Actually, with the exception of the deletion of config.sub, the other
half of this patch was already present in 2.12.3; not sure why you're
trying to build an older version.

Sorry for that, but it looks like fault of apt-get:

$ apt-get source lilypond
Reading package lists... Done
Building dependency tree
Reading state information... Done
Skipping already downloaded file 'lilypond_2.12.2-1.dsc'
Skipping already downloaded file 'lilypond_2.12.2.orig.tar.gz'
Skipping already downloaded file 'lilypond_2.12.2-1.diff.gz'
Need to get 0B of source archives.
Skipping unpack of already unpacked source in lilypond-2.12.2



$ cat /etc/apt/sources.list

deb http://ftp.cz.debian.org/debian unstable main
deb-src http://ftp.cz.debian.org/debian unstable main

deb http://ftp.de.debian.org/debian unstable main
deb-src http://ftp.de.debian.org/debian unstable main



$ apt-cache showsrc lilypond | grep Version
Version: 2.12.2-1
Standards-Version: 3.7.3
Version: 2.12.3-6
Standards-Version: 3.8.4
Version: 2.12.2-1
Standards-Version: 3.7.3
Version: 2.12.3-6
Standards-Version: 3.8.4


even after removing lilypond*:


$ apt-get -t unstable source lilypond
Reading package lists... Done
Building dependency tree
Reading state information... Done
Need to get 4616kB of source archives.
Get:1 http://ftp.cz.debian.org unstable/main lilypond 2.12.2-1 (dsc) [1720B] Get:2 http://ftp.cz.debian.org unstable/main lilypond 2.12.2-1 (tar) [4576kB] Get:3 http://ftp.cz.debian.org unstable/main lilypond 2.12.2-1 (diff) [38.7kB]
Fetched 4616kB in 0s (63.3MB/s)

The /var/lib/apt/lists/*unstable_main_source_Sources contains
two entries for lilypond, the first one is

Package: lilypond
Binary: lilypond, lilypond-data, lilypond-doc
Version: 2.12.2-1
Priority: optional

and the second one

Package: lilypond
Binary: lilypond, lilypond-data, lilypond-doc
Version: 2.12.3-6
Priority: optional

It looks like apt-get just uses the first occurence of source,
not the one with highest version number.

Sorry again

                Petr




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