diff options
Diffstat (limited to 'tests/data/spool/archive/95/26095.log')
| -rw-r--r-- | tests/data/spool/archive/95/26095.log | 6099 |
1 files changed, 6099 insertions, 0 deletions
diff --git a/tests/data/spool/archive/95/26095.log b/tests/data/spool/archive/95/26095.log new file mode 100644 index 0000000..0ce0092 --- /dev/null +++ b/tests/data/spool/archive/95/26095.log @@ -0,0 +1,6099 @@ + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489480202 --> +<strong>Report forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: R: do not build recommended packages +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 08:30:02 +0000 +Resent-Message-ID: <handler.26095.B.14894801591162@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: report 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +X-Debbugs-Original-To: guix-patches@gnu.org +Received: via spool by submit@debbugs.gnu.org id=B.14894801591162 + (code B ref -1); Tue, 14 Mar 2017 08:30:02 +0000 +Received: (at submit) by debbugs.gnu.org; 14 Mar 2017 08:29:19 +0000 +Received: from localhost ([127.0.0.1]:54721 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cnhpW-0000Ig-O5 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:18 -0400 +Received: from eggs.gnu.org ([208.118.235.92]:54571) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cnhpV-0000IT-2c + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:17 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpO-00014S-RV + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:11 -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 autolearn=disabled + version=3.3.2 +Received: from lists.gnu.org ([2001:4830:134:3::11]:46586) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpO-00014O-PH + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from eggs.gnu.org ([2001:4830:134:3::10]:45510) + by lists.gnu.org with esmtp (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpM-0005M2-GH + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpH-00011R-KO + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:08 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21020) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpH-00010f-E4 + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:03 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489480138371144.2514938811363; + Tue, 14 Mar 2017 01:28:58 -0700 (PDT) +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Tue, 14 Mar 2017 09:28:55 +0100 +Message-ID: <87h92w1cu0.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x +X-Received-From: 2001:4830:134:3::11 +X-Spam-Score: -4.0 (----) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -4.0 (----) + +This relates to bug 25598 “R packages are not bit-reproducible”. R +itself does not build reproducibly. One of the reasons is that it +includes recommended packages that are built in a random temporary +directory. The build paths for each of these packages is then embedded +in the packages’ “paths.rds” files. + +We don’t have this problem when building the packages with the +“r-build-system” like any other R package. + +This patch set adds package expressions for each of the recommended +packages, disables building of recommended packages, and adds some of +these packages to those R packages that need them. + +I’ve successfully rebuilt all R packages to make sure that these changes +don’t break anything. + +I also have an unpolished patch to fix bug 25598, but it depends on this +patch set. + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + + + + +<!-- request_addr: Ricardo Wurmus <rekado@example.com> --> +<!-- time:1489480202 --> +<strong>Acknowledgement sent</strong> +to <code>Ricardo Wurmus <rekado@example.com></code>:<br> +New bug report received and forwarded. Copy sent to <code>guix-patches@gnu.org</code>. + + +-t + +Content-Disposition: inline +Content-Transfer-Encoding: quoted-printable +MIME-Version: 1.0 +X-Mailer: MIME-tools 5.505 (Entity 5.505) +Content-Type: text/plain; charset=utf-8 +X-Loop: help-debbugs@gnu.org +From: help-debbugs@gnu.org (GNU bug Tracking System) +To: Ricardo Wurmus <rekado@example.com> +Subject: bug#26095: Acknowledgement (R: do not build recommended packages) +Message-ID: <handler.26095.B.14894801591162.ack@debbugs.gnu.org> +References: <87h92w1cu0.fsf@example.com> +X-Gnu-PR-Message: ack 26095 +X-Gnu-PR-Package: guix-patches +Reply-To: 26095@debbugs.gnu.org +Date: Tue, 14 Mar 2017 08:30:02 +0000 + +Thank you for filing a new bug report with debbugs.gnu.org. + +This is an automatically generated reply to let you know your message +has been received. + +Your message is being forwarded to the package maintainers and other +interested parties for their attention; they will reply in due course. + +Your message has been sent to the package maintainer(s): + guix-patches@gnu.org + +If you wish to submit further information on this problem, please +send it to 26095@debbugs.gnu.org. + +Please do not send mail to help-debbugs@gnu.org unless you wish +to report a problem with the Bug-tracking system. + +--=20 +26095: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D26095 +GNU Bug Tracking System +Contact help-debbugs@gnu.org with problems + + + +Received: (at submit) by debbugs.gnu.org; 14 Mar 2017 08:29:19 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 04:29:18 2017 +Received: from localhost ([127.0.0.1]:54721 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cnhpW-0000Ig-O5 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:18 -0400 +Received: from eggs.gnu.org ([208.118.235.92]:54571) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cnhpV-0000IT-2c + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:17 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpO-00014S-RV + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:11 -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 autolearn=disabled + version=3.3.2 +Received: from lists.gnu.org ([2001:4830:134:3::11]:46586) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpO-00014O-PH + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from eggs.gnu.org ([2001:4830:134:3::10]:45510) + by lists.gnu.org with esmtp (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpM-0005M2-GH + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpH-00011R-KO + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:08 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21020) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpH-00010f-E4 + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:03 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489480138371144.2514938811363; + Tue, 14 Mar 2017 01:28:58 -0700 (PDT) +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +To: guix-patches@gnu.org +Subject: R: do not build recommended packages +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Tue, 14 Mar 2017 09:28:55 +0100 +Message-ID: <87h92w1cu0.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x +X-Received-From: 2001:4830:134:3::11 +X-Spam-Score: -4.0 (----) +X-Debbugs-Envelope-To: submit +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -4.0 (----) + +This relates to bug 25598 “R packages are not bit-reproducible”. R +itself does not build reproducibly. One of the reasons is that it +includes recommended packages that are built in a random temporary +directory. The build paths for each of these packages is then embedded +in the packages’ “paths.rds” files. + +We don’t have this problem when building the packages with the +“r-build-system” like any other R package. + +This patch set adds package expressions for each of the recommended +packages, disables building of recommended packages, and adds some of +these packages to those R packages that need them. + +I’ve successfully rebuilt all R packages to make sure that these changes +don’t break anything. + +I also have an unpolished patch to fix bug 25598, but it depends on this +patch set. + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482241 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 02/17] gnu: Add r-mass. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:01 +0000 +Resent-Message-ID: <handler.26095.B26095.148948219010932@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948219010932 + (code B ref 26095); Tue, 14 Mar 2017 09:04:01 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:10 +0000 +Received: from localhost ([127.0.0.1]:54736 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMH-0002qE-Pe + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:09 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21033) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMG-0002q0-8j + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:08 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482184868114.23117059581193; + Tue, 14 Mar 2017 02:03:04 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:41 +0100 +Message-Id: <20170314090256.7695-2-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-mass): New variable. +--- + gnu/packages/statistics.scm | 21 +++++++++++++++++++++ + 1 file changed, 21 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 54305a2f8..189a1d299 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -241,6 +241,27 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") + ;; Unlimited distribution + (license (license:non-copyleft "file://R/bootfuns.q")))) + ++(define-public r-mass ++ (package ++ (name "r-mass") ++ (version "7.3-45") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "MASS" version)) ++ (sha256 ++ (base32 ++ "13lp5919h2bnpmf8rbmkar8a41yx62fnx66pkvljvqf60wa29qsx")))) ++ (properties `((upstream-name . "MASS"))) ++ (build-system r-build-system) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "Support functions and datasets for Venables and Ripley's MASS") ++ (description ++ "This package provides functions and datasets for the book \"Modern ++Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") ++ ;; Either version may be picked. ++ (license (list license:gpl2 license:gpl3)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:10 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:10 2017 +Received: from localhost ([127.0.0.1]:54736 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMH-0002qE-Pe + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:09 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21033) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMG-0002q0-8j + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:08 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482184868114.23117059581193; + Tue, 14 Mar 2017 02:03:04 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 02/17] gnu: Add r-mass. +Date: Tue, 14 Mar 2017 10:02:41 +0100 +Message-Id: <20170314090256.7695-2-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-mass): New variable. +--- + gnu/packages/statistics.scm | 21 +++++++++++++++++++++ + 1 file changed, 21 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 54305a2f8..189a1d299 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -241,6 +241,27 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") + ;; Unlimited distribution + (license (license:non-copyleft "file://R/bootfuns.q")))) + ++(define-public r-mass ++ (package ++ (name "r-mass") ++ (version "7.3-45") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "MASS" version)) ++ (sha256 ++ (base32 ++ "13lp5919h2bnpmf8rbmkar8a41yx62fnx66pkvljvqf60wa29qsx")))) ++ (properties `((upstream-name . "MASS"))) ++ (build-system r-build-system) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "Support functions and datasets for Venables and Ripley's MASS") ++ (description ++ "This package provides functions and datasets for the book \"Modern ++Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") ++ ;; Either version may be picked. ++ (license (list license:gpl2 license:gpl3)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482242 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 01/17] gnu: Add r-boot. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:02 +0000 +Resent-Message-ID: <handler.26095.B26095.148948219110941@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948219110941 + (code B ref 26095); Tue, 14 Mar 2017 09:04:02 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:11 +0000 +Received: from localhost ([127.0.0.1]:54738 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMI-0002qH-0U + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:11 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21014) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMG-0002py-62 + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:09 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482181810718.3930901673849; + Tue, 14 Mar 2017 02:03:01 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:40 +0100 +Message-Id: <20170314090256.7695-1-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <87h92w1cu0.fsf@example.com> +References: <87h92w1cu0.fsf@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-boot): New variable. +--- + gnu/packages/statistics.scm | 21 +++++++++++++++++++++ + 1 file changed, 21 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 75bdb5df8..54305a2f8 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -220,6 +220,27 @@ publication-quality data plots. A large amount of 3rd-party packages are + available, greatly increasing its breadth and scope.") + (license license:gpl3+))) + ++(define-public r-boot ++ (package ++ (name "r-boot") ++ (version "1.3-18") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "boot" version)) ++ (sha256 ++ (base32 ++ "0pi348vvgzn1ny54yxhw6kq6nl7rx9bpr9ji1a6wqs8ah5zj7z8j")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/boot") ++ (synopsis "Bootstrap functions for R") ++ (description ++ "This package provides functions and datasets for bootstrapping from the ++book \"Bootstrap Methods and Their Application\" by A.C. Davison and ++D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") ++ ;; Unlimited distribution ++ (license (license:non-copyleft "file://R/bootfuns.q")))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:11 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:11 2017 +Received: from localhost ([127.0.0.1]:54738 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMI-0002qH-0U + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:11 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21014) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMG-0002py-62 + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:09 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482181810718.3930901673849; + Tue, 14 Mar 2017 02:03:01 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 01/17] gnu: Add r-boot. +Date: Tue, 14 Mar 2017 10:02:40 +0100 +Message-Id: <20170314090256.7695-1-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <87h92w1cu0.fsf@example.com> +References: <87h92w1cu0.fsf@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-boot): New variable. +--- + gnu/packages/statistics.scm | 21 +++++++++++++++++++++ + 1 file changed, 21 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 75bdb5df8..54305a2f8 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -220,6 +220,27 @@ publication-quality data plots. A large amount of 3rd-party packages are + available, greatly increasing its breadth and scope.") + (license license:gpl3+))) + ++(define-public r-boot ++ (package ++ (name "r-boot") ++ (version "1.3-18") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "boot" version)) ++ (sha256 ++ (base32 ++ "0pi348vvgzn1ny54yxhw6kq6nl7rx9bpr9ji1a6wqs8ah5zj7z8j")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/boot") ++ (synopsis "Bootstrap functions for R") ++ (description ++ "This package provides functions and datasets for bootstrapping from the ++book \"Bootstrap Methods and Their Application\" by A.C. Davison and ++D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") ++ ;; Unlimited distribution ++ (license (license:non-copyleft "file://R/bootfuns.q")))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482242 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 03/17] gnu: Add r-class. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:02 +0000 +Resent-Message-ID: <handler.26095.B26095.148948219310954@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948219310954 + (code B ref 26095); Tue, 14 Mar 2017 09:04:02 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:13 +0000 +Received: from localhost ([127.0.0.1]:54741 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniML-0002qc-9W + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:13 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21109) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMI-0002qN-MO + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:11 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482187941337.1994676040965; + Tue, 14 Mar 2017 02:03:07 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:42 +0100 +Message-Id: <20170314090256.7695-3-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-class): New variable. +--- + gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ + 1 file changed, 22 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 189a1d299..9199c0b9e 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -262,6 +262,28 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") + ;; Either version may be picked. + (license (list license:gpl2 license:gpl3)))) + ++(define-public r-class ++ (package ++ (name "r-class") ++ (version "7.3-14") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "class" version)) ++ (sha256 ++ (base32 ++ "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-mass" ,r-mass))) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "R functions for classification") ++ (description ++ "This package provides various functions for classification, including ++k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") ++ ;; Either of the two versions can be picked. ++ (license (list license:gpl2 license:gpl3)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:13 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:13 2017 +Received: from localhost ([127.0.0.1]:54741 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniML-0002qc-9W + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:13 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21109) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMI-0002qN-MO + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:11 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482187941337.1994676040965; + Tue, 14 Mar 2017 02:03:07 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 03/17] gnu: Add r-class. +Date: Tue, 14 Mar 2017 10:02:42 +0100 +Message-Id: <20170314090256.7695-3-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-class): New variable. +--- + gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ + 1 file changed, 22 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 189a1d299..9199c0b9e 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -262,6 +262,28 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") + ;; Either version may be picked. + (license (list license:gpl2 license:gpl3)))) + ++(define-public r-class ++ (package ++ (name "r-class") ++ (version "7.3-14") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "class" version)) ++ (sha256 ++ (base32 ++ "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-mass" ,r-mass))) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "R functions for classification") ++ (description ++ "This package provides various functions for classification, including ++k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") ++ ;; Either of the two versions can be picked. ++ (license (list license:gpl2 license:gpl3)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482243 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 04/17] gnu: Add r-cluster. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:03 +0000 +Resent-Message-ID: <handler.26095.B26095.148948219610971@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948219610971 + (code B ref 26095); Tue, 14 Mar 2017 09:04:03 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:16 +0000 +Received: from localhost ([127.0.0.1]:54744 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMO-0002qs-Ha + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:16 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21116) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMM-0002qk-Qm + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:15 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482191021786.5984999866124; + Tue, 14 Mar 2017 02:03:11 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:43 +0100 +Message-Id: <20170314090256.7695-4-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-cluster): New variable. +--- + gnu/packages/statistics.scm | 20 ++++++++++++++++++++ + 1 file changed, 20 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 9199c0b9e..1492dccfb 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -284,6 +284,26 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") + ;; Either of the two versions can be picked. + (license (list license:gpl2 license:gpl3)))) + ++(define-public r-cluster ++ (package ++ (name "r-cluster") ++ (version "2.0.5") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "cluster" version)) ++ (sha256 ++ (base32 ++ "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/cluster") ++ (synopsis "Methods for cluster analysis") ++ (description ++ "This package provides methods for cluster analysis. It is a much ++extended version of the original from Peter Rousseeuw, Anja Struyf and Mia ++Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:16 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:16 2017 +Received: from localhost ([127.0.0.1]:54744 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMO-0002qs-Ha + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:16 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21116) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMM-0002qk-Qm + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:15 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482191021786.5984999866124; + Tue, 14 Mar 2017 02:03:11 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 04/17] gnu: Add r-cluster. +Date: Tue, 14 Mar 2017 10:02:43 +0100 +Message-Id: <20170314090256.7695-4-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-cluster): New variable. +--- + gnu/packages/statistics.scm | 20 ++++++++++++++++++++ + 1 file changed, 20 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 9199c0b9e..1492dccfb 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -284,6 +284,26 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") + ;; Either of the two versions can be picked. + (license (list license:gpl2 license:gpl3)))) + ++(define-public r-cluster ++ (package ++ (name "r-cluster") ++ (version "2.0.5") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "cluster" version)) ++ (sha256 ++ (base32 ++ "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/cluster") ++ (synopsis "Methods for cluster analysis") ++ (description ++ "This package provides methods for cluster analysis. It is a much ++extended version of the original from Peter Rousseeuw, Anja Struyf and Mia ++Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482243 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 05/17] gnu: Add r-codetools. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:03 +0000 +Resent-Message-ID: <handler.26095.B26095.148948219910986@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948219910986 + (code B ref 26095); Tue, 14 Mar 2017 09:04:03 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:19 +0000 +Received: from localhost ([127.0.0.1]:54747 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMQ-0002r7-Ow + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:18 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21119) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMO-0002qt-Sg + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:17 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482193896711.7762833516957; + Tue, 14 Mar 2017 02:03:13 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:44 +0100 +Message-Id: <20170314090256.7695-5-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-codetools): New variable. +--- + gnu/packages/statistics.scm | 18 ++++++++++++++++++ + 1 file changed, 18 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 1492dccfb..cbf5c14b1 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -304,6 +304,24 @@ extended version of the original from Peter Rousseeuw, Anja Struyf and Mia + Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") + (license license:gpl2+))) + ++(define-public r-codetools ++ (package ++ (name "r-codetools") ++ (version "0.2-15") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "codetools" version)) ++ (sha256 ++ (base32 ++ "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/codetools") ++ (synopsis "Code analysis tools for R") ++ (description "This package provides code analysis tools for R.") ++ ;; Any version of the GPL. ++ (license (list license:gpl2+ license:gpl3+)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:19 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:19 2017 +Received: from localhost ([127.0.0.1]:54747 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMQ-0002r7-Ow + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:18 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21119) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMO-0002qt-Sg + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:17 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482193896711.7762833516957; + Tue, 14 Mar 2017 02:03:13 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 05/17] gnu: Add r-codetools. +Date: Tue, 14 Mar 2017 10:02:44 +0100 +Message-Id: <20170314090256.7695-5-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-codetools): New variable. +--- + gnu/packages/statistics.scm | 18 ++++++++++++++++++ + 1 file changed, 18 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 1492dccfb..cbf5c14b1 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -304,6 +304,24 @@ extended version of the original from Peter Rousseeuw, Anja Struyf and Mia + Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") + (license license:gpl2+))) + ++(define-public r-codetools ++ (package ++ (name "r-codetools") ++ (version "0.2-15") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "codetools" version)) ++ (sha256 ++ (base32 ++ "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/codetools") ++ (synopsis "Code analysis tools for R") ++ (description "This package provides code analysis tools for R.") ++ ;; Any version of the GPL. ++ (license (list license:gpl2+ license:gpl3+)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482243 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 06/17] gnu: Add r-foreign. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:03 +0000 +Resent-Message-ID: <handler.26095.B26095.148948220411010@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948220411010 + (code B ref 26095); Tue, 14 Mar 2017 09:04:03 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:24 +0000 +Received: from localhost ([127.0.0.1]:54751 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMW-0002rV-0b + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:24 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21132) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMV-0002rJ-17 + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:23 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482196923552.914063811571; + Tue, 14 Mar 2017 02:03:16 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:45 +0100 +Message-Id: <20170314090256.7695-6-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-foreign): New variable. +--- + gnu/packages/statistics.scm | 20 ++++++++++++++++++++ + 1 file changed, 20 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index cbf5c14b1..2317b37c3 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -322,6 +322,26 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + ++(define-public r-foreign ++ (package ++ (name "r-foreign") ++ (version "0.8-67") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "foreign" version)) ++ (sha256 ++ (base32 ++ "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/foreign") ++ (synopsis "Read data stored by other statistics software") ++ (description ++ "This package provides functions for reading and writing data stored by ++some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and ++for reading and writing some dBase files.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:24 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:24 2017 +Received: from localhost ([127.0.0.1]:54751 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMW-0002rV-0b + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:24 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21132) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMV-0002rJ-17 + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:23 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482196923552.914063811571; + Tue, 14 Mar 2017 02:03:16 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 06/17] gnu: Add r-foreign. +Date: Tue, 14 Mar 2017 10:02:45 +0100 +Message-Id: <20170314090256.7695-6-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-foreign): New variable. +--- + gnu/packages/statistics.scm | 20 ++++++++++++++++++++ + 1 file changed, 20 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index cbf5c14b1..2317b37c3 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -322,6 +322,26 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + ++(define-public r-foreign ++ (package ++ (name "r-foreign") ++ (version "0.8-67") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "foreign" version)) ++ (sha256 ++ (base32 ++ "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/foreign") ++ (synopsis "Read data stored by other statistics software") ++ (description ++ "This package provides functions for reading and writing data stored by ++some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and ++for reading and writing some dBase files.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482244 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 07/17] gnu: Add r-kernsmooth. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:04 +0000 +Resent-Message-ID: <handler.26095.B26095.148948220411017@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948220411017 + (code B ref 26095); Tue, 14 Mar 2017 09:04:04 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:24 +0000 +Received: from localhost ([127.0.0.1]:54753 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMW-0002rX-8N + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:24 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21130) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMV-0002rI-17 + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:23 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482199917634.0397872636701; + Tue, 14 Mar 2017 02:03:19 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:46 +0100 +Message-Id: <20170314090256.7695-7-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-kernsmooth): New variable. +--- + gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ + 1 file changed, 22 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 2317b37c3..0b092ed15 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -342,6 +342,28 @@ some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and + for reading and writing some dBase files.") + (license license:gpl2+))) + ++(define-public r-kernsmooth ++ (package ++ (name "r-kernsmooth") ++ (version "2.23-15") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "KernSmooth" version)) ++ (sha256 ++ (base32 ++ "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) ++ (properties `((upstream-name . "KernSmooth"))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/KernSmooth") ++ (synopsis "Functions for kernel smoothing") ++ (description ++ "This package provides functions for kernel smoothing (and density ++estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) ++\"Kernel Smoothing\".") ++ ;; Unlimited distribution ++ (license (license:non-copyleft "file://LICENCE.note")))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:24 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:24 2017 +Received: from localhost ([127.0.0.1]:54753 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMW-0002rX-8N + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:24 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21130) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMV-0002rI-17 + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:23 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482199917634.0397872636701; + Tue, 14 Mar 2017 02:03:19 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 07/17] gnu: Add r-kernsmooth. +Date: Tue, 14 Mar 2017 10:02:46 +0100 +Message-Id: <20170314090256.7695-7-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-kernsmooth): New variable. +--- + gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ + 1 file changed, 22 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 2317b37c3..0b092ed15 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -342,6 +342,28 @@ some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and + for reading and writing some dBase files.") + (license license:gpl2+))) + ++(define-public r-kernsmooth ++ (package ++ (name "r-kernsmooth") ++ (version "2.23-15") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "KernSmooth" version)) ++ (sha256 ++ (base32 ++ "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) ++ (properties `((upstream-name . "KernSmooth"))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/KernSmooth") ++ (synopsis "Functions for kernel smoothing") ++ (description ++ "This package provides functions for kernel smoothing (and density ++estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) ++\"Kernel Smoothing\".") ++ ;; Unlimited distribution ++ (license (license:non-copyleft "file://LICENCE.note")))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482244 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 08/17] gnu: r-lattice: Move to other recommended R packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:04 +0000 +Resent-Message-ID: <handler.26095.B26095.148948220811040@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948220811040 + (code B ref 26095); Tue, 14 Mar 2017 09:04:04 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:28 +0000 +Received: from localhost ([127.0.0.1]:54757 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMa-0002rz-Ge + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:28 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21068) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMY-0002rl-AQ + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:26 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 148948220270532.832375765680126; + Tue, 14 Mar 2017 02:03:22 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:47 +0100 +Message-Id: <20170314090256.7695-8-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R +packages. +--- + gnu/packages/statistics.scm | 40 ++++++++++++++++++++-------------------- + 1 file changed, 20 insertions(+), 20 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 0b092ed15..0fa3be42c 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -364,6 +364,26 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) + ;; Unlimited distribution + (license (license:non-copyleft "file://LICENCE.note")))) + ++(define-public r-lattice ++ (package ++ (name "r-lattice") ++ (version "0.20-34") ++ (source (origin ++ (method url-fetch) ++ (uri (cran-uri "lattice" version)) ++ (sha256 ++ (base32 ++ "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) ++ (build-system r-build-system) ++ (home-page "http://lattice.r-forge.r-project.org/") ++ (synopsis "High-level data visualization system") ++ (description ++ "The lattice package provides a powerful and elegant high-level data ++visualization system inspired by Trellis graphics, with an emphasis on ++multivariate data. Lattice is sufficient for typical graphics needs, and is ++also flexible enough to handle most nonstandard requirements.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -2171,26 +2191,6 @@ scaling functions for R.") + "This package provides an integration of base and grid graphics for R.") + (license license:gpl2+))) + +-(define-public r-lattice +- (package +- (name "r-lattice") +- (version "0.20-34") +- (source (origin +- (method url-fetch) +- (uri (cran-uri "lattice" version)) +- (sha256 +- (base32 +- "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) +- (build-system r-build-system) +- (home-page "http://lattice.r-forge.r-project.org/") +- (synopsis "High-level data visualization system") +- (description +- "The lattice package provides a powerful and elegant high-level data +-visualization system inspired by Trellis graphics, with an emphasis on +-multivariate data. Lattice is sufficient for typical graphics needs, and is +-also flexible enough to handle most nonstandard requirements.") +- (license license:gpl2+))) +- + (define-public r-latticeextra + (package + (name "r-latticeextra") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:28 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:28 2017 +Received: from localhost ([127.0.0.1]:54757 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMa-0002rz-Ge + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:28 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21068) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMY-0002rl-AQ + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:26 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 148948220270532.832375765680126; + Tue, 14 Mar 2017 02:03:22 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 08/17] gnu: r-lattice: Move to other recommended R packages. +Date: Tue, 14 Mar 2017 10:02:47 +0100 +Message-Id: <20170314090256.7695-8-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R +packages. +--- + gnu/packages/statistics.scm | 40 ++++++++++++++++++++-------------------- + 1 file changed, 20 insertions(+), 20 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 0b092ed15..0fa3be42c 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -364,6 +364,26 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) + ;; Unlimited distribution + (license (license:non-copyleft "file://LICENCE.note")))) + ++(define-public r-lattice ++ (package ++ (name "r-lattice") ++ (version "0.20-34") ++ (source (origin ++ (method url-fetch) ++ (uri (cran-uri "lattice" version)) ++ (sha256 ++ (base32 ++ "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) ++ (build-system r-build-system) ++ (home-page "http://lattice.r-forge.r-project.org/") ++ (synopsis "High-level data visualization system") ++ (description ++ "The lattice package provides a powerful and elegant high-level data ++visualization system inspired by Trellis graphics, with an emphasis on ++multivariate data. Lattice is sufficient for typical graphics needs, and is ++also flexible enough to handle most nonstandard requirements.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -2171,26 +2191,6 @@ scaling functions for R.") + "This package provides an integration of base and grid graphics for R.") + (license license:gpl2+))) + +-(define-public r-lattice +- (package +- (name "r-lattice") +- (version "0.20-34") +- (source (origin +- (method url-fetch) +- (uri (cran-uri "lattice" version)) +- (sha256 +- (base32 +- "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) +- (build-system r-build-system) +- (home-page "http://lattice.r-forge.r-project.org/") +- (synopsis "High-level data visualization system") +- (description +- "The lattice package provides a powerful and elegant high-level data +-visualization system inspired by Trellis graphics, with an emphasis on +-multivariate data. Lattice is sufficient for typical graphics needs, and is +-also flexible enough to handle most nonstandard requirements.") +- (license license:gpl2+))) +- + (define-public r-latticeextra + (package + (name "r-latticeextra") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482245 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 09/17] gnu: r-matrix: Move to set of recommended R packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:05 +0000 +Resent-Message-ID: <handler.26095.B26095.148948221111051@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948221111051 + (code B ref 26095); Tue, 14 Mar 2017 09:04:05 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:31 +0000 +Received: from localhost ([127.0.0.1]:54759 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMc-0002s9-Om + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:31 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21055) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMa-0002rt-3B + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:28 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482205494208.0975189395151; + Tue, 14 Mar 2017 02:03:25 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:48 +0100 +Message-Id: <20170314090256.7695-9-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R +packages. +--- + gnu/packages/statistics.scm | 44 ++++++++++++++++++++++---------------------- + 1 file changed, 22 insertions(+), 22 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 0fa3be42c..23d6c9392 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -384,6 +384,28 @@ multivariate data. Lattice is sufficient for typical graphics needs, and is + also flexible enough to handle most nonstandard requirements.") + (license license:gpl2+))) + ++(define-public r-matrix ++ (package ++ (name "r-matrix") ++ (version "1.2-7.1") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "Matrix" version)) ++ (sha256 ++ (base32 ++ "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) ++ (properties `((upstream-name . "Matrix"))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) ++ (home-page "http://Matrix.R-forge.R-project.org/") ++ (synopsis "Sparse and dense matrix classes and methods") ++ (description ++ "This package provides classes and methods for dense and sparse matrices ++and operations on them using LAPACK and SuiteSparse.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -623,28 +645,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see + 'citation(\"Rcpp\")' for details on these last two.") + (license license:gpl2+))) + +-(define-public r-matrix +- (package +- (name "r-matrix") +- (version "1.2-7.1") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "Matrix" version)) +- (sha256 +- (base32 +- "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) +- (properties `((upstream-name . "Matrix"))) +- (build-system r-build-system) +- (propagated-inputs +- `(("r-lattice" ,r-lattice))) +- (home-page "http://Matrix.R-forge.R-project.org/") +- (synopsis "Sparse and dense matrix classes and methods") +- (description +- "This package provides classes and methods for dense and sparse matrices +-and operations on them using LAPACK and SuiteSparse.") +- (license license:gpl2+))) +- + (define-public r-mgcv + (package + (name "r-mgcv") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:31 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:31 2017 +Received: from localhost ([127.0.0.1]:54759 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMc-0002s9-Om + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:31 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21055) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMa-0002rt-3B + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:28 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482205494208.0975189395151; + Tue, 14 Mar 2017 02:03:25 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 09/17] gnu: r-matrix: Move to set of recommended R packages. +Date: Tue, 14 Mar 2017 10:02:48 +0100 +Message-Id: <20170314090256.7695-9-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R +packages. +--- + gnu/packages/statistics.scm | 44 ++++++++++++++++++++++---------------------- + 1 file changed, 22 insertions(+), 22 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 0fa3be42c..23d6c9392 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -384,6 +384,28 @@ multivariate data. Lattice is sufficient for typical graphics needs, and is + also flexible enough to handle most nonstandard requirements.") + (license license:gpl2+))) + ++(define-public r-matrix ++ (package ++ (name "r-matrix") ++ (version "1.2-7.1") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "Matrix" version)) ++ (sha256 ++ (base32 ++ "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) ++ (properties `((upstream-name . "Matrix"))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) ++ (home-page "http://Matrix.R-forge.R-project.org/") ++ (synopsis "Sparse and dense matrix classes and methods") ++ (description ++ "This package provides classes and methods for dense and sparse matrices ++and operations on them using LAPACK and SuiteSparse.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -623,28 +645,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see + 'citation(\"Rcpp\")' for details on these last two.") + (license license:gpl2+))) + +-(define-public r-matrix +- (package +- (name "r-matrix") +- (version "1.2-7.1") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "Matrix" version)) +- (sha256 +- (base32 +- "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) +- (properties `((upstream-name . "Matrix"))) +- (build-system r-build-system) +- (propagated-inputs +- `(("r-lattice" ,r-lattice))) +- (home-page "http://Matrix.R-forge.R-project.org/") +- (synopsis "Sparse and dense matrix classes and methods") +- (description +- "This package provides classes and methods for dense and sparse matrices +-and operations on them using LAPACK and SuiteSparse.") +- (license license:gpl2+))) +- + (define-public r-mgcv + (package + (name "r-mgcv") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482245 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 10/17] gnu: Add r-nlme. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:05 +0000 +Resent-Message-ID: <handler.26095.B26095.148948221211064@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948221211064 + (code B ref 26095); Tue, 14 Mar 2017 09:04:05 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:32 +0000 +Received: from localhost ([127.0.0.1]:54762 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMe-0002sO-67 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:32 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21001) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMd-0002sA-7N + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:31 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482208236363.193775120444; + Tue, 14 Mar 2017 02:03:28 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:49 +0100 +Message-Id: <20170314090256.7695-10-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-nlme): New variable. +--- + gnu/packages/statistics.scm | 23 +++++++++++++++++++++++ + 1 file changed, 23 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 23d6c9392..c072bcbcb 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -406,6 +406,29 @@ also flexible enough to handle most nonstandard requirements.") + and operations on them using LAPACK and SuiteSparse.") + (license license:gpl2+))) + ++(define-public r-nlme ++ (package ++ (name "r-nlme") ++ (version "3.1-131") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "nlme" version)) ++ (sha256 ++ (base32 ++ "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) ++ (native-inputs ++ `(("gfortran" ,gfortran))) ++ (home-page "http://cran.r-project.org/web/packages/nlme") ++ (synopsis "Linear and nonlinear mixed effects models") ++ (description ++ "This package provides tools to fit and compare Gaussian linear and ++nonlinear mixed-effects models.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:32 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:32 2017 +Received: from localhost ([127.0.0.1]:54762 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMe-0002sO-67 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:32 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21001) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMd-0002sA-7N + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:31 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482208236363.193775120444; + Tue, 14 Mar 2017 02:03:28 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 10/17] gnu: Add r-nlme. +Date: Tue, 14 Mar 2017 10:02:49 +0100 +Message-Id: <20170314090256.7695-10-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-nlme): New variable. +--- + gnu/packages/statistics.scm | 23 +++++++++++++++++++++++ + 1 file changed, 23 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 23d6c9392..c072bcbcb 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -406,6 +406,29 @@ also flexible enough to handle most nonstandard requirements.") + and operations on them using LAPACK and SuiteSparse.") + (license license:gpl2+))) + ++(define-public r-nlme ++ (package ++ (name "r-nlme") ++ (version "3.1-131") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "nlme" version)) ++ (sha256 ++ (base32 ++ "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) ++ (native-inputs ++ `(("gfortran" ,gfortran))) ++ (home-page "http://cran.r-project.org/web/packages/nlme") ++ (synopsis "Linear and nonlinear mixed effects models") ++ (description ++ "This package provides tools to fit and compare Gaussian linear and ++nonlinear mixed-effects models.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482246 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 11/17] gnu: r-mgcv: Move to set of recommended R packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:06 +0000 +Resent-Message-ID: <handler.26095.B26095.148948221511080@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948221511080 + (code B ref 26095); Tue, 14 Mar 2017 09:04:06 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:35 +0000 +Received: from localhost ([127.0.0.1]:54765 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMh-0002sd-DZ + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:35 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21064) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMg-0002sW-8b + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:34 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482211038530.2017426969343; + Tue, 14 Mar 2017 02:03:31 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:50 +0100 +Message-Id: <20170314090256.7695-11-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R +packages. +--- + gnu/packages/statistics.scm | 45 ++++++++++++++++++++++++--------------------- + 1 file changed, 24 insertions(+), 21 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index c072bcbcb..e5237d509 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -429,6 +429,30 @@ and operations on them using LAPACK and SuiteSparse.") + nonlinear mixed-effects models.") + (license license:gpl2+))) + ++(define-public r-mgcv ++ (package ++ (name "r-mgcv") ++ (version "1.8-16") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "mgcv" version)) ++ (sha256 ++ (base32 ++ "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix) ++ ("r-nlme" ,r-nlme))) ++ (home-page "http://cran.r-project.org/web/packages/mgcv") ++ (synopsis "Mixed generalised additive model computation") ++ (description ++ "GAMs, GAMMs and other generalized ridge regression with multiple smoothing ++parameter estimation by GCV, REML or UBRE/AIC. The library includes a ++@code{gam()} function, a wide variety of smoothers, JAGS support and ++distributions beyond the exponential family.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -668,27 +692,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see + 'citation(\"Rcpp\")' for details on these last two.") + (license license:gpl2+))) + +-(define-public r-mgcv +- (package +- (name "r-mgcv") +- (version "1.8-16") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "mgcv" version)) +- (sha256 +- (base32 +- "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) +- (build-system r-build-system) +- (home-page "http://cran.r-project.org/web/packages/mgcv") +- (synopsis "Mixed generalised additive model computation") +- (description +- "GAMs, GAMMs and other generalized ridge regression with multiple smoothing +-parameter estimation by GCV, REML or UBRE/AIC. The library includes a +-@code{gam()} function, a wide variety of smoothers, JAGS support and +-distributions beyond the exponential family.") +- (license license:gpl2+))) +- + (define-public r-permute + (package + (name "r-permute") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:35 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:35 2017 +Received: from localhost ([127.0.0.1]:54765 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMh-0002sd-DZ + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:35 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21064) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMg-0002sW-8b + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:34 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482211038530.2017426969343; + Tue, 14 Mar 2017 02:03:31 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 11/17] gnu: r-mgcv: Move to set of recommended R packages. +Date: Tue, 14 Mar 2017 10:02:50 +0100 +Message-Id: <20170314090256.7695-11-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R +packages. +--- + gnu/packages/statistics.scm | 45 ++++++++++++++++++++++++--------------------- + 1 file changed, 24 insertions(+), 21 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index c072bcbcb..e5237d509 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -429,6 +429,30 @@ and operations on them using LAPACK and SuiteSparse.") + nonlinear mixed-effects models.") + (license license:gpl2+))) + ++(define-public r-mgcv ++ (package ++ (name "r-mgcv") ++ (version "1.8-16") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "mgcv" version)) ++ (sha256 ++ (base32 ++ "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix) ++ ("r-nlme" ,r-nlme))) ++ (home-page "http://cran.r-project.org/web/packages/mgcv") ++ (synopsis "Mixed generalised additive model computation") ++ (description ++ "GAMs, GAMMs and other generalized ridge regression with multiple smoothing ++parameter estimation by GCV, REML or UBRE/AIC. The library includes a ++@code{gam()} function, a wide variety of smoothers, JAGS support and ++distributions beyond the exponential family.") ++ (license license:gpl2+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -668,27 +692,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see + 'citation(\"Rcpp\")' for details on these last two.") + (license license:gpl2+))) + +-(define-public r-mgcv +- (package +- (name "r-mgcv") +- (version "1.8-16") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "mgcv" version)) +- (sha256 +- (base32 +- "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) +- (build-system r-build-system) +- (home-page "http://cran.r-project.org/web/packages/mgcv") +- (synopsis "Mixed generalised additive model computation") +- (description +- "GAMs, GAMMs and other generalized ridge regression with multiple smoothing +-parameter estimation by GCV, REML or UBRE/AIC. The library includes a +-@code{gam()} function, a wide variety of smoothers, JAGS support and +-distributions beyond the exponential family.") +- (license license:gpl2+))) +- + (define-public r-permute + (package + (name "r-permute") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482246 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 12/17] gnu: r-nnet: Move to set of recommended R packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:06 +0000 +Resent-Message-ID: <handler.26095.B26095.148948221911098@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948221911098 + (code B ref 26095); Tue, 14 Mar 2017 09:04:06 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:39 +0000 +Received: from localhost ([127.0.0.1]:54768 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMk-0002st-MI + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:38 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21086) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMj-0002sm-1u + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:37 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482213900182.87795641098103; + Tue, 14 Mar 2017 02:03:33 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:51 +0100 +Message-Id: <20170314090256.7695-12-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/machine-learning.scm (r-nnet): Move from here... +* gnu/packages/statistics.scm (r-nnet): ...to here because the other +recommended R packages are here. +--- + gnu/packages/machine-learning.scm | 19 ------------------- + gnu/packages/statistics.scm | 19 +++++++++++++++++++ + 2 files changed, 19 insertions(+), 19 deletions(-) + +diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm +index 7bad833b3..73c78744f 100644 +--- a/gnu/packages/machine-learning.scm ++++ b/gnu/packages/machine-learning.scm +@@ -460,25 +460,6 @@ adaptive sparsity and the Wong algorithm for adaptively sparse gaussian + geometric models.") + (license license:lgpl3+))) + +-(define-public r-nnet +- (package +- (name "r-nnet") +- (version "7.3-12") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "nnet" version)) +- (sha256 +- (base32 +- "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7")))) +- (build-system r-build-system) +- (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") +- (synopsis "Feed-forward neural networks and multinomial log-linear models") +- (description +- "This package provides functions for feed-forward neural networks with a +-single hidden layer, and for multinomial log-linear models.") +- (license (list license:gpl2+ license:gpl3+)))) +- + (define-public r-kernlab + (package + (name "r-kernlab") +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index e5237d509..29cf32a60 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -453,6 +453,25 @@ parameter estimation by GCV, REML or UBRE/AIC. The library includes a + distributions beyond the exponential family.") + (license license:gpl2+))) + ++(define-public r-nnet ++ (package ++ (name "r-nnet") ++ (version "7.3-12") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "nnet" version)) ++ (sha256 ++ (base32 ++ "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7")))) ++ (build-system r-build-system) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "Feed-forward neural networks and multinomial log-linear models") ++ (description ++ "This package provides functions for feed-forward neural networks with a ++single hidden layer, and for multinomial log-linear models.") ++ (license (list license:gpl2+ license:gpl3+)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:39 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:38 2017 +Received: from localhost ([127.0.0.1]:54768 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMk-0002st-MI + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:38 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21086) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMj-0002sm-1u + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:37 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482213900182.87795641098103; + Tue, 14 Mar 2017 02:03:33 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 12/17] gnu: r-nnet: Move to set of recommended R packages. +Date: Tue, 14 Mar 2017 10:02:51 +0100 +Message-Id: <20170314090256.7695-12-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/machine-learning.scm (r-nnet): Move from here... +* gnu/packages/statistics.scm (r-nnet): ...to here because the other +recommended R packages are here. +--- + gnu/packages/machine-learning.scm | 19 ------------------- + gnu/packages/statistics.scm | 19 +++++++++++++++++++ + 2 files changed, 19 insertions(+), 19 deletions(-) + +diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm +index 7bad833b3..73c78744f 100644 +--- a/gnu/packages/machine-learning.scm ++++ b/gnu/packages/machine-learning.scm +@@ -460,25 +460,6 @@ adaptive sparsity and the Wong algorithm for adaptively sparse gaussian + geometric models.") + (license license:lgpl3+))) + +-(define-public r-nnet +- (package +- (name "r-nnet") +- (version "7.3-12") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "nnet" version)) +- (sha256 +- (base32 +- "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7")))) +- (build-system r-build-system) +- (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") +- (synopsis "Feed-forward neural networks and multinomial log-linear models") +- (description +- "This package provides functions for feed-forward neural networks with a +-single hidden layer, and for multinomial log-linear models.") +- (license (list license:gpl2+ license:gpl3+)))) +- + (define-public r-kernlab + (package + (name "r-kernlab") +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index e5237d509..29cf32a60 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -453,6 +453,25 @@ parameter estimation by GCV, REML or UBRE/AIC. The library includes a + distributions beyond the exponential family.") + (license license:gpl2+))) + ++(define-public r-nnet ++ (package ++ (name "r-nnet") ++ (version "7.3-12") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "nnet" version)) ++ (sha256 ++ (base32 ++ "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7")))) ++ (build-system r-build-system) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "Feed-forward neural networks and multinomial log-linear models") ++ (description ++ "This package provides functions for feed-forward neural networks with a ++single hidden layer, and for multinomial log-linear models.") ++ (license (list license:gpl2+ license:gpl3+)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482247 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 13/17] gnu: r-rpart: Move to the set of recommended packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:07 +0000 +Resent-Message-ID: <handler.26095.B26095.148948222211116@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948222211116 + (code B ref 26095); Tue, 14 Mar 2017 09:04:07 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:42 +0000 +Received: from localhost ([127.0.0.1]:54771 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMn-0002tB-UO + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:42 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21077) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMm-0002t4-GJ + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:40 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482216717193.69834246919174; + Tue, 14 Mar 2017 02:03:36 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:52 +0100 +Message-Id: <20170314090256.7695-13-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended +packages. +--- + gnu/packages/statistics.scm | 38 +++++++++++++++++++------------------- + 1 file changed, 19 insertions(+), 19 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 29cf32a60..8780027d3 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -472,6 +472,25 @@ distributions beyond the exponential family.") + single hidden layer, and for multinomial log-linear models.") + (license (list license:gpl2+ license:gpl3+)))) + ++(define-public r-rpart ++ (package ++ (name "r-rpart") ++ (version "4.1-10") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "rpart" version)) ++ (sha256 ++ (base32 ++ "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/rpart") ++ (synopsis "Recursive partitioning and regression trees") ++ (description ++ "This package provides recursive partitioning functions for ++classification, regression and survival trees.") ++ (license (list license:gpl2+ license:gpl3+)))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -3644,25 +3663,6 @@ following problems: + @end enumerate\n") + (license license:gpl3+))) + +-(define-public r-rpart +- (package +- (name "r-rpart") +- (version "4.1-10") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "rpart" version)) +- (sha256 +- (base32 +- "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) +- (build-system r-build-system) +- (home-page "http://cran.r-project.org/web/packages/rpart") +- (synopsis "Recursive partitioning and regression trees") +- (description +- "This package provides recursive partitioning functions for +-classification, regression and survival trees.") +- (license (list license:gpl2+ license:gpl3+)))) +- + (define-public r-survival + (package + (name "r-survival") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:42 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:42 2017 +Received: from localhost ([127.0.0.1]:54771 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMn-0002tB-UO + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:42 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21077) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMm-0002t4-GJ + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:40 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482216717193.69834246919174; + Tue, 14 Mar 2017 02:03:36 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 13/17] gnu: r-rpart: Move to the set of recommended packages. +Date: Tue, 14 Mar 2017 10:02:52 +0100 +Message-Id: <20170314090256.7695-13-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended +packages. +--- + gnu/packages/statistics.scm | 38 +++++++++++++++++++------------------- + 1 file changed, 19 insertions(+), 19 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 29cf32a60..8780027d3 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -472,6 +472,25 @@ distributions beyond the exponential family.") + single hidden layer, and for multinomial log-linear models.") + (license (list license:gpl2+ license:gpl3+)))) + ++(define-public r-rpart ++ (package ++ (name "r-rpart") ++ (version "4.1-10") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "rpart" version)) ++ (sha256 ++ (base32 ++ "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) ++ (build-system r-build-system) ++ (home-page "http://cran.r-project.org/web/packages/rpart") ++ (synopsis "Recursive partitioning and regression trees") ++ (description ++ "This package provides recursive partitioning functions for ++classification, regression and survival trees.") ++ (license (list license:gpl2+ license:gpl3+)))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -3644,25 +3663,6 @@ following problems: + @end enumerate\n") + (license license:gpl3+))) + +-(define-public r-rpart +- (package +- (name "r-rpart") +- (version "4.1-10") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "rpart" version)) +- (sha256 +- (base32 +- "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) +- (build-system r-build-system) +- (home-page "http://cran.r-project.org/web/packages/rpart") +- (synopsis "Recursive partitioning and regression trees") +- (description +- "This package provides recursive partitioning functions for +-classification, regression and survival trees.") +- (license (list license:gpl2+ license:gpl3+)))) +- + (define-public r-survival + (package + (name "r-survival") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482247 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 14/17] gnu: Add r-spatial. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:07 +0000 +Resent-Message-ID: <handler.26095.B26095.148948222511130@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948222511130 + (code B ref 26095); Tue, 14 Mar 2017 09:04:07 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:45 +0000 +Received: from localhost ([127.0.0.1]:54774 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMr-0002tS-90 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:45 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21139) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMo-0002tC-8Y + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:42 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482219504537.9036992197271; + Tue, 14 Mar 2017 02:03:39 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:53 +0100 +Message-Id: <20170314090256.7695-14-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-spatial): New variable. +--- + gnu/packages/statistics.scm | 20 ++++++++++++++++++++ + 1 file changed, 20 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 8780027d3..b338efcda 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -491,6 +491,26 @@ single hidden layer, and for multinomial log-linear models.") + classification, regression and survival trees.") + (license (list license:gpl2+ license:gpl3+)))) + ++(define-public r-spatial ++ (package ++ (name "r-spatial") ++ (version "7.3-11") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "spatial" version)) ++ (sha256 ++ (base32 ++ "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32")))) ++ (build-system r-build-system) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "Functions for kriging and point pattern analysis") ++ (description ++ "This package provides functions for kriging and point pattern ++analysis.") ++ ;; Either version may be picked. ++ (license (list license:gpl2 license:gpl3)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:45 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:45 2017 +Received: from localhost ([127.0.0.1]:54774 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMr-0002tS-90 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:45 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21139) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMo-0002tC-8Y + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:42 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482219504537.9036992197271; + Tue, 14 Mar 2017 02:03:39 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 14/17] gnu: Add r-spatial. +Date: Tue, 14 Mar 2017 10:02:53 +0100 +Message-Id: <20170314090256.7695-14-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-spatial): New variable. +--- + gnu/packages/statistics.scm | 20 ++++++++++++++++++++ + 1 file changed, 20 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index 8780027d3..b338efcda 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -491,6 +491,26 @@ single hidden layer, and for multinomial log-linear models.") + classification, regression and survival trees.") + (license (list license:gpl2+ license:gpl3+)))) + ++(define-public r-spatial ++ (package ++ (name "r-spatial") ++ (version "7.3-11") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "spatial" version)) ++ (sha256 ++ (base32 ++ "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32")))) ++ (build-system r-build-system) ++ (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") ++ (synopsis "Functions for kriging and point pattern analysis") ++ (description ++ "This package provides functions for kriging and point pattern ++analysis.") ++ ;; Either version may be picked. ++ (license (list license:gpl2 license:gpl3)))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482248 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 15/17] gnu: r-survival: Move to set of recommended R packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:08 +0000 +Resent-Message-ID: <handler.26095.B26095.148948222911148@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948222911148 + (code B ref 26095); Tue, 14 Mar 2017 09:04:08 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:49 +0000 +Received: from localhost ([127.0.0.1]:54778 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMu-0002tj-FN + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:49 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21146) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMs-0002ta-AD + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:46 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482222312655.0922279479503; + Tue, 14 Mar 2017 02:03:42 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:54 +0100 +Message-Id: <20170314090256.7695-15-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R +packages. +--- + gnu/packages/statistics.scm | 42 ++++++++++++++++++++++-------------------- + 1 file changed, 22 insertions(+), 20 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index b338efcda..c836409b6 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -511,6 +511,28 @@ analysis.") + ;; Either version may be picked. + (license (list license:gpl2 license:gpl3)))) + ++(define-public r-survival ++ (package ++ (name "r-survival") ++ (version "2.40-1") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "survival" version)) ++ (sha256 ++ (base32 ++ "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix))) ++ (home-page "https://github.com/therneau/survival") ++ (synopsis "Survival analysis") ++ (description ++ "This package contains the core survival analysis routines, including ++definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) ++curves, Cox models, and parametric accelerated failure time models.") ++ (license license:lgpl2.0+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -3683,26 +3705,6 @@ following problems: + @end enumerate\n") + (license license:gpl3+))) + +-(define-public r-survival +- (package +- (name "r-survival") +- (version "2.40-1") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "survival" version)) +- (sha256 +- (base32 +- "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) +- (build-system r-build-system) +- (home-page "https://github.com/therneau/survival") +- (synopsis "Survival analysis") +- (description +- "This package contains the core survival analysis routines, including +-definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) +-curves, Cox models, and parametric accelerated failure time models.") +- (license license:lgpl2.0+))) +- + (define-public r-base64 + (package + (name "r-base64") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:49 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:49 2017 +Received: from localhost ([127.0.0.1]:54778 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMu-0002tj-FN + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:49 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21146) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMs-0002ta-AD + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:46 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482222312655.0922279479503; + Tue, 14 Mar 2017 02:03:42 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 15/17] gnu: r-survival: Move to set of recommended R packages. +Date: Tue, 14 Mar 2017 10:02:54 +0100 +Message-Id: <20170314090256.7695-15-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R +packages. +--- + gnu/packages/statistics.scm | 42 ++++++++++++++++++++++-------------------- + 1 file changed, 22 insertions(+), 20 deletions(-) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index b338efcda..c836409b6 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -511,6 +511,28 @@ analysis.") + ;; Either version may be picked. + (license (list license:gpl2 license:gpl3)))) + ++(define-public r-survival ++ (package ++ (name "r-survival") ++ (version "2.40-1") ++ (source ++ (origin ++ (method url-fetch) ++ (uri (cran-uri "survival" version)) ++ (sha256 ++ (base32 ++ "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) ++ (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix))) ++ (home-page "https://github.com/therneau/survival") ++ (synopsis "Survival analysis") ++ (description ++ "This package contains the core survival analysis routines, including ++definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) ++curves, Cox models, and parametric accelerated failure time models.") ++ (license license:lgpl2.0+))) ++ + (define-public r-bit + (package + (name "r-bit") +@@ -3683,26 +3705,6 @@ following problems: + @end enumerate\n") + (license license:gpl3+))) + +-(define-public r-survival +- (package +- (name "r-survival") +- (version "2.40-1") +- (source +- (origin +- (method url-fetch) +- (uri (cran-uri "survival" version)) +- (sha256 +- (base32 +- "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) +- (build-system r-build-system) +- (home-page "https://github.com/therneau/survival") +- (synopsis "Survival analysis") +- (description +- "This package contains the core survival analysis routines, including +-definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) +-curves, Cox models, and parametric accelerated failure time models.") +- (license license:lgpl2.0+))) +- + (define-public r-base64 + (package + (name "r-base64") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482248 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 16/17] gnu: r: Do not build recommended packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:08 +0000 +Resent-Message-ID: <handler.26095.B26095.148948224111182@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948224111182 + (code B ref 26095); Tue, 14 Mar 2017 09:04:08 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:04:01 +0000 +Received: from localhost ([127.0.0.1]:54780 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMx-0002tz-Mk + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:04:01 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21085) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMs-0002tb-Hi + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:50 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482225338842.7746612780102; + Tue, 14 Mar 2017 02:03:45 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:55 +0100 +Message-Id: <20170314090256.7695-16-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r)[arguments]: Rename phase +"build-recommended-packages-reproducibly" to "build-reproducibly"; add +configure flag "--without-recommended-packages". +* guix/import/cran.scm (default-r-packages): Remove recommended packages. +* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice +and r-nlme. +(r-vegan)[propagated-inputs]: Add r-mass. +(r-genefilter)[propagated-inputs]: Add r-survival. +(r-grohmm)[propagated-inputs]: Add r-mass. +(r-bioccheck)[propagated-inputs]: Add r-codetools. +(r-summarizedexperiment)[propagated-inputs]: Add r-matrix. +(r-topgo)[propagated-inputs]: Add r-lattice. +(r-sva)[propagated-inputs]: Add r-mgcv. +(r-raremetals2)[propagated-inputs]: Add r-mass. +(r-vsn)[propagated-inputs]: Add r-lattice. +(r-pcamethods)[propagated-inputs]: Add r-mass. +* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass. +(r-locfit)[propagated-inputs]: Add r-lattice. +(r-coda)[propagated-inputs]: Add r-lattice. +(r-irlba)[propagated-inputs]: Add r-matrix. +(r-glmnet)[propagated-inputs]: Add r-matrix. +(r-e1071)[propagated-inputs]: Add r-class. +(r-spams)[propagated-inputs]: Add r-lattice and r-matrix. +(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and +r-rpart. +(r-zoo)[propagated-inputs]: Add r-lattice. +(r-mixtools)[propagated-inputs]: Add r-boot and r-mass. +(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet. +(r-prabclus)[propagated-inputs]: Add r-mass. +(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass. +(r-rcppeigen)[propagated-inputs]: Add r-matrix. +(r-matrixmodels)[propagated-inputs]: Add r-matrix. +(r-lme4)[propagated-inputs]: Add r-mass and r-nlme. +(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix. +(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet. +(r-tclust)[propagated-inputs]: Add r-cluster. +--- + gnu/packages/bioinformatics.scm | 21 +++++++++-- + gnu/packages/statistics.scm | 83 ++++++++++++++++++++++++++++++----------- + guix/import/cran.scm | 18 +-------- + 3 files changed, 80 insertions(+), 42 deletions(-) + +diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm +index 770bea7e3..daef0f6de 100644 +--- a/gnu/packages/bioinformatics.scm ++++ b/gnu/packages/bioinformatics.scm +@@ -108,6 +108,9 @@ + (base32 + "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice) ++ ("r-nlme" ,r-nlme))) + (home-page "http://ape-package.ird.fr/") + (synopsis "Analyses of phylogenetics and evolution") + (description +@@ -5344,6 +5347,7 @@ information as possible.") + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice) ++ ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-permute" ,r-permute))) + (home-page "https://cran.r-project.org/web/packages/vegan") +@@ -5425,7 +5429,8 @@ microarrays.") + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) +- ("r-s4vectors" ,r-s4vectors))) ++ ("r-s4vectors" ,r-s4vectors) ++ ("r-survival" ,r-survival))) + (home-page "http://bioconductor.org/packages/genefilter") + (synopsis "Filter genes from high-throughput experiments") + (description +@@ -5723,6 +5728,7 @@ annotation infrastructure.") + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) ++ ("r-mass" ,r-mass) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/Kraus-Lab/groHMM") +@@ -6122,7 +6128,8 @@ functionality.") + (native-inputs + `(("which" ,which))) + (propagated-inputs +- `(("r-graph" ,r-graph) ++ `(("r-codetools" ,r-codetools) ++ ("r-graph" ,r-graph) + ("r-knitr" ,r-knitr) + ("r-httr" ,r-httr) + ("r-optparse" ,r-optparse) +@@ -6650,6 +6657,7 @@ files.") + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) ++ ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://bioconductor.org/packages/SummarizedExperiment") + (synopsis "Container for representing genomic ranges by sample") +@@ -6841,8 +6849,9 @@ information about the latest version of the Gene Ontologies.") + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) +- ("r-matrixstats" ,r-matrixstats) + ("r-graph" ,r-graph) ++ ("r-lattice" ,r-lattice) ++ ("r-matrixstats" ,r-matrixstats) + ("r-sparsem" ,r-sparsem))) + (home-page "http://bioconductor.org/packages/topGO") + (synopsis "Enrichment analysis for gene ontology") +@@ -8234,7 +8243,8 @@ number detection tools.") + "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-genefilter" ,r-genefilter))) ++ `(("r-genefilter" ,r-genefilter) ++ ("r-mgcv" ,r-mgcv))) + (home-page "http://bioconductor.org/packages/sva") + (synopsis "Surrogate variable analysis") + (description +@@ -8286,6 +8296,7 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") + (propagated-inputs + `(("r-seqminer" ,r-seqminer) + ("r-mvtnorm" ,r-mvtnorm) ++ ("r-mass" ,r-mass) + ("r-compquadform" ,r-compquadform) + ("r-getopt" ,r-getopt))) + (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") +@@ -8444,6 +8455,7 @@ analysis.") + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) ++ ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma))) + (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") +@@ -8507,6 +8519,7 @@ specific parser.") + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) ++ ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hredestig/pcamethods") + (synopsis "Collection of PCA methods") +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index c836409b6..b8abbf62d 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -99,6 +99,9 @@ can be imported from spreadsheets, text files and database sources and it can + be output in text, PostScript, PDF or HTML.") + (license license:gpl3+))) + ++;; Update this package together with the set of recommended packages: r-boot, ++;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, ++;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. + (define-public r + (package + (name "r") +@@ -128,12 +131,8 @@ be output in text, PostScript, PDF or HTML.") + (substitute* "src/scripts/R.sh.in" + (("uname") uname-bin))) + #t)) +- (add-after 'unpack 'build-recommended-packages-reproducibly ++ (add-after 'unpack 'build-reproducibly + (lambda _ +- (substitute* "src/library/Recommended/Makefile.in" +- (("INSTALL_OPTS =(.*)" line rest ) +- (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01" +- rest))) + ;; Ensure that gzipped files are reproducible + (substitute* '("src/library/grDevices/Makefile.in" + "doc/manual/Makefile.in") +@@ -162,7 +161,12 @@ be output in text, PostScript, PDF or HTML.") + (add-after 'build 'install-info + (lambda _ (zero? (system* "make" "install-info"))))) + #:configure-flags +- '("--with-cairo" ++ '(;; Do not build the recommended packages. The build system creates ++ ;; random temporary directories and embeds their names in some ++ ;; package files. We build these packages with the r-build-system ++ ;; instead. ++ "--without-recommended-packages" ++ "--with-cairo" + "--with-blas=-lopenblas" + "--with-libpng" + "--with-jpeglib" +@@ -991,6 +995,7 @@ legends.") + ("r-gtable" ,r-gtable) + ("r-plyr" ,r-plyr) + ("r-lazyeval" ,r-lazyeval) ++ ("r-mass" ,r-mass) + ("r-tibble" ,r-tibble) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) +@@ -1611,6 +1616,8 @@ side.") + (base32 + "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) + (home-page "http://cran.r-project.org/web/packages/locfit") + (synopsis "Local regression, likelihood and density estimation") + (description +@@ -1788,6 +1795,8 @@ inference for statistical models.") + (base32 + "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) + (home-page "http://cran.r-project.org/web/packages/coda") + (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") + (description "This package provides functions for summarizing and plotting +@@ -2936,6 +2945,8 @@ flexible than the orphaned \"base64\" package.") + (base32 + "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix))) + (home-page "http://cran.r-project.org/web/packages/irlba") + (synopsis "Methods for eigendecomposition of large matrices") + (description +@@ -2956,10 +2967,11 @@ analysis of large sparse or dense matrices.") + (base32 + "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) + (build-system r-build-system) +- (inputs +- `(("gfortran" ,gfortran))) ++ (inputs ++ `(("gfortran" ,gfortran))) + (propagated-inputs +- `(("r-foreach" ,r-foreach))) ++ `(("r-foreach" ,r-foreach) ++ ("r-matrix" ,r-matrix))) + (home-page "http://www.jstatsoft.org/v33/i01") + (synopsis "Lasso and elastic-net regularized generalized linear models") + (description +@@ -3077,6 +3089,8 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") + (base32 + "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-class" ,r-class))) + (home-page "http://cran.r-project.org/web/packages/e1071") + (synopsis "Miscellaneous functions for probability theory") + (description +@@ -3688,6 +3702,9 @@ from within R.") + (("if isnan\\(lambda\\) \\{") + "if (isnan(lambda)) {")) + #t))))) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice) ++ ("r-matrix" ,r-matrix))) + (home-page "http://spams-devel.gforge.inria.fr") + (synopsis "Toolbox for solving sparse estimation problems") + (description "SPAMS (SPArse Modeling Software) is an optimization toolbox +@@ -3746,17 +3763,20 @@ package instead.") + `(("r-acepack" ,r-acepack) + ("r-base64" ,r-base64) + ("r-base64enc" ,r-base64enc) ++ ("r-cluster" ,r-cluster) + ("r-data-table" ,r-data-table) ++ ("r-foreign" ,r-foreign) + ("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) +- ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival +- ;; package that comes with R 3.3.2. +- ("r-survival" ,r-survival) ++ ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-htmltable" ,r-htmltable) + ("r-htmltools" ,r-htmltools) ++ ("r-nnet" ,r-nnet) ++ ("r-rpart" ,r-rpart) ++ ("r-survival" ,r-survival) + ("r-viridis" ,r-viridis))) + (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") + (synopsis "Miscellaneous data analysis and graphics functions") +@@ -4041,6 +4061,8 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) + (base32 + "167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) + (home-page "http://zoo.R-Forge.R-project.org/") + (synopsis "S3 infrastructure for regular and irregular time series") + (description "This package contains an S3 class with methods for totally +@@ -4307,7 +4329,9 @@ letters, as is often required for scientific publications.") + "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-segmented" ,r-segmented))) ++ `(("r-boot" ,r-boot) ++ ("r-mass" ,r-mass) ++ ("r-segmented" ,r-segmented))) + (home-page "http://cran.r-project.org/web/packages/mixtools") + (synopsis "Tools for analyzing finite mixture models") + (description +@@ -4437,7 +4461,9 @@ to change in the future.") + "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-modeltools" ,r-modeltools))) ++ `(("r-lattice" ,r-lattice) ++ ("r-modeltools" ,r-modeltools) ++ ("r-nnet" ,r-nnet))) + (home-page "http://cran.r-project.org/web/packages/flexmix") + (synopsis "Flexible mixture modeling") + (description +@@ -4484,7 +4510,8 @@ and resampling-based inference.") + "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-mclust" ,r-mclust))) ++ `(("r-mass" ,r-mass) ++ ("r-mclust" ,r-mclust))) + (home-page "https://cran.r-project.org/web/packages/prabclus") + (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") + (description +@@ -4573,9 +4600,12 @@ of the points.") + "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-diptest" ,r-diptest) ++ `(("r-class" ,r-class) ++ ("r-cluster" ,r-cluster) ++ ("r-diptest" ,r-diptest) + ("r-flexmix" ,r-flexmix) + ("r-kernlab" ,r-kernlab) ++ ("r-mass" ,r-mass) + ("r-mclust" ,r-mclust) + ("r-mvtnorm" ,r-mvtnorm) + ("r-prabclus" ,r-prabclus) +@@ -4694,7 +4724,8 @@ based on an interface to Fortran implementations by M. J. D. Powell.") + (properties `((upstream-name . "RcppEigen"))) + (build-system r-build-system) + (propagated-inputs +- `(("r-rcpp" ,r-rcpp))) ++ `(("r-rcpp" ,r-rcpp) ++ ("r-matrix" ,r-matrix))) + (home-page "http://eigen.tuxfamily.org") + (synopsis "Rcpp integration for the Eigen templated linear algebra library") + (description +@@ -4739,6 +4770,8 @@ metrics for evaluating models.") + "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy")))) + (properties `((upstream-name . "MatrixModels"))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/MatrixModels") + (synopsis "Modelling with sparse and dense matrices") + (description +@@ -4816,7 +4849,9 @@ algorithms.") + ("r-rcppeigen" ,r-rcppeigen))) + (propagated-inputs + `(("r-minqa" ,r-minqa) +- ("r-nloptr" ,r-nloptr))) ++ ("r-nloptr" ,r-nloptr) ++ ("r-mass" ,r-mass) ++ ("r-nlme" ,r-nlme))) + (home-page "http://cran.r-project.org/web/packages/lme4") + (synopsis "Linear mixed-effects models using eigen and S4") + (description +@@ -4839,7 +4874,9 @@ C++ library for numerical linear algebra and RcppEigen glue.") + "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-lme4" ,r-lme4))) ++ `(("r-lme4" ,r-lme4) ++ ("r-mass" ,r-mass) ++ ("r-matrix" ,r-matrix))) + (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/") + (synopsis "Methods for linear mixed model comparison") + (description +@@ -4861,7 +4898,10 @@ bootstrap test for generalized linear mixed models.") + "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-pbkrtest" ,r-pbkrtest) ++ `(("r-mass" ,r-mass) ++ ("r-mgcv" ,r-mgcv) ++ ("r-nnet" ,r-nnet) ++ ("r-pbkrtest" ,r-pbkrtest) + ("r-quantreg" ,r-quantreg))) + (home-page "https://r-forge.r-project.org/projects/car/") + (synopsis "Companion to applied regression") +@@ -5000,7 +5040,8 @@ multivariate case.") + "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-mclust" ,r-mclust) ++ `(("r-cluster" ,r-cluster) ++ ("r-mclust" ,r-mclust) + ("r-mvtnorm" ,r-mvtnorm) + ("r-sn" ,r-sn))) + (home-page "http://cran.r-project.org/web/packages/tclust") +diff --git a/guix/import/cran.scm b/guix/import/cran.scm +index 40cdea029..7521a39bc 100644 +--- a/guix/import/cran.scm ++++ b/guix/import/cran.scm +@@ -164,32 +164,16 @@ empty list when the FIELD cannot be found." + (map string-trim-both items)))))) + + (define default-r-packages +- (list "KernSmooth" +- "MASS" +- "Matrix" +- "base" +- "boot" +- "class" +- "cluster" +- "codetools" ++ (list "base" + "compiler" +- "datasets" +- "foreign" + "grDevices" + "graphics" + "grid" +- "lattice" + "methods" +- "mgcv" +- "nlme" +- "nnet" + "parallel" +- "rpart" +- "spatial" + "splines" + "stats" + "stats4" +- "survival" + "tcltk" + "tools" + "translations" +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:04:01 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:04:01 2017 +Received: from localhost ([127.0.0.1]:54780 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniMx-0002tz-Mk + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:04:01 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21085) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMs-0002tb-Hi + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:50 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482225338842.7746612780102; + Tue, 14 Mar 2017 02:03:45 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 16/17] gnu: r: Do not build recommended packages. +Date: Tue, 14 Mar 2017 10:02:55 +0100 +Message-Id: <20170314090256.7695-16-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r)[arguments]: Rename phase +"build-recommended-packages-reproducibly" to "build-reproducibly"; add +configure flag "--without-recommended-packages". +* guix/import/cran.scm (default-r-packages): Remove recommended packages. +* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice +and r-nlme. +(r-vegan)[propagated-inputs]: Add r-mass. +(r-genefilter)[propagated-inputs]: Add r-survival. +(r-grohmm)[propagated-inputs]: Add r-mass. +(r-bioccheck)[propagated-inputs]: Add r-codetools. +(r-summarizedexperiment)[propagated-inputs]: Add r-matrix. +(r-topgo)[propagated-inputs]: Add r-lattice. +(r-sva)[propagated-inputs]: Add r-mgcv. +(r-raremetals2)[propagated-inputs]: Add r-mass. +(r-vsn)[propagated-inputs]: Add r-lattice. +(r-pcamethods)[propagated-inputs]: Add r-mass. +* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass. +(r-locfit)[propagated-inputs]: Add r-lattice. +(r-coda)[propagated-inputs]: Add r-lattice. +(r-irlba)[propagated-inputs]: Add r-matrix. +(r-glmnet)[propagated-inputs]: Add r-matrix. +(r-e1071)[propagated-inputs]: Add r-class. +(r-spams)[propagated-inputs]: Add r-lattice and r-matrix. +(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and +r-rpart. +(r-zoo)[propagated-inputs]: Add r-lattice. +(r-mixtools)[propagated-inputs]: Add r-boot and r-mass. +(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet. +(r-prabclus)[propagated-inputs]: Add r-mass. +(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass. +(r-rcppeigen)[propagated-inputs]: Add r-matrix. +(r-matrixmodels)[propagated-inputs]: Add r-matrix. +(r-lme4)[propagated-inputs]: Add r-mass and r-nlme. +(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix. +(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet. +(r-tclust)[propagated-inputs]: Add r-cluster. +--- + gnu/packages/bioinformatics.scm | 21 +++++++++-- + gnu/packages/statistics.scm | 83 ++++++++++++++++++++++++++++++----------- + guix/import/cran.scm | 18 +-------- + 3 files changed, 80 insertions(+), 42 deletions(-) + +diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm +index 770bea7e3..daef0f6de 100644 +--- a/gnu/packages/bioinformatics.scm ++++ b/gnu/packages/bioinformatics.scm +@@ -108,6 +108,9 @@ + (base32 + "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice) ++ ("r-nlme" ,r-nlme))) + (home-page "http://ape-package.ird.fr/") + (synopsis "Analyses of phylogenetics and evolution") + (description +@@ -5344,6 +5347,7 @@ information as possible.") + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice) ++ ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-permute" ,r-permute))) + (home-page "https://cran.r-project.org/web/packages/vegan") +@@ -5425,7 +5429,8 @@ microarrays.") + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) +- ("r-s4vectors" ,r-s4vectors))) ++ ("r-s4vectors" ,r-s4vectors) ++ ("r-survival" ,r-survival))) + (home-page "http://bioconductor.org/packages/genefilter") + (synopsis "Filter genes from high-throughput experiments") + (description +@@ -5723,6 +5728,7 @@ annotation infrastructure.") + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) ++ ("r-mass" ,r-mass) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/Kraus-Lab/groHMM") +@@ -6122,7 +6128,8 @@ functionality.") + (native-inputs + `(("which" ,which))) + (propagated-inputs +- `(("r-graph" ,r-graph) ++ `(("r-codetools" ,r-codetools) ++ ("r-graph" ,r-graph) + ("r-knitr" ,r-knitr) + ("r-httr" ,r-httr) + ("r-optparse" ,r-optparse) +@@ -6650,6 +6657,7 @@ files.") + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) ++ ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://bioconductor.org/packages/SummarizedExperiment") + (synopsis "Container for representing genomic ranges by sample") +@@ -6841,8 +6849,9 @@ information about the latest version of the Gene Ontologies.") + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) +- ("r-matrixstats" ,r-matrixstats) + ("r-graph" ,r-graph) ++ ("r-lattice" ,r-lattice) ++ ("r-matrixstats" ,r-matrixstats) + ("r-sparsem" ,r-sparsem))) + (home-page "http://bioconductor.org/packages/topGO") + (synopsis "Enrichment analysis for gene ontology") +@@ -8234,7 +8243,8 @@ number detection tools.") + "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-genefilter" ,r-genefilter))) ++ `(("r-genefilter" ,r-genefilter) ++ ("r-mgcv" ,r-mgcv))) + (home-page "http://bioconductor.org/packages/sva") + (synopsis "Surrogate variable analysis") + (description +@@ -8286,6 +8296,7 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") + (propagated-inputs + `(("r-seqminer" ,r-seqminer) + ("r-mvtnorm" ,r-mvtnorm) ++ ("r-mass" ,r-mass) + ("r-compquadform" ,r-compquadform) + ("r-getopt" ,r-getopt))) + (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") +@@ -8444,6 +8455,7 @@ analysis.") + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) ++ ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma))) + (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") +@@ -8507,6 +8519,7 @@ specific parser.") + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) ++ ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hredestig/pcamethods") + (synopsis "Collection of PCA methods") +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index c836409b6..b8abbf62d 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -99,6 +99,9 @@ can be imported from spreadsheets, text files and database sources and it can + be output in text, PostScript, PDF or HTML.") + (license license:gpl3+))) + ++;; Update this package together with the set of recommended packages: r-boot, ++;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, ++;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. + (define-public r + (package + (name "r") +@@ -128,12 +131,8 @@ be output in text, PostScript, PDF or HTML.") + (substitute* "src/scripts/R.sh.in" + (("uname") uname-bin))) + #t)) +- (add-after 'unpack 'build-recommended-packages-reproducibly ++ (add-after 'unpack 'build-reproducibly + (lambda _ +- (substitute* "src/library/Recommended/Makefile.in" +- (("INSTALL_OPTS =(.*)" line rest ) +- (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01" +- rest))) + ;; Ensure that gzipped files are reproducible + (substitute* '("src/library/grDevices/Makefile.in" + "doc/manual/Makefile.in") +@@ -162,7 +161,12 @@ be output in text, PostScript, PDF or HTML.") + (add-after 'build 'install-info + (lambda _ (zero? (system* "make" "install-info"))))) + #:configure-flags +- '("--with-cairo" ++ '(;; Do not build the recommended packages. The build system creates ++ ;; random temporary directories and embeds their names in some ++ ;; package files. We build these packages with the r-build-system ++ ;; instead. ++ "--without-recommended-packages" ++ "--with-cairo" + "--with-blas=-lopenblas" + "--with-libpng" + "--with-jpeglib" +@@ -991,6 +995,7 @@ legends.") + ("r-gtable" ,r-gtable) + ("r-plyr" ,r-plyr) + ("r-lazyeval" ,r-lazyeval) ++ ("r-mass" ,r-mass) + ("r-tibble" ,r-tibble) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) +@@ -1611,6 +1616,8 @@ side.") + (base32 + "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) + (home-page "http://cran.r-project.org/web/packages/locfit") + (synopsis "Local regression, likelihood and density estimation") + (description +@@ -1788,6 +1795,8 @@ inference for statistical models.") + (base32 + "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) + (home-page "http://cran.r-project.org/web/packages/coda") + (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") + (description "This package provides functions for summarizing and plotting +@@ -2936,6 +2945,8 @@ flexible than the orphaned \"base64\" package.") + (base32 + "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix))) + (home-page "http://cran.r-project.org/web/packages/irlba") + (synopsis "Methods for eigendecomposition of large matrices") + (description +@@ -2956,10 +2967,11 @@ analysis of large sparse or dense matrices.") + (base32 + "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) + (build-system r-build-system) +- (inputs +- `(("gfortran" ,gfortran))) ++ (inputs ++ `(("gfortran" ,gfortran))) + (propagated-inputs +- `(("r-foreach" ,r-foreach))) ++ `(("r-foreach" ,r-foreach) ++ ("r-matrix" ,r-matrix))) + (home-page "http://www.jstatsoft.org/v33/i01") + (synopsis "Lasso and elastic-net regularized generalized linear models") + (description +@@ -3077,6 +3089,8 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") + (base32 + "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-class" ,r-class))) + (home-page "http://cran.r-project.org/web/packages/e1071") + (synopsis "Miscellaneous functions for probability theory") + (description +@@ -3688,6 +3702,9 @@ from within R.") + (("if isnan\\(lambda\\) \\{") + "if (isnan(lambda)) {")) + #t))))) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice) ++ ("r-matrix" ,r-matrix))) + (home-page "http://spams-devel.gforge.inria.fr") + (synopsis "Toolbox for solving sparse estimation problems") + (description "SPAMS (SPArse Modeling Software) is an optimization toolbox +@@ -3746,17 +3763,20 @@ package instead.") + `(("r-acepack" ,r-acepack) + ("r-base64" ,r-base64) + ("r-base64enc" ,r-base64enc) ++ ("r-cluster" ,r-cluster) + ("r-data-table" ,r-data-table) ++ ("r-foreign" ,r-foreign) + ("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) +- ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival +- ;; package that comes with R 3.3.2. +- ("r-survival" ,r-survival) ++ ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-htmltable" ,r-htmltable) + ("r-htmltools" ,r-htmltools) ++ ("r-nnet" ,r-nnet) ++ ("r-rpart" ,r-rpart) ++ ("r-survival" ,r-survival) + ("r-viridis" ,r-viridis))) + (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") + (synopsis "Miscellaneous data analysis and graphics functions") +@@ -4041,6 +4061,8 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) + (base32 + "167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28")))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-lattice" ,r-lattice))) + (home-page "http://zoo.R-Forge.R-project.org/") + (synopsis "S3 infrastructure for regular and irregular time series") + (description "This package contains an S3 class with methods for totally +@@ -4307,7 +4329,9 @@ letters, as is often required for scientific publications.") + "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-segmented" ,r-segmented))) ++ `(("r-boot" ,r-boot) ++ ("r-mass" ,r-mass) ++ ("r-segmented" ,r-segmented))) + (home-page "http://cran.r-project.org/web/packages/mixtools") + (synopsis "Tools for analyzing finite mixture models") + (description +@@ -4437,7 +4461,9 @@ to change in the future.") + "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-modeltools" ,r-modeltools))) ++ `(("r-lattice" ,r-lattice) ++ ("r-modeltools" ,r-modeltools) ++ ("r-nnet" ,r-nnet))) + (home-page "http://cran.r-project.org/web/packages/flexmix") + (synopsis "Flexible mixture modeling") + (description +@@ -4484,7 +4510,8 @@ and resampling-based inference.") + "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-mclust" ,r-mclust))) ++ `(("r-mass" ,r-mass) ++ ("r-mclust" ,r-mclust))) + (home-page "https://cran.r-project.org/web/packages/prabclus") + (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") + (description +@@ -4573,9 +4600,12 @@ of the points.") + "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-diptest" ,r-diptest) ++ `(("r-class" ,r-class) ++ ("r-cluster" ,r-cluster) ++ ("r-diptest" ,r-diptest) + ("r-flexmix" ,r-flexmix) + ("r-kernlab" ,r-kernlab) ++ ("r-mass" ,r-mass) + ("r-mclust" ,r-mclust) + ("r-mvtnorm" ,r-mvtnorm) + ("r-prabclus" ,r-prabclus) +@@ -4694,7 +4724,8 @@ based on an interface to Fortran implementations by M. J. D. Powell.") + (properties `((upstream-name . "RcppEigen"))) + (build-system r-build-system) + (propagated-inputs +- `(("r-rcpp" ,r-rcpp))) ++ `(("r-rcpp" ,r-rcpp) ++ ("r-matrix" ,r-matrix))) + (home-page "http://eigen.tuxfamily.org") + (synopsis "Rcpp integration for the Eigen templated linear algebra library") + (description +@@ -4739,6 +4770,8 @@ metrics for evaluating models.") + "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy")))) + (properties `((upstream-name . "MatrixModels"))) + (build-system r-build-system) ++ (propagated-inputs ++ `(("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/MatrixModels") + (synopsis "Modelling with sparse and dense matrices") + (description +@@ -4816,7 +4849,9 @@ algorithms.") + ("r-rcppeigen" ,r-rcppeigen))) + (propagated-inputs + `(("r-minqa" ,r-minqa) +- ("r-nloptr" ,r-nloptr))) ++ ("r-nloptr" ,r-nloptr) ++ ("r-mass" ,r-mass) ++ ("r-nlme" ,r-nlme))) + (home-page "http://cran.r-project.org/web/packages/lme4") + (synopsis "Linear mixed-effects models using eigen and S4") + (description +@@ -4839,7 +4874,9 @@ C++ library for numerical linear algebra and RcppEigen glue.") + "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-lme4" ,r-lme4))) ++ `(("r-lme4" ,r-lme4) ++ ("r-mass" ,r-mass) ++ ("r-matrix" ,r-matrix))) + (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/") + (synopsis "Methods for linear mixed model comparison") + (description +@@ -4861,7 +4898,10 @@ bootstrap test for generalized linear mixed models.") + "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-pbkrtest" ,r-pbkrtest) ++ `(("r-mass" ,r-mass) ++ ("r-mgcv" ,r-mgcv) ++ ("r-nnet" ,r-nnet) ++ ("r-pbkrtest" ,r-pbkrtest) + ("r-quantreg" ,r-quantreg))) + (home-page "https://r-forge.r-project.org/projects/car/") + (synopsis "Companion to applied regression") +@@ -5000,7 +5040,8 @@ multivariate case.") + "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp")))) + (build-system r-build-system) + (propagated-inputs +- `(("r-mclust" ,r-mclust) ++ `(("r-cluster" ,r-cluster) ++ ("r-mclust" ,r-mclust) + ("r-mvtnorm" ,r-mvtnorm) + ("r-sn" ,r-sn))) + (home-page "http://cran.r-project.org/web/packages/tclust") +diff --git a/guix/import/cran.scm b/guix/import/cran.scm +index 40cdea029..7521a39bc 100644 +--- a/guix/import/cran.scm ++++ b/guix/import/cran.scm +@@ -164,32 +164,16 @@ empty list when the FIELD cannot be found." + (map string-trim-both items)))))) + + (define default-r-packages +- (list "KernSmooth" +- "MASS" +- "Matrix" +- "base" +- "boot" +- "class" +- "cluster" +- "codetools" ++ (list "base" + "compiler" +- "datasets" +- "foreign" + "grDevices" + "graphics" + "grid" +- "lattice" + "methods" +- "mgcv" +- "nlme" +- "nnet" + "parallel" +- "rpart" +- "spatial" + "splines" + "stats" + "stats4" +- "survival" + "tcltk" + "tools" + "translations" +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489482248 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: [PATCH 17/17] gnu: Add r-with-recommended-packages. +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Tue, 14 Mar 2017 09:04:08 +0000 +Resent-Message-ID: <handler.26095.B26095.148948224111191@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: Ricardo Wurmus <rekado@example.com> +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948224111191 + (code B ref 26095); Tue, 14 Mar 2017 09:04:08 +0000 +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:04:01 +0000 +Received: from localhost ([127.0.0.1]:54783 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniN7-0002uN-8S + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:04:01 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21030) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMx-0002ty-OD + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:52 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482228129150.34783315355207; + Tue, 14 Mar 2017 02:03:48 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +Date: Tue, 14 Mar 2017 10:02:56 +0100 +Message-Id: <20170314090256.7695-17-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-with-recommended-packages): New variable. +--- + gnu/packages/statistics.scm | 25 +++++++++++++++++++++++++ + 1 file changed, 25 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index b8abbf62d..656895273 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -31,6 +31,7 @@ + #:use-module (guix build-system gnu) + #:use-module (guix build-system r) + #:use-module (guix build-system python) ++ #:use-module (guix build-system trivial) + #:use-module (gnu packages) + #:use-module (gnu packages compression) + #:use-module (gnu packages curl) +@@ -537,6 +538,30 @@ definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) + curves, Cox models, and parametric accelerated failure time models.") + (license license:lgpl2.0+))) + ++(define-public r-with-recommended-packages ++ (package (inherit r) ++ (name "r-with-recommended-packages") ++ (source #f) ++ (build-system trivial-build-system) ++ (arguments '(#:builder (mkdir %output))) ++ (propagated-inputs ++ `(("r" ,r) ++ ("r-boot" ,r-boot) ++ ("r-class" ,r-class) ++ ("r-cluster" ,r-cluster) ++ ("r-codetools" ,r-codetools) ++ ("r-foreign" ,r-foreign) ++ ("r-kernsmooth" ,r-kernsmooth) ++ ("r-lattice" ,r-lattice) ++ ("r-mass" ,r-mass) ++ ("r-matrix" ,r-matrix) ++ ("r-mgcv" ,r-mgcv) ++ ("r-nlme" ,r-nlme) ++ ("r-nnet" ,r-nnet) ++ ("r-rpart" ,r-rpart) ++ ("r-spatial" ,r-spatial) ++ ("r-survival" ,r-survival))))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:04:01 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:04:01 2017 +Received: from localhost ([127.0.0.1]:54783 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cniN7-0002uN-8S + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:04:01 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21030) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cniMx-0002ty-OD + for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:52 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489482228129150.34783315355207; + Tue, 14 Mar 2017 02:03:48 -0700 (PDT) +From: Ricardo Wurmus <rekado@example.com> +To: 26095@debbugs.gnu.org +Subject: [PATCH 17/17] gnu: Add r-with-recommended-packages. +Date: Tue, 14 Mar 2017 10:02:56 +0100 +Message-Id: <20170314090256.7695-17-rekado@example.com> +X-Mailer: git-send-email 2.12.0 +In-Reply-To: <20170314090256.7695-1-rekado@example.com> +References: <87h92w1cu0.fsf@example.com> + <20170314090256.7695-1-rekado@example.com> +X-Spam-Score: 1.0 (+) +X-Debbugs-Envelope-To: 26095 +Cc: Ricardo Wurmus <rekado@example.com> +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: 1.0 (+) + +* gnu/packages/statistics.scm (r-with-recommended-packages): New variable. +--- + gnu/packages/statistics.scm | 25 +++++++++++++++++++++++++ + 1 file changed, 25 insertions(+) + +diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm +index b8abbf62d..656895273 100644 +--- a/gnu/packages/statistics.scm ++++ b/gnu/packages/statistics.scm +@@ -31,6 +31,7 @@ + #:use-module (guix build-system gnu) + #:use-module (guix build-system r) + #:use-module (guix build-system python) ++ #:use-module (guix build-system trivial) + #:use-module (gnu packages) + #:use-module (gnu packages compression) + #:use-module (gnu packages curl) +@@ -537,6 +538,30 @@ definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) + curves, Cox models, and parametric accelerated failure time models.") + (license license:lgpl2.0+))) + ++(define-public r-with-recommended-packages ++ (package (inherit r) ++ (name "r-with-recommended-packages") ++ (source #f) ++ (build-system trivial-build-system) ++ (arguments '(#:builder (mkdir %output))) ++ (propagated-inputs ++ `(("r" ,r) ++ ("r-boot" ,r-boot) ++ ("r-class" ,r-class) ++ ("r-cluster" ,r-cluster) ++ ("r-codetools" ,r-codetools) ++ ("r-foreign" ,r-foreign) ++ ("r-kernsmooth" ,r-kernsmooth) ++ ("r-lattice" ,r-lattice) ++ ("r-mass" ,r-mass) ++ ("r-matrix" ,r-matrix) ++ ("r-mgcv" ,r-mgcv) ++ ("r-nlme" ,r-nlme) ++ ("r-nnet" ,r-nnet) ++ ("r-rpart" ,r-rpart) ++ ("r-spatial" ,r-spatial) ++ ("r-survival" ,r-survival))))) ++ + (define-public r-bit + (package + (name "r-bit") +-- +2.12.0 + + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489611122 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: R: do not build recommended packages +Resent-From: John Lennon <john@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Wed, 15 Mar 2017 20:52:02 +0000 +Resent-Message-ID: <handler.26095.B26095.148961110731504@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: Ricardo Wurmus <rekado@example.com> +Cc: 26095@debbugs.gnu.org +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148961110731504 + (code B ref 26095); Wed, 15 Mar 2017 20:52:02 +0000 +Received: (at 26095) by debbugs.gnu.org; 15 Mar 2017 20:51:47 +0000 +Received: from localhost ([127.0.0.1]:57580 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coFtb-0008C4-Ig + for submit@debbugs.gnu.org; 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charset=utf-8 +Content-Disposition: inline +Content-Transfer-Encoding: quoted-printable + +On Tue, Mar 14, 2017 at 09:28:55AM +0100, Ricardo Wurmus wrote: +> This relates to bug 25598 =E2=80=9CR packages are not bit-reproducible=E2= +=80=9D. R +> itself does not build reproducibly. One of the reasons is that it +> includes recommended packages that are built in a random temporary +> directory. The build paths for each of these packages is then embedded +> in the packages=E2=80=99 =E2=80=9Cpaths.rds=E2=80=9D files. +>=20 +> We don=E2=80=99t have this problem when building the packages with the +> =E2=80=9Cr-build-system=E2=80=9D like any other R package. +>=20 +> This patch set adds package expressions for each of the recommended +> packages, disables building of recommended packages, and adds some of +> these packages to those R packages that need them. +>=20 +> I=E2=80=99ve successfully rebuilt all R packages to make sure that these = +changes +> don=E2=80=99t break anything. +>=20 +> I also have an unpolished patch to fix bug 25598, but it depends on this +> patch set. + +Overall this patch series LGTM. I leave it up to you and the other +bio-info hackers to decide if it's the best solution. + +--dDRMvlgZJXvWKvBx +Content-Type: application/pgp-signature; name="signature.asc" + +-----BEGIN PGP SIGNATURE----- + +iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAljJqVsACgkQJkb6MLrK +fwiQ6Q/7BBpEjBQmW4lvdYHX6HT45miDp6/sr4oJiJUrHu2/ELFz/m0EcgwKr1tr +mvSzyarLtev8kyw1FNMPJ+ia5xVLtLq9nCPo8wVU/c+5DvhkaEqpqkLnCJUymsyQ +hVUZzmRQSh71ig9gkRWsaD/etusOCkFfOBmRM4whkuvJP2U40jtxAVxcRmxw4I8Z +74GcsO9S9t9nJsz4ZIrnFitUGlv4z/pG51yMG3hh0vf9nC5l2cBPFW8jsSNtLqxK +Qh2jdUHC3vh+UQdSAhw8CJAb6CGWL21fif3AcAMfYCTt2vfWZGGI4wcpolrRSLkL +5SLIKeKL1is5nlygN5Pmh8X1+wVWVvs5ChYBXr2WPu3Dw/0WlpaXkRUz/+hME+oe +F2T+1tAyjLSSO3TaCu8yPtvtHcz4OW+jtEb9SraEVtd++GH1LPTk0JbzTwrcZjZp +UlKisEMWZS7U92o0r+nkNCaHp5zP4Br9At7pGaIuRnXMbDIEeHwwHUFB2fb+yluE +mQcyORp8lhH6jynbooWddseswNbpXpyvz/3usYerYJL357zEksAF+pYiLJ1KULAo +1volJclcqyj5lujJvGPGWXcyUp6pRmQdPe7c+srh6+OPtLYHc9O1o5n2Y0imWJK8 +KZcz+2wnxe4iHAqPn4A2uvlz7rOLF76teOnC1JwmagCShuB7xmo= +=/ddK +-----END PGP SIGNATURE----- + +--dDRMvlgZJXvWKvBx-- + + + + + +Received: (at 26095) by debbugs.gnu.org; 15 Mar 2017 20:51:47 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 15 16:51:47 2017 +Received: from localhost ([127.0.0.1]:57580 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coFtb-0008C4-Ig + for submit@debbugs.gnu.org; Wed, 15 Mar 2017 16:51:47 -0400 +Received: from out1-smtp.messagingengine.com ([66.111.4.25]:46186) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <john@example.com>) id 1coFtZ-0008Bw-EG + for 26095@debbugs.gnu.org; Wed, 15 Mar 2017 16:51:45 -0400 +Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) + by mailout.nyi.internal (Postfix) with ESMTP id A4AD8206C8; + Wed, 15 Mar 2017 16:51:44 -0400 (EDT) +Received: from frontend2 ([10.202.2.161]) + by compute4.internal (MEProxy); Wed, 15 Mar 2017 16:51:44 -0400 +DKIM-Signature: v=1; a=rsa-sha1; c=relaxed/relaxed; d=example.com; h= + cc:content-type:date:from:in-reply-to:message-id:mime-version + :references:subject:to:x-me-sender:x-me-sender:x-sasl-enc + :x-sasl-enc; s=mesmtp; bh=QWXNjeVPZtZXOpw/B+fy6sIWj5k=; b=rcyYoP + 1DvNi4bLXAv88YLel4MBIPEQlcquQakzeTThmE2AL45IFazv0j3tNnsVtItH9+Qr + 33LyiHtE4D4VtJcgc3fnQF0qVG7mQz4+CD5gjnWQP/t+IRjYZuNIECu4A92jwK5W + OUyOH07fw1Ff+eqM9S3yu0lf6xxuxd2a/4Pd8= +DKIM-Signature: v=1; a=rsa-sha1; c=relaxed/relaxed; d= + messagingengine.com; h=cc:content-type:date:from:in-reply-to + :message-id:mime-version:references:subject:to:x-me-sender + :x-me-sender:x-sasl-enc:x-sasl-enc; s=smtpout; bh=QWXNjeVPZtZXOp + w/B+fy6sIWj5k=; b=sVIW9p0kVwpb1udbrq7FidGigO6kkfjS4B2HDOGyE0Cnvu + 9w8lQV6SwA99Xn6+dBE9tDx1JVykxdT2RwcmOANLIyrDxLhWEZXVeistdDMjb5ul + /aMR+MiSc7WmzjrVzXcIjCYPQ/Eps7v4l+RavkTHvMQiANUmS+SreAuK87wcE= +X-ME-Sender: <xms:YKnJWHI2nAY3zy522vzr_iyExBWT5D6PVV0qEab9_N249bkgx6gUFw> +X-Sasl-enc: i27KY9gkGYFnlp2bwmNl/fN9zZ9BZYL5Cn1ce5WRCePG 1489611104 +Received: from localhost (unknown [73.81.116.201]) + by mail.messagingengine.com (Postfix) with ESMTPA id 5CA32240AE; + Wed, 15 Mar 2017 16:51:44 -0400 (EDT) +Date: Wed, 15 Mar 2017 16:51:43 -0400 +From: John Lennon <john@example.com> +To: Ricardo Wurmus <rekado@example.com> +Subject: Re: bug#26095: R: do not build recommended packages +Message-ID: <20170315205143.GA7417@jasmine> +References: <87h92w1cu0.fsf@example.com> +MIME-Version: 1.0 +Content-Type: multipart/signed; micalg=pgp-sha256; + protocol="application/pgp-signature"; boundary="dDRMvlgZJXvWKvBx" +Content-Disposition: inline +In-Reply-To: <87h92w1cu0.fsf@example.com> +User-Agent: Mutt/1.8.0 (2017-02-23) +X-Spam-Score: -0.7 (/) +X-Debbugs-Envelope-To: 26095 +Cc: 26095@debbugs.gnu.org +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -0.7 (/) + + +--dDRMvlgZJXvWKvBx +Content-Type: text/plain; charset=utf-8 +Content-Disposition: inline +Content-Transfer-Encoding: quoted-printable + +On Tue, Mar 14, 2017 at 09:28:55AM +0100, Ricardo Wurmus wrote: +> This relates to bug 25598 =E2=80=9CR packages are not bit-reproducible=E2= +=80=9D. R +> itself does not build reproducibly. One of the reasons is that it +> includes recommended packages that are built in a random temporary +> directory. The build paths for each of these packages is then embedded +> in the packages=E2=80=99 =E2=80=9Cpaths.rds=E2=80=9D files. +>=20 +> We don=E2=80=99t have this problem when building the packages with the +> =E2=80=9Cr-build-system=E2=80=9D like any other R package. +>=20 +> This patch set adds package expressions for each of the recommended +> packages, disables building of recommended packages, and adds some of +> these packages to those R packages that need them. +>=20 +> I=E2=80=99ve successfully rebuilt all R packages to make sure that these = +changes +> don=E2=80=99t break anything. +>=20 +> I also have an unpolished patch to fix bug 25598, but it depends on this +> patch set. + +Overall this patch series LGTM. I leave it up to you and the other +bio-info hackers to decide if it's the best solution. + +--dDRMvlgZJXvWKvBx +Content-Type: application/pgp-signature; name="signature.asc" + +-----BEGIN PGP SIGNATURE----- + +iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAljJqVsACgkQJkb6MLrK +fwiQ6Q/7BBpEjBQmW4lvdYHX6HT45miDp6/sr4oJiJUrHu2/ELFz/m0EcgwKr1tr +mvSzyarLtev8kyw1FNMPJ+ia5xVLtLq9nCPo8wVU/c+5DvhkaEqpqkLnCJUymsyQ +hVUZzmRQSh71ig9gkRWsaD/etusOCkFfOBmRM4whkuvJP2U40jtxAVxcRmxw4I8Z +74GcsO9S9t9nJsz4ZIrnFitUGlv4z/pG51yMG3hh0vf9nC5l2cBPFW8jsSNtLqxK +Qh2jdUHC3vh+UQdSAhw8CJAb6CGWL21fif3AcAMfYCTt2vfWZGGI4wcpolrRSLkL +5SLIKeKL1is5nlygN5Pmh8X1+wVWVvs5ChYBXr2WPu3Dw/0WlpaXkRUz/+hME+oe +F2T+1tAyjLSSO3TaCu8yPtvtHcz4OW+jtEb9SraEVtd++GH1LPTk0JbzTwrcZjZp +UlKisEMWZS7U92o0r+nkNCaHp5zP4Br9At7pGaIuRnXMbDIEeHwwHUFB2fb+yluE +mQcyORp8lhH6jynbooWddseswNbpXpyvz/3usYerYJL357zEksAF+pYiLJ1KULAo +1volJclcqyj5lujJvGPGWXcyUp6pRmQdPe7c+srh6+OPtLYHc9O1o5n2Y0imWJK8 +KZcz+2wnxe4iHAqPn4A2uvlz7rOLF76teOnC1JwmagCShuB7xmo= +=/ddK +-----END PGP SIGNATURE----- + +--dDRMvlgZJXvWKvBx-- + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489616582 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: R: do not build recommended packages +Resent-From: Paul McCartney <p.mccartney@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Wed, 15 Mar 2017 22:23:02 +0000 +Resent-Message-ID: <handler.26095.B26095.14896165667752@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: Ricardo Wurmus <rekado@example.com>, 26095@debbugs.gnu.org +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.14896165667752 + (code B ref 26095); Wed, 15 Mar 2017 22:23:02 +0000 +Received: (at 26095) by debbugs.gnu.org; 15 Mar 2017 22:22:46 +0000 +Received: from localhost ([127.0.0.1]:57640 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coHJe-00020y-ML + for submit@debbugs.gnu.org; Wed, 15 Mar 2017 18:22:46 -0400 +Received: from mailhub2.soe.example.com ([130.102.132.209]:45140 + helo=newmailhub.example.com) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <p.mccartney@example.com>) id 1coHJc-00020n-Aa + for 26095@debbugs.gnu.org; Wed, 15 Mar 2017 18:22:45 -0400 +Received: from smtp1.soe.example.com (smtp1.soe.example.com [10.138.113.40]) + by newmailhub.example.com (8.14.5/8.14.5) with ESMTP id v2FMMeJT017835; + Thu, 16 Mar 2017 08:22:41 +1000 +Received: from [172.23.208.246] (scmb-bwoodc.biosci.example.com [172.23.208.246]) + (authenticated bits=0) + by smtp1.soe.example.com (8.14.5/8.14.5) with ESMTP id v2FMMd8e010652 + (version=TLSv1.2 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); + Thu, 16 Mar 2017 08:22:40 +1000 +References: <87h92w1cu0.fsf@example.com> +From: Paul McCartney <p.mccartney@example.com> +Message-ID: <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> +Date: Thu, 16 Mar 2017 08:22:39 +1000 +User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 + Thunderbird/45.7.0 +MIME-Version: 1.0 +In-Reply-To: <87h92w1cu0.fsf@example.com> +Content-Type: text/plain; charset=utf-8; format=flowed +Content-Transfer-Encoding: 7bit +X-UQ-FilterTime: 1489616561 +X-Scanned-By: MIMEDefang 2.73 on UQ Mailhub +X-Spam-Score: -2.3 (--) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -2.3 (--) + +Hi Ricardo, + +Good stuff. + +On 14/03/17 18:28, Ricardo Wurmus wrote: +> [..] +> +> This patch set adds package expressions for each of the recommended +> packages, disables building of recommended packages, and adds some of +> these packages to those R packages that need them. +What do you think about having an "r" and +"r-without-recommended-packages" instead of +"r-with-recommended-packages" and "r", respectively? When people load R, +they expect to have the recommended packages, don't they? + +Thanks, +ben + + + + + +Received: (at 26095) by debbugs.gnu.org; 15 Mar 2017 22:22:46 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 15 18:22:46 2017 +Received: from localhost ([127.0.0.1]:57640 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coHJe-00020y-ML + for submit@debbugs.gnu.org; Wed, 15 Mar 2017 18:22:46 -0400 +Received: from mailhub2.soe.example.com ([130.102.132.209]:45140 + helo=newmailhub.example.com) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <p.mccartney@example.com>) id 1coHJc-00020n-Aa + for 26095@debbugs.gnu.org; Wed, 15 Mar 2017 18:22:45 -0400 +Received: from smtp1.soe.example.com (smtp1.soe.example.com [10.138.113.40]) + by newmailhub.example.com (8.14.5/8.14.5) with ESMTP id v2FMMeJT017835; + Thu, 16 Mar 2017 08:22:41 +1000 +Received: from [172.23.208.246] (scmb-bwoodc.biosci.example.com [172.23.208.246]) + (authenticated bits=0) + by smtp1.soe.example.com (8.14.5/8.14.5) with ESMTP id v2FMMd8e010652 + (version=TLSv1.2 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); + Thu, 16 Mar 2017 08:22:40 +1000 +Subject: Re: bug#26095: R: do not build recommended packages +To: Ricardo Wurmus <rekado@example.com>, 26095@debbugs.gnu.org +References: <87h92w1cu0.fsf@example.com> +From: Paul McCartney <p.mccartney@example.com> +Message-ID: <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> +Date: Thu, 16 Mar 2017 08:22:39 +1000 +User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 + Thunderbird/45.7.0 +MIME-Version: 1.0 +In-Reply-To: <87h92w1cu0.fsf@example.com> +Content-Type: text/plain; charset=utf-8; format=flowed +Content-Transfer-Encoding: 7bit +X-UQ-FilterTime: 1489616561 +X-Scanned-By: MIMEDefang 2.73 on UQ Mailhub +X-Spam-Score: -2.3 (--) +X-Debbugs-Envelope-To: 26095 +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -2.3 (--) + +Hi Ricardo, + +Good stuff. + +On 14/03/17 18:28, Ricardo Wurmus wrote: +> [..] +> +> This patch set adds package expressions for each of the recommended +> packages, disables building of recommended packages, and adds some of +> these packages to those R packages that need them. +What do you think about having an "r" and +"r-without-recommended-packages" instead of +"r-with-recommended-packages" and "r", respectively? When people load R, +they expect to have the recommended packages, don't they? + +Thanks, +ben + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489672381 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: R: do not build recommended packages +Resent-From: Ricardo Wurmus <rekado@example.com> +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Thu, 16 Mar 2017 13:53:01 +0000 +Resent-Message-ID: <handler.26095.B26095.148967237323157@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: Paul McCartney <p.mccartney@example.com> +Cc: 26095@debbugs.gnu.org +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148967237323157 + (code B ref 26095); Thu, 16 Mar 2017 13:53:01 +0000 +Received: (at 26095) by debbugs.gnu.org; 16 Mar 2017 13:52:53 +0000 +Received: from localhost ([127.0.0.1]:58188 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coVpl-00061R-LS + for submit@debbugs.gnu.org; Thu, 16 Mar 2017 09:52:53 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21019) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1coVpj-00061I-Oa + for 26095@debbugs.gnu.org; Thu, 16 Mar 2017 09:52:52 -0400 +Received: from localhost (141.80.148.144 [141.80.148.144]) by mx.zohomail.com + with SMTPS id 1489672369603818.7135798037732; + Thu, 16 Mar 2017 06:52:49 -0700 (PDT) +References: <87h92w1cu0.fsf@example.com> + <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +In-reply-to: <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Thu, 16 Mar 2017 14:52:49 +0100 +Message-ID: <87pohhuy4u.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-Spam-Score: -1.8 (-) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -1.8 (-) + +Hi Ben, + +> What do you think about having an "r" and +> "r-without-recommended-packages" instead of +> "r-with-recommended-packages" and "r", respectively? + +> When people load R, they expect to have the recommended packages, +> don't they? + +I’m not sure. On the one hand it seems good to offer R with recommended +packages. On the other hand, people who already use R from Guix would +probably install R packages from Guix as well. + +If we offered R without the recommended packages by default, we would +still use the R variant without recommended packages for the +r-build-system. + +This means that we’d have a package variable “r” with the package name +“r-without-recommended-packages” and a package variable +“r-with-recommended-packages” with the package name “r”. + +Alternatively, we could change the r-build-system to use “r-minimal” by +default, rename “r” to “r-minimal” (both variable and package name), and +then rename “r-with-recommended-packages” to just “r” (both variable and +package name). + +What do you think? + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + + + + +Received: (at 26095) by debbugs.gnu.org; 16 Mar 2017 13:52:53 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 16 09:52:53 2017 +Received: from localhost ([127.0.0.1]:58188 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coVpl-00061R-LS + for submit@debbugs.gnu.org; Thu, 16 Mar 2017 09:52:53 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21019) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1coVpj-00061I-Oa + for 26095@debbugs.gnu.org; Thu, 16 Mar 2017 09:52:52 -0400 +Received: from localhost (141.80.148.144 [141.80.148.144]) by mx.zohomail.com + with SMTPS id 1489672369603818.7135798037732; + Thu, 16 Mar 2017 06:52:49 -0700 (PDT) +References: <87h92w1cu0.fsf@example.com> + <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +To: Paul McCartney <p.mccartney@example.com> +Subject: Re: bug#26095: R: do not build recommended packages +In-reply-to: <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Thu, 16 Mar 2017 14:52:49 +0100 +Message-ID: <87pohhuy4u.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-Spam-Score: -1.8 (-) +X-Debbugs-Envelope-To: 26095 +Cc: 26095@debbugs.gnu.org +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -1.8 (-) + +Hi Ben, + +> What do you think about having an "r" and +> "r-without-recommended-packages" instead of +> "r-with-recommended-packages" and "r", respectively? + +> When people load R, they expect to have the recommended packages, +> don't they? + +I’m not sure. On the one hand it seems good to offer R with recommended +packages. On the other hand, people who already use R from Guix would +probably install R packages from Guix as well. + +If we offered R without the recommended packages by default, we would +still use the R variant without recommended packages for the +r-build-system. + +This means that we’d have a package variable “r” with the package name +“r-without-recommended-packages” and a package variable +“r-with-recommended-packages” with the package name “r”. + +Alternatively, we could change the r-build-system to use “r-minimal” by +default, rename “r” to “r-minimal” (both variable and package name), and +then rename “r-with-recommended-packages” to just “r” (both variable and +package name). + +What do you think? + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + + + + +<!-- request_addr: Ricardo Wurmus <rekado@example.com> --> +<!-- time:1489742222 --> +<strong>Reply sent</strong> +to <code>Ricardo Wurmus <rekado@example.com></code>:<br> +You have taken responsibility. + + +-t + +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: Ricardo Wurmus <rekado@example.com> +Subject: bug#26095: closed (R: do not build recommended packages) +CC: tracker@debbugs.gnu.org +Message-ID: <handler.26095.D26095.148974222027144.ackdone@debbugs.gnu.org> +References: <8737ecz2im.fsf@example.com> <87h92w1cu0.fsf@example.com> +X-Gnu-PR-Message: closed 26095 +X-Gnu-PR-Package: guix-patches +Date: Fri, 17 Mar 2017 09:17:02 +0000 +Content-Type: multipart/mixed; boundary="----------=_1489742222-27156-0" + +This is a multi-part message in MIME format... + +------------=_1489742222-27156-0 +Content-Disposition: inline +Content-Transfer-Encoding: quoted-printable +Content-Type: text/plain; charset=utf-8 + +Your message dated Fri, 17 Mar 2017 10:16:49 +0100 +with message-id <8737ecz2im.fsf@example.com> +and subject line Re: bug#26095: R: do not build recommended packages +has caused the debbugs.gnu.org bug report #26095, +regarding R: do not build recommended packages +to be marked as done. + +(If you believe you have received this mail in error, please contact +help-debbugs@gnu.org.) + + +--=20 +26095: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D26095 +GNU Bug Tracking System +Contact help-debbugs@gnu.org with problems + +------------=_1489742222-27156-0 +Content-Type: message/rfc822 +Content-Disposition: inline +Content-Transfer-Encoding: 7bit + +Received: (at submit) by debbugs.gnu.org; 14 Mar 2017 08:29:19 +0000 +Received: from localhost ([127.0.0.1]:54721 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cnhpW-0000Ig-O5 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:18 -0400 +Received: from eggs.gnu.org ([208.118.235.92]:54571) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cnhpV-0000IT-2c + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:17 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpO-00014S-RV + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:11 -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 autolearn=disabled + version=3.3.2 +Received: from lists.gnu.org ([2001:4830:134:3::11]:46586) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpO-00014O-PH + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from eggs.gnu.org ([2001:4830:134:3::10]:45510) + by lists.gnu.org with esmtp (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpM-0005M2-GH + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpH-00011R-KO + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:08 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21020) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpH-00010f-E4 + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:03 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489480138371144.2514938811363; + Tue, 14 Mar 2017 01:28:58 -0700 (PDT) +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +To: guix-patches@gnu.org +Subject: R: do not build recommended packages +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Tue, 14 Mar 2017 09:28:55 +0100 +Message-ID: <87h92w1cu0.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x +X-Received-From: 2001:4830:134:3::11 +X-Spam-Score: -4.0 (----) +X-Debbugs-Envelope-To: submit +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -4.0 (----) + +This relates to bug 25598 “R packages are not bit-reproducible”. R +itself does not build reproducibly. One of the reasons is that it +includes recommended packages that are built in a random temporary +directory. The build paths for each of these packages is then embedded +in the packages’ “paths.rds” files. + +We don’t have this problem when building the packages with the +“r-build-system” like any other R package. + +This patch set adds package expressions for each of the recommended +packages, disables building of recommended packages, and adds some of +these packages to those R packages that need them. + +I’ve successfully rebuilt all R packages to make sure that these changes +don’t break anything. + +I also have an unpolished patch to fix bug 25598, but it depends on this +patch set. + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + + +------------=_1489742222-27156-0 +Content-Type: message/rfc822 +Content-Disposition: inline +Content-Transfer-Encoding: 7bit + +Received: (at 26095-done) by debbugs.gnu.org; 17 Mar 2017 09:17:00 +0000 +Received: from localhost ([127.0.0.1]:59601 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coo0J-00073k-Vj + for submit@debbugs.gnu.org; Fri, 17 Mar 2017 05:17:00 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21115) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1coo0I-00073b-KX + for 26095-done@debbugs.gnu.org; Fri, 17 Mar 2017 05:16:59 -0400 +Received: from localhost (141.80.148.179 [141.80.148.179]) by mx.zohomail.com + with SMTPS id 148974221224770.0071204243684; + Fri, 17 Mar 2017 02:16:52 -0700 (PDT) +References: <87h92w1cu0.fsf@example.com> + <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> <87pohhuy4u.fsf@example.com> +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +To: Paul McCartney <p.mccartney@example.com> +Subject: Re: bug#26095: R: do not build recommended packages +In-reply-to: <87pohhuy4u.fsf@example.com> +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Fri, 17 Mar 2017 10:16:49 +0100 +Message-ID: <8737ecz2im.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-Spam-Score: -1.8 (-) +X-Debbugs-Envelope-To: 26095-done +Cc: 26095-done@debbugs.gnu.org +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -1.8 (-) + + +>> What do you think about having an "r" and +>> "r-without-recommended-packages" instead of +>> "r-with-recommended-packages" and "r", respectively? + +[…] + +> Alternatively, we could change the r-build-system to use “r-minimal” by +> default, rename “r” to “r-minimal” (both variable and package name), and +> then rename “r-with-recommended-packages” to just “r” (both variable and +> package name). + +I went ahead and implemented this in a follow-up commit. (Doing this +all at once turned out to be a little too cluttered.) I’ve pushed this +to master with commit 2d7c4ae3ee83841ef827a160b0d23c1d10d2570d. + +Thanks for the review and the discussion! + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + +------------=_1489742222-27156-0-- + + + +<!-- request_addr: Ricardo Wurmus <rekado@example.com> --> +<!-- time:1489742222 --> +<strong>Notification sent</strong> +to <code>Ricardo Wurmus <rekado@example.com></code>:<br> +bug acknowledged by developer. + + +-t + +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: Ricardo Wurmus <rekado@example.com> +Subject: bug#26095: closed (Re: bug#26095: R: do not build recommended + packages) +Message-ID: <handler.26095.D26095.148974222027144.notifdone@debbugs.gnu.org> +References: <8737ecz2im.fsf@example.com> <87h92w1cu0.fsf@example.com> +X-Gnu-PR-Message: they-closed 26095 +X-Gnu-PR-Package: guix-patches +Reply-To: 26095@debbugs.gnu.org +Date: Fri, 17 Mar 2017 09:17:02 +0000 +Content-Type: multipart/mixed; boundary="----------=_1489742222-27156-1" + +This is a multi-part message in MIME format... + +------------=_1489742222-27156-1 +Content-Disposition: inline +Content-Transfer-Encoding: quoted-printable +Content-Type: text/plain; charset="utf-8" + +Your bug report + +#26095: R: do not build recommended packages + +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 26095@debbugs.gnu.org. + +--=20 +26095: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D26095 +GNU Bug Tracking System +Contact help-debbugs@gnu.org with problems + +------------=_1489742222-27156-1 +Content-Type: message/rfc822 +Content-Disposition: inline +Content-Transfer-Encoding: 7bit + +Received: (at 26095-done) by debbugs.gnu.org; 17 Mar 2017 09:17:00 +0000 +Received: from localhost ([127.0.0.1]:59601 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coo0J-00073k-Vj + for submit@debbugs.gnu.org; Fri, 17 Mar 2017 05:17:00 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21115) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1coo0I-00073b-KX + for 26095-done@debbugs.gnu.org; Fri, 17 Mar 2017 05:16:59 -0400 +Received: from localhost (141.80.148.179 [141.80.148.179]) by mx.zohomail.com + with SMTPS id 148974221224770.0071204243684; + Fri, 17 Mar 2017 02:16:52 -0700 (PDT) +References: <87h92w1cu0.fsf@example.com> + <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> <87pohhuy4u.fsf@example.com> +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +To: Paul McCartney <p.mccartney@example.com> +Subject: Re: bug#26095: R: do not build recommended packages +In-reply-to: <87pohhuy4u.fsf@example.com> +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Fri, 17 Mar 2017 10:16:49 +0100 +Message-ID: <8737ecz2im.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-Spam-Score: -1.8 (-) +X-Debbugs-Envelope-To: 26095-done +Cc: 26095-done@debbugs.gnu.org +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -1.8 (-) + + +>> What do you think about having an "r" and +>> "r-without-recommended-packages" instead of +>> "r-with-recommended-packages" and "r", respectively? + +[…] + +> Alternatively, we could change the r-build-system to use “r-minimal” by +> default, rename “r” to “r-minimal” (both variable and package name), and +> then rename “r-with-recommended-packages” to just “r” (both variable and +> package name). + +I went ahead and implemented this in a follow-up commit. (Doing this +all at once turned out to be a little too cluttered.) I’ve pushed this +to master with commit 2d7c4ae3ee83841ef827a160b0d23c1d10d2570d. + +Thanks for the review and the discussion! + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + +------------=_1489742222-27156-1 +Content-Type: message/rfc822 +Content-Disposition: inline +Content-Transfer-Encoding: 7bit + +Received: (at submit) by debbugs.gnu.org; 14 Mar 2017 08:29:19 +0000 +Received: from localhost ([127.0.0.1]:54721 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1cnhpW-0000Ig-O5 + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:18 -0400 +Received: from eggs.gnu.org ([208.118.235.92]:54571) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1cnhpV-0000IT-2c + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:17 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpO-00014S-RV + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:11 -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 autolearn=disabled + version=3.3.2 +Received: from lists.gnu.org ([2001:4830:134:3::11]:46586) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpO-00014O-PH + for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from eggs.gnu.org ([2001:4830:134:3::10]:45510) + by lists.gnu.org with esmtp (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpM-0005M2-GH + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:10 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <rekado@example.com>) id 1cnhpH-00011R-KO + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:08 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21020) + by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) + (Exim 4.71) (envelope-from <rekado@example.com>) id 1cnhpH-00010f-E4 + for guix-patches@gnu.org; Tue, 14 Mar 2017 04:29:03 -0400 +Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by + mx.zohomail.com with SMTPS id 1489480138371144.2514938811363; + Tue, 14 Mar 2017 01:28:58 -0700 (PDT) +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +To: guix-patches@gnu.org +Subject: R: do not build recommended packages +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Tue, 14 Mar 2017 09:28:55 +0100 +Message-ID: <87h92w1cu0.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x +X-Received-From: 2001:4830:134:3::11 +X-Spam-Score: -4.0 (----) +X-Debbugs-Envelope-To: submit +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -4.0 (----) + +This relates to bug 25598 “R packages are not bit-reproducible”. R +itself does not build reproducibly. One of the reasons is that it +includes recommended packages that are built in a random temporary +directory. The build paths for each of these packages is then embedded +in the packages’ “paths.rds” files. + +We don’t have this problem when building the packages with the +“r-build-system” like any other R package. + +This patch set adds package expressions for each of the recommended +packages, disables building of recommended packages, and adds some of +these packages to those R packages that need them. + +I’ve successfully rebuilt all R packages to make sure that these changes +don’t break anything. + +I also have an unpolished patch to fix bug 25598, but it depends on this +patch set. + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + + +------------=_1489742222-27156-1-- + + + +Received: (at 26095-done) by debbugs.gnu.org; 17 Mar 2017 09:17:00 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 17 05:17:00 2017 +Received: from localhost ([127.0.0.1]:59601 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coo0J-00073k-Vj + for submit@debbugs.gnu.org; Fri, 17 Mar 2017 05:17:00 -0400 +Received: from sender-of-o51.zoho.com ([135.84.80.216]:21115) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <rekado@example.com>) id 1coo0I-00073b-KX + for 26095-done@debbugs.gnu.org; Fri, 17 Mar 2017 05:16:59 -0400 +Received: from localhost (141.80.148.179 [141.80.148.179]) by mx.zohomail.com + with SMTPS id 148974221224770.0071204243684; + Fri, 17 Mar 2017 02:16:52 -0700 (PDT) +References: <87h92w1cu0.fsf@example.com> + <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> <87pohhuy4u.fsf@example.com> +User-agent: mu4e 0.9.18; emacs 25.1.1 +From: Ricardo Wurmus <rekado@example.com> +To: Paul McCartney <p.mccartney@example.com> +Subject: Re: bug#26095: R: do not build recommended packages +In-reply-to: <87pohhuy4u.fsf@example.com> +X-URL: https://example.com +X-PGP-Key: https://example.com/rekado.pubkey +X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +Date: Fri, 17 Mar 2017 10:16:49 +0100 +Message-ID: <8737ecz2im.fsf@example.com> +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: 8bit +X-Spam-Score: -1.8 (-) +X-Debbugs-Envelope-To: 26095-done +Cc: 26095-done@debbugs.gnu.org +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -1.8 (-) + + +>> What do you think about having an "r" and +>> "r-without-recommended-packages" instead of +>> "r-with-recommended-packages" and "r", respectively? + +[…] + +> Alternatively, we could change the r-build-system to use “r-minimal” by +> default, rename “r” to “r-minimal” (both variable and package name), and +> then rename “r-with-recommended-packages” to just “r” (both variable and +> package name). + +I went ahead and implemented this in a follow-up commit. (Doing this +all at once turned out to be a little too cluttered.) I’ve pushed this +to master with commit 2d7c4ae3ee83841ef827a160b0d23c1d10d2570d. + +Thanks for the review and the discussion! + +-- +Ricardo + +GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC +https://example.com + + + + + + +<!-- request_addr: guix-patches@gnu.org --> +<!-- time:1489745161 --> +<strong>Information forwarded</strong> +to <code>guix-patches@gnu.org</code>:<br> +<code>bug#26095</code>; Package <code>guix-patches</code>. + + +guix-patches@gnu.org + +X-Loop: help-debbugs@gnu.org +Subject: bug#26095: R: do not build recommended packages +Resent-From: ludo@example.com (Ludovic =?UTF-8?Q?Court=C3=A8s?=) +Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +Resent-CC: guix-patches@gnu.org +Resent-Date: Fri, 17 Mar 2017 10:06:01 +0000 +Resent-Message-ID: <handler.26095.B26095.148974515431823@debbugs.gnu.org> +Resent-Sender: help-debbugs@gnu.org +X-GNU-PR-Message: followup 26095 +X-GNU-PR-Package: guix-patches +X-GNU-PR-Keywords: +To: 26095@debbugs.gnu.org +Cc: rekado@example.com +Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148974515431823 + (code B ref 26095); Fri, 17 Mar 2017 10:06:01 +0000 +Received: (at 26095) by debbugs.gnu.org; 17 Mar 2017 10:05:54 +0000 +Received: from localhost ([127.0.0.1]:59645 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coold-0008HC-JH + for submit@debbugs.gnu.org; Fri, 17 Mar 2017 06:05:54 -0400 +Received: from eggs.gnu.org ([208.118.235.92]:35368) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <ludo@example.com>) id 1coolb-0008Gz-8e + for 26095@debbugs.gnu.org; Fri, 17 Mar 2017 06:05:51 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <ludo@example.com>) id 1coolV-0001Ix-4G + for 26095@debbugs.gnu.org; Fri, 17 Mar 2017 06:05:46 -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_20,RP_MATCHES_RCVD + autolearn=disabled version=3.3.2 +Received: from fencepost.gnu.org ([2001:4830:134:3::e]:33667) + by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from <ludo@example.com>) + id 1coolN-0001Ed-G4; Fri, 17 Mar 2017 06:05:37 -0400 +Received: from [193.50.110.167] (port=39122 helo=ribbon) + by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) + (Exim 4.82) (envelope-from <ludo@example.com>) + id 1coolN-0003Qj-23; Fri, 17 Mar 2017 06:05:37 -0400 +From: ludo@example.com (Ludovic =?UTF-8?Q?Court=C3=A8s?=) +References: <87h92w1cu0.fsf@example.com> + <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> + <87pohhuy4u.fsf@example.com> <8737ecz2im.fsf@example.com> +X-URL: http://www.fdn.fr/~lcourtes/ +X-Revolutionary-Date: 27 =?UTF-8?Q?Vent=C3=B4se?= an 225 de la =?UTF-8?Q?R=C3=A9volution?= +X-PGP-Key-ID: 0x090B11993D9AEBB5 +X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc +X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 +X-OS: x86_64-unknown-linux-gnu +Date: Fri, 17 Mar 2017 11:05:33 +0100 +In-Reply-To: <8737ecz2im.fsf@example.com> (Ricardo Wurmus's message of "Fri, + 17 Mar 2017 10:16:49 +0100") +Message-ID: <87mvckgqvm.fsf@gnu.org> +User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: quoted-printable +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] +X-Received-From: 2001:4830:134:3::e +X-Spam-Score: -5.0 (-----) +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -5.0 (-----) + +Ricardo Wurmus <rekado@example.com> skribis: + +>>> What do you think about having an "r" and +>>> "r-without-recommended-packages" instead of +>>> "r-with-recommended-packages" and "r", respectively? +> +> [=E2=80=A6] +> +>> Alternatively, we could change the r-build-system to use =E2=80=9Cr-mini= +mal=E2=80=9D by +>> default, rename =E2=80=9Cr=E2=80=9D to =E2=80=9Cr-minimal=E2=80=9D (both= + variable and package name), and +>> then rename =E2=80=9Cr-with-recommended-packages=E2=80=9D to just =E2=80= +=9Cr=E2=80=9D (both variable and +>> package name). +> +> I went ahead and implemented this in a follow-up commit. (Doing this +> all at once turned out to be a little too cluttered.) I=E2=80=99ve pushe= +d this +> to master with commit 2d7c4ae3ee83841ef827a160b0d23c1d10d2570d. + +Great work. It=E2=80=99s good to see more modularity! + +Ludo=E2=80=99. + + + + + +Received: (at 26095) by debbugs.gnu.org; 17 Mar 2017 10:05:54 +0000 +From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 17 06:05:54 2017 +Received: from localhost ([127.0.0.1]:59645 helo=debbugs.gnu.org) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>) + id 1coold-0008HC-JH + for submit@debbugs.gnu.org; Fri, 17 Mar 2017 06:05:54 -0400 +Received: from eggs.gnu.org ([208.118.235.92]:35368) + by debbugs.gnu.org with esmtp (Exim 4.84_2) + (envelope-from <ludo@example.com>) id 1coolb-0008Gz-8e + for 26095@debbugs.gnu.org; Fri, 17 Mar 2017 06:05:51 -0400 +Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) + (envelope-from <ludo@example.com>) id 1coolV-0001Ix-4G + for 26095@debbugs.gnu.org; Fri, 17 Mar 2017 06:05:46 -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_20,RP_MATCHES_RCVD + autolearn=disabled version=3.3.2 +Received: from fencepost.gnu.org ([2001:4830:134:3::e]:33667) + by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from <ludo@example.com>) + id 1coolN-0001Ed-G4; Fri, 17 Mar 2017 06:05:37 -0400 +Received: from [193.50.110.167] (port=39122 helo=ribbon) + by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) + (Exim 4.82) (envelope-from <ludo@example.com>) + id 1coolN-0003Qj-23; Fri, 17 Mar 2017 06:05:37 -0400 +From: ludo@example.com (Ludovic =?utf-8?Q?Court=C3=A8s?=) +To: 26095@debbugs.gnu.org +Subject: Re: bug#26095: R: do not build recommended packages +References: <87h92w1cu0.fsf@example.com> + <4d4ea5ba-1414-0362-3d9a-49be575308d2@example.com> + <87pohhuy4u.fsf@example.com> <8737ecz2im.fsf@example.com> +X-URL: http://www.fdn.fr/~lcourtes/ +X-Revolutionary-Date: 27 =?utf-8?Q?Vent=C3=B4se?= an 225 de la =?utf-8?Q?R?= + =?utf-8?Q?=C3=A9volution?= +X-PGP-Key-ID: 0x090B11993D9AEBB5 +X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc +X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 +X-OS: x86_64-unknown-linux-gnu +Date: Fri, 17 Mar 2017 11:05:33 +0100 +In-Reply-To: <8737ecz2im.fsf@example.com> (Ricardo Wurmus's message of "Fri, + 17 Mar 2017 10:16:49 +0100") +Message-ID: <87mvckgqvm.fsf@gnu.org> +User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: quoted-printable +X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] +X-Received-From: 2001:4830:134:3::e +X-Spam-Score: -5.0 (-----) +X-Debbugs-Envelope-To: 26095 +Cc: rekado@example.com +X-BeenThere: debbugs-submit@debbugs.gnu.org +X-Mailman-Version: 2.1.18 +Precedence: list +List-Id: <debbugs-submit.debbugs.gnu.org> +List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe> +List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> +List-Post: <mailto:debbugs-submit@debbugs.gnu.org> +List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help> +List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, + <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe> +Errors-To: debbugs-submit-bounces@debbugs.gnu.org +Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> +X-Spam-Score: -5.0 (-----) + +Ricardo Wurmus <rekado@example.com> skribis: + +>>> What do you think about having an "r" and +>>> "r-without-recommended-packages" instead of +>>> "r-with-recommended-packages" and "r", respectively? +> +> [=E2=80=A6] +> +>> Alternatively, we could change the r-build-system to use =E2=80=9Cr-mini= +mal=E2=80=9D by +>> default, rename =E2=80=9Cr=E2=80=9D to =E2=80=9Cr-minimal=E2=80=9D (both= + variable and package name), and +>> then rename =E2=80=9Cr-with-recommended-packages=E2=80=9D to just =E2=80= +=9Cr=E2=80=9D (both variable and +>> package name). +> +> I went ahead and implemented this in a follow-up commit. (Doing this +> all at once turned out to be a little too cluttered.) I=E2=80=99ve pushe= +d this +> to master with commit 2d7c4ae3ee83841ef827a160b0d23c1d10d2570d. + +Great work. It=E2=80=99s good to see more modularity! + +Ludo=E2=80=99. + + + + + +<!-- command:archive --> +<!-- requester: Debbugs Internal Request <help-debbugs@gnu.org> --> +<!-- request_addr: internal_control@debbugs.gnu.org --> +<!-- time:1492169045 --> +<!-- new_data: +$new_data = {}; +--> +<!-- old_data: +$old_data = {}; +--> +<strong>bug archived.</strong> +Request was from <code>Debbugs Internal Request <help-debbugs@gnu.org></code> +to <code>internal_control@debbugs.gnu.org</code>. + + +Received: (at fakecontrol) by fakecontrolmessage; +To: internal_control@debbugs.gnu.org +From: Debbugs Internal Request <help-debbugs@gnu.org> +Subject: Internal Control +Message-Id: bug archived. +Date: Fri, 14 Apr 2017 11:24:05 +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 + + |