From unknown Sun Aug 10 09:46:33 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#35207 <35207@debbugs.gnu.org> To: bug#35207 <35207@debbugs.gnu.org> Subject: Status: [PATCH] Resurrect pplacer. Reply-To: bug#35207 <35207@debbugs.gnu.org> Date: Sun, 10 Aug 2025 16:46:33 +0000 retitle 35207 [PATCH] Resurrect pplacer. reassign 35207 guix-patches submitter 35207 Ricardo Wurmus severity 35207 normal tag 35207 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 09 09:02:23 2019 Received: (at submit) by debbugs.gnu.org; 9 Apr 2019 13:02:23 +0000 Received: from localhost ([127.0.0.1]:50725 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqOM-0000XK-Va for submit@debbugs.gnu.org; Tue, 09 Apr 2019 09:02:23 -0400 Received: from eggs.gnu.org ([209.51.188.92]:39606) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqOK-0000X7-IG for submit@debbugs.gnu.org; Tue, 09 Apr 2019 09:02:21 -0400 Received: from lists.gnu.org ([209.51.188.17]:53505) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hDqOF-00038i-8x for submit@debbugs.gnu.org; Tue, 09 Apr 2019 09:02:15 -0400 Received: from eggs.gnu.org ([209.51.188.92]:53940) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hDqOE-0001lU-6g for guix-patches@gnu.org; Tue, 09 Apr 2019 09:02:15 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=BAYES_40,URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hDqO9-0002uG-4u for guix-patches@gnu.org; Tue, 09 Apr 2019 09:02:14 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21307) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hDqO6-0001K2-T8 for guix-patches@gnu.org; Tue, 09 Apr 2019 09:02:09 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554814808; cv=none; d=zoho.com; s=zohoarc; b=CUlVmMqrAONFmytM/5s3OJ6yCMhly+K2EBUL05YUfuUs7M7KVQEQsukUySdqH9+TW3vJoRC+JT/lOcyftc6/5s//LzBDTsIJXYVUC0tdDcLnk6YzToUczZU6s3sFOqYya5Mz+X2r4K+lFnj9BNeGVWTcWjcVUOQHrfb6W8fzjjI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554814808; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To:ARC-Authentication-Results; bh=nO9CfNIFNQK1Ec7muWv61/kpcCJDiSxI1z/o2u7Z8cA=; b=LJUQ6SeUA4GlA6S+VJk4V4E1yFRViwgSemlpGFqh7vnb3Mesl/BJuE2GWc41C8w5giZrnChacZbkZIWAaKU751HpwcCuXtS2q9U5Ar91yOTzQoPqKUCwTYFP5FzaxXT0c961+4UwmfNiJHNlIFmp2Efo3N6oQY0Y1ia/2dE1r1E= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554814808; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Subject:Date:Message-ID:MIME-Version:Content-Type; l=136; bh=nO9CfNIFNQK1Ec7muWv61/kpcCJDiSxI1z/o2u7Z8cA=; b=U5Rgnch5EGFEaaSyMbt0WlZ+HuH5DKHpLEu8A8qTYPg3AettKE/UkOv9wFpc/590 4IXlalk/Lrre0DdGvJkly31/ZSrhWujVvaUlZ9RPqh0P+w2pup9vnL7Wh9Vs85sGx8A FAsKZlZmhaTCq2EvKEJ22gpRZIRmYaGcja4q/Hec= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 1554814806001546.1903934961518; Tue, 9 Apr 2019 06:00:06 -0700 (PDT) User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: guix-patches@gnu.org Subject: [PATCH] Resurrect pplacer. X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 09 Apr 2019 15:00:02 +0200 Message-ID: <87zhoze3l9.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 136.143.188.53 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: 1.0 (+) 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: -0.0 (/) Hi Guix, this patch series adds pplacer, which had been removed due to its dependency on the vulnerable OCaml 4.01. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 09 09:19:58 2019 Received: (at 35207) by debbugs.gnu.org; 9 Apr 2019 13:19:58 +0000 Received: from localhost ([127.0.0.1]:50754 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqfN-0000zi-Gy for submit@debbugs.gnu.org; Tue, 09 Apr 2019 09:19:57 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21336) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqfK-0000zS-BO for 35207@debbugs.gnu.org; Tue, 09 Apr 2019 09:19:55 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554815979; cv=none; d=zoho.com; s=zohoarc; b=m2PikMBchOFQPWs4e869lVEYykfHPd+Wiulsg/DLZhMM4wiZBjogtCzpYeGnXIZ167FStz9XFA2/97xbtQNf3MptgHPYnC0bdXz/RvhVvo+iDTzbcWwIuoKocg6CeAHBH+NlUuPVhPn+LMHx+KCbxdBnf2WCRycLHD1I3l2iu6U= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554815979; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:MIME-Version:Message-ID:Subject:To:ARC-Authentication-Results; bh=Is9vu6aDCcvofDsWg2XFQSVUSnBi6KHFOyeIA8mF7rU=; b=PO37Xi+1iciOMl2qdpGFOdx6qQ2z+fgOQbuYkwrwNDbb/YvsOoXtf/DySD8jRK6VaAHv+QsnOXBAgWyMe16re52fLOz1rn6+7xsrRyFs0JctE/KJy1I3nR6SQ9DdoiQEaSVSYm8meMvFC1VUaOqcL9HXdTcf6vW5Qb4DyWQBx6U= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554815979; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Message-ID:Subject:Date:MIME-Version:Content-Transfer-Encoding:Content-Type; l=647; bh=Is9vu6aDCcvofDsWg2XFQSVUSnBi6KHFOyeIA8mF7rU=; b=JRAeW/N03atri/hLHdDn56Bq9e5fp97hDDtChgrMqY3NYCMl0fGr1xHNsVX1avH9 qpqRvT1pJDRBZtmehTFyOiM2vPeSRjyjW1lGXsIyedhvGcePsiMdlFyfwYctf26ldCq LSkp33qjE1TRCEZcdIosT6fg4zvnBJnggg6yxuYo= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 1554815977480540.6285492215573; Tue, 9 Apr 2019 06:19:37 -0700 (PDT) From: Ricardo Wurmus To: 35207@debbugs.gnu.org Message-ID: <20190409131330.12089-1-rekado@elephly.net> Subject: [PATCH 1/3] gnu: Add ocaml4.02-mcl. Date: Tue, 9 Apr 2019 15:13:28 +0200 X-Mailer: git-send-email 2.20.1 MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Content-Type: text/plain; charset=utf8 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 Cc: Ricardo Wurmus 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 (-) * gnu/packages/machine-learning.scm (ocaml4.02-mcl): New variable. --- gnu/packages/machine-learning.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learn= ing.scm index 10aff22206..5b2786b61c 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -334,6 +334,9 @@ networks) based on simulation of (stochastic) flow in g= raphs.") algorithm.") (license license:gpl3))) =20 +(define-public ocaml4.02-mcl + (package-with-ocaml4.02 ocaml-mcl)) + (define-public randomjungle (package (name "randomjungle") --=20 2.20.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 09 09:20:00 2019 Received: (at 35207) by debbugs.gnu.org; 9 Apr 2019 13:20:00 +0000 Received: from localhost ([127.0.0.1]:50757 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqfP-0000zw-VY for submit@debbugs.gnu.org; Tue, 09 Apr 2019 09:20:00 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21354) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqfM-0000za-I4 for 35207@debbugs.gnu.org; Tue, 09 Apr 2019 09:19:56 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554815983; cv=none; d=zoho.com; s=zohoarc; b=I0rHXCpOzazEYO3Jvc6uoivsDNOIc6Wl7nVA68Urwk+O+EUCHBcGmxyuy68yf3h527CPzuuzNHukyAfK7vzOkEieBVthYzG08Wh6Ho1OOEA+9wzCh84MLaLP/WDSi8epmlhgKHv0X1906yQ2XciTv6DsCKC3Nkkexz3jc8OVFXQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554815983; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=l6du7TjnpLCq+v9VGS/+1J9U/K6G+3I/Dpi1NLVLMfA=; b=IV5uBOlHkB7+uYhO5mIzVwQT6XSDusLyuauw8jGc8d0C33PTQjXXxqNepoE5Jec1/sf9i3ffp0GJ9DKxq93H2iRtRNwWZvN1gRevtpTnT4+pfZ4rCfqyl/4XBxRdUA4heYABQflPqrUKPwicJBGf1yUZJwZR/QKhSYfTkGEY/k8= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554815983; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Message-ID:Subject:Date:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Content-Type; l=1136; bh=l6du7TjnpLCq+v9VGS/+1J9U/K6G+3I/Dpi1NLVLMfA=; b=KFe9RBPfgxxu82/w41A0lLkZwPlRv08QUT2sbVlm32QRdsJqbiMmFP4S6K2jLh0r 6S1/2BQAWkeVaLJx8iYOdt91deAqh1+w7XIOStyL7Eho26oBbhuVICPoC7pocw9i08P zuAX/WOXw1ZEkTAYcC64zvjz9gKda/ALw4c2xSog= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 1554815981724704.8984858955747; Tue, 9 Apr 2019 06:19:41 -0700 (PDT) From: Ricardo Wurmus To: 35207@debbugs.gnu.org Message-ID: <20190409131330.12089-2-rekado@elephly.net> Subject: [PATCH 2/3] gnu: Add ocaml4.02-gsl. Date: Tue, 9 Apr 2019 15:13:29 +0200 X-Mailer: git-send-email 2.20.1 In-Reply-To: <20190409131330.12089-1-rekado@elephly.net> References: <20190409131330.12089-1-rekado@elephly.net> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Content-Type: text/plain; charset=utf8 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 Cc: Ricardo Wurmus 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 (-) * gnu/packages/ocaml.scm (ocaml4.02-gsl): New variable. --- gnu/packages/ocaml.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 7bebf3921b..bf5d39db6c 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -4824,6 +4824,28 @@ Atom.") the OCaml language.") (license license:gpl3+))) =20 +;; This is the last version that can be built with without ocaml-base, whi= ch +;; cannot be built with OCaml 4.02. +(define-public ocaml4.02-gsl + (package + (inherit (package-with-ocaml4.02 ocaml-gsl)) + (version "1.19.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/mmottl/gsl-ocaml" + "/releases/download/v" + version "/gsl-ocaml-" version ".tar.gz")= ) + (sha256 + (base32 + "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh")))) + (build-system ocaml-build-system) + (inputs + `(("gsl" ,gsl))) + (arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib)) + (propagated-inputs '()))) + (define-public cubicle (package (name "cubicle") --=20 2.20.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 09 09:20:05 2019 Received: (at 35207) by debbugs.gnu.org; 9 Apr 2019 13:20:05 +0000 Received: from localhost ([127.0.0.1]:50759 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqfQ-0000zz-8y for submit@debbugs.gnu.org; Tue, 09 Apr 2019 09:20:03 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21358) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDqfN-0000zh-GV for 35207@debbugs.gnu.org; Tue, 09 Apr 2019 09:19:58 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554815987; cv=none; d=zoho.com; s=zohoarc; b=ojq4YrOPLuFO9Dsdod10RL3PdttHuj17zjbHj/iIoBQAhrNoJxUaYQ1y8fU5rwkODmJGLGybgDe6FwQq4V1jG8SOTAHBRmT61oUtJ8bsoUCeZG5M2injJoWQpSjB4lsPZGl6uzzvA+LfhIqzaB7iCsblOo+98fbjUJv03ve68t0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554815987; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=Vr1mjiUTC90bb7B9DdZZSFP1nhgIpOPrUuQdWE6DowE=; b=AmjfIZ/5WcvH9DUgkzGMKkdLGe7R7tGLfvA37M1su4zyxdfn/Sns9VVb+DIyB3H1qY9xpnI3uodFb6KdObsXb414Wc5LbfoGqlW5wRAWCd4oISphl1YAx9KZmKUzxDaPL9YwIBfnXmApwrbqnby8ysEWAGM/rBygWZ2sF2cwOms= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554815987; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Message-ID:Subject:Date:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Content-Type; l=5635; bh=Vr1mjiUTC90bb7B9DdZZSFP1nhgIpOPrUuQdWE6DowE=; b=TzlxoAesrEGp5GEebb08H/pCNiLtIsO9dv6KkOGO1Qg+qjfWBVudqrRU0sj8dKd6 2ILcNVpcGN4bf8go9aPkDz/L68KEUWW6a/8VuJ3lC8/+3titTxYm/XLY4/fY5zsu7mS Y9bh/JsphBU5FS2F+oRI87ZiR3Gb6DqJlGwmmQac= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 155481598555070.68352761901212; Tue, 9 Apr 2019 06:19:45 -0700 (PDT) From: Ricardo Wurmus To: 35207@debbugs.gnu.org Message-ID: <20190409131330.12089-3-rekado@elephly.net> Subject: [PATCH 3/3] gnu: Add pplacer. Date: Tue, 9 Apr 2019 15:13:30 +0200 X-Mailer: git-send-email 2.20.1 In-Reply-To: <20190409131330.12089-1-rekado@elephly.net> References: <20190409131330.12089-1-rekado@elephly.net> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Content-Type: text/plain; charset=utf8 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 Cc: Ricardo Wurmus 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 (-) * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables= . --- gnu/packages/bioinformatics.scm | 151 ++++++++++++++++++++++++++++++++ 1 file changed, 151 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 4cd032abd4..c073519dc3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14555,3 +14555,154 @@ overlapping paired-ended reads into (longer) cons= ensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapte= r sequence for paired-ended data, for which this information is not availabl= e.") (license license:gpl3+))) + +(define-public pplacer + (let ((commit "807f6f3")) + (package + (name "pplacer") + ;; The commit should be updated with each version change. + (version "1.1.alpha19") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/matsen/pplacer.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))= )) + (build-system ocaml-build-system) + (arguments + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:modules ((guix build ocaml-build-system) + (guix build utils) + (ice-9 ftw)) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'fix-build-with-ocaml-4.02 + (lambda _ + (substitute* "myocamlbuild.ml" + (("let run_and_read" m) + (string-append " +let split s ch =3D + let x =3D ref [] in + let rec go s =3D + let pos =3D String.index s ch in + x :=3D (String.before s pos)::!x; + go (String.after s (pos + 1)) + in + try go s + with Not_found -> !x +let split_nl s =3D split s '\\n' +let before_space s =3D + try String.before s (String.index s ' ') + with Not_found -> s + +" m)) + (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m) + (string-append "List.map before_space (split_nl & " m ")= ")) + ((" blank_sep_strings &") "") + ((" Lexing.from_string &") "")) + #t)) + (add-after 'unpack 'replace-bundled-cddlib + (lambda* (#:key inputs #:allow-other-keys) + (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) + (local-dir "cddlib_guix")) + (mkdir local-dir) + (with-directory-excursion local-dir + (invoke "tar" "xvf" cddlib-src)) + (let ((cddlib-src-folder + (string-append local-dir "/" + (list-ref (scandir local-dir) 2) + "/lib-src"))) + (for-each make-file-writable (find-files "cdd_src" ".*"= )) + (for-each + (lambda (file) + (copy-file file + (string-append "cdd_src/" (basename file)= ))) + (find-files cddlib-src-folder ".*[ch]$"))) + #t))) + (add-after 'unpack 'fix-makefile + (lambda _ + ;; Remove system calls to 'git'. + (substitute* "Makefile" + (("^DESCRIPT:=3Dpplacer-.*") + (string-append + "DESCRIPT:=3Dpplacer-$(shell uname)-v" ,version "\n"))) + (substitute* "myocamlbuild.ml" + (("git describe --tags --long .*\\\" with") + (string-append + "echo -n v" ,version "-" ,commit "\" with"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (copy-recursively "bin" bin)) + #t))))) + (inputs + `(("zlib" ,zlib "static") + ("gsl" ,gsl) + ("ocaml-ounit" ,ocaml4.02-ounit) + ("ocaml-batteries" ,ocaml4.02-batteries) + ("ocaml-camlzip" ,ocaml4.02-camlzip) + ("ocaml-csv" ,ocaml4.02-csv) + ("ocaml-sqlite3" ,ocaml4.02-sqlite3) + ("ocaml-xmlm" ,ocaml4.02-xmlm) + ("ocaml-mcl" ,ocaml4.02-mcl) + ("ocaml-gsl" ,ocaml4.02-gsl))) + (native-inputs + `(("cddlib-src" ,(package-source cddlib)) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("pplacer-scripts" ,pplacer-scripts))) + (synopsis "Phylogenetic placement of biological sequences") + (description + "Pplacer places query sequences on a fixed reference phylogenetic t= ree +to maximize phylogenetic likelihood or posterior probability according to = a +reference alignment. Pplacer is designed to be fast, to give useful +information about uncertainty, and to offer advanced visualization and +downstream analysis.") + (home-page "http://matsen.fhcrc.org/pplacer") + (license license:gpl3)))) + +;; This package is installed alongside 'pplacer'. It is a separate packag= e so +;; that it can use the python-build-system for the scripts that are +;; distributed alongside the main OCaml binaries. +(define pplacer-scripts + (package + (inherit pplacer) + (name "pplacer-scripts") + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-scripts-dir + (lambda _ (chdir "scripts") #t)) + (replace 'check + (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)= ) + (add-after 'install 'wrap-executables + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (let ((path (string-append + (assoc-ref inputs "hmmer") "/bin:" + (assoc-ref inputs "infernal") "/bin"))) + (display path) + (wrap-program (string-append bin "/refpkg_align.py") + `("PATH" ":" prefix (,path)))) + (let ((path (string-append + (assoc-ref inputs "hmmer") "/bin"))) + (wrap-program (string-append bin "/hrefpkg_query.py") + `("PATH" ":" prefix (,path))))) + #t))))) + (inputs + `(("infernal" ,infernal) + ("hmmer" ,hmmer))) + (propagated-inputs + `(("python-biopython" ,python2-biopython) + ("taxtastic" ,taxtastic))) + (synopsis "Pplacer Python scripts"))) --=20 2.20.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 09 13:12:54 2019 Received: (at 35207) by debbugs.gnu.org; 9 Apr 2019 17:12:54 +0000 Received: from localhost ([127.0.0.1]:51924 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDuIo-0007QH-En for submit@debbugs.gnu.org; Tue, 09 Apr 2019 13:12:54 -0400 Received: from lepiller.eu ([89.234.186.109]:59414) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDuIn-0007Q8-2B for 35207@debbugs.gnu.org; Tue, 09 Apr 2019 13:12:53 -0400 Received: from [10.186.132.204] (exit05.brasshorncomms.uk [185.104.120.5]) by lepiller.eu (OpenSMTPD) with ESMTPSA id 9a20784e (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256:NO); Tue, 9 Apr 2019 17:12:48 +0000 (UTC) Date: Tue, 09 Apr 2019 19:12:43 +0200 User-Agent: K-9 Mail for Android In-Reply-To: <87zhoze3l9.fsf@elephly.net> References: <87zhoze3l9.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Subject: Re: [bug#35207] [PATCH] Resurrect pplacer. To: Ricardo Wurmus ,35207@debbugs.gnu.org From: Julien Lepiller Message-ID: X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 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 (-) Le 9 avril 2019 15:00:02 GMT+02:00, Ricardo Wurmus a= =C3=A9crit : >Hi Guix, > >this patch series adds pplacer, which had been removed due to its >dependency on the vulnerable OCaml 4=2E01=2E We're going to have the same issue with ocaml-4=2E02, so I don't think we = should add more dependents=2E I'd like to remove ocaml-4=2E02 but I'm a bit= stuck because of bap right now=2E What's the most recent version of ocaml pplacer can use? From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 09 13:41:55 2019 Received: (at 35207) by debbugs.gnu.org; 9 Apr 2019 17:41:55 +0000 Received: from localhost ([127.0.0.1]:51932 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDukt-0008BH-CX for submit@debbugs.gnu.org; Tue, 09 Apr 2019 13:41:55 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21282) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hDukr-0008B8-46 for 35207@debbugs.gnu.org; Tue, 09 Apr 2019 13:41:54 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554831693; cv=none; d=zoho.com; s=zohoarc; b=gfHYfZxFzQw4Y+1MrDmaqieVrGf3SK3sgFeFaKazXOq8uO/pCVCSAZUBy/ULQEul1T7acevtHB+crfrxkUpGxGaFSoN7FftNFFvbKSSHPKdlGAnqrVnx7WtT8yYv6FS5L9n+n/oMfvl67/8GjsVapslE3l8tUININpgvWO24BN0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554831693; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=15dT0vhrYdcUa82aubE46WEBccptYZ1kjat7v4OGRxM=; b=NV1E9nxfU0gqwBrgK+gfJiI30z+sAor9qJoT4AH8SyGAHramM/+aNu8tTkXJxxlAoBl52DuYkbM6R1rBGtJn2SdrlRY4C4lhMi0fYWKAB9wKe2Y749Y/h5lUGijbropgOzt+77aKPb6wnmsPG3gKxFij66I8zomkpNRrziQCNC8= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554831693; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=266; bh=15dT0vhrYdcUa82aubE46WEBccptYZ1kjat7v4OGRxM=; b=hrbsAf/ZFL8Si79pwd3Cl2TNWMlQ4YiRm8OkbQ6HZ8XfssnNK2YOMi662VLP8o73 wPrlgwV7Vr22CGhsA2dQ4p8z2+SqswuteZddLreiIztcfOsZWmURmofBbGRQxeeRgSJ QGAFFHna+lstnJbLp0JeH4mRbDu8inTcUFPThvSw= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 1554831691510114.39339467754849; Tue, 9 Apr 2019 10:41:31 -0700 (PDT) References: <87zhoze3l9.fsf@elephly.net> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Julien Lepiller Subject: Re: [bug#35207] [PATCH] Resurrect pplacer. In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 09 Apr 2019 19:41:27 +0200 Message-ID: <87r2abdqk8.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 Cc: 35207@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: -1.0 (-) Julien Lepiller writes: > What's the most recent version of ocaml pplacer can use? It=E2=80=99s actually 4.01. I don=E2=80=99t know how much effort it=E2=80= =99s going to be to make it work with the latest version. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 11 08:56:22 2019 Received: (at 35207) by debbugs.gnu.org; 11 Apr 2019 12:56:22 +0000 Received: from localhost ([127.0.0.1]:54012 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEZFe-0001QT-2E for submit@debbugs.gnu.org; Thu, 11 Apr 2019 08:56:22 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21362) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEZFY-0001QA-Bt for 35207@debbugs.gnu.org; Thu, 11 Apr 2019 08:56:18 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554987348; cv=none; d=zoho.com; s=zohoarc; b=gPylXsX8Zj2+OL2jUvJpb7ZrxjtqpJbfp89/HqtYnS1KNP//DkW8aGRpOeZB7yxLdmzmDyWeqReOFgju0sUHXQs4iV/N2BGuw36qg7gEABaBOsZoOOMlL7seZG231WQeXxrrI8sr9P6i2BU9Zstbj5DLYeQ3QpFAuV0L0o6qChw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554987348; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=SgKeQNLyMS8dvnp6zHAsNvSqVfVMrsljfoZHdOTzsY4=; b=SclKpJ7UwjaUhCBXlihtpj4mfErDbICBudkejLRYSbjvFPbRuh6YUpgW+zX7X+jkfD9TchSOZHpvsaXPLCOv8FAmsKtZnXyMxf4ZzwWl/IFaBCGtba68YTMeienmHzdMWnykfb4mWus/2IkF+S1hDoFdm1MFbVN3VT+YdGk/bQk= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554987348; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=660; bh=SgKeQNLyMS8dvnp6zHAsNvSqVfVMrsljfoZHdOTzsY4=; b=CpM2Nzp3wqgx0CfC6cNU6zL2wJUYlZWXw0CIkeEPgAkE6RB8RRPgxx0zF9BFt1ot yCEHbuiOmM7F6vjtvGap3uLZtWxY6iio1OoSIrUKH2uyaTH4Ok2SSg+pQ+aqjeE5V9S pQWgSiy5DSgtOOyVUMZEULX/G2MG20wTpkp3DdAQ= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 1554987348090469.5545858061856; Thu, 11 Apr 2019 05:55:48 -0700 (PDT) References: <87zhoze3l9.fsf@elephly.net> <87r2abdqk8.fsf@elephly.net> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Julien Lepiller Subject: Re: [bug#35207] [PATCH] Resurrect pplacer. In-reply-to: <87r2abdqk8.fsf@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 11 Apr 2019 14:55:44 +0200 Message-ID: <87v9zkitv3.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 Cc: 35207@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: -1.0 (-) Ricardo Wurmus writes: > Julien Lepiller writes: > >> What's the most recent version of ocaml pplacer can use? > > It=E2=80=99s actually 4.01. I don=E2=80=99t know how much effort it=E2= =80=99s going to be to > make it work with the latest version. I gave patching pplacer a try, but in more recent versions of OCaml strings are byte streams, so it=E2=80=99s quite a bit of work to figure out where exactly to convert strings to byte streams and back again. I=E2=80=99ll keep working on this for a while, but for now I=E2=80=99d like= to get pplacer resurrected with 4.02 first. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 11 09:02:39 2019 Received: (at 35207) by debbugs.gnu.org; 11 Apr 2019 13:02:39 +0000 Received: from localhost ([127.0.0.1]:54021 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEZLj-0001bS-34 for submit@debbugs.gnu.org; Thu, 11 Apr 2019 09:02:39 -0400 Received: from lepiller.eu ([89.234.186.109]:59460) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEZLf-0001bG-OF for 35207@debbugs.gnu.org; Thu, 11 Apr 2019 09:02:37 -0400 Received: from [100.95.17.185] (89.144.12.17 [89.144.12.17]) by lepiller.eu (OpenSMTPD) with ESMTPSA id 83d7014a (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256:NO); Thu, 11 Apr 2019 13:02:33 +0000 (UTC) Date: Thu, 11 Apr 2019 15:02:28 +0200 User-Agent: K-9 Mail for Android In-Reply-To: <87v9zkitv3.fsf@elephly.net> References: <87zhoze3l9.fsf@elephly.net> <87r2abdqk8.fsf@elephly.net> <87v9zkitv3.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Subject: Re: [bug#35207] [PATCH] Resurrect pplacer. To: Ricardo Wurmus From: Julien Lepiller Message-ID: <9091683B-549B-483B-B476-1B16B22EDA84@lepiller.eu> X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 Cc: 35207@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: -1.0 (-) Le 11 avril 2019 14:55:44 GMT+02:00, Ricardo Wurmus = a =C3=A9crit : > >Ricardo Wurmus writes: > >> Julien Lepiller writes: >> >>> What's the most recent version of ocaml pplacer can use? >> >> It=E2=80=99s actually 4=2E01=2E I don=E2=80=99t know how much effort i= t=E2=80=99s going to be to >> make it work with the latest version=2E > >I gave patching pplacer a try, but in more recent versions of OCaml >strings are byte streams, so it=E2=80=99s quite a bit of work to figure o= ut >where exactly to convert strings to byte streams and back again=2E > >I=E2=80=99ll keep working on this for a while, but for now I=E2=80=99d li= ke to get >pplacer resurrected with 4=2E02 first=2E > >-- >Ricardo Ok, I guess it's acceptable=2E I'll fully review your patches later today= =2E From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 11 10:57:11 2019 Received: (at 35207) by debbugs.gnu.org; 11 Apr 2019 14:57:11 +0000 Received: from localhost ([127.0.0.1]:55022 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEb8Z-0004jn-GT for submit@debbugs.gnu.org; Thu, 11 Apr 2019 10:57:11 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21207) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEb8X-0004jc-9V for 35207@debbugs.gnu.org; Thu, 11 Apr 2019 10:57:10 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554994599; cv=none; d=zoho.com; s=zohoarc; b=KNVGw4Gsz7W8utiaDITQ+k97DTZkm41F1CTp2GU/NsaPlk4vLy5p64NYKHRoX1v+B7cjiQz+BCJjBhK5tsCDYNP84leTd+YW4GRvYznZwTEJZgNx4ZX1dCs0yj9IpS8O4/rcvhsxtDsfOOa3/7GzGiPxNotSN4tPnCCj0Q66mzQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554994599; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=srozYJi2CP0/1jpl0zaRTwow5gt5Cx1+erafAeY4p2A=; b=MYMqS8Q7Y9KInUAh4Yf9nK/wQYquncX3xLscVs8fsMhawCfGThWqBWNjB9fu13VwT2f9MjKPfF2c/47DoXj4DwoGCt+zJkO8RHeZWq6pjnC+lAVSAi2mY0+9PPhGXoK4ncGW+g2mxwdNEPfmR7kvcL4b5Sk/YdZk4Y1fyv38UUE= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554994599; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=1163; bh=srozYJi2CP0/1jpl0zaRTwow5gt5Cx1+erafAeY4p2A=; b=hUb/THk27Nqav5Kg2z1xoL+mDg7uZFFik7CzPBX169Cco+us5CGrvF6WOsZGFIEk Ta/zMqigSnK4vc/X95pEstzggWY3zv32IGEAGlTah5/qyPQ4EWUPD04W3xo7hipcxQU Z9g61CVzB9Z84Hi/UbB0fvHhcqRkLuyRH6RAtBD4= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 1554994597461670.9133375571216; Thu, 11 Apr 2019 07:56:37 -0700 (PDT) References: <87zhoze3l9.fsf@elephly.net> <87r2abdqk8.fsf@elephly.net> <87v9zkitv3.fsf@elephly.net> <9091683B-549B-483B-B476-1B16B22EDA84@lepiller.eu> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Julien Lepiller Subject: Re: [bug#35207] [PATCH] Resurrect pplacer. In-reply-to: <9091683B-549B-483B-B476-1B16B22EDA84@lepiller.eu> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 11 Apr 2019 16:56:32 +0200 Message-ID: <87sguoio9r.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207 Cc: 35207@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: -1.0 (-) Julien Lepiller writes: > Le 11 avril 2019 14:55:44 GMT+02:00, Ricardo Wurmus = a =C3=A9crit : >> >>Ricardo Wurmus writes: >> >>> Julien Lepiller writes: >>> >>>> What's the most recent version of ocaml pplacer can use? >>> >>> It=E2=80=99s actually 4.01. I don=E2=80=99t know how much effort it=E2= =80=99s going to be to >>> make it work with the latest version. >> >>I gave patching pplacer a try, but in more recent versions of OCaml >>strings are byte streams, so it=E2=80=99s quite a bit of work to figure o= ut >>where exactly to convert strings to byte streams and back again. >> >>I=E2=80=99ll keep working on this for a while, but for now I=E2=80=99d li= ke to get >>pplacer resurrected with 4.02 first. >> >>-- >>Ricardo > > Ok, I guess it's acceptable. I'll fully review your patches later today. Thanks for the offer, but it won=E2=80=99t be necessary after all. I figur= ed out how to make it work with the latest OCaml. I had to also patch ocaml-mcl, but that seems okay. New patches coming in a few minutes! -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 11 11:39:02 2019 Received: (at 35207-done) by debbugs.gnu.org; 11 Apr 2019 15:39:02 +0000 Received: from localhost ([127.0.0.1]:55043 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEbn3-0005nh-Sw for submit@debbugs.gnu.org; Thu, 11 Apr 2019 11:39:02 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21265) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hEbn1-0005nI-Aq for 35207-done@debbugs.gnu.org; Thu, 11 Apr 2019 11:39:00 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1554996208; cv=none; d=zoho.com; s=zohoarc; b=CEqV2Nr4btHEE3iEo7aZj9jzX8+VuRrwJM15MHryBXJwwVbkDpssnrYdkskBGtXzMZ9t5pmH4lYQOrFa8VqbZeqfPD2qB4cSCFrV3kkWw9Fpf4WPjnjmXUHB6HCentvRACCQJbvZECG5UYkgmFptUUMrOYaIADZpGp6XImfB/hw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1554996208; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=lfWAmqUmfxBycp7AJrodMzG1iq6Z1PAhr4SuppCWDv8=; b=Q0OQ9MIiLDMCJK9VtScLDbx74SyhhIuzjjC/9Pehxspz1raTYQBbR6mKKLmf71xpI8Umw7EowyzrakAEHpLRwEEikZUqGmdlTmuoKs/ucS6ab35EiyG6XxfLBFhg7qDWHzADnko73Cgj8s3SNG0y5woYPr0vf2gCw2RFM1BDYtg= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1554996208; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=1342; bh=lfWAmqUmfxBycp7AJrodMzG1iq6Z1PAhr4SuppCWDv8=; b=QD/DLQ8drfKLh4OtkTEjy3Jc+WR+hzYx2zW110ktq4bXB5GMnNixO9zkUZmHma32 WLH1inkU2AUTFJZTpHAZmaoJJEFDD65w6Lc0uPfkioNlkepn8HYrJ9GFgTHvp9vjAPM v1gFaRccmDADH0xoAkOZCzWRhZVO9IR0+QXwRVtc= Received: from localhost (141.80.247.154 [141.80.247.154]) by mx.zohomail.com with SMTPS id 1554996204462560.1927106848323; Thu, 11 Apr 2019 08:23:24 -0700 (PDT) References: <87zhoze3l9.fsf@elephly.net> <87r2abdqk8.fsf@elephly.net> <87v9zkitv3.fsf@elephly.net> <9091683B-549B-483B-B476-1B16B22EDA84@lepiller.eu> <87sguoio9r.fsf@elephly.net> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Julien Lepiller Subject: Re: [bug#35207] [PATCH] Resurrect pplacer. In-reply-to: <87sguoio9r.fsf@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 11 Apr 2019 17:23:21 +0200 Message-ID: <87pnpsin12.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35207-done Cc: 35207-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: -1.0 (-) Ricardo Wurmus writes: > Julien Lepiller writes: > >> Le 11 avril 2019 14:55:44 GMT+02:00, Ricardo Wurmus = a =C3=A9crit : >>> >>>Ricardo Wurmus writes: >>> >>>> Julien Lepiller writes: >>>> >>>>> What's the most recent version of ocaml pplacer can use? >>>> >>>> It=E2=80=99s actually 4.01. I don=E2=80=99t know how much effort it= =E2=80=99s going to be to >>>> make it work with the latest version. >>> >>>I gave patching pplacer a try, but in more recent versions of OCaml >>>strings are byte streams, so it=E2=80=99s quite a bit of work to figure = out >>>where exactly to convert strings to byte streams and back again. >>> >>>I=E2=80=99ll keep working on this for a while, but for now I=E2=80=99d l= ike to get >>>pplacer resurrected with 4.02 first. >>> >>>-- >>>Ricardo >> >> Ok, I guess it's acceptable. I'll fully review your patches later today. > > Thanks for the offer, but it won=E2=80=99t be necessary after all. I fig= ured > out how to make it work with the latest OCaml. I had to also patch > ocaml-mcl, but that seems okay. > > New patches coming in a few minutes! I pushed the new patches to the =E2=80=9Cmaster=E2=80=9D branch with commit= 12327d7447. --=20 Ricardo From unknown Sun Aug 10 09:46:33 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 10 May 2019 11:24:04 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator