I have seen a similar issue using 'yum check-update' on Ubunty Trusty with libxml2=2.9.1+dfsg1-3ubuntu4.8 failing to parse the primary.xml.gz index.

$ yum check-update
                                                                                                                              
custom-repo: [########################################################################### ] 6900/6903
(process:1482): GLib-WARNING **: GError set over the top of a previous GError or uninitialized memory.
This indicates a bug in someone's code. You must ensure an error is NULL before it's set.
The overwriting error message was: Parsing primary.xml error: attributes construct error


(process:1482): GLib-WARNING **: GError set over the top of a previous GError or uninitialized memory.
This indicates a bug in someone's code. You must ensure an error is NULL before it's set.
The overwriting error message was: Parsing primary.xml error: Couldn't find end of Start Tag size line 238347


(process:1482): GLib-WARNING **: GError set over the top of a previous GError or uninitialized memory.
This indicates a bug in someone's code. You must ensure an error is NULL before it's set.
The overwriting error message was: Parsing primary.xml error: Premature end of data in tag package line 238338


(process:1482): GLib-WARNING **: GError set over the top of a previous GError or uninitialized memory.
This indicates a bug in someone's code. You must ensure an error is NULL before it's set.
The overwriting error message was: Parsing primary.xml error: Premature end of data in tag metadata line 2

Traceback (most recent call last):
  File "/usr/bin/yum", line 29, in <module>
    yummain.user_main(sys.argv[1:], exit_code=True)
  File "/usr/share/yum-cli/yummain.py", line 288, in user_main
    errcode = main(args)
  File "/usr/share/yum-cli/yummain.py", line 140, in main
    result, resultmsgs = base.doCommands()
  File "/usr/share/yum-cli/cli.py", line 436, in doCommands
    self._getTs(needTsRemove)
  File "/usr/lib/python2.7/dist-packages/yum/depsolve.py", line 101, in _getTs
    self._getTsInfo(remove_only)
  File "/usr/lib/python2.7/dist-packages/yum/depsolve.py", line 112, in _getTsInfo
    pkgSack = self.pkgSack
  File "/usr/lib/python2.7/dist-packages/yum/__init__.py", line 892, in <lambda>
    pkgSack = property(fget=lambda self: self._getSacks(),
  File "/usr/lib/python2.7/dist-packages/yum/__init__.py", line 673, in _getSacks
    self.repos.populateSack(which=repos)
  File "/usr/lib/python2.7/dist-packages/yum/repos.py", line 294, in populateSack
    sack.populate(repo, mdtype, callback, cacheonly)
  File "/usr/lib/python2.7/dist-packages/yum/yumRepo.py", line 190, in populate
    dobj = repo_cache_function(xml, csum)
  File "/usr/lib/python2.7/dist-packages/sqlitecachec.py", line 46, in getPrimary
    self.repoid))
TypeError: Parsing primary.xml error: Specification mandate value for attribute archive

I have seen this a few times, but never took the time to dig into it until recently.  What I found was the size of the primary.xml.gz file is what seems to be causing the failure.  If (size of file in bytes)/(8192 bytes) has a remainder of 1 byte this failure will occur. Basically, in the case of "yum check-update", if the last read (that returns more than 0 bytes) on the primary.xml.gz file ONLY contains a single null character it fails.

strace excerpt (with the primary.xml.gz as fd 5):

read(5, "\0", 8192)                     = 1
read(5, "", 8191)                       = 0

After the above it fails immediately.

Updating libxml2 to v2.9.3+dfsg1-1ubuntu0.2 from the Ubuntu Xenial repos seems to fix the problem, but that is not an acceptable solution in my case because the Xenial package brings in some other dependencies that I cannot update to.

Any chance someone could fix this issue for Ubuntu Trusty?