[Debian-med-packaging] Bug#856424: libvcflib-tools: vcflib cannot find its programs in /usr/lib/vcflib/binaries

[John Hensley]

Package: libvcflib-tools
Version: 1.0.0~rc1+dfsg1-1
Severity: grave
Justification: renders package unusable

Dear Maintainer,

* What led up to the situation?

I installed libvcflib-tools on testing/stretch. When I ran 'vcflib', I
saw this:

$ vcflib
Usage: /usr/bin/vcflib <program>                                                                                                                                                                                                                                                                       Existing programs are:                                                                                                                                                                                                                                                                             ls: cannot access '/usr/lib/vcflib/bin': No such file or directory

* What exactly did you do (or not do) that was effective (or
  ineffective)?

For now, I created a symlink from /usr/lib/vcflib/binaries to
/usr/lib/vcflib/bin.

* What was the outcome of this action?

Now vcflib can find its programs:

$ vcflib
Usage: /usr/bin/vcflib <program>
  Existing programs are:
abba-baba              LD             plotHaps           vcf2dag
[...]

It looks like the 'keep_R_files' patch from September 2016 changed the
path to which programs are installed, while trying to keep the R
scripts from being purged by 'make clean'.

These R scripts reside in a 'scripts' directory upstream; maybe moving
them in the Debian package as well, reverting BIN_DIR in the Makefile,
and installing them from the scripts directory would fix this.

-- System Information:
Debian Release: 9.0
  APT prefers testing
  APT policy: (500, 'testing'), (50, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-1-amd64 (SMP w/80 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages libvcflib-tools depends on:
ii  libc6              2.24-9
ii  libdisorder0       0.0.2-1
ii  libfastahack0      0.0+20160702-1
ii  libgcc1            1:6.3.0-6
ii  libgomp1           6.3.0-6
ii  libhts1            1.3.2-2
ii  libsmithwaterman0  0.0+20160702-1
ii  libstdc++6         6.3.0-6
ii  libtabixpp0        1.0.0-2
ii  libvcflib1         1.0.0~rc1+dfsg1-1
ii  zlib1g             1:1.2.8.dfsg-5

libvcflib-tools recommends no packages.

libvcflib-tools suggests no packages.

-- no debconf information