[Bug 1597525] [NEW] data corruption in unbutu package version

[Kevin Horan]

Public bug reported:

When running the command "obabel -L descriptors", the output contains garbage characters:
# obabel -L descriptors
abonds    `�V
atoms    
bonds    p�
           cansmi    Canonical SMILES
cansmiNS    Canonical SMILES without isotopes or stereo
    ,S
formula    Chemical formula
HBA1    Number of Hydrogen Bond Acceptors 1 (JoelLib)
HBA2    Number of Hydrogen Bond Acceptors 2 (JoelLib)
HBD    Number of Hydrogen Bond Donors (JoelLib)
InChI    IUPAC InChI identifier
InChIKey    InChIKey
abonds    InChIKey    InChIKey
logP    octanol/water partition coefficient
MP    Melting point
MR    molar refractivity
MW    Molecular Weight filter
nF    Number of Fluorine Atoms
s    SMARTS filter
sbonds    SmartsDescriptor
smarts    SMARTS filter
tbonds    iptor is definable
title    For comparing a molecule's title
TPSA    topological polar surface area

In particular, the descriptors "cansmi", "formula", and "title" are
corrupted (it appears on the line above each of these names). The
corruption appears to be in the names themselves because when I use the
openbabel library (C++ code) in my own application and try to use any
one of these descriptors, it fails to even find the descriptor,
presumably because the name does not match (due to the corruption). All
other available descriptors work fine.

I have compiled the upstream source code from openbabel directly on the same machine and the output does not contain any corruption and my C++ code finds these descriptors without problem.
Here is the output with the upstream version:

# obabel -L descriptors
cansmi    Canonical SMILES
cansmiNS    Canonical SMILES without isotopes or stereo
formula    Chemical formula
HBA1    Number of Hydrogen Bond Acceptors 1 (JoelLib)
HBA2    Number of Hydrogen Bond Acceptors 2 (JoelLib)
HBD    Number of Hydrogen Bond Donors (JoelLib)
InChI    IUPAC InChI identifier
InChIKey    InChIKey
logP    octanol/water partition coefficient
MR    molar refractivity
MW    Molecular Weight filter
nF    Number of Fluorine Atoms
s    SMARTS filter
smarts    SMARTS filter
title    For comparing a molecule's title
TPSA    topological polar surface area

I tried downloading the source package of openbabel from Ubuntu and building the package myself, which I was able do successfully, but the corrupt output remained. 
 

System Info
-------------
# lsb_release -rd
Description:    Ubuntu 16.04 LTS
Release:        16.04

# apt-cache policy openbabel
openbabel:
  Installed: 2.3.2+dfsg-2.2build1
  Candidate: 2.3.2+dfsg-2.2build1
  Version table:
 *** 2.3.2+dfsg-2.2build1 500
        500 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
        100 /var/lib/dpkg/status


# apt-cache policy libopenbabel4v5
libopenbabel4v5:
  Installed: 2.3.2+dfsg-2.2build1
  Candidate: 2.3.2+dfsg-2.2build1
  Version table:
     2.3.2+dfsg-2.2build1 500
        500 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
 *** 2.3.2+dfsg-2.2build1 100
        100 /var/lib/dpkg/status

** Affects: openbabel (Ubuntu)
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/1597525

Title:
  data corruption in unbutu package version

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