{"id":7346,"date":"2014-06-07T02:29:51","date_gmt":"2014-06-07T02:29:51","guid":{"rendered":"https:\/\/unknownerror.org\/index.php\/2014\/06\/07\/bundler-wont-update-because-of-nokogiri-already-installed-libxml2-what-is-the-issue-collection-of-common-programming-errors\/"},"modified":"2014-06-07T02:29:51","modified_gmt":"2014-06-07T02:29:51","slug":"bundler-wont-update-because-of-nokogiri-already-installed-libxml2-what-is-the-issue-collection-of-common-programming-errors","status":"publish","type":"post","link":"https:\/\/unknownerror.org\/index.php\/2014\/06\/07\/bundler-wont-update-because-of-nokogiri-already-installed-libxml2-what-is-the-issue-collection-of-common-programming-errors\/","title":{"rendered":"Bundler won't update because of nokogiri, already installed libxml2, what is the issue?-Collection of common programming errors"},"content":{"rendered":"

In Max OS X Mountain Lion (10.8.3): I’m following the railstutorial.org tutorial, and on chapter 3 we started to include \"gem 'rspec-rails', '2.11.0'\"<\/code> in the gemfile. Since then I can’t seem to get ‘bundle update’ to work in my application because it’s trying to install nokogiri, which doesn’t like me…why?<\/p>\n

This is what happens in console when I run<\/p>\n

\n

bundle update<\/code><\/p>\n<\/blockquote>\n

Fetching gem metadata from https:\/\/rubygems.org\/.........\nFetching gem metadata from https:\/\/rubygems.org\/..\nResolving dependencies...\nUsing rake (10.0.4) \nUsing i18n (0.6.1) \nUsing multi_json (1.7.2) \nUsing activesupport (3.2.13) \nUsing builder (3.0.4) \nUsing activemodel (3.2.13) \nUsing erubis (2.7.0) \nUsing journey (1.0.4) \nUsing rack (1.4.5) \nUsing rack-cache (1.2) \nUsing rack-test (0.6.2) \nUsing hike (1.2.1) \nUsing tilt (1.3.6) \nUsing sprockets (2.2.2) \nUsing actionpack (3.2.13) \nUsing mime-types (1.22) \nUsing polyglot (0.3.3) \nUsing treetop (1.4.12) \nUsing mail (2.5.3) \nUsing actionmailer (3.2.13) \nUsing arel (3.0.2) \nUsing tzinfo (0.3.37) \nUsing activerecord (3.2.13) \nUsing activeresource (3.2.13) \n> Using bundler (1.3.5) \n> Installing nokogiri (1.5.9) \n> Gem::Installer::ExtensionBuildError: ERROR: Failed to build gem native extension.\n\n    \/usr\/local\/rvm\/rubies\/ruby-1.9.3-p392\/bin\/ruby extconf.rb \n\n>checking for libxml\/parser.h... yes\n\n> checking for libxslt\/xslt.h... yes\n\n>checking for libexslt\/exslt.h... yes\n\n>checking for iconv_open() in iconv.h... no\n\n>checking for iconv_open() in -liconv... no\n\n>checking for iconv_open() in -liconv... yes\n\n>checking for xmlParseDoc() in -lxml2... yes\n\n>checking for xsltParseStylesheetDoc() in -lxslt... yes\n\n>checking for exsltFuncRegister() in -lexslt... yes\n\n>checking for xmlHasFeature()... yes\n\n>checking for xmlFirstElementChild()... yes\n\n>checking for xmlRelaxNGSetParserStructuredErrors()... yes\n\n>checking for xmlRelaxNGSetParserStructuredErrors()... yes\n\n>checking for xmlRelaxNGSetValidStructuredErrors()... yes\n\n>checking for xmlSchemaSetValidStructuredErrors()... yes\n\n>checking for xmlSchemaSetParserStructuredErrors()... yes\n\n>creating Makefile\n\nmake\n\ncompiling html_document.c\n\ncompiling html_element_description.c\n\nhtml_element_description.c: In function \u2018get_description\u2019:\n\nhtml_element_description.c:249: warning: cast discards qualifiers from pointer target type\n\ncompiling html_entity_lookup.c\n\ncompiling html_sax_parser_context.c\n\ncompiling html_sax_push_parser.c\n\ncompiling nokogiri.c\n\ncompiling xml_attr.c\n\ncompiling xml_attribute_decl.c\n\ncompiling xml_cdata.c\n\ncompiling xml_comment.c\n\ncompiling xml_document.c\n\nxml_document.c: In function \u2018set_encoding\u2019:\n\nxml_document.c:159: warning: cast discards qualifiers from pointer target type\n\nxml_document.c: In function \u2018canonicalize\u2019:\n\nxml_document.c:505: warning: cast discards qualifiers from pointer target type\n\nxml_document.c: In function \u2018Nokogiri_wrap_xml_document\u2019:\n\nxml_document.c:569: warning: passing argument 1 of \u2018st_init_numtable_with_size\u2019 with \n\ndifferent width due to prototype\n\ncompiling xml_document_fragment.c\n\ncompiling xml_dtd.c\n\ncompiling xml_element_content.c\n\ncompiling xml_element_decl.c\n\ncompiling xml_encoding_handler.c\n\ncompiling xml_entity_decl.c\n\ncompiling xml_entity_reference.c\n\ncompiling xml_io.c\n\nxml_io.c: In function \u2018io_read_callback\u2019:\n\nxml_io.c:20: warning: passing argument 4 of \u2018rb_rescue\u2019 with different width due to \nprototype\n\nxml_io.c: In function \u2018io_write_callback\u2019:\n\nxml_io.c:45: warning: passing argument 4 of \u2018rb_rescue\u2019 with different width due to prototype\n\ncompiling xml_libxml2_hacks.c\n\ncompiling xml_namespace.c\n\ncompiling xml_node.c\n\ncompiling xml_node_set.c\n\nxml_node_set.c: In function \u2018dealloc_namespace\u2019:\n\nxml_node_set.c:9: warning: cast discards qualifiers from pointer target type\n\nxml_node_set.c:11: warning: cast discards qualifiers from pointer target type\n\nxml_node_set.c: In function \u2018deallocate\u2019:\n\nxml_node_set.c:52: warning: passing argument 3 of \u2018st_foreach\u2019 with different width due to \nprototype\n\ncompiling xml_processing_instruction.c\n\ncompiling xml_reader.c\n\ncompiling xml_relax_ng.c\n\ncompiling xml_sax_parser.c\n\nxml_sax_parser.c: In function \u2018start_element\u2019:\n\nxml_sax_parser.c:69: warning: passing argument 1 of \u2018rb_ary_new3\u2019 with different width due to prototype\n\ncompiling xml_sax_parser_context.c\n\ncompiling xml_sax_push_parser.c\n\ncompiling xml_schema.c\n\ncompiling xml_syntax_error.c\n\ncompiling xml_text.c\n\ncompiling xml_xpath_context.c\n\ncompiling xslt_stylesheet.c\n\nxslt_stylesheet.c: In function \u2018parse_stylesheet_doc\u2019:\n\nxslt_stylesheet.c:72: warning: passing argument 2 of \u2018rb_str_new\u2019 with different width due to prototype\n\nxslt_stylesheet.c: In function \u2018transform\u2019:\n\nxslt_stylesheet.c:166: warning: passing argument 2 of \u2018rb_str_new\u2019 with different width due to prototype\n\nlinking shared-object nokogiri\/nokogiri.bundle\n\nld: warning: directory not found for option '-L\/opt\/local\/lib'\n\nld: in \/usr\/local\/lib\/libz.1.dylib, file was built for unsupported file format which is not the architecture being linked (x86_64) for architecture x86_64\n\ncollect2: ld returned 1 exit status\nmake: *** [nokogiri.bundle] Error 1\n\n\nGem files will remain installed in \/usr\/local\/rvm\/gems\/ruby-1.9.3-p392\/gems\/nokogiri-1.5.9 for inspection.\nResults logged to \/usr\/local\/rvm\/gems\/ruby-1.9.3-p392\/gems\/nokogiri-1.5.9\/ext\/nokogiri\/gem_make.out\n\n>An error occurred while installing nokogiri (1.5.9), and Bundler cannot\n>continue.\n>Make sure that `gem install nokogiri -v '1.5.9'` succeeds before bundling.\n<\/code><\/pre>\n
This is the gem_make.out file:<\/p>\n
\/usr\/local\/rvm\/rubies\/ruby-1.9.3-p392\/bin\/ruby extconf.rb \nchecking for libxml\/parser.h... yes\nchecking for libxslt\/xslt.h... yes\nchecking for libexslt\/exslt.h... yes\nchecking for iconv_open() in iconv.h... no\nchecking for iconv_open() in -liconv... no\nchecking for iconv_open() in -liconv... yes\nchecking for xmlParseDoc() in -lxml2... yes\nchecking for xsltParseStylesheetDoc() in -lxslt... yes\nchecking for exsltFuncRegister() in -lexslt... yes\nchecking for xmlHasFeature()... yes\nchecking for xmlFirstElementChild()... yes\nchecking for xmlRelaxNGSetParserStructuredErrors()... yes\nchecking for xmlRelaxNGSetParserStructuredErrors()... yes\nchecking for xmlRelaxNGSetValidStructuredErrors()... yes\nchecking for xmlSchemaSetValidStructuredErrors()... yes\nchecking for xmlSchemaSetParserStructuredErrors()... yes\ncreating Makefile\n\nmake\ncompiling html_document.c\ncompiling html_element_description.c\nhtml_element_description.c: In function \u2018get_description\u2019:\nhtml_element_description.c:249: warning: cast discards qualifiers from pointer target type\ncompiling html_entity_lookup.c\ncompiling html_sax_parser_context.c\ncompiling html_sax_push_parser.c\ncompiling nokogiri.c\ncompiling xml_attr.c\ncompiling xml_attribute_decl.c\ncompiling xml_cdata.c\ncompiling xml_comment.c\ncompiling xml_document.c\nxml_document.c: In function \u2018set_encoding\u2019:\nxml_document.c:159: warning: cast discards qualifiers from pointer target type\nxml_document.c: In function \u2018canonicalize\u2019:\nxml_document.c:505: warning: cast discards qualifiers from pointer target type\nxml_document.c: In function \u2018Nokogiri_wrap_xml_document\u2019:\nxml_document.c:569: warning: passing argument 1 of \u2018st_init_numtable_with_size\u2019 with different width due to prototype\ncompiling xml_document_fragment.c\ncompiling xml_dtd.c\ncompiling xml_element_content.c\ncompiling xml_element_decl.c\ncompiling xml_encoding_handler.c\ncompiling xml_entity_decl.c\ncompiling xml_entity_reference.c\ncompiling xml_io.c\nxml_io.c: In function \u2018io_read_callback\u2019:\nxml_io.c:20: warning: passing argument 4 of \u2018rb_rescue\u2019 with different width due to prototype\nxml_io.c: In function \u2018io_write_callback\u2019:\nxml_io.c:45: warning: passing argument 4 of \u2018rb_rescue\u2019 with different width due to prototype\ncompiling xml_libxml2_hacks.c\ncompiling xml_namespace.c\ncompiling xml_node.c\ncompiling xml_node_set.c\nxml_node_set.c: In function \u2018dealloc_namespace\u2019:\nxml_node_set.c:9: warning: cast discards qualifiers from pointer target type\nxml_node_set.c:11: warning: cast discards qualifiers from pointer target type\nxml_node_set.c: In function \u2018deallocate\u2019:\nxml_node_set.c:52: warning: passing argument 3 of \u2018st_foreach\u2019 with different width due to prototype\ncompiling xml_processing_instruction.c\ncompiling xml_reader.c\ncompiling xml_relax_ng.c\ncompiling xml_sax_parser.c\nxml_sax_parser.c: In function \u2018start_element\u2019:\nxml_sax_parser.c:69: warning: passing argument 1 of \u2018rb_ary_new3\u2019 with different width due to prototype\ncompiling xml_sax_parser_context.c\ncompiling xml_sax_push_parser.c\ncompiling xml_schema.c\ncompiling xml_syntax_error.c\ncompiling xml_text.c\ncompiling xml_xpath_context.c\ncompiling xslt_stylesheet.c\nxslt_stylesheet.c: In function \u2018parse_stylesheet_doc\u2019:\nxslt_stylesheet.c:72: warning: passing argument 2 of \u2018rb_str_new\u2019 with different width due to prototype\nxslt_stylesheet.c: In function \u2018transform\u2019:\nxslt_stylesheet.c:166: warning: passing argument 2 of \u2018rb_str_new\u2019 with different width due to prototype\nlinking shared-object nokogiri\/nokogiri.bundle\nld: warning: directory not found for option '-L\/opt\/local\/lib'\nld: in \/usr\/local\/lib\/libz.1.dylib, file was built for unsupported file format which is not the architecture being linked (x86_64) for architecture x86_64\ncollect2: ld returned 1 exit status\nmake: *** [nokogiri.bundle] Error 1\n<\/code><\/pre>\n
Update:<\/p>\n
just running ‘bundle’ in the application directory gets the same message in console:<\/p>\n
“An error occurred while installing nokogiri (1.5.9), and Bundler cannot continue. Make sure that gem install nokogiri -v '1.5.9'<\/code> succeeds before bundling.”<\/p>\n
Tried ‘gem install nokogiri’ – Outputs this in console:<\/p>\n
'$ gem install nokogiri\nBuilding native extensions.  This could take a while...\nERROR:  Error installing nokogiri:\n    ERROR: Failed to build gem native extension.\n\n    \/usr\/local\/rvm\/rubies\/ruby-1.9.3-p392\/bin\/ruby extconf.rb\nchecking for libxml\/parser.h... yes\nchecking for libxslt\/xslt.h... yes\nchecking for libexslt\/exslt.h... yes\nchecking for iconv_open() in iconv.h... no\nchecking for iconv_open() in -liconv... yes\nchecking for xmlParseDoc() in -lxml2... yes\nchecking for xsltParseStylesheetDoc() in -lxslt... yes\nchecking for exsltFuncRegister() in -lexslt... yes\nchecking for xmlHasFeature()... yes\nchecking for xmlFirstElementChild()... yes\nchecking for xmlRelaxNGSetParserStructuredErrors()... yes\nchecking for xmlRelaxNGSetParserStructuredErrors()... yes\nchecking for xmlRelaxNGSetValidStructuredErrors()... yes\nchecking for xmlSchemaSetValidStructuredErrors()... yes\nchecking for xmlSchemaSetParserStructuredErrors()... yes\ncreating Makefile\n\nmake\ncompiling html_document.c\ncompiling html_element_description.c\nhtml_element_description.c: In function \u2018get_description\u2019:\nhtml_element_description.c:249: warning: cast discards qualifiers from pointer target type\ncompiling html_entity_lookup.c\ncompiling html_sax_parser_context.c\ncompiling html_sax_push_parser.c\ncompiling nokogiri.c\ncompiling xml_attr.c\ncompiling xml_attribute_decl.c\ncompiling xml_cdata.c\ncompiling xml_comment.c\ncompiling xml_document.c\nxml_document.c: In function \u2018set_encoding\u2019:\nxml_document.c:159: warning: cast discards qualifiers from pointer target type\nxml_document.c: In function \u2018canonicalize\u2019:\nxml_document.c:505: warning: cast discards qualifiers from pointer target type\nxml_document.c: In function \u2018Nokogiri_wrap_xml_document\u2019:\nxml_document.c:569: warning: passing argument 1 of \u2018st_init_numtable_with_size\u2019 with different width due to prototype\ncompiling xml_document_fragment.c\ncompiling xml_dtd.c\ncompiling xml_element_content.c\ncompiling xml_element_decl.c\ncompiling xml_encoding_handler.c\ncompiling xml_entity_decl.c\ncompiling xml_entity_reference.c\ncompiling xml_io.c\nxml_io.c: In function \u2018io_read_callback\u2019:\nxml_io.c:20: warning: passing argument 4 of \u2018rb_rescue\u2019 with different width due to prototype\nxml_io.c: In function \u2018io_write_callback\u2019:\nxml_io.c:45: warning: passing argument 4 of \u2018rb_rescue\u2019 with different width due to prototype\ncompiling xml_libxml2_hacks.c\ncompiling xml_namespace.c\ncompiling xml_node.c\ncompiling xml_node_set.c\nxml_node_set.c: In function \u2018dealloc_namespace\u2019:\nxml_node_set.c:9: warning: cast discards qualifiers from pointer target type\nxml_node_set.c:11: warning: cast discards qualifiers from pointer target type\nxml_node_set.c: In function \u2018deallocate\u2019:\nxml_node_set.c:52: warning: passing argument 3 of \u2018st_foreach\u2019 with different width due to prototype\ncompiling xml_processing_instruction.c\ncompiling xml_reader.c\ncompiling xml_relax_ng.c\ncompiling xml_sax_parser.c\nxml_sax_parser.c: In function \u2018start_element\u2019:\nxml_sax_parser.c:69: warning: passing argument 1 of \u2018rb_ary_new3\u2019 with different width due to prototype\ncompiling xml_sax_parser_context.c\ncompiling xml_sax_push_parser.c\ncompiling xml_schema.c\ncompiling xml_syntax_error.c\ncompiling xml_text.c\ncompiling xml_xpath_context.c\ncompiling xslt_stylesheet.c\nxslt_stylesheet.c: In function \u2018parse_stylesheet_doc\u2019:\nxslt_stylesheet.c:72: warning: passing argument 2 of \u2018rb_str_new\u2019 with different width due to prototype\nxslt_stylesheet.c: In function \u2018transform\u2019:\nxslt_stylesheet.c:166: warning: passing argument 2 of \u2018rb_str_new\u2019 with different width due to prototype\nlinking shared-object nokogiri\/nokogiri.bundle\nld: warning: directory not found for option '-L\/opt\/local\/lib'\nld: in '\/usr\/local\/lib\/libz.1.dylib', file was built for unsupported file format ( 0xce 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 0 0x 3 0x 0 0x 0 0x 0 0x 6 0x 0 0x 0 0x 0 ) which is not the architecture being linked (x86_64): \/usr\/local\/lib\/libz.1.dylib for architecture x86_64\ncollect2: ld returned 1 exit status\nmake: *** [nokogiri.bundle] Error 1\n\n\nGem files will remain installed in \/usr\/local\/rvm\/gems\/ruby-1.9.3-p392\/gems\/nokogiri-1.5.9 for inspection.\nResults logged to \/usr\/local\/rvm\/gems\/ruby-1.9.3-p392\/gems\/nokogiri-1.5.9\/ext\/nokogiri\/gem_make.out\n<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
In Max OS X Mountain Lion (10.8.3): I’m following the railstutorial.org tutorial, and on chapter 3 we started to include “gem ‘rspec-rails’, ‘2.11.0’” in the gemfile. Since then I can’t seem to get ‘bundle update’ to work in my application because it’s trying to install nokogiri, which doesn’t like me…why? This is what happens in […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-7346","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/posts\/7346","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/comments?post=7346"}],"version-history":[{"count":0,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/posts\/7346\/revisions"}],"wp:attachment":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/media?parent=7346"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/categories?post=7346"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/tags?post=7346"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}