1.6.2 install: "Failed to complete patch task" #1095

mattbrictson · 2014-05-13T00:44:40Z

1.6.1 installs fine, but 1.6.2 fails while patching. I'm on Mac OS X Mavericks.

$ ruby -v
ruby 2.1.2p95 (2014-05-08 revision 45877) [x86_64-darwin13.0]

$ gem install nokogiri -v '1.6.2'
Building native extensions.  This could take a while...
Building nokogiri using packaged libraries.
Building libxml2-2.8.0 for nokogiri with the following patches applied:
    - 0001-Fix-parser-local-buffers-size-problems.patch
    - 0002-Fix-entities-local-buffers-size-problems.patch
    - 0003-Fix-an-error-in-previous-commit.patch
    - 0004-Fix-potential-out-of-bound-access.patch
    - 0005-Detect-excessive-entities-expansion-upon-replacement.patch
    - 0006-Do-not-fetch-external-parsed-entities.patch
    - 0007-Enforce-XML_PARSER_EOF-state-handling-through-the-pa.patch
    - 0008-Improve-handling-of-xmlStopParser.patch
    - 0009-Fix-a-couple-of-return-without-value.patch
    - 0010-Keep-non-significant-blanks-node-in-HTML-parser.patch
    - 0011-Do-not-fetch-external-parameter-entities.patch
************************************************************************
IMPORTANT!  Nokogiri builds and uses a packaged version of libxml2.

[snip]

Running 'patch' for libxml2 2.8.0... ERROR, review 'tmp/x86_64-apple-darwin13.1.0/ports/libxml2/2.8.0/patch.log' to see what happened.
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
    --with-opt-dir
    --without-opt-dir
    --with-opt-include
    --without-opt-include=${opt-dir}/include
    --with-opt-lib
    --without-opt-lib=${opt-dir}/lib
    --with-make-prog
    --without-make-prog
    --srcdir=.
    --curdir
    --ruby=/Users/mbrictson/.rbenv/versions/2.1.2/bin/ruby
    --help
    --clean
    --use-system-libraries
    --enable-static
    --disable-static
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${zlib-dir}/include
    --with-zlib-lib
    --without-zlib-lib=${zlib-dir}/lib
    --enable-cross-build
    --disable-cross-build
/Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/mini_portile-0.5.3/lib/mini_portile.rb:278:in `block in execute': Failed to complete patch task (RuntimeError)
    from /Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/mini_portile-0.5.3/lib/mini_portile.rb:270:in `chdir'
    from /Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/mini_portile-0.5.3/lib/mini_portile.rb:270:in `execute'
    from /Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/mini_portile-0.5.3/lib/mini_portile.rb:47:in `block in patch'
    from /Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/mini_portile-0.5.3/lib/mini_portile.rb:44:in `each'
    from /Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/mini_portile-0.5.3/lib/mini_portile.rb:44:in `patch'
    from /Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/mini_portile-0.5.3/lib/mini_portile.rb:107:in `cook'
    from extconf.rb:247:in `block in process_recipe'
    from extconf.rb:176:in `tap'
    from extconf.rb:176:in `process_recipe'
    from extconf.rb:364:in `<main>'

$ cat tmp/x86_64-apple-darwin13.1.0/ports/libxml2/2.8.0/patch.log
/Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/nokogiri-1.6.2/ports/patches/libxml2/0010-Keep-non-significant-blanks-node-in-HTML-parser.patch:170: trailing whitespace.
<html>
/Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/nokogiri-1.6.2/ports/patches/libxml2/0010-Keep-non-significant-blanks-node-in-HTML-parser.patch:171: trailing whitespace.
<body bgcolor="#FFFFFF">
/Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/nokogiri-1.6.2/ports/patches/libxml2/0010-Keep-non-significant-blanks-node-in-HTML-parser.patch:172: trailing whitespace.
                <a href="mailto:katherine@cbfanc.org,website@bis.doc.gov?subject=South%20San%20Francisco%20BIS%20Seminar%20-%20October%2016th"></a><br>
/Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/nokogiri-1.6.2/ports/patches/libxml2/0010-Keep-non-significant-blanks-node-in-HTML-parser.patch:173: trailing whitespace.
</body>
/Users/mbrictson/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/nokogiri-1.6.2/ports/patches/libxml2/0010-Keep-non-significant-blanks-node-in-HTML-parser.patch:245: trailing whitespace.
<title>BP6.com #1 online resource for the BP6 Mobo....</title>
error: patch failed: result/HTML/attrents.html:1
error: result/HTML/attrents.html: patch does not apply
error: patch failed: result/HTML/doc3.htm:1
error: result/HTML/doc3.htm: patch does not apply
error: patch failed: result/HTML/test3.html:1
error: result/HTML/test3.html: patch does not apply
error: patch failed: result/HTML/wired.html:3
error: result/HTML/wired.html: patch does not apply

The text was updated successfully, but these errors were encountered:

knu · 2014-05-13T01:12:55Z

Hmm, this doesn't reproduce for me on OS X Mavericks or FreeBSD 10.

Maybe there is something wrong with patch(1)? (maybe too recent, too old, or broken somehow)
Try type patch (or which patch) / patch --version to start with.

mattbrictson · 2014-05-13T01:25:14Z

$ which patch
/usr/bin/patch
$ patch --version
patch 2.5.8

I will test the installation on another Mavericks machine and see if I can reproduce.

knu · 2014-05-13T02:52:47Z

On my MBP, looks like the same version of patch could successfully find the diff --git a/HTMLparser.c b/HTMLparser.c header and proceed.
I wonder what the difference is. LANG/LC_* perhaps?

knu · 2014-05-13T02:58:19Z

I'll try gem install nokogiri -- --disable-clean and compare my successful case with yours later.

knu · 2014-05-13T03:10:48Z

Un, no, tmp/ will be removed regardless of --disable-clean.
I'll have to try building nokogiri manually.

mattbrictson · 2014-05-13T04:18:52Z

I asked another developer to test gem install nokogiri -v '1.6.2' on his Mavericks machine and he is getting the same error.

I tried manually running patch for the failing patch (0010-Keep-non-significant-blanks-node-in-HTML-parser.patch) and it applied fine. I'm stumped.

$ cd .rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/nokogiri-1.6.2/
$ patch -p1 -d ext/nokogiri/tmp/x86_64-apple-darwin13.1.0/ports/libxml2/2.8.0/libxml2-2.8.0 < ports/patches/libxml2/0010-Keep-non-significant-blanks-node-in-HTML-parser.patch
patching file HTMLparser.c
Hunk #1 succeeded at 2941 (offset -40 lines).
Hunk #2 succeeded at 2979 (offset -40 lines).
Hunk #3 succeeded at 5665 (offset -33 lines).
patching file result/HTML/53867.html
patching file result/HTML/Down.html
patching file result/HTML/attrents.html
patching file result/HTML/autoclose.html
patching file result/HTML/cf_128.html
patching file result/HTML/doc2.htm
patching file result/HTML/doc3.htm
patching file result/HTML/entities.html
patching file result/HTML/entities2.html
patching file result/HTML/fp40.htm
patching file result/HTML/html5_enc.html
patching file result/HTML/liclose.html
patching file result/HTML/lt.html
patching file result/HTML/noscript.html
patching file result/HTML/pre.html
patching file result/HTML/python.html
patching file result/HTML/reg1.html
patching file result/HTML/reg2.html
patching file result/HTML/reg3.html
patching file result/HTML/reg4.html
patching file result/HTML/repeat.html
patching file result/HTML/script.html
patching file result/HTML/script2.html
patching file result/HTML/test2.html
patching file result/HTML/test3.html
patching file result/HTML/utf8bug.html
patching file result/HTML/wired.html
patching file xmllint.c
Hunk #1 succeeded at 3339 (offset -1 lines).

knu · 2014-05-13T04:35:25Z

OK, it wasn't patch(1) but git-apply(1) which is used by mini_portile to apply patches.

Mavericks should have 1.8.5.2 in /usr/bin with which the build succeeded for me:

% /usr/bin/git --version
git version 1.8.5.2 (Apple Git-48)

What's the version of git you are using?

gsong · 2014-05-13T04:41:21Z

Homebrew's Git 1.9.2.

mattbrictson · 2014-05-13T04:43:15Z

I use Homebrew's 1.9.3.

Just now I tried uninstalling it so that I am now using 1.8.5.2 (Apple Git-48). However, nokogiri still fails to install with the same error.

sorah · 2014-05-13T04:43:49Z

Succeeded using

(▰╹◡╹) git --version
git version 1.9.1
(▰╹◡╹) /usr/bin/git --version
git version 1.8.5.2 (Apple Git-48)
(▰╹◡╹) patch --version
patch 2.5.8
Copyright (C) 1988 Larry Wall
Copyright (C) 2002 Free Software Foundation, Inc.

This program comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of this program
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.

written by Larry Wall and Paul Eggert

mattbrictson · 2014-05-13T04:49:49Z

Interesting! If I revert this commit in mini_portile (i.e. go back to using patch -p1 instead of git apply), then the nokogiri install succeeds.

flavorjones/mini_portile@4f4abd5

So somehow git apply is not working for me and @gsong.

mattbrictson · 2014-05-13T05:09:18Z

Solved!

My ~/.gitconfig had the setting autocrlf = input. When I remove this setting the nokogiri build succeeds.

sorah · 2014-05-13T05:13:40Z

Thanks, it worked for my co-workers -- is this mini_portile's issue?

sorah · 2014-05-13T05:14:11Z

@mbrictson good work 👏

knu · 2014-05-13T05:20:46Z

@mbrictson Good job! ~~A tentative cure could be to prefix env GIT_CONFIG=/dev/null with a gem or bundle command line that triggers installation of the nokogiri gem.~~ <- Doesn't work 😞

martinb3 · 2014-05-13T20:10:48Z

Just to add to what @mbrictson said, nokogiri utlilizes mini_portile but doesn't explicitly depend on git being installed (mini_portile currently requires git). This also means that anything wrong with git will break the install (like various flavors of Ubuntu not coming with git installed at all).

flavorjones · 2014-05-14T00:03:35Z

There are quite a few duplicates of this issue, so I'm closing this one. Please follow along for updates on this issue at #1102.

emaildanwilson · 2015-04-14T21:30:09Z

annoying... I just hit this too. appears that mini_portile doesn't check for it's patch dependency at all.

knu mentioned this issue May 13, 2014

Install of Nokogiri 1.6.2 fails on Ubuntu 12.04 #1098

Closed

mattbrictson closed this as completed May 13, 2014

mattbrictson mentioned this issue May 13, 2014

git apply fails depending on git configuration flavorjones/mini_portile#32

Closed

knu mentioned this issue May 13, 2014

Install of Nokogiri 1.6.2 fails on Mavericks #1096

Closed

GiboMac mentioned this issue May 13, 2014

Spree 2-2-Stable on Rails 4.0.3 fail installation on building libxml2 spree/spree#4681

Closed

martinb3 mentioned this issue May 13, 2014

Nokogiri's dependency on mini_portile has introduced a dependency on git #1102

Closed

cantino mentioned this issue Sep 14, 2014

Huginn setup fails while bundling nokogiri huginn/huginn#497

Closed

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1.6.2 install: "Failed to complete patch task" #1095

1.6.2 install: "Failed to complete patch task" #1095

mattbrictson commented May 13, 2014

knu commented May 13, 2014

mattbrictson commented May 13, 2014

knu commented May 13, 2014

knu commented May 13, 2014

knu commented May 13, 2014

mattbrictson commented May 13, 2014

knu commented May 13, 2014

gsong commented May 13, 2014

mattbrictson commented May 13, 2014

sorah commented May 13, 2014

mattbrictson commented May 13, 2014

mattbrictson commented May 13, 2014

sorah commented May 13, 2014

sorah commented May 13, 2014

knu commented May 13, 2014

martinb3 commented May 13, 2014

flavorjones commented May 14, 2014

emaildanwilson commented Apr 14, 2015

1.6.2 install: "Failed to complete patch task" #1095

1.6.2 install: "Failed to complete patch task" #1095

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mattbrictson commented May 13, 2014

knu commented May 13, 2014

mattbrictson commented May 13, 2014

knu commented May 13, 2014

knu commented May 13, 2014

knu commented May 13, 2014

mattbrictson commented May 13, 2014

knu commented May 13, 2014

gsong commented May 13, 2014

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sorah commented May 13, 2014

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sorah commented May 13, 2014

sorah commented May 13, 2014

knu commented May 13, 2014

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flavorjones commented May 14, 2014

emaildanwilson commented Apr 14, 2015