From unknown Tue Aug 19 10:08:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#44613] [PATCH] Fix build for bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 11:02:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44613@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16052652855014 (code B ref -1); Fri, 13 Nov 2020 11:02:01 +0000 Received: (at submit) by debbugs.gnu.org; 13 Nov 2020 11:01:25 +0000 Received: from localhost ([127.0.0.1]:46868 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpY-0001Io-P0 for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:25 -0500 Received: from lists.gnu.org ([209.51.188.17]:60528) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpX-0001Ig-1s for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:23 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:42704) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdWpP-0006a6-Nz for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:19 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:48998) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdWpL-0003H1-IN for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:14 -0500 Received: from [143.121.239.14] (port=45168 helo=[10.132.152.6]) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kdWpG-0002NT-Ip for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:10 -0500 Message-ID: From: Roel Janssen Date: Fri, 13 Nov 2020 12:01:04 +0100 Content-Type: multipart/mixed; boundary="=-A3Jh9HcEN31wwMB5f/Iy" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-A3Jh9HcEN31wwMB5f/Iy Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Dear Guix, By updating samtools to 1.11, I introduced a build failure for bedtools. More precisely, the tests for intersect break in precisely this way: https://github.com/arq5x/bedtools2/issues/814 With the following patches, I'd like to add samtools-1.9, htslib-1.9 (samtools depends on that) to fix this problem with bedtools. Alternatively we could add a patch to disable the failing bedtools tests. I manually inspected the test results, and seem to match perfectly (indicating that there's no problem with bedtools). Kind regards, Roel Janssen --=-A3Jh9HcEN31wwMB5f/Iy Content-Disposition: attachment; filename="0003-gnu-bedtools-Use-samtools-1.9.patch" Content-Type: text/x-patch; name="0003-gnu-bedtools-Use-samtools-1.9.patch"; charset="UTF-8" Content-Transfer-Encoding: base64 RnJvbSAyNTQxYjNjNDRlNjk1ZmYxYTZiNTYxMjhiNmVmYTcyYzQ2M2MwYjBhIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiBSb2VsIEphbnNzZW4gPHJvZWxAZ251Lm9yZz4KRGF0ZTogRnJp LCAxMyBOb3YgMjAyMCAxMToyOTozOCArMDEwMApTdWJqZWN0OiBbUEFUQ0ggMy8zXSBnbnU6IGJl ZHRvb2xzOiBVc2Ugc2FtdG9vbHMtMS45LgoKVGhlIGJ1aWxkIGZvciBiZWR0b29scyB3aXRoIHNh bXRvb2xzIDEuMTEgdHJpZ2dlcnMgYSB0ZXN0c3VpdGUKZmFpbHVyZSB3aGljaCBpcyByZXBvcnRl ZCBoZXJlOgpodHRwczovL2dpdGh1Yi5jb20vYXJxNXgvYmVkdG9vbHMyL2lzc3Vlcy84MTQKCiog Z251L3BhY2thZ2VzL2Jpb2luZm9ybWF0aWNzLnNjbSAoYmVkdG9vbHMpOiBVc2Ugc2FtdG9vbHMt MS45LgotLS0KIGdudS9wYWNrYWdlcy9iaW9pbmZvcm1hdGljcy5zY20gfCAyICstCiAxIGZpbGUg Y2hhbmdlZCwgMSBpbnNlcnRpb24oKyksIDEgZGVsZXRpb24oLSkKCmRpZmYgLS1naXQgYS9nbnUv cGFja2FnZXMvYmlvaW5mb3JtYXRpY3Muc2NtIGIvZ251L3BhY2thZ2VzL2Jpb2luZm9ybWF0aWNz LnNjbQppbmRleCBlMDQ3YWViZDFkLi44YWQzOGFjNDk4IDEwMDY0NAotLS0gYS9nbnUvcGFja2Fn ZXMvYmlvaW5mb3JtYXRpY3Muc2NtCisrKyBiL2dudS9wYWNrYWdlcy9iaW9pbmZvcm1hdGljcy5z Y20KQEAgLTQzNyw3ICs0MzcsNyBAQCBjb21wdXRhdGlvbmFsIGNsdXN0ZXIuIikKICAgICAobmF0 aXZlLWlucHV0cwogICAgICBgKCgicHl0aG9uIiAscHl0aG9uLXdyYXBwZXIpKSkKICAgICAoaW5w dXRzCi0gICAgIGAoKCJzYW10b29scyIgLHNhbXRvb2xzKQorICAgICBgKCgic2FtdG9vbHMiICxz YW10b29scy0xLjkpCiAgICAgICAgKCJ6bGliIiAsemxpYikpKQogICAgIChob21lLXBhZ2UgImh0 dHBzOi8vZ2l0aHViLmNvbS9hcnE1eC9iZWR0b29sczIiKQogICAgIChzeW5vcHNpcyAiVG9vbHMg Zm9yIGdlbm9tZSBhbmFseXNpcyBhbmQgYXJpdGhtZXRpYyIpCi0tIAoyLjI5LjIKCg== --=-A3Jh9HcEN31wwMB5f/Iy Content-Disposition: attachment; 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Fri, 13 Nov 2020 04:43:15 -0800 (PST) From: zimoun In-Reply-To: References: Date: Fri, 13 Nov 2020 13:39:56 +0100 Message-ID: <86v9e9e8gz.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Roel, On Fri, 13 Nov 2020 at 12:01, Roel Janssen wrote: > With the following patches, I'd like to add samtools-1.9, htslib-1.9 > (samtools depends on that) to fix this problem with bedtools. Recently, investigating why the substitute of =E2=80=99python-pysam=E2=80= =99 was not available, I decided then to give a try at fixing the TODO: --8<---------------cut here---------------start------------->8--- (snippet '(begin ;; Drop bundled htslib. TODO: Also remove samtools ;; and bcftools. (delete-file-recursively "htslib") #t)))) --8<---------------cut here---------------end--------------->8--- And the bundled version is 1.9 (if I remember correctly), therefore because of: --8<---------------cut here---------------start------------->8--- (native-inputs `(("python-cython" ,python-cython) ;; Dependencies below are are for tests only. ("samtools" ,samtools) ("bcftools" ,bcftools) ("python-nose" ,python-nose))) --8<---------------cut here---------------end--------------->8--- some tests are unhappy. That=E2=80=99s said, these additions seem fine with me. :-) All the best, simon From unknown Tue Aug 19 10:08:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#44613] [PATCH] Fix build for bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 12:56:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: zimoun , 44613@debbugs.gnu.org Received: via spool by 44613-submit@debbugs.gnu.org id=B44613.160527214132660 (code B ref 44613); Fri, 13 Nov 2020 12:56:02 +0000 Received: (at 44613) by debbugs.gnu.org; 13 Nov 2020 12:55:41 +0000 Received: from localhost ([127.0.0.1]:47248 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdYc8-0008Ui-OY for submit@debbugs.gnu.org; Fri, 13 Nov 2020 07:55:40 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43840) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdYc6-0008UU-EC for 44613@debbugs.gnu.org; Fri, 13 Nov 2020 07:55:39 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:56966) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdYc1-0002yi-26; Fri, 13 Nov 2020 07:55:33 -0500 Received: from [143.121.239.14] (port=45972 helo=[10.132.152.6]) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kdYby-00059k-SX; Fri, 13 Nov 2020 07:55:32 -0500 Message-ID: <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> From: Roel Janssen Date: Fri, 13 Nov 2020 13:55:29 +0100 In-Reply-To: <86v9e9e8gz.fsf@gmail.com> References: <86v9e9e8gz.fsf@gmail.com> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hi Simon, On Fri, 2020-11-13 at 13:39 +0100, zimoun wrote: > Hi Roel, > > On Fri, 13 Nov 2020 at 12:01, Roel Janssen wrote: > > > With the following patches, I'd like to add samtools-1.9, htslib- > > 1.9 > > (samtools depends on that) to fix this problem with bedtools. > > Recently, investigating why the substitute of ’python-pysam’ was not > available, I decided then to give a try at fixing the TODO: > > --8<---------------cut here---------------start------------->8--- >               (snippet '(begin >                           ;; Drop bundled htslib. TODO: Also remove > samtools >                           ;; and bcftools. >                           (delete-file-recursively "htslib") >                           #t)))) > --8<---------------cut here---------------end--------------->8--- > > And the bundled version is 1.9 (if I remember correctly), therefore > because of: > > --8<---------------cut here---------------start------------->8--- >     (native-inputs >      `(("python-cython" ,python-cython) >        ;; Dependencies below are are for tests only. >        ("samtools" ,samtools) >        ("bcftools" ,bcftools) >        ("python-nose" ,python-nose))) > --8<---------------cut here---------------end--------------->8--- > > some tests are unhappy. > > That’s said, these additions seem fine with me. :-) > I also tried removing the bundled htslib for bedtools, but didn't go this route for two reasons: - The bundled htslib for bedtools seems "slightly modified" (I didn't investigate further) - Replacing the references to libhts.a with $(pkg-config htslib -- cflags --libs) produced various linker errors. So I stopped right there. I'm sure more tools will likely have failed because of the htslib upgrade (sorry about this!), so having htslib-1.9 around for some time may be a good fallback for now. Just to double-check: Is it OK to push the proposed patches? Kind regards, Roel Janssen From unknown Tue Aug 19 10:08:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#44613] [PATCH] Fix build for bedtools Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 13:39:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen , 44613@debbugs.gnu.org Received: via spool by 44613-submit@debbugs.gnu.org id=B44613.16052747044039 (code B ref 44613); Fri, 13 Nov 2020 13:39:02 +0000 Received: (at 44613) by debbugs.gnu.org; 13 Nov 2020 13:38:24 +0000 Received: from localhost ([127.0.0.1]:47264 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZHU-000135-AJ for submit@debbugs.gnu.org; Fri, 13 Nov 2020 08:38:24 -0500 Received: from mail-wm1-f66.google.com ([209.85.128.66]:39610) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZHS-00012q-MR for 44613@debbugs.gnu.org; Fri, 13 Nov 2020 08:38:23 -0500 Received: by mail-wm1-f66.google.com with SMTP id s13so8519478wmh.4 for <44613@debbugs.gnu.org>; Fri, 13 Nov 2020 05:38:22 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:in-reply-to:references:date:message-id:mime-version :content-transfer-encoding; bh=zSw2QQZW4vWDV71p5cy8617NNxK3pYBbvybT3A5l1pw=; b=o6ZG2qDtjYYz132girfkQ87dHWfjY4KPm7b+iUJO23N9/vu3Of0tadDTSbmFpMm6RS pRngdVqH1DWF7TIRfjRIUPeWaGb/WfyShBgVzTTb3Ucr6u9WVoh+k7MpTSieEAwXJX0z p/SUdsUwy6OkClFYtIB18jpoE6KxBPwOBp0RZyOwu0H7QQMTdOdgJGt8DkL3wx81kqFm GZ/KD0GcZn3epqDkiu+bqSw2TLOWZA/kkfkzgUs/5yRr8z9yNgrXNEUDlGXxl4Nfgktu I1UX6onZf3uM4+GP0vjvnVKBXZCGF8q7zWm9B0f+qqxSKjoWdgfbldNEXX4OXgGxX6j6 7mWQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:in-reply-to:references:date :message-id:mime-version:content-transfer-encoding; bh=zSw2QQZW4vWDV71p5cy8617NNxK3pYBbvybT3A5l1pw=; b=DRRoi/IHNeiZCKrO7ChKn9D6wJZA8bu8IFiTsPJOLuYrILEQBR2uiwjiXy5LmdCFJV ygqBCT8XkfM5SAhOFJ9BuaEfAX3IdVL+JFBIRXKmw0cfocyrLOuOqp3LyK8V/EDs2SdB lfKSBD3iGMNgp+mPeEnA1MB3jcxkke2REvv0jNuagD40sieusBWG5rbUxP+UGRSkJ6RE MqbbfuvNBKMnAaUkd4EFXaKIhlXy4isgnYObsVQ7nDh6Rd9ZAzsS/NbdC+IhN5XNHy1U xmJNJVI/9tpiNDAKG+QYeyDSci1SQMdIcGVndSL8wBKd9W+qVXNSZqup1IUgEmk7nLTo HWbQ== X-Gm-Message-State: AOAM5304b44H8sqxE465FhFhWwK5M1SUZe19ZG0pxMnJzlhuckA2dejz WVpc+HGFlFpDmC1zoAuhnioRbw0fajeZjQ== X-Google-Smtp-Source: ABdhPJwxE8D0usZk6mDVSt1bPBQnvnxAHmCYkoxedsDJSW1luhi0DmXUAicy5UsxF/WChR0iK2OA/Q== X-Received: by 2002:a1c:230e:: with SMTP id j14mr2534530wmj.187.1605274696332; Fri, 13 Nov 2020 05:38:16 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id d3sm11971436wrg.16.2020.11.13.05.38.15 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 13 Nov 2020 05:38:15 -0800 (PST) From: zimoun In-Reply-To: <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> References: <86v9e9e8gz.fsf@gmail.com> <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> Date: Fri, 13 Nov 2020 14:34:06 +0100 Message-ID: <86k0upe5yp.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Roel, On Fri, 13 Nov 2020 at 13:55, Roel Janssen wrote: > I also tried removing the bundled htslib for bedtools, but didn't go > this route for two reasons: > - The bundled htslib for bedtools seems "slightly modified" (I didn't > investigate further) > - Replacing the references to libhts.a with $(pkg-config htslib -- > cflags --libs) produced various linker errors. So I stopped right > there. > > I'm sure more tools will likely have failed because of the htslib > upgrade (sorry about this!), so having htslib-1.9 around for some time > may be a good fallback for now. Thank for your explanations. > Just to double-check: Is it OK to push the proposed patches? I have not tried them but they LGTM. All the best, simon PS: I am always confused if the removal should be done in =E2=80=99origin=E2=80= =99 or in the =E2=80=99add-after 'unpack=E2=80=99 phase; especially when the bundle is fr= ee software. Other said, what should an user expect when fetching with =E2=80=9Cguix bui= ld -S=E2=80=9D? Anyway! :-) From unknown Tue Aug 19 10:08:17 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Roel Janssen Subject: bug#44613: closed (Re: [bug#44613] [PATCH] Fix build for bedtools) Message-ID: References: X-Gnu-PR-Message: they-closed 44613 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 44613@debbugs.gnu.org Date: Fri, 13 Nov 2020 14:02:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1605276122-6410-1" This is a multi-part message in MIME format... ------------=_1605276122-6410-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #44613: [PATCH] Fix build for bedtools which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 44613@debbugs.gnu.org. --=20 44613: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D44613 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1605276122-6410-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 44613-done) by debbugs.gnu.org; 13 Nov 2020 14:01:11 +0000 Received: from localhost ([127.0.0.1]:47285 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZdX-0001dz-44 for submit@debbugs.gnu.org; Fri, 13 Nov 2020 09:01:11 -0500 Received: from eggs.gnu.org ([209.51.188.92]:60626) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZdR-0001dK-PL for 44613-done@debbugs.gnu.org; Fri, 13 Nov 2020 09:01:09 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:59444) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdZdM-000148-Em; Fri, 13 Nov 2020 09:01:00 -0500 Received: from [143.121.239.14] (port=46298 helo=[10.132.152.6]) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kdZdL-00056v-5C; Fri, 13 Nov 2020 09:00:59 -0500 Message-ID: Subject: Re: [bug#44613] [PATCH] Fix build for bedtools From: Roel Janssen To: zimoun Date: Fri, 13 Nov 2020 15:00:57 +0100 In-Reply-To: <86k0upe5yp.fsf@gmail.com> References: <86v9e9e8gz.fsf@gmail.com> <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> <86k0upe5yp.fsf@gmail.com> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 44613-done Cc: 44613-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hi Simon, On Fri, 2020-11-13 at 14:34 +0100, zimoun wrote: > Hi Roel, > > On Fri, 13 Nov 2020 at 13:55, Roel Janssen wrote: > > > I also tried removing the bundled htslib for bedtools, but didn't > > go > > this route for two reasons: > > - The bundled htslib for bedtools seems "slightly modified" (I > > didn't > > investigate further) > > - Replacing the references to libhts.a with $(pkg-config htslib -- > > cflags --libs) produced various linker errors. So I stopped right > > there. > > > > I'm sure more tools will likely have failed because of the htslib > > upgrade (sorry about this!), so having htslib-1.9 around for some > > time > > may be a good fallback for now. > > Thank for your explanations. > > > > Just to double-check: Is it OK to push the proposed patches? > > I have not tried them but they LGTM. > Thanks for the quick review. I pushed the patches in c3232fcc7785abc1057a0d4b5b1832f1e39c9c1b, da4a38edad52f7bb5a8d41465d09f3f0197fd0b7, and 3ede804f6d4c38ff0b9a5705544a8c35f6827ff1. Kind regards, Roel Janssen ------------=_1605276122-6410-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 13 Nov 2020 11:01:25 +0000 Received: from localhost ([127.0.0.1]:46868 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpY-0001Io-P0 for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:25 -0500 Received: from lists.gnu.org ([209.51.188.17]:60528) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpX-0001Ig-1s for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:23 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:42704) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdWpP-0006a6-Nz for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:19 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:48998) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdWpL-0003H1-IN for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:14 -0500 Received: from [143.121.239.14] (port=45168 helo=[10.132.152.6]) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kdWpG-0002NT-Ip for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:10 -0500 Message-ID: Subject: [PATCH] Fix build for bedtools From: Roel Janssen To: guix-patches@gnu.org Date: Fri, 13 Nov 2020 12:01:04 +0100 Content-Type: multipart/mixed; boundary="=-A3Jh9HcEN31wwMB5f/Iy" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-A3Jh9HcEN31wwMB5f/Iy Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Dear Guix, By updating samtools to 1.11, I introduced a build failure for bedtools. More precisely, the tests for intersect break in precisely this way: https://github.com/arq5x/bedtools2/issues/814 With the following patches, I'd like to add samtools-1.9, htslib-1.9 (samtools depends on that) to fix this problem with bedtools. Alternatively we could add a patch to disable the failing bedtools tests. I manually inspected the test results, and seem to match perfectly (indicating that there's no problem with bedtools). 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Fri, 13 Nov 2020 15:09:02 +0000 Received: (at 44613) by debbugs.gnu.org; 13 Nov 2020 15:08:38 +0000 Received: from localhost ([127.0.0.1]:49067 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdago-0003m1-5a for submit@debbugs.gnu.org; Fri, 13 Nov 2020 10:08:38 -0500 Received: from eggs.gnu.org ([209.51.188.92]:51652) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdagm-0003lp-Qp for 44613@debbugs.gnu.org; Fri, 13 Nov 2020 10:08:37 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:60936) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdagh-00008N-Gt; Fri, 13 Nov 2020 10:08:31 -0500 Received: from host-37-191-236-253.lynet.no ([37.191.236.253]:56640 helo=localhost) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kdagg-0004rp-1J; Fri, 13 Nov 2020 10:08:30 -0500 From: Marius Bakke In-Reply-To: <86k0upe5yp.fsf@gmail.com> References: <86v9e9e8gz.fsf@gmail.com> <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> <86k0upe5yp.fsf@gmail.com> Date: Fri, 13 Nov 2020 16:08:27 +0100 Message-ID: <87o8k1b8gk.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable zimoun writes: > PS: > I am always confused if the removal should be done in =E2=80=99origin=E2= =80=99 or in the > =E2=80=99add-after 'unpack=E2=80=99 phase; especially when the bundle is = free software. > Other said, what should an user expect when fetching with =E2=80=9Cguix b= uild -S=E2=80=9D? > Anyway! :-) Unbundling is always better to do in a snippet. It leads to less bandwidth usage, and users can more easily inspect the (actual) code. For other kinds of patching the boundary is less clear. Generally, Guix-specific tweaks should be in a phase, but "universal" bug fixes may well be in a snippet. I sometimes imagine a downstream distribution that use Guix sources, but not the build scripts, to draw the line. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFDBAEBCgAtFiEEu7At3yzq9qgNHeZDoqBt8qM6VPoFAl+uoWsPHG1hcml1c0Bn bnUub3JnAAoJEKKgbfKjOlT6u5YH/izJ3w/QKYfoL97jfU83PDBlEETIpp/S5wZT ExBEA+pTy7UucE4b4AWBuR3TH56SEi6cVr+N1poHzngOrisPovASE1ZCv6pUk4sv EEf3jUBIEuruS5le/5Ihg3lQu8KcyIypUvOKUl+X4FMSgzHxdAdUll0rvdQwVswb bjEC9B730jpbPMWTEEK62VnHoE5AD5LIJgG//kCxgUjXDaBTNih2NN5ihCuEC4NE nbcbadCtZxXMI0aOpSOEylWbAM/h0ydDoceTyru+WpZvKLaPUKRIDzVInPO5givx elS/RIj2nFHgT49KUDZVuMEszXvbf3zKwyphn/UK2zU/uB03l9Q= =H285 -----END PGP SIGNATURE----- --=-=-=-- From unknown Tue Aug 19 10:08:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#44613] what =?UTF-8?Q?=E2=80=9Cguix?= build =?UTF-8?Q?-S=E2=80=9D?= should return? Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 16:02:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Marius Bakke , Roel Janssen , 44613@debbugs.gnu.org Received: via spool by 44613-submit@debbugs.gnu.org id=B44613.160528329119616 (code B ref 44613); Fri, 13 Nov 2020 16:02:02 +0000 Received: (at 44613) by debbugs.gnu.org; 13 Nov 2020 16:01:31 +0000 Received: from localhost ([127.0.0.1]:49165 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdbVy-00056K-JG for submit@debbugs.gnu.org; Fri, 13 Nov 2020 11:01:30 -0500 Received: from mail-wm1-f53.google.com ([209.85.128.53]:53506) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdbVw-000560-91 for 44613@debbugs.gnu.org; Fri, 13 Nov 2020 11:01:28 -0500 Received: by mail-wm1-f53.google.com with SMTP id p22so8540459wmg.3 for <44613@debbugs.gnu.org>; Fri, 13 Nov 2020 08:01:28 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:in-reply-to:references:date:message-id:mime-version :content-transfer-encoding; bh=2BCsQuEQKqsJxDSTf1/r2YdgBUtvi+Ng+NnQ7si9uYY=; b=PVRXjc0XgP1TBO17iEg7v/GK7yheZ7gaCz3DQQZVSxrHgeB5zE5TguPRh9zQjLNSB3 XzpVh2FEt6gQd83Eg05sDERO1JYlxRO5HiQKmj2s/ln/w4KQyoPDvhgeevTzlR9cEsa2 flR0KTAVUg8SvdvIyQh+WKydaf0bXaZTz4eTS/XN1+ZMIvyFzg5wft8ltTzWR0YnF5Kn PE6Td/Zpz6sfYLetgTazYccw/wEwaTCrS2k1RxlXKb9KmzgAwZhGCWNcAQ6iB5/I7W3p R07v8SvUzAI2bECKMTVDTQEyOc5Mh/1PhJeTGvY2nJUiDQv9/efWiwVtHDPWSvAoTCIO 70Gg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:in-reply-to:references:date :message-id:mime-version:content-transfer-encoding; bh=2BCsQuEQKqsJxDSTf1/r2YdgBUtvi+Ng+NnQ7si9uYY=; b=Iur8uZakAyBy4bmxCc7dpFtsz9qWJuaZC33LfKuvCXu4I8/I05pMccJqBLHiPOPrlx IciPqKzdud89UgDzVHaFL7rNuYI9M7VOcW/TIzMdKWtFBCJI2pcTMql/d3+Ea+NmsQJ8 d1SeOoJrToVsPOc6aoIii9yXfXLTcMdjxUj9FJZWfmnk7kD8CH6GCynsizQDAS+XryuB Ljz9F/LBYUhVvz10FS1Lw++GVBIu8wPZhFbHTjQJ+rNH9djIKSF+gJZlya9QL5FUYjh/ VRw85IBan5rgis0S134UR1ZxOVnlbtHNkQ/Uo2JCcaBdhG/5dP/tdUYb9t0A6H04hpga DAdA== X-Gm-Message-State: AOAM532P0Befub8BDtIsuOqhgDKMT7XaD3ZIZUv7ZdLfxldWnfU2STEa 6fpTATnv4CbSvF6OxKznvLB+Jg+xAZzaMg== X-Google-Smtp-Source: ABdhPJzump4/Z5eOCChiKWa66IXiQnxvEJ/r8hS78TjMvh/cr5w0TrTp0Vigb0olBWzGUxTefsGjlQ== X-Received: by 2002:a1c:4646:: with SMTP id t67mr3366969wma.40.1605283276456; Fri, 13 Nov 2020 08:01:16 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id b8sm12216193wrv.57.2020.11.13.08.01.15 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 13 Nov 2020 08:01:15 -0800 (PST) From: zimoun In-Reply-To: <87o8k1b8gk.fsf@gnu.org> References: <86v9e9e8gz.fsf@gmail.com> <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> <86k0upe5yp.fsf@gmail.com> <87o8k1b8gk.fsf@gnu.org> Date: Fri, 13 Nov 2020 16:51:46 +0100 Message-ID: <86eekxdzl9.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Marius, Thank you for the explanations. On Fri, 13 Nov 2020 at 16:08, Marius Bakke wrote: > zimoun writes: > >> PS: >> I am always confused if the removal should be done in =E2=80=99origin=E2= =80=99 or in the >> =E2=80=99add-after 'unpack=E2=80=99 phase; especially when the bundle is= free software. >> Other said, what should an user expect when fetching with =E2=80=9Cguix = build -S=E2=80=9D? >> Anyway! :-) > > Unbundling is always better to do in a snippet. It leads to less > bandwidth usage, and users can more easily inspect the (actual) code. Well, I do not know. For example, I could do this workflow: guix environment bedtools tar -xvf $(guix build -S bedtools) make which probably fails because removing the bundles often needs some extra tweaks. Concretely, see python-pysam for instance: --8<---------------cut here---------------start------------->8--- (snippet '(begin ;; Drop bundled htslib. TODO: Also remove samtools ;; and bcftools. (delete-file-recursively "htslib") #t)))) [...] #:phases (modify-phases %standard-phases (add-before 'build 'set-flags (lambda* (#:key inputs #:allow-other-keys) (setenv "HTSLIB_MODE" "external") (setenv "HTSLIB_LIBRARY_DIR" (string-append (assoc-ref inputs "htslib") "/lib")) (setenv "HTSLIB_INCLUDE_DIR" (string-append (assoc-ref inputs "htslib") "/include")) --8<---------------cut here---------------end--------------->8--- Then, I am not convince that: guix build bedtools --with-git-url=3Dhttp://example.org works too. Or =E2=80=99--with-source=3D=E2=80=99 as well. I remember a di= scussion initiated by Mark and Maxim about this: snippet vs phases but I am not able to reach it. > For other kinds of patching the boundary is less clear. Generally, > Guix-specific tweaks should be in a phase, but "universal" bug fixes may > well be in a snippet. I agree that non-free and bug fixes should go to snippet. Then I am still confused and my feelings are mixed about Guix specific tweaks. > I sometimes imagine a downstream distribution that use Guix sources, but > not the build scripts, to draw the line. It seems a good criteria to draw the line. And in the case of bedtools or python-pysam or many others, =E2=80=99snippet=E2=80=99 removes (free sof= tware) bundles because of an implicit and non-uniform Guix policy that a downstream distribution could choose differently. Well, my mind is not clear about this topic. :-) All the best, simon