Problems with gnupg-2.1.9 (and gpgme-1.6.0)

[Andrew Savchenko]

Hello,

I updated to gnupg-2.1.9 from 2.0.x on both my desktop and laptop
and now I have big problems. My OS is Gentoo Linux.

1. gpgme is now broken.

Gpgme consumers (e.g. sylpheed, mcabber) can verify, encrypt and
decrypt messages, but can't sign them. On signing I have the
following issues:

Please enter your PGP passphrase: 
[17:26:06] GPGME signature error: Unusable secret key

Or:
** Sylpheed-WARNING: pgp_sign(): signing failed: User defined error code 1

I _can_ sign using the very same keys and plain
  gpg -s --default-key $id
command. GPG itself works fine, something is amiss with gmgme.

I updated gpgme, libgcrypt, libgpg-error and libassuan to the
latest versions (gpgme-1.6.0, libgcrypt-1.6.4, libgpg-error-1.20,
libassuan-2.3.0) and rebuilt consumer applications. Of course,
keys were migrated to the new format using
  gpg --import ~/.gnupg/secring.gpg
and gpg-agent was restarted (I even rebooted the whole host), but
problem is still here.

The problem is even more strange, since I found a workaround way to
sign messages in sylpheed. Program has three options for key
selection:
a) use default GPG key;
b) select key by e-mail;
c) use key with provided ID.

Options b) and c) cause the error above, while option a) works, so
by editing gpg.conf I can set default key id to what I need to sign
a message. This is very inconvenient (since I have many keys), but
at least works somehow.

I attach a GPGME_DEBUG=3 log for the case where key was selected
by id. I don't want to attach more verbose logs, since they contain
a lot of binary data and I don't want to risk data leak. See
sylpheed-gpgme.log.


2. I have duplicated keys in the ring with the same ID and
fingerprint.

Duplication happens only to _some_ of my keys where I have a secret
key, fetched public keys of other users are not duplicated.

Examples:
a) Here I have the very same key twice:

$ gpg --fingerprint -K 0x8EE705C07CFA83D3
sec   rsa4096/0x8EE705C07CFA83D3 2012-09-11 [expired: 2015-09-11]
      Key fingerprint = 3F2D 1E49 4F96 2CE6 1597  F217 8EE7 05C0 7CFA 83D3
uid                   [ expired] Bircoph <bircoph at jabber.ru>

sec   rsa4096/0x8EE705C07CFA83D3 2012-09-11 [expired: 2015-09-11]
      Key fingerprint = 3F2D 1E49 4F96 2CE6 1597  F217 8EE7 05C0 7CFA 83D3
uid                   [ expired] Bircoph <bircoph at jabber.ru>

b) Now it becomes more interesting:

$ gpg --fingerprint -K 0x565953B95372756C
sec   rsa4096/0x565953B95372756C 2013-02-27 [expires: 2018-02-26]
      Key fingerprint = 63EB 04FA A30C 76E2 952E  6ED6 5659 53B9 5372 756C
uid                   [ultimate] Andrew Savchenko <bircoph at gmail.com>
uid                   [ultimate] Andrew A. Savchenko (NRNU MEPhI) <aasavchenko at mephi.ru>
uid                   [ultimate] Andrew A. Savchenko (UT Department) <aasavchenko at ut.mephi.ru>
uid                   [ultimate] Andrew Savchenko (Gentoo Dev) <bircoph at gentoo.org>
uid                   [ultimate] Andrew A. Savchenko (XMPP) <bircoph at jabber.ru>
uid                   [ultimate] Andrew A. Savchenko (UT Department) <bircoph at ut.mephi.ru> uid                   [ultimate] Andrey Savchenko (RHIC) <bircoph at rcf.rhic.bnl.gov>
ssb   rsa4096/0x7AB649CA518C8321 2013-02-27 [expires: 2018-02-26]
ssb   rsa4096/0xF6535A33BA1EE48D 2015-01-13 [expires: 2018-01-12]

sec   rsa4096/0x565953B95372756C 2013-02-27 [expires: 2018-02-26]
uid                   [ultimate] Andrew A. Savchenko (NRNU MEPhI) <aasavchenko at mephi.ru>
uid                   [ultimate] Andrew Savchenko <bircoph at gmail.com>
uid                   [ultimate] Andrew Savchenko (Gentoo Dev) <bircoph at gentoo.org>
uid                   [ultimate] Andrew A. Savchenko (XMPP) <bircoph at jabber.ru>
uid                   [ultimate] Andrew A. Savchenko (UT Department) <bircoph at ut.mephi.ru>
uid                   [ultimate] Andrew A. Savchenko (UT Department) <aasavchenko at ut.mephi.ru>
ssb   rsa4096/0x7AB649CA518C8321 2013-02-27 [expires: 2018-02-26]
ssb   rsa4096/0xF6535A33BA1EE48D 2015-01-13 [expires: 2018-01-12]

I have two versions of the same key: the latest and previous one 
(before I added one more e-mail uid to the key).

This problem may be related to the first one, may be not, I'm not
sure. It is possible that gpgme goes crazy with these duplicates.

I have no idea how to remove duplicates and old versions. All gpg
commands are tied to either key id, e-mail or fingerprint. They
are all not unique to delete such duplicates.

I have though that this may happen due to both secring.gpg and
private-keys-v1.d present, but moving secring.gpg away doesn't
help.

Maybe manual editing of pubring.gpg will help to remove duplicates,
but it will be quite hard to handle this binary format.


Googling gave me very litte here:

1st issue: may happen for some custom gpgme client software, but
no data on global failures after gnupg update.

2nd issue: may happen when key is stored in multiple sources and
fetched from them, but I have no --keyring options in my gpg.conf
(see attached file).

Any ideas how to fix these issues, especially the signing failure
are much appreciated.

Best regards,
Andrew Savchenko
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