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Thu, 29 Apr 2021 02:44:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43102) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lc0P4-0001yP-AG for guix-patches@gnu.org; Thu, 29 Apr 2021 02:44:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lc0P4-0002KK-7X for guix-patches@gnu.org; Thu, 29 Apr 2021 02:44:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 29 Apr 2021 06:44:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47821 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen Cc: 47821@debbugs.gnu.org Received: via spool by 47821-submit@debbugs.gnu.org id=B47821.16196786268913 (code B ref 47821); Thu, 29 Apr 2021 06:44:02 +0000 Received: (at 47821) by debbugs.gnu.org; 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aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: -4.05 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 613251EAE9 X-Spam-Score: -4.05 X-Migadu-Scanner: scn0.migadu.com X-TUID: fMhWd3Ck9++p --2Uv/FEvIbMBUf7Mb Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Wed, Apr 28, 2021 at 04:05:09PM +0200, Roel Janssen wrote: > On Tue, 2021-04-27 at 10:32 +0300, Efraim Flashner wrote: > > On Fri, Apr 16, 2021 at 11:55:39AM +0200, Roel Janssen wrote: > > > Hi Guix, > > >=20 > > > The following patches update htslib, bcftools, samtools, and > > > bedtools. > > > I've succesfully built bedtools with the latest samtools instead of > > > the > > > 1.9 version. > >=20 > > These look good and are ready for merging. Can you take a look at > > python-pybedtools? There's a new version out which I hope builds with > > the newer version of bedtools. > >=20 > > Thanks. > >=20 >=20 > I looked at python-pybedtools and came up with the following patch. > The test phase is still not entirely happy because it ends with: >=20 > --- > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 497 passed, 3 xfailed, 4= 26 warnings in 25.49s > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > Error in atexit._run_exitfuncs: > Traceback (most recent call last): > File "/gnu/store/rz42ba0my9vrgbkjpkzr2drmnjk5ah50-python- > 3.8.2/lib/python3.8/shutil.py", line 704, in rmtree > orig_st =3D os.lstat(path) > --- >=20 > I attached the patch that I have that at least builds the newer version > of python-pybedtools. I don't know how to further test it. >=20 > Can I in the meantime already push the patches for updating htslib, > bcftools, samtools and bedtools? >=20 Yeah, those patches LGTM. --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --2Uv/FEvIbMBUf7Mb Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmCKVZMACgkQQarn3Mo9 g1GkOQ/7Bcn+havSbfk0vW4SFs5DpFfKhlxg2ejfoZU8pODokK4eCO2reCugRxno 2YAe5Aa82K3LoE8mEml0BdQS+5aPrMhduGneHXsGWBfatSD6CVDg1U1hvmYjoVSY 7O5KZAv38iVLFBKLqAj4abnQDVsFctI5qMROo9YbOEitAoH6G3ae7K0l4IZgnYHq +M/6278SDM0rq4q3NklfQ722SVHXhMERr8QN99VN88tNpgysv/66A+8FZ6VaCtk5 HluLp+pp3YftWMS34/qDuXG8G0suJETZ+gKMHDXJqq+qeMg4Xq75SksTeNdGcLna RslLQJl253pmkQbHodXKVtNbG+jh4wrbcfo30x/8gI/FxQecdjFs2vJydV5B6uqZ WW+STVkUUN94z9/ZZSGwMIfIHbakg4TIhG7+TqLQAPv6dtlVuOpVblVYfcz3mTpE 6hw+b9LXqNIuHNMywvGwliYqbWCi2HQxUYlpACx20Ac0jLVtE2ewp/sqoyyeONtl exlxqm4daYsxLpsyzaMCSnZbVhZ7WqWeO7Hi1X7j0rsilJ20klSMxnhI80d4LOYm d19k9b8XwoiNMQ/54vUXnPJWcZta6J2Fra8eBTrCIzl+zVySL3lE5eilIij/FUw+ lq+1foFJikzCsuPUX5BvbUzI3bkCYBJinmM94vvQudZHMlplqH8= =fcRb -----END PGP SIGNATURE----- --2Uv/FEvIbMBUf7Mb--