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'asciidoctor-mathematical' could not be loaded #23

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harumo11 opened this issue Nov 20, 2016 · 13 comments
Closed

'asciidoctor-mathematical' could not be loaded #23

harumo11 opened this issue Nov 20, 2016 · 13 comments
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@ProgramFan
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@harumo11
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Hello. everyone.

I want to write equations in my document.
When I executed this command:

$ asciidoctor-pdf --trace -r asciidoctor-mathematical -o test.pdf research.asciidoc

I got this error:

harumo@harumo-X250 ~/Documents/research $ asciidoctor-pdf --trace -r asciidoctor-mathematical -o test.pdf research.asciidoc 
/usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- asciidoctor-mathematical (LoadError)
	from /usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
	from /var/lib/gems/2.3.0/gems/polyglot-0.3.5/lib/polyglot.rb:65:in `require'
	from /usr/lib/ruby/vendor_ruby/asciidoctor/cli/options.rb:219:in `block in parse!'
	from /usr/lib/ruby/vendor_ruby/asciidoctor/cli/options.rb:217:in `each'
	from /usr/lib/ruby/vendor_ruby/asciidoctor/cli/options.rb:217:in `parse!'
	from /var/lib/gems/2.3.0/gems/asciidoctor-pdf-1.5.0.alpha.13/bin/asciidoctor-pdf:25:in `<top (required)>'
	from /usr/local/bin/asciidoctor-pdf:23:in `load'
	from /usr/local/bin/asciidoctor-pdf:23:in `<main>'

I know next to nothing about asciidoc. but I know that it is a great tool for writing.
What am I doing wrong?

Thanks in advance.
@ProgramFan
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What is the result of:

asciidoctor -r asciidoctor-pdf -r asciidoctor-mathematical -b pdf -o test.pdf research.asciidoc

?

@ProgramFan ProgramFan self-assigned this Nov 20, 2016
@harumo11
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Hi. @ProgramFan

Bellow is my result.

harumo@harumo-X250 ~/Documents/research $ asciidoctor -r asciidoctor-pdf -r asciidoctor-mathematical -b pdf -o test.pdf research.asciidoc
asciidoctor: FAILED: 'asciidoctor-mathematical' could not be loaded
  Use --trace for backtrace

And When I use --trace option, I get following result.

harumo@harumo-X250 ~/Documents/research $ asciidoctor --trace -r asciidoctor-pdf -r asciidoctor-mathematical -b pdf -o test.pdf research.asciidoc
/usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- asciidoctor-mathematical (LoadError)
    from /usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /var/lib/gems/2.3.0/gems/polyglot-0.3.5/lib/polyglot.rb:65:in `require'
    from /var/lib/gems/2.3.0/gems/asciidoctor-1.5.5/lib/asciidoctor/cli/options.rb:219:in `block in parse!'
    from /var/lib/gems/2.3.0/gems/asciidoctor-1.5.5/lib/asciidoctor/cli/options.rb:217:in `each'
    from /var/lib/gems/2.3.0/gems/asciidoctor-1.5.5/lib/asciidoctor/cli/options.rb:217:in `parse!'
    from /var/lib/gems/2.3.0/gems/asciidoctor-1.5.5/lib/asciidoctor/cli/options.rb:33:in `parse!'
    from /var/lib/gems/2.3.0/gems/asciidoctor-1.5.5/lib/asciidoctor/cli/invoker.rb:22:in `initialize'
    from /var/lib/gems/2.3.0/gems/asciidoctor-1.5.5/bin/asciidoctor:12:in `new'
    from /var/lib/gems/2.3.0/gems/asciidoctor-1.5.5/bin/asciidoctor:12:in `<top (required)>'
    from /usr/local/bin/asciidoctor:23:in `load'
    from /usr/local/bin/asciidoctor:23:in `<main>'

My environment is as bellow.

os ruby version asciidoctor version
Ubuntu 16.04 2.3.1 1.5.5

@ProgramFan
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I have never met this before. I use asciidoctor-mathematical on macOS and Fedora 24 with rvm, and have no experiences of ruby on ubuntu. So the following are my guesses.

I doubt your installation of asciidoctor-mathematical is not clean. You may have updated your system but asciidoctor-mathematical and its dependencies are not updated, so load errors can occur. Does remove asciidoctor-mathematical and mathematical and reinstall them work?

@tstumm
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tstumm commented Nov 21, 2016

Please post the output of gem list | grep asciidoctor-mathematical

If you don't get any result from this command try running gem install asciidoctor-mathematical.

@harumo11
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@ProgramFan @tstumm

I run gem list | grep asciidoctor-mathematical command, but I get no result.
Then, I run this:gem install asciidoctor-mathematical .
It shows below error message.

harumo@harumo-X250 ~ $ sudo gem install asciidoctor-mathematicalBuilding native extensions.  This could take a while...
ERROR:  Error installing asciidoctor-mathematical:
	ERROR: Failed to build gem native extension.

    current directory: /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical
/usr/bin/ruby2.3 -r ./siteconf20161123-5639-zm8nop.rb extconf.rb
checking for cmake... yes
checking for main() in -lxml2... yes
checking for main() in -lpangocairo-1.0... yes
checking for libxml/tree.h in /include/libxml2,/usr/include/libxml2,/usr/local/include/libxml2... yes
checking for libxml/parser.h in /include/libxml2,/usr/include/libxml2,/usr/local/include/libxml2... yes
checking for libxml/xpath.h in /include/libxml2,/usr/include/libxml2,/usr/local/include/libxml2... yes
checking for libxml/xpathInternals.h in /include/libxml2,/usr/include/libxml2,/usr/local/include/libxml2... yes
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found BISON: /usr/bin/bison (found version "3.0.4") 
-- Found FLEX: /usr/bin/flex (found version "2.6.0") 
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Found PythonInterp: /usr/bin/python (found version "2.7.12") 
-- Configuring done
-- Generating done
-- Build files have been written to: /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/build
[ 11%] [FLEX][MTEX2MMLSCANNER] Building scanner with flex 2.6.0
[ 22%] [BISON][MTEX2MMLPARSER] Building parser with bison 3.0.4
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/parser.y: warning: 5270 shift/reduce conflicts [-Wconflicts-sr]
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/parser.y: warning: 613 reduce/reduce conflicts [-Wconflicts-rr]
Scanning dependencies of target libmtex2MML_static
[ 33%] Building C object CMakeFiles/libmtex2MML_static.dir/src/environment.c.o
In file included from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.h:5:0,
                 from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:7:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c: In function ‘mtex2MML_perform_replacement’:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:223:91: warning: signed and unsigned type in conditional expression [-Wsign-compare]
 #define utarray_eltidx(a,e) (((char*)(e) >= (a)->d) ? (((char*)(e) - (a)->d)/(a)->icd.sz) : -1)
                                                                                           ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:221:62: note: in expansion of macro ‘utarray_eltidx’
 #define utarray_prev(a,e) (((e)==NULL) ? utarray_back(a) : ((utarray_eltidx(a,e) > 0) ? _utarray_eltptr(a,utarray_eltidx(a,e)-1) : NULL))
                                                              ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:309:22: note: in expansion of macro ‘utarray_prev’
   while ( (o=(char**)utarray_prev(rowlines_stack,o))) {
                      ^
In file included from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.h:5:0,
                 from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:7:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:223:91: warning: signed and unsigned type in conditional expression [-Wsign-compare]
 #define utarray_eltidx(a,e) (((char*)(e) >= (a)->d) ? (((char*)(e) - (a)->d)/(a)->icd.sz) : -1)
                                                                                           ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:122:56: note: in definition of macro ‘_utarray_eltptr’
 #define _utarray_eltptr(a,j) ((a)->d + ((a)->icd.sz * (j)))
                                                        ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:221:107: note: in expansion of macro ‘utarray_eltidx’
 #define utarray_prev(a,e) (((e)==NULL) ? utarray_back(a) : ((utarray_eltidx(a,e) > 0) ? _utarray_eltptr(a,utarray_eltidx(a,e)-1) : NULL))
                                                                                                           ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:309:22: note: in expansion of macro ‘utarray_prev’
   while ( (o=(char**)utarray_prev(rowlines_stack,o))) {
                      ^
In file included from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.h:5:0,
                 from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:7:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:223:91: warning: signed and unsigned type in conditional expression [-Wsign-compare]
 #define utarray_eltidx(a,e) (((char*)(e) >= (a)->d) ? (((char*)(e) - (a)->d)/(a)->icd.sz) : -1)
                                                                                           ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:221:62: note: in expansion of macro ‘utarray_eltidx’
 #define utarray_prev(a,e) (((e)==NULL) ? utarray_back(a) : ((utarray_eltidx(a,e) > 0) ? _utarray_eltptr(a,utarray_eltidx(a,e)-1) : NULL))
                                                              ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:322:22: note: in expansion of macro ‘utarray_prev’
   while ( (p=(char**)utarray_prev(row_spacing_stack,p))) {
                      ^
In file included from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.h:5:0,
                 from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:7:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:223:91: warning: signed and unsigned type in conditional expression [-Wsign-compare]
 #define utarray_eltidx(a,e) (((char*)(e) >= (a)->d) ? (((char*)(e) - (a)->d)/(a)->icd.sz) : -1)
                                                                                           ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:122:56: note: in definition of macro ‘_utarray_eltptr’
 #define _utarray_eltptr(a,j) ((a)->d + ((a)->icd.sz * (j)))
                                                        ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/utarray.h:221:107: note: in expansion of macro ‘utarray_eltidx’
 #define utarray_prev(a,e) (((e)==NULL) ? utarray_back(a) : ((utarray_eltidx(a,e) > 0) ? _utarray_eltptr(a,utarray_eltidx(a,e)-1) : NULL))
                                                                                                           ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.c:322:22: note: in expansion of macro ‘utarray_prev’
   while ( (p=(char**)utarray_prev(row_spacing_stack,p))) {
                      ^
[ 44%] Building C object CMakeFiles/libmtex2MML_static.dir/src/colors.c.o
[ 55%] Building C object CMakeFiles/libmtex2MML_static.dir/src/em.c.o
[ 66%] Building C object CMakeFiles/libmtex2MML_static.dir/src/string_extras.c.o
[ 77%] Building C object CMakeFiles/libmtex2MML_static.dir/parser.c.o
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/parser.y: In function ‘mtex2MML_yyerror’:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/parser.y:56:30: warning: unused parameter ‘ret_str’ [-Wunused-parameter]
  static void yyerror (char **ret_str, const char * s)
                              ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/parser.y: At top level:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/parser.y:68:14: warning: ‘mtex2MML_default_write’ defined but not used [-Wunused-function]
  static void mtex2MML_default_write (const char * buffer, unsigned long length)
              ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/parser.y:79:14: warning: ‘mtex2MML_default_write_mathml’ defined but not used [-Wunused-function]
  static void mtex2MML_default_write_mathml (const char * mathml)
              ^
[ 88%] Building C object CMakeFiles/libmtex2MML_static.dir/lexer.c.o
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/build/lexer.c: In function ‘yy_get_next_buffer’:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/build/lexer.c:8042:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ( number_to_move == YY_MORE_ADJ )
                       ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/build/lexer.c:8059:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if ((int) ((yy_n_chars) + number_to_move) > YY_CURRENT_BUFFER_LVALUE->yy_buf_size) {
                                            ^
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/lexer.l: At top level:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/build/lexer.c:8178:16: warning: ‘input’ defined but not used [-Wunused-function]
     static int input  (void)
                ^
[100%] Linking C static library libmtex2MML.a
[100%] Built target libmtex2MML_static
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
-- Checking for module 'glib-2.0'
--   Found glib-2.0, version 2.48.1
-- Checking for module 'cairo'
--   Found cairo, version 1.14.6
-- Checking for module 'pango'
--   Found pango, version 1.38.1
-- Checking for module 'gdk-pixbuf-2.0'
--   Found gdk-pixbuf-2.0, version 2.32.2
-- Checking for module 'libxml-2.0'
--   Found libxml-2.0, version 2.9.3
-- Checking for module 'gio-2.0'
--   Found gio-2.0, version 2.48.1
-- Checking for module 'pangocairo'
--   Found pangocairo, version 1.38.1
-- Configuring done
-- Generating done
-- Build files have been written to: /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/lasem/build
Scanning dependencies of target lasem
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checking for mtex2MML.h in /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src... yes
creating Makefile

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/mathematical-1.6.7/mkmf.log

current directory: /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical
make "DESTDIR=" clean

current directory: /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical
make "DESTDIR="
compiling cairo_callbacks.c
compiling lasem_overrides.c
In file included from /usr/include/string.h:630:0,
                 from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/uthash.h:29,
                 from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/environment.h:4,
                 from /var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/mtex2MML.h:12,
                 from lasem_overrides.c:5:
/var/lib/gems/2.3.0/gems/mathematical-1.6.7/ext/mathematical/mtex2MML/src/../deps/uthash/../strdup/strdup.h:24:1: error: expected identifier or ‘(’ before ‘__extension__’
 strdup(const char *str);
 ^
Makefile:239: recipe for target 'lasem_overrides.o' failed
make: *** [lasem_overrides.o] Error 1

make failed, exit code 2

Gem files will remain installed in /var/lib/gems/2.3.0/gems/mathematical-1.6.7 for inspection.
Results logged to /var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/mathematical-1.6.7/gem_make.out

I also tried to remove and re-install asciidoctor and asciidoctor-mathematical.
But, I got same result.

@ProgramFan
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See gjtorikian/mathematical#64

@ProgramFan
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Since this is not a problem of asciidoctor-mathematical, I will close this issue, but feel free to ask new questions.

@harumo11
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Thank you.
I solved the problem.

@mojavelinux
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Can you please document this in the README?

@mojavelinux
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I can confirm that the fix proposed by Garen works, but it would have saved me time had I seen it in the README first.

ProgramFan added a commit that referenced this issue Feb 4, 2017
@ProgramFan
Add a trouble shooting for mathematical building issue (address #23)
00a63d5
@mojavelinux
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@ProgramFan Thanks!

@akosma
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akosma commented Oct 21, 2018

This fix does not work on macOS Mojave 10.14, and the gem does not work on it. I've reported this to the mathematical maintainers too.

@ProgramFan
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This shall go to mathematical indeed. I don't understand why someone would override strdup. This type of tricks always introduces nasty bugs and compatibility problems.

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@ProgramFan @akosma @mojavelinux @tstumm @harumo11