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SuperNEMO-DBD / homebrew-cadfael

Instructions on using/installing the SuperNEMO Software are now at: https://github.com/SuperNEMO-DBD/brew
MIT License
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Cadfael toolchain failed at resource libxml2--patch #10

Closed goliviero closed 7 years ago

goliviero commented 7 years ago

Hi Ben, all

I'm reinstalling Cadfael from scratch due to an upgrade of my system (kubuntu 14.04 -> kubuntu 16.04). After the git clone, i try to install cadfael brew with the command :

./brew cadfael-bootstrap

Checkings are good and some things download and install but it failed at : 

=> Installing dependencies for git-flow-avh: libxml2, gettext, gnu-getopt
==> Installing git-flow-avh dependency: libxml2
==> Downloading http://xmlsoft.org/sources/libxml2-2.9.4.tar.gz
Already downloaded: /home/goliviero/.cache/Homebrew/libxml2-2.9.4.tar.gz
==> Downloading https://mirrors.ocf.berkeley.edu/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.1.debian.tar.xz

curl: (22) The requested URL returned error: 404 Not Found
Trying a mirror...
==> Downloading https://mirrorservice.org/sites/ftp.debian.org/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.1.debian.tar.xz

curl: (22) The requested URL returned error: 404 Not Found
Error: Failed to download resource "libxml2--patch"
Download failed: https://mirrorservice.org/sites/ftp.debian.org/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.1.debian.tar.xz
Error: Failed to bootstrap cadfael toolchain

Here is a brew doctor 

 Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Setting LD_* vars can break dynamic linking.
Set variables:
  LD_LIBRARY_PATH: /opt/intel/composer_xe_2015.1.133/compiler/lib/intel64:/opt/intel/composer_xe_2015.1.133/mpirt/lib/intel64:/opt/intel/composer_xe_2015.1.133/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2015.1.133/ipp/lib/intel64:/opt/intel/composer_xe_2015.1.133/compiler/lib/intel64:/opt/intel/composer_xe_2015.1.133/mkl/lib/intel64:/opt/intel/composer_xe_2015.1.133/tbb/lib/intel64/gcc4.1

Warning: Homebrew's share was not found in your XDG_DATA_DIRS but you have
this variable set to include other locations.
Some programs like `vapigen` may not work correctly.
Consider setting the XDG_DATA_DIRS for example like so
    echo 'export XDG_DATA_DIRS="/home/goliviero/software/Cadfael/cadfaelbrew.git/share:$XDG_DATA_DIRS"' >> ~/.bash_profile

Can you help me with this ?

Thanks, Guillaume

drbenmorgan commented 7 years ago

This is an issue with the upstream linuxbrew/homebrew-core repo, and subsequently the upstream source of the patches removing the patch file. The fix is in homebrew/homebrew-core as of a few hours ago( https://github.com/Homebrew/homebrew-core/pull/9663), so should be merged into linuxbrew in the next day or two.

In the meantime, you can do the following to patch that formula (assumes brew is in PATH):

$ cd $(brew --prefix)
$ cd Library/Taps/homebrew/homebrew-core
$ git remote add upstream https://github.com/homebrew/homebrew-core
$ git fetch upstream
$ git checkout -p upstream/master -- Formula/libxml2.rb
... This will start an interactive session to select parts of the diff - say 'y' to the first (the patches), 'n' to the second (need to retain the zlib dep), 'n' to the third (need linuxbrew additions), and 'y' tp the forth.
...
$ cd $(brew --prefix)
$ brew install git-flow-avh
... or if you prefer ...
$ brew cadfael-bootstrap

The same process can be applied to any other formulae that need updating.

goliviero commented 7 years ago

I exactly did what you propose and i have the same issue. When i execute : brew cadfael-bootstrap, it fails again and the link for download is not the updated link but the old one... Is the "Updating brew" restore the old link ? Here is my error after your patch : 

Already up-to-date.
==> About to bootstrap cadfael toolchain. This may take some time
==> Bootstrapping Cadfael toolchain
==> Cadfael tool patchelf already installed
==> Cadfael tool python already installed
==> Cadfael tool ninja already installed
==> Cadfael tool cmake already installed
==> Installing Cadfael tool git-flow-avh
==> Installing dependencies for git-flow-avh: libxml2, gettext, gnu-getopt
==> Installing git-flow-avh dependency: libxml2
==> Downloading http://xmlsoft.org/sources/libxml2-2.9.4.tar.gz
Already downloaded: /home/goliviero/.cache/Homebrew/libxml2-2.9.4.tar.gz
==> Downloading https://mirrors.ocf.berkeley.edu/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.1.debian.tar.xz

curl: (22) The requested URL returned error: 404 Not Found
Trying a mirror...
==> Downloading https://mirrorservice.org/sites/ftp.debian.org/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.1.debian.tar.xz

curl: (22) The requested URL returned error: 404 Not Found
Error: Failed to download resource "libxml2--patch"
Download failed: https://mirrorservice.org/sites/ftp.debian.org/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.1.debian.tar.xz
Error: Failed to bootstrap cadfael toolchain
goliviero commented 7 years ago

Ok it seems to work when i do a 'direct' installation of libxml2.rb with brew install Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb I think the brew update in the cadfael-bootstrap erase my changes.

==> Bootstrap of toolchain complete, installed formulae
unzip 6.0_2
sqlite 3.16.2
gpatch 2.7.5
openssl 1.0.2k
pkg-config 0.29.1_2
zlib 1.2.8
xz 5.2.3
curl 7.52.1
ncurses 6.0_2
m4 1.4.18
ninja 1.7.2
python 2.7.13
cmake 3.7.2
gettext 0.19.8.1
bison 3.0.4
sphinx-doc 1.5.1
gdbm 1.12
readline 7.0.1
git-flow-avh 1.10.2
gnu-getopt 1.1.6
bzip2 1.0.6_1
patchelf 0.9_1
libxml2 2.9.4_2
Bootstrap of CadfaelBrew complete under
drbenmorgan commented 7 years ago

I think if it had overwritten the file, the direct install would not have worked - but does the current libxml2.rb file reflect the upstream changes (i.e. has the "...2.2.debian.tar.xz patch file?

goliviero commented 7 years ago

I do the direct installation just after a new git checkout of course. The file : Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb reflect the upstream changes with this inside : 

 stable do
    url "http://xmlsoft.org/sources/libxml2-2.9.4.tar.gz"
    mirror "ftp://xmlsoft.org/libxml2/libxml2-2.9.4.tar.gz"
    sha256 "ffb911191e509b966deb55de705387f14156e1a56b21824357cdf0053233633c"

    # All patches upstream already. Remove whenever 2.9.5 is released.
    # Fixes CVE-2016-4658, CVE-2016-5131.
    patch do
      url "https://mirrors.ocf.berkeley.edu/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.2.debian.tar.xz"
      mirror "https://mirrorservice.org/sites/ftp.debian.org/debian/pool/main/libx/libxml2/libxml2_2.9.4+dfsg1-2.2.debian.tar.xz"
      sha256 "c038bba02a56164cef7728509ba3c8f1856018573769ee9ffcc48c565e90bdc9"
      apply "patches/0003-Fix-NULL-pointer-deref-in-XPointer-range-to.patch",
            "patches/0004-Fix-comparison-with-root-node-in-xmlXPathCmpNodes.patch",
            "patches/0005-Fix-XPointer-paths-beginning-with-range-to.patch",
            "patches/0006-Disallow-namespace-nodes-in-XPointer-ranges.patch",
            "patches/0007-Fix-more-NULL-pointer-derefs-in-xpointer.c.patch",
            "patches/0008-Fix-attribute-decoding-during-XML-schema-validation.patch"
    end
drbenmorgan commented 7 years ago

O.k., just to check the behaviour, you could try 

$ brew uninstall libxml2
$ brew update
$ brew install libxml2

That would confirm if the update overwrites. If it does, then the changes to libxml2.rb should be commited, i.e., after patching:

$ cd $(brew --prefix)
$ cd Library/Taps/homebrew/homebrew-core
... patching ...
$ git add Formula/libxml2.rb
$ git commit -m "Apply patch from homebrew/homebrew-core for missing debian patch file"

Certainly, a commit should prevent any overwriting...

goliviero commented 7 years ago

When i do an uninstall / update and reinstall it seems to work. A git diff show me no difference now, maybe the master version was updated with the change ? Thank you anyway for your help, it seems to work now.