Your message dated Tue, 24 Sep 2024 07:19:05 +0000
with message-id <[email protected]>
and subject line Bug#1082109: fixed in inchi 1.07.1+dfsg-4
has caused the Debian Bug report #1082109,
regarding inchi: support for .sdf (v3000 dialect) is not functional
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1082109: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1082109
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: libinchi1.07
Version: 1.07.1+dfsg-3
Severity: normal
File: inchi
X-Debbugs-Cc: [email protected]
Dear Maintainer,
The compiled reference executable of InChI 1.07.1[1] for Linux 64bit assigns
InChI for .sdf in either v2000, or v3000 dialect. While replying to an issue
report,[2] I noticed `inchi_main` as packaged by DebiChem currently supports
only the elder v2000 style. I suggest to amend the package's functionality
to allow either input format be accepted.
See the log attached below:
```shell
@debian:~/Desktop/issue_debian$ obabel -:"C" -h --gen3d -O style_2000.sdf
1 molecule converted
@debian:~/Desktop/issue_debian$ inchi_main style_2000.sdf
InChI version 1, Software v. 1.07 (Library call example, classic API)
Linux 64-bit Build (gcc 14.2.0) of Sep 3 2024 05:44:57
Opened log file 'style_2000.sdf.log'
Opened input file 'style_2000.sdf'
Opened output file 'style_2000.sdf.txt'
Opened problem file 'style_2000.sdf.prb'
Generating standard InChI
Input format: MOLfile
Output format: Plain text
Full Aux. info
Timeout per structure: 60000 msec
Up to 1024 atoms per structure
Structure 2 could not be read: Detected end of file.
Processed 1 structure, 0 errors.
@debian:~/Desktop/issue_debian$ cat style_2000.sdf.txt
* Input_File: "style_2000.sdf"
Structure: 1
InChI=1S/CH4/h1H4
AuxInfo=1/0/N:1/rA:5nCHHHH/rB:s1;s1;s1;s1;/rC:.93,-.0596,.0392;2.0222,-.0596,.0392;.5659,-.4666,.9851;.5659,-.6753,-.7862;.5659,.963,-.0813;
@debian:~/Desktop/issue_debian$
@debian:~/Desktop/issue_debian$ obabel -:"C" -h --gen3d -O style_3000.sdf -x3
1 molecule converted
@debian:~/Desktop/issue_debian$ inchi_main style_3000.sdf
InChI version 1, Software v. 1.07 (Library call example, classic API)
Linux 64-bit Build (gcc 14.2.0) of Sep 3 2024 05:44:57
Opened log file 'style_3000.sdf.log'
Opened input file 'style_3000.sdf'
Opened output file 'style_3000.sdf.txt'
Opened problem file 'style_3000.sdf.prb'
Generating standard InChI
Input format: MOLfile
Output format: Plain text
Full Aux. info
Timeout per structure: 60000 msec
Up to 1024 atoms per structure
Error 171 (no INChI; Molfile V3000 input is not supported) inp structure #1.
Structure 2 could not be read: Detected end of file.
Processed 1 structure, 1 error.
@debian:~/Desktop/issue_debian$ cat style_3000.sdf.txt
* Input_File: "style_3000.sdf"
InChI=1S//
@debian:~/Desktop/issue_debian$
```
Regards,
Norwid Behrnd
[1] https://github.com/openbabel/openbabel/releases
[2] https://github.com/IUPAC-InChI/InChI/issues/52
-- System Information:
Debian Release: trixie/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.9.10-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages libinchi1.07 depends on:
ii libc6 2.40-2
libinchi1.07 recommends no packages.
libinchi1.07 suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: inchi
Source-Version: 1.07.1+dfsg-4
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
inchi, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (supplier of updated inchi package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 24 Sep 2024 02:59:00 -0400
Source: inchi
Architecture: source
Version: 1.07.1+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1082109
Changes:
inchi (1.07.1+dfsg-4) unstable; urgency=medium
.
* Build and install inchi-1 executable (Closes: #1082109)
* Update debian/inchi_main.1.txt.
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