp ./bxh_eventmerge.xsl ./bxh_eventmerge.xsl
cp: cannot stat `./bxh_eventmerge.xsl': No such file or directory
make[1]: *** [scripts] Error 1
make[1]: Leaving directory `/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/utils'
make: *** [utils] Error 2
ln -s bxhabsorb afni2xcede
ln -s bxhabsorb analyze2bxh
ln -s bxhabsorb analyze2xcede
cp ./bxh_eventmerge.xsl ./bxh_eventmerge.xsl
cp: cannot stat `./bxh_eventmerge.xsl': No such file or directory
make[1]: *** [scripts] Error 1
make[1]: Leaving directory `/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/utils'
make: *** [utils] Error 2
Again - thanks for any help...
Matthew
Mar 26, 2011 01:03 AM | Syam Gadde
RE: Error bulding docs
I assume you are building in the same directory as the
source? I think I have fixed this. Please do:
svn update
./config.status
make
The config.status will rebuild the Makefile, which is where the problem was. Thanks.
svn update
./config.status
make
The config.status will rebuild the Makefile, which is where the problem was. Thanks.
Mar 26, 2011 01:03 AM | Matthew Brett
RE: Error bulding docs
Originally posted by Syam Gadde:
Ah - sorry - I hope I have the right version - but testing 'make' again after updating I now get this:
I assume you are building in the same directory
as the source? I think I have fixed this. Please
do:
svn update
./config.status
make
The config.status will rebuild the Makefile, which is where the problem was. Thanks.
svn update
./config.status
make
The config.status will rebuild the Makefile, which is where the problem was. Thanks.
Ah - sorry - I hope I have the right version - but testing 'make' again after updating I now get this:
...
g++
./bxh_epochavg.cpp -c -o bxh_epochavg.o
-DXMLH_VERSIONSTR="\"BXH/XCEDE utilities (1.9.9.6pre)\"" -I.
-I../libsrc -I..//libsrc -g -O2 -pthread
-I/usr/include/libxml2 -I/usr/include/libxml2
-I/usr/include/libgdome -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include
-I/usr/include/libxml2 -I. -g -DBIAC=1
-DHAVE_CONFIG_H
./bxh_epochavg.cpp: In function ‘int main(int, char**)’:
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:1343: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1343: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:1360: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1360: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:1390: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1390: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:1736: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1736: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:2098: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:2098: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2219: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:2219: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:2327: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’
./bxh_epochavg.cpp:2327: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘size_t’
./bxh_epochavg.cpp:2520: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:2520: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
make[1]: *** [bxh_epochavg.o] Error 1
make[1]: Leaving directory `/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/utils'
make: *** [utils] Error 2
./bxh_epochavg.cpp: In function ‘int main(int, char**)’:
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:583: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:584: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:1343: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1343: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:1360: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1360: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:1390: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1390: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:1736: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:1736: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:2098: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:2098: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2214: warning: deprecated conversion from string constant to ‘char*’
./bxh_epochavg.cpp:2219: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:2219: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
./bxh_epochavg.cpp:2327: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’
./bxh_epochavg.cpp:2327: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘size_t’
./bxh_epochavg.cpp:2520: error: invalid conversion from ‘char**’ to ‘const char**’
./bxh_epochavg.cpp:2520: error: initializing argument 5 of ‘int bxh_dataReadFileStart(const char*, const char*, const char*, int, const char**, char**, bxhdataread*)’
make[1]: *** [bxh_epochavg.o] Error 1
make[1]: Leaving directory `/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/utils'
make: *** [utils] Error 2
Mar 26, 2011 02:03 PM | Syam Gadde
RE: Error bulding docs
I'm not sure why I didn't catch those when I compiled on
Ubuntu. Anyway, I have committed some updates that I hope
will fix this. I won't be able to actually compile on Ubuntu
until Monday, but the same errors you got were resolved by these
latest fixes on Fedora 13.
Mar 26, 2011 06:03 PM | Matthew Brett
RE: Error bulding docs
Originally posted by Syam Gadde:
Sorry to keep on with bad news, but I now get:
I made some effort at trying to work out what was going on, but got a little lost in the make machinery. It is true that there is not such file ``eprime2xml`` in the codebase, but I suppose it needs to be built.
Thanks again,
Matthew
I'm not sure why I didn't catch those when I
compiled on Ubuntu. Anyway, I have committed some updates
that I hope will fix this. I won't be able to actually
compile on Ubuntu until Monday, but the same errors you got were
resolved by these latest fixes on Fedora 13.
Sorry to keep on with bad news, but I now get:
...
ln -s
bxhabsorb afni2bxh
ln -s
bxhabsorb afni2xcede
ln -s
bxhabsorb analyze2bxh
ln -s
bxhabsorb analyze2xcede
cp
./eprime2xml ./eventstable2xml
cp: cannot
stat `./eprime2xml': No such file or directory
make[1]: ***
[scripts] Error 1
make[1]:
Leaving directory
`/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/utils'
make: ***
[utils] Error 2
I made some effort at trying to work out what was going on, but got a little lost in the make machinery. It is true that there is not such file ``eprime2xml`` in the codebase, but I suppose it needs to be built.
Thanks again,
Matthew
Mar 28, 2011 01:03 PM | Syam Gadde
RE: Error bulding docs
Sorry, I don't do a lot of building in the source directory.
The Makefile was removing some files on "make clean" that it
shouldn't have been removing. I think this is fixed now:
svn update
./config.status
make
svn update
./config.status
make
Mar 28, 2011 05:03 PM | Matthew Brett
RE: Error bulding docs
Originally posted by Syam Gadde:
Thanks for the feedback. Now with the in-place build I get this:
For the own-directory build I get this:
Indeed there doesn't seem to be a file 'wrapusage.sh' in my code tree.
Thanks again,
Matthew
Sorry, I don't do a lot of building in the
source directory. The Makefile was removing some files on
"make clean" that it shouldn't have been removing. I think
this is fixed now:
svn update
./config.status
make
svn update
./config.status
make
Thanks for the feedback. Now with the in-place build I get this:
Getting help
message for afni2bxh
bash:
./wrapusage.sh: No such file or directory
Getting help
message for analyze2bxh
bash:
./wrapusage.sh: No such file or directory
Getting help
message for batch_showplay2xml
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh2analyze
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh2pgm
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh2ppm
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxhabsorb
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_brainmask
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_correlate
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_epochavg
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_event2table
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_eventmerge
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_eventresp
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_eventstats
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_eventstats_standardize
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_mean
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxhreorient
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxhselect
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxhsetorient
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_tfilter
bash:
./wrapusage.sh: No such file or directory
Getting help
message for bxh_ttest
bash:
./wrapusage.sh: No such file or directory
Getting help
message for dumpheader
bash:
./wrapusage.sh: No such file or directory
Getting help
message for eprime2xml
bash:
./wrapusage.sh: No such file or directory
Getting help
message for eventstable2xml
bash:
./wrapusage.sh: No such file or directory
Getting help
message for extractimagedata
bash:
./wrapusage.sh: No such file or directory
Getting help
message for extractxyztdata
bash:
./wrapusage.sh: No such file or directory
Getting help
message for ffile2bxh
bash:
./wrapusage.sh: No such file or directory
Getting help
message for iowa-signafive2bxh
bash:
./wrapusage.sh: No such file or directory
Getting help
message for pfile2bxh
bash:
./wrapusage.sh: No such file or directory
Getting help
message for presentation2xml
bash:
./wrapusage.sh: No such file or directory
Getting help
message for printfrags
bash:
./wrapusage.sh: No such file or directory
Getting help
message for showplay2xml
bash:
./wrapusage.sh: No such file or directory
Getting help
message for signafive2bxh
bash:
./wrapusage.sh: No such file or directory
Getting help
message for ximg2bxh
bash:
./wrapusage.sh: No such file or directory
Getting help
message for xcede_extract_schedules.pl
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_count
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_generate.pl
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_minmax
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_oediff
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_phantomqa
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_phantomqa.pl
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_spikiness
bash:
./wrapusage.sh: No such file or directory
Getting help
message for fmriqa_volmeasures
bash:
./wrapusage.sh: No such file or directory
cp ./*.xml
.
cp:
`./app_toolusage.xml' and `./app_toolusage.xml' are the same
file
cp:
`./overview.xml' and `./overview.xml' are the same
file
cp:
`./qa.xml' and `./qa.xml' are the same file
cp:
`./tool_afni2bxh.xml' and `./tool_afni2bxh.xml' are the same
file
cp:
`./tool_analyze2bxh.xml' and `./tool_analyze2bxh.xml' are the same
file
cp:
`./tool_batch_showplay2xml.xml' and `./tool_batch_showplay2xml.xml'
are the same file
cp:
`./tool_bxh2analyze.xml' and `./tool_bxh2analyze.xml' are the same
file
cp:
`./tool_bxh2pgm.xml' and `./tool_bxh2pgm.xml' are the same
file
cp:
`./tool_bxh2ppm.xml' and `./tool_bxh2ppm.xml' are the same
file
cp:
`./tool_bxhabsorb.xml' and `./tool_bxhabsorb.xml' are the same
file
cp:
`./tool_bxh_brainmask.xml' and `./tool_bxh_brainmask.xml' are the
same file
cp:
`./tool_bxh_correlate.xml' and `./tool_bxh_correlate.xml' are the
same file
cp:
`./tool_bxh_epochavg.xml' and `./tool_bxh_epochavg.xml' are the
same file
cp:
`./tool_bxh_event2table.xml' and `./tool_bxh_event2table.xml' are
the same file
cp:
`./tool_bxh_eventmerge.xml' and `./tool_bxh_eventmerge.xml' are the
same file
cp:
`./tool_bxh_eventresp.xml' and `./tool_bxh_eventresp.xml' are the
same file
cp:
`./tool_bxh_eventstats_standardize.xml' and
`./tool_bxh_eventstats_standardize.xml' are the same
file
cp:
`./tool_bxh_eventstats.xml' and `./tool_bxh_eventstats.xml' are the
same file
cp:
`./tool_bxh_mean.xml' and `./tool_bxh_mean.xml' are the same
file
cp:
`./tool_bxhreorient.xml' and `./tool_bxhreorient.xml' are the same
file
cp:
`./tool_bxhselect.xml' and `./tool_bxhselect.xml' are the same
file
cp:
`./tool_bxhsetorient.xml' and `./tool_bxhsetorient.xml' are the
same file
cp:
`./tool_bxh_tfilter.xml' and `./tool_bxh_tfilter.xml' are the same
file
cp:
`./tool_bxh_ttest.xml' and `./tool_bxh_ttest.xml' are the same
file
cp:
`./tool_dumpheader.xml' and `./tool_dumpheader.xml' are the same
file
cp:
`./tool_eprime2xml.xml' and `./tool_eprime2xml.xml' are the same
file
cp:
`./tool_eventstable2xml.xml' and `./tool_eventstable2xml.xml' are
the same file
cp:
`./tool_extractimagedata.xml' and `./tool_extractimagedata.xml' are
the same file
cp:
`./tool_extractxyztdata.xml' and `./tool_extractxyztdata.xml' are
the same file
cp:
`./tool_ffile2bxh.xml' and `./tool_ffile2bxh.xml' are the same
file
cp:
`./tool_fmriqa_count.xml' and `./tool_fmriqa_count.xml' are the
same file
cp:
`./tool_fmriqa_generate.pl.xml' and `./tool_fmriqa_generate.pl.xml'
are the same file
cp:
`./tool_fmriqa_minmax.xml' and `./tool_fmriqa_minmax.xml' are the
same file
cp:
`./tool_fmriqa_oediff.xml' and `./tool_fmriqa_oediff.xml' are the
same file
cp:
`./tool_fmriqa_phantomqa.pl.xml' and
`./tool_fmriqa_phantomqa.pl.xml' are the same file
cp:
`./tool_fmriqa_phantomqa.xml' and `./tool_fmriqa_phantomqa.xml' are
the same file
cp:
`./tool_fmriqa_spikiness.xml' and `./tool_fmriqa_spikiness.xml' are
the same file
cp:
`./tool_fmriqa_volmeasures.xml' and `./tool_fmriqa_volmeasures.xml'
are the same file
cp:
`./tool_iowa-signafive2bxh.xml' and `./tool_iowa-signafive2bxh.xml'
are the same file
cp:
`./tool_pfile2bxh.xml' and `./tool_pfile2bxh.xml' are the same
file
cp:
`./tool_presentation2xml.xml' and `./tool_presentation2xml.xml' are
the same file
cp:
`./tool_printfrags.xml' and `./tool_printfrags.xml' are the same
file
cp:
`./tool_showplay2xml.xml' and `./tool_showplay2xml.xml' are the
same file
cp:
`./tool_signafive2bxh.xml' and `./tool_signafive2bxh.xml' are the
same file
cp:
`./tool_xcede_extract_schedules.pl.xml' and
`./tool_xcede_extract_schedules.pl.xml' are the same
file
cp:
`./tool_ximg2bxh.xml' and `./tool_ximg2bxh.xml' are the same
file
cp:
`./usermanual.xml' and `./usermanual.xml' are the same
file
make[1]: ***
[usermanual_full.xml] Error 1
make[1]:
Leaving directory
`/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/docs/usedocs'
make: ***
[docs/usedocs] Error 2
For the own-directory build I get this:
Getting help
message for fmriqa_spikiness
bash:
../../../../bxh-xcede-tools/bxh_xcede_tools/docs/usedocs/wrapusage.sh:
No such file or directory
Getting help
message for fmriqa_volmeasures
bash:
../../../../bxh-xcede-tools/bxh_xcede_tools/docs/usedocs/wrapusage.sh:
No such file or directory
cp
../../../../bxh-xcede-tools/bxh_xcede_tools/docs/usedocs/*.xml
.
xmllint
--xinclude usermanual.xml > usermanual_full.xml
tool_afni2bxh.xml:1: parser error : Document is
empty
^
tool_afni2bxh.xml:1: parser error : Start tag
expected, '<' not found
^
app_toolusage.xml:5: element include: XInclude
error : could not load tool_afni2bxh.xml, and no fallback was
found
tool_analyze2bxh.xml:1: parser error : Document is
empty
Indeed there doesn't seem to be a file 'wrapusage.sh' in my code tree.
Thanks again,
Matthew
Mar 31, 2011 01:03 AM | Syam Gadde
RE: Error bulding docs
> I have gotten rid of those errors now, and was able to compile
the docs with the following:
svn update
./configure --prefix=/home/gadde/install --with-fop=/usr/bin/fop
--with-xalan-j=/usr/share/java
--with-docbook-xsl=/usr/share/sgml/docbook/xsl-stylesheets
make clean all
Let me know if you get any other errors.
svn update
./configure --prefix=/home/gadde/install --with-fop=/usr/bin/fop
--with-xalan-j=/usr/share/java
--with-docbook-xsl=/usr/share/sgml/docbook/xsl-stylesheets
make clean all
Let me know if you get any other errors.
Mar 31, 2011 05:03 AM | Matthew Brett
RE: Error bulding docs
Hi,
Thanks for persisting. Now I think we're getting to Ubuntu / Fedora
territory. The build:
./configure --with-fop=/usr/bin/fop --with-xalan-j=/usr/share/java
--with-docbook-xsl=/usr/share/xml/docbook/stylesheet
--prefix=/home/mb312/usr/local
fails with
...
xmllint --xinclude usermanual.xml > usermanual_full.xml
warning: failed to load external entity "tool_dicom2bxh.xml"
app_toolusage.xml:26: element include: XInclude error : could not load
tool_dicom2bxh.xml, and no fallback was found
java -cp /usr/share/java/xalan-j2.jar:/usr/share/java/xercesImpl.jar:/usr/share/java/xml-apis.jar
-Djava.endorsed.dirs= org.apache.xalan.xslt.Process -PARAM
use.extensions 1 -PARAM textinsert.extension 1 -PARAM
hyphenate.verbatim 1 -PARAM xref.with.number.and.title 0 -PARAM
section.autolabel 1 -PARAM section.label.includes.component.label 1
-PARAM header.column.widths '30 40 30' -PARAM footer.column.widths '30
40 30' -PARAM tex.math.in.alt tex -PARAM fop1.extensions 1 -XSL
./docbook_custom.xsl -IN usermanual_full.xml -OUT usermanual_full.fo
Exception in thread "main" java.lang.NoClassDefFoundError:
org/apache/xalan/xslt/Process
Caused by: java.lang.ClassNotFoundException: org.apache.xalan.xslt.Process
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: org.apache.xalan.xslt.Process. Program will exit.
make[1]: *** [usermanual_full.fo] Error 1
make[1]: Leaving directory
`/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/docs/usedocs'
make: *** [docs/usedocs] Error 2
In the java -cp line above /usr/share/java/xalan-j2.jar does not
exist but /usr/share/java/xalan2.jar does. Replacing in that command
and rerunning by hand gives:
file:///home/mb312/dev_trees/bxh-xcede-t...
Line #5; Column #80; Had IO Exception with stylesheet file:
/usr/share/sgml/docbook/xsl-stylesheets/fo/docbook.xsl
file:///home/mb312/dev_trees/bxh-xcede-t...
Line #14; Column #45; org.xml.sax.SAXException: ElemTemplateElement
error: inline.monoseq
javax.xml.transform.TransformerException: ElemTemplateElement error:
inline.monoseq
which also makes sense because
/usr/share/sgml/docbook/xsl-stylesheets/fo/docbook.xsl does not exist,
probably in fact being
/usr/share/sgml/docbook/stylesheet/xsl/docbook-xsl/fo/docbook.xsl
which does exist.
At that stage I'm afraid I declared myself lost again :)
Thanks,
Matthew
Thanks for persisting. Now I think we're getting to Ubuntu / Fedora
territory. The build:
./configure --with-fop=/usr/bin/fop --with-xalan-j=/usr/share/java
--with-docbook-xsl=/usr/share/xml/docbook/stylesheet
--prefix=/home/mb312/usr/local
fails with
...
xmllint --xinclude usermanual.xml > usermanual_full.xml
warning: failed to load external entity "tool_dicom2bxh.xml"
app_toolusage.xml:26: element include: XInclude error : could not load
tool_dicom2bxh.xml, and no fallback was found
java -cp /usr/share/java/xalan-j2.jar:/usr/share/java/xercesImpl.jar:/usr/share/java/xml-apis.jar
-Djava.endorsed.dirs= org.apache.xalan.xslt.Process -PARAM
use.extensions 1 -PARAM textinsert.extension 1 -PARAM
hyphenate.verbatim 1 -PARAM xref.with.number.and.title 0 -PARAM
section.autolabel 1 -PARAM section.label.includes.component.label 1
-PARAM header.column.widths '30 40 30' -PARAM footer.column.widths '30
40 30' -PARAM tex.math.in.alt tex -PARAM fop1.extensions 1 -XSL
./docbook_custom.xsl -IN usermanual_full.xml -OUT usermanual_full.fo
Exception in thread "main" java.lang.NoClassDefFoundError:
org/apache/xalan/xslt/Process
Caused by: java.lang.ClassNotFoundException: org.apache.xalan.xslt.Process
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: org.apache.xalan.xslt.Process. Program will exit.
make[1]: *** [usermanual_full.fo] Error 1
make[1]: Leaving directory
`/home/mb312/dev_trees/bxh-xcede-tools/bxh_xcede_tools/docs/usedocs'
make: *** [docs/usedocs] Error 2
In the java -cp line above /usr/share/java/xalan-j2.jar does not
exist but /usr/share/java/xalan2.jar does. Replacing in that command
and rerunning by hand gives:
file:///home/mb312/dev_trees/bxh-xcede-t...
Line #5; Column #80; Had IO Exception with stylesheet file:
/usr/share/sgml/docbook/xsl-stylesheets/fo/docbook.xsl
file:///home/mb312/dev_trees/bxh-xcede-t...
Line #14; Column #45; org.xml.sax.SAXException: ElemTemplateElement
error: inline.monoseq
javax.xml.transform.TransformerException: ElemTemplateElement error:
inline.monoseq
which also makes sense because
/usr/share/sgml/docbook/xsl-stylesheets/fo/docbook.xsl does not exist,
probably in fact being
/usr/share/sgml/docbook/stylesheet/xsl/docbook-xsl/fo/docbook.xsl
which does exist.
At that stage I'm afraid I declared myself lost again :)
Thanks,
Matthew
Mar 31, 2011 07:03 PM | Syam Gadde
RE: Error bulding docs
OK, please try one more time. I have also added some
intelligence to search for fop, docbook-xsl, xalan-j and java in
standard places in RedHat and Ubunutu systems. Having all
those installed I was able to configure without any "--with-"
options. So:
svn update
./configure --prefix=/path/to/install
make clean all
svn update
./configure --prefix=/path/to/install
make clean all
Mar 31, 2011 07:03 PM | Matthew Brett
RE: Error bulding docs
Thanks - nice job - that's much easier...
In case it's helpful:
sudo apt-get install libgdome2-dev
sudo apt-get install libxslt-dev
sudo apt-get install fop
sudo apt-get install libxalan2-java
./configure
make clean all
Gives (Maverick):
Getting help message for fmriqa_spikiness
Getting help message for fmriqa_volmeasures
xmllint --xinclude usermanual.xml > usermanual_full.xml
warning: failed to load external entity "tool_dicom2bxh.xml"
app_toolusage.xml:26: element include: XInclude error : could not load
tool_dicom2bxh.xml, and no fallback was found
java -cp /usr/share/java/xalan2.jar
-Djava.endorsed.dirs=/usr/share/java org.apache.xalan.xslt.Process
-PARAM use.extensions 1 -PARAM textinsert.extension 1 -PARAM
hyphenate.verbatim 1 -PARAM xref.with.number.and.title 0 -PARAM
section.autolabel 1 -PARAM section.label.includes.component.label 1
-PARAM header.column.widths '30 40 30' -PARAM footer.column.widths '30
40 30' -PARAM tex.math.in.alt tex -PARAM fop1.extensions 1 -XSL
./docbook_custom.xsl -IN usermanual_full.xml -OUT usermanual_full.fo
Exception during runtime initialization
make[1]: *** [usermanual_full.fo] Aborted
make[1]: Leaving directory
`/home/mb312/gcmirrors/bxh-xcede-tools/bxh_xcede_tools/docs/usedocs'
make: *** [docs/usedocs] Error 2
The error is a bit longer for lucid:
Getting help message for eventstable2xml
Getting help message for presentation2xml
java -cp /usr/share/java/xalan2.jar
-Djava.endorsed.dirs=/usr/share/java org.apache.xalan.xslt.Process
-PARAM use.extensions 1 -PARAM textinsert.extension 1 -PARAM
hyphenate.verbatim 1 -PARAM xref.with.number.and.title 0 -PARAM
section.autolabel 1 -PARAM section.label.includes.component.label 1
-PARAM header.column.widths '30 40 30' -PARAM footer.column.widths '30
40 30' -PARAM tex.math.in.alt tex -PARAM fop1.extensions 1 -XSL
./docbook_custom.xsl -IN usermanual_full.xml -OUT usermanual_full.fo
Error occurred during initialization of VM
java.lang.StackOverflowError
at java.lang.Throwable.fillInStackTrace(Throwable.java:498)
at java.lang.Throwable.(Throwable.java:159)
at java.lang.Error.(Error.java:81)
at java.lang.LinkageError.(LinkageError.java:72)
at java.lang.IncompatibleClassChangeError.(IncompatibleClassChangeError.java:71)
at java.lang.NoSuchMethodError.(NoSuchMethodError.java:72)
at java.lang.VMThrowable.fillInStackTrace(Native Method)
at java.lang.Throwable.fillInStackTrace(Throwable.java:498
...
at java.lang.Error.(Error.java:81)
at java.lang.LinkageError.(LinkageError.java:72)
at java.lang.IncompatibleClassChangeError.(IncompatibleClassChangeError.java:71)
at java.lang.NoSuchMethodError.(NoSuchMethodError.java:72)
at java.lang.VMThrowable.fillInStackTrace(Native Method)
at java.lang.Throwable.fillInStackTrace(Throwable.java:498)
at java.lang.Throwable.(Throwable.java:159)
make[1]: *** [usermanual_full.fo] Error 1
Sorry - again I am out of my depth,
Thanks,
Matthew
In case it's helpful:
sudo apt-get install libgdome2-dev
sudo apt-get install libxslt-dev
sudo apt-get install fop
sudo apt-get install libxalan2-java
./configure
make clean all
Gives (Maverick):
Getting help message for fmriqa_spikiness
Getting help message for fmriqa_volmeasures
xmllint --xinclude usermanual.xml > usermanual_full.xml
warning: failed to load external entity "tool_dicom2bxh.xml"
app_toolusage.xml:26: element include: XInclude error : could not load
tool_dicom2bxh.xml, and no fallback was found
java -cp /usr/share/java/xalan2.jar
-Djava.endorsed.dirs=/usr/share/java org.apache.xalan.xslt.Process
-PARAM use.extensions 1 -PARAM textinsert.extension 1 -PARAM
hyphenate.verbatim 1 -PARAM xref.with.number.and.title 0 -PARAM
section.autolabel 1 -PARAM section.label.includes.component.label 1
-PARAM header.column.widths '30 40 30' -PARAM footer.column.widths '30
40 30' -PARAM tex.math.in.alt tex -PARAM fop1.extensions 1 -XSL
./docbook_custom.xsl -IN usermanual_full.xml -OUT usermanual_full.fo
Exception during runtime initialization
make[1]: *** [usermanual_full.fo] Aborted
make[1]: Leaving directory
`/home/mb312/gcmirrors/bxh-xcede-tools/bxh_xcede_tools/docs/usedocs'
make: *** [docs/usedocs] Error 2
The error is a bit longer for lucid:
Getting help message for eventstable2xml
Getting help message for presentation2xml
java -cp /usr/share/java/xalan2.jar
-Djava.endorsed.dirs=/usr/share/java org.apache.xalan.xslt.Process
-PARAM use.extensions 1 -PARAM textinsert.extension 1 -PARAM
hyphenate.verbatim 1 -PARAM xref.with.number.and.title 0 -PARAM
section.autolabel 1 -PARAM section.label.includes.component.label 1
-PARAM header.column.widths '30 40 30' -PARAM footer.column.widths '30
40 30' -PARAM tex.math.in.alt tex -PARAM fop1.extensions 1 -XSL
./docbook_custom.xsl -IN usermanual_full.xml -OUT usermanual_full.fo
Error occurred during initialization of VM
java.lang.StackOverflowError
at java.lang.Throwable.fillInStackTrace(Throwable.java:498)
at java.lang.Throwable.(Throwable.java:159)
at java.lang.Error.(Error.java:81)
at java.lang.LinkageError.(LinkageError.java:72)
at java.lang.IncompatibleClassChangeError.(IncompatibleClassChangeError.java:71)
at java.lang.NoSuchMethodError.(NoSuchMethodError.java:72)
at java.lang.VMThrowable.fillInStackTrace(Native Method)
at java.lang.Throwable.fillInStackTrace(Throwable.java:498
...
at java.lang.Error.(Error.java:81)
at java.lang.LinkageError.(LinkageError.java:72)
at java.lang.IncompatibleClassChangeError.(IncompatibleClassChangeError.java:71)
at java.lang.NoSuchMethodError.(NoSuchMethodError.java:72)
at java.lang.VMThrowable.fillInStackTrace(Native Method)
at java.lang.Throwable.fillInStackTrace(Throwable.java:498)
at java.lang.Throwable.(Throwable.java:159)
make[1]: *** [usermanual_full.fo] Error 1
Sorry - again I am out of my depth,
Thanks,
Matthew