>> I still suspect a Pango bug that has probably been fixed in the not
>> too distant past.  What version are you using?  Can you upgrade to the
>> most recent one?  On my 32bit GNU/Linux I use a quite recent git
>> version of Pango, which should behave identically to the last release
>> (1.36.8), and everything's just fine.
> 
> GUB's pango is 1.26.0.
> https://github.com/gperciva/gub/blob/master/gub/specs/pango.py#L18
> I think that it is too old.
> 
> Pango 1.26.2 and 1.28.0 had some ligature related bugfixes.
> https://git.gnome.org/browse/pango/tree/NEWS#n306
> https://git.gnome.org/browse/pango/tree/NEWS#n288
> 
> I'll try to upgrade GUB's pango to 1.28.3 or 1.26.2.
> Pango 1.28.4 requires glib 2.24.0.
> However, GUB's glib is 2.21.5.
> Therefore, in order to upgrade to newer pango,
> it is necessary to also upgrade glib.

I've succeed to upgrade GUB's pango to 1.28.3.
https://github.com/trueroad/gub/tree/pango-1.28

Then, I've checked some environments.
The results are following:

  linux-64 binary on Ubuntu 14.04 LTS 64 bit:
    ligatured pdf is generated.

  linux-x86 binary on Ubuntu 14.04 LTS 64 bit:
    ligatured pdf is generated.

  linux-x86 binary on Ubuntu 14.04 LTS 32 bit (minimal install):
    Serif font (CenturySchL-Roma) is ligatured.
    Sans-serif font (TakaoPGothic) is non-ligatured.

    I think that the reason is that
    the system doesn't have ligature possible sans-serif fonts.
    In other environment, selected sans-serif font is DejaVuSans.

  mingw (Windows) on Windows 8.1 64 bit:
    ligatured pdf is generated.

Note that I haven't build all platform's lilypond installer, yet.

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