tests: Add missing test data.
[software/mumi.git] / tests / data / spool / archive / 95 / 26095.log
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11 X-Loop: help-debbugs@gnu.org
12 Subject: bug#26095: R: do not build recommended packages
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89
90 This relates to bug 25598 “R packages are not bit-reproducible”. R
91 itself does not build reproducibly. One of the reasons is that it
92 includes recommended packages that are built in a random temporary
93 directory. The build paths for each of these packages is then embedded
94 in the packages’ “paths.rds” files.
95
96 We don’t have this problem when building the packages with the
97 “r-build-system” like any other R package.
98
99 This patch set adds package expressions for each of the recommended
100 packages, disables building of recommended packages, and adds some of
101 these packages to those R packages that need them.
102
103 I’ve successfully rebuilt all R packages to make sure that these changes
104 don’t break anything.
105
106 I also have an unpolished patch to fix bug 25598, but it depends on this
107 patch set.
108
109 --
110 Ricardo
111
112 GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
113 https://example.com
114
115
116
117
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120 <!-- request_addr: Ricardo Wurmus &lt;rekado@example.com&gt; -->
121 <!-- time:1489480202 -->
122 <strong>Acknowledgement sent</strong>
123 to <code>Ricardo Wurmus &lt;rekado@example.com&gt;</code>:<br>
124 New bug report received and forwarded. Copy sent to <code>guix-patches@gnu.org</code>.
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135 From: help-debbugs@gnu.org (GNU bug Tracking System)
136 To: Ricardo Wurmus <rekado@example.com>
137 Subject: bug#26095: Acknowledgement (R: do not build recommended packages)
138 Message-ID: <handler.26095.B.14894801591162.ack@debbugs.gnu.org>
139 References: <87h92w1cu0.fsf@example.com>
140 X-Gnu-PR-Message: ack 26095
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142 Reply-To: 26095@debbugs.gnu.org
143 Date: Tue, 14 Mar 2017 08:30:02 +0000
144
145 Thank you for filing a new bug report with debbugs.gnu.org.
146
147 This is an automatically generated reply to let you know your message
148 has been received.
149
150 Your message is being forwarded to the package maintainers and other
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158
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161
162 --=20
163 26095: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D26095
164 GNU Bug Tracking System
165 Contact help-debbugs@gnu.org with problems
166
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208 Subject: R: do not build recommended packages
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236
237 This relates to bug 25598 “R packages are not bit-reproducible”. R
238 itself does not build reproducibly. One of the reasons is that it
239 includes recommended packages that are built in a random temporary
240 directory. The build paths for each of these packages is then embedded
241 in the packages’ “paths.rds” files.
242
243 We don’t have this problem when building the packages with the
244 “r-build-system” like any other R package.
245
246 This patch set adds package expressions for each of the recommended
247 packages, disables building of recommended packages, and adds some of
248 these packages to those R packages that need them.
249
250 I’ve successfully rebuilt all R packages to make sure that these changes
251 don’t break anything.
252
253 I also have an unpolished patch to fix bug 25598, but it depends on this
254 patch set.
255
256 --
257 Ricardo
258
259 GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
260 https://example.com
261
262
263
264
265 \ 3
266 \ 6
267 <!-- request_addr: guix-patches@gnu.org -->
268 <!-- time:1489482241 -->
269 <strong>Information forwarded</strong>
270 to <code>guix-patches@gnu.org</code>:<br>
271 <code>bug#26095</code>; Package <code>guix-patches</code>.
272 \ 3
273 \ 2
274 guix-patches@gnu.org
275 \ 5
276 X-Loop: help-debbugs@gnu.org
277 Subject: bug#26095: [PATCH 02/17] gnu: Add r-mass.
278 Resent-From: Ricardo Wurmus <rekado@example.com>
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326
327 * gnu/packages/statistics.scm (r-mass): New variable.
328 ---
329 gnu/packages/statistics.scm | 21 +++++++++++++++++++++
330 1 file changed, 21 insertions(+)
331
332 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
333 index 54305a2f8..189a1d299 100644
334 --- a/gnu/packages/statistics.scm
335 +++ b/gnu/packages/statistics.scm
336 @@ -241,6 +241,27 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
337 ;; Unlimited distribution
338 (license (license:non-copyleft "file://R/bootfuns.q"))))
339
340 +(define-public r-mass
341 + (package
342 + (name "r-mass")
343 + (version "7.3-45")
344 + (source
345 + (origin
346 + (method url-fetch)
347 + (uri (cran-uri "MASS" version))
348 + (sha256
349 + (base32
350 + "13lp5919h2bnpmf8rbmkar8a41yx62fnx66pkvljvqf60wa29qsx"))))
351 + (properties `((upstream-name . "MASS")))
352 + (build-system r-build-system)
353 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
354 + (synopsis "Support functions and datasets for Venables and Ripley's MASS")
355 + (description
356 + "This package provides functions and datasets for the book \"Modern
357 +Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
358 + ;; Either version may be picked.
359 + (license (list license:gpl2 license:gpl3))))
360 +
361 (define-public r-bit
362 (package
363 (name "r-bit")
364 --
365 2.12.0
366
367
368
369
370
371 \ 3
372 \a
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386 Tue, 14 Mar 2017 02:03:04 -0700 (PDT)
387 From: Ricardo Wurmus <rekado@example.com>
388 To: 26095@debbugs.gnu.org
389 Subject: [PATCH 02/17] gnu: Add r-mass.
390 Date: Tue, 14 Mar 2017 10:02:41 +0100
391 Message-Id: <20170314090256.7695-2-rekado@example.com>
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413
414 * gnu/packages/statistics.scm (r-mass): New variable.
415 ---
416 gnu/packages/statistics.scm | 21 +++++++++++++++++++++
417 1 file changed, 21 insertions(+)
418
419 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
420 index 54305a2f8..189a1d299 100644
421 --- a/gnu/packages/statistics.scm
422 +++ b/gnu/packages/statistics.scm
423 @@ -241,6 +241,27 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
424 ;; Unlimited distribution
425 (license (license:non-copyleft "file://R/bootfuns.q"))))
426
427 +(define-public r-mass
428 + (package
429 + (name "r-mass")
430 + (version "7.3-45")
431 + (source
432 + (origin
433 + (method url-fetch)
434 + (uri (cran-uri "MASS" version))
435 + (sha256
436 + (base32
437 + "13lp5919h2bnpmf8rbmkar8a41yx62fnx66pkvljvqf60wa29qsx"))))
438 + (properties `((upstream-name . "MASS")))
439 + (build-system r-build-system)
440 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
441 + (synopsis "Support functions and datasets for Venables and Ripley's MASS")
442 + (description
443 + "This package provides functions and datasets for the book \"Modern
444 +Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
445 + ;; Either version may be picked.
446 + (license (list license:gpl2 license:gpl3))))
447 +
448 (define-public r-bit
449 (package
450 (name "r-bit")
451 --
452 2.12.0
453
454
455
456
457
458 \ 3
459 \ 6
460 <!-- request_addr: guix-patches@gnu.org -->
461 <!-- time:1489482242 -->
462 <strong>Information forwarded</strong>
463 to <code>guix-patches@gnu.org</code>:<br>
464 <code>bug#26095</code>; Package <code>guix-patches</code>.
465 \ 3
466 \ 2
467 guix-patches@gnu.org
468 \ 5
469 X-Loop: help-debbugs@gnu.org
470 Subject: bug#26095: [PATCH 01/17] gnu: Add r-boot.
471 Resent-From: Ricardo Wurmus <rekado@example.com>
472 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
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496 Tue, 14 Mar 2017 02:03:01 -0700 (PDT)
497 From: Ricardo Wurmus <rekado@example.com>
498 Date: Tue, 14 Mar 2017 10:02:40 +0100
499 Message-Id: <20170314090256.7695-1-rekado@example.com>
500 X-Mailer: git-send-email 2.12.0
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518
519 * gnu/packages/statistics.scm (r-boot): New variable.
520 ---
521 gnu/packages/statistics.scm | 21 +++++++++++++++++++++
522 1 file changed, 21 insertions(+)
523
524 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
525 index 75bdb5df8..54305a2f8 100644
526 --- a/gnu/packages/statistics.scm
527 +++ b/gnu/packages/statistics.scm
528 @@ -220,6 +220,27 @@ publication-quality data plots. A large amount of 3rd-party packages are
529 available, greatly increasing its breadth and scope.")
530 (license license:gpl3+)))
531
532 +(define-public r-boot
533 + (package
534 + (name "r-boot")
535 + (version "1.3-18")
536 + (source
537 + (origin
538 + (method url-fetch)
539 + (uri (cran-uri "boot" version))
540 + (sha256
541 + (base32
542 + "0pi348vvgzn1ny54yxhw6kq6nl7rx9bpr9ji1a6wqs8ah5zj7z8j"))))
543 + (build-system r-build-system)
544 + (home-page "http://cran.r-project.org/web/packages/boot")
545 + (synopsis "Bootstrap functions for R")
546 + (description
547 + "This package provides functions and datasets for bootstrapping from the
548 +book \"Bootstrap Methods and Their Application\" by A.C. Davison and
549 +D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
550 + ;; Unlimited distribution
551 + (license (license:non-copyleft "file://R/bootfuns.q"))))
552 +
553 (define-public r-bit
554 (package
555 (name "r-bit")
556 --
557 2.12.0
558
559
560
561
562
563 \ 3
564 \a
565 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:11 +0000
566 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:11 2017
567 Received: from localhost ([127.0.0.1]:54738 helo=debbugs.gnu.org)
568 by debbugs.gnu.org with esmtp (Exim 4.84_2)
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571 for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:11 -0400
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575 for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:09 -0400
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578 Tue, 14 Mar 2017 02:03:01 -0700 (PDT)
579 From: Ricardo Wurmus <rekado@example.com>
580 To: 26095@debbugs.gnu.org
581 Subject: [PATCH 01/17] gnu: Add r-boot.
582 Date: Tue, 14 Mar 2017 10:02:40 +0100
583 Message-Id: <20170314090256.7695-1-rekado@example.com>
584 X-Mailer: git-send-email 2.12.0
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604
605 * gnu/packages/statistics.scm (r-boot): New variable.
606 ---
607 gnu/packages/statistics.scm | 21 +++++++++++++++++++++
608 1 file changed, 21 insertions(+)
609
610 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
611 index 75bdb5df8..54305a2f8 100644
612 --- a/gnu/packages/statistics.scm
613 +++ b/gnu/packages/statistics.scm
614 @@ -220,6 +220,27 @@ publication-quality data plots. A large amount of 3rd-party packages are
615 available, greatly increasing its breadth and scope.")
616 (license license:gpl3+)))
617
618 +(define-public r-boot
619 + (package
620 + (name "r-boot")
621 + (version "1.3-18")
622 + (source
623 + (origin
624 + (method url-fetch)
625 + (uri (cran-uri "boot" version))
626 + (sha256
627 + (base32
628 + "0pi348vvgzn1ny54yxhw6kq6nl7rx9bpr9ji1a6wqs8ah5zj7z8j"))))
629 + (build-system r-build-system)
630 + (home-page "http://cran.r-project.org/web/packages/boot")
631 + (synopsis "Bootstrap functions for R")
632 + (description
633 + "This package provides functions and datasets for bootstrapping from the
634 +book \"Bootstrap Methods and Their Application\" by A.C. Davison and
635 +D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
636 + ;; Unlimited distribution
637 + (license (license:non-copyleft "file://R/bootfuns.q"))))
638 +
639 (define-public r-bit
640 (package
641 (name "r-bit")
642 --
643 2.12.0
644
645
646
647
648
649 \ 3
650 \ 6
651 <!-- request_addr: guix-patches@gnu.org -->
652 <!-- time:1489482242 -->
653 <strong>Information forwarded</strong>
654 to <code>guix-patches@gnu.org</code>:<br>
655 <code>bug#26095</code>; Package <code>guix-patches</code>.
656 \ 3
657 \ 2
658 guix-patches@gnu.org
659 \ 5
660 X-Loop: help-debbugs@gnu.org
661 Subject: bug#26095: [PATCH 03/17] gnu: Add r-class.
662 Resent-From: Ricardo Wurmus <rekado@example.com>
663 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
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671 To: 26095@debbugs.gnu.org
672 Cc: Ricardo Wurmus <rekado@example.com>
673 Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948219310954
674 (code B ref 26095); Tue, 14 Mar 2017 09:04:02 +0000
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687 Tue, 14 Mar 2017 02:03:07 -0700 (PDT)
688 From: Ricardo Wurmus <rekado@example.com>
689 Date: Tue, 14 Mar 2017 10:02:42 +0100
690 Message-Id: <20170314090256.7695-3-rekado@example.com>
691 X-Mailer: git-send-email 2.12.0
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710
711 * gnu/packages/statistics.scm (r-class): New variable.
712 ---
713 gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
714 1 file changed, 22 insertions(+)
715
716 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
717 index 189a1d299..9199c0b9e 100644
718 --- a/gnu/packages/statistics.scm
719 +++ b/gnu/packages/statistics.scm
720 @@ -262,6 +262,28 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
721 ;; Either version may be picked.
722 (license (list license:gpl2 license:gpl3))))
723
724 +(define-public r-class
725 + (package
726 + (name "r-class")
727 + (version "7.3-14")
728 + (source
729 + (origin
730 + (method url-fetch)
731 + (uri (cran-uri "class" version))
732 + (sha256
733 + (base32
734 + "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
735 + (build-system r-build-system)
736 + (propagated-inputs
737 + `(("r-mass" ,r-mass)))
738 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
739 + (synopsis "R functions for classification")
740 + (description
741 + "This package provides various functions for classification, including
742 +k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
743 + ;; Either of the two versions can be picked.
744 + (license (list license:gpl2 license:gpl3))))
745 +
746 (define-public r-bit
747 (package
748 (name "r-bit")
749 --
750 2.12.0
751
752
753
754
755
756 \ 3
757 \a
758 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:13 +0000
759 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:13 2017
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771 Tue, 14 Mar 2017 02:03:07 -0700 (PDT)
772 From: Ricardo Wurmus <rekado@example.com>
773 To: 26095@debbugs.gnu.org
774 Subject: [PATCH 03/17] gnu: Add r-class.
775 Date: Tue, 14 Mar 2017 10:02:42 +0100
776 Message-Id: <20170314090256.7695-3-rekado@example.com>
777 X-Mailer: git-send-email 2.12.0
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798
799 * gnu/packages/statistics.scm (r-class): New variable.
800 ---
801 gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
802 1 file changed, 22 insertions(+)
803
804 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
805 index 189a1d299..9199c0b9e 100644
806 --- a/gnu/packages/statistics.scm
807 +++ b/gnu/packages/statistics.scm
808 @@ -262,6 +262,28 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
809 ;; Either version may be picked.
810 (license (list license:gpl2 license:gpl3))))
811
812 +(define-public r-class
813 + (package
814 + (name "r-class")
815 + (version "7.3-14")
816 + (source
817 + (origin
818 + (method url-fetch)
819 + (uri (cran-uri "class" version))
820 + (sha256
821 + (base32
822 + "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
823 + (build-system r-build-system)
824 + (propagated-inputs
825 + `(("r-mass" ,r-mass)))
826 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
827 + (synopsis "R functions for classification")
828 + (description
829 + "This package provides various functions for classification, including
830 +k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
831 + ;; Either of the two versions can be picked.
832 + (license (list license:gpl2 license:gpl3))))
833 +
834 (define-public r-bit
835 (package
836 (name "r-bit")
837 --
838 2.12.0
839
840
841
842
843
844 \ 3
845 \ 6
846 <!-- request_addr: guix-patches@gnu.org -->
847 <!-- time:1489482243 -->
848 <strong>Information forwarded</strong>
849 to <code>guix-patches@gnu.org</code>:<br>
850 <code>bug#26095</code>; Package <code>guix-patches</code>.
851 \ 3
852 \ 2
853 guix-patches@gnu.org
854 \ 5
855 X-Loop: help-debbugs@gnu.org
856 Subject: bug#26095: [PATCH 04/17] gnu: Add r-cluster.
857 Resent-From: Ricardo Wurmus <rekado@example.com>
858 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
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883 From: Ricardo Wurmus <rekado@example.com>
884 Date: Tue, 14 Mar 2017 10:02:43 +0100
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905
906 * gnu/packages/statistics.scm (r-cluster): New variable.
907 ---
908 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
909 1 file changed, 20 insertions(+)
910
911 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
912 index 9199c0b9e..1492dccfb 100644
913 --- a/gnu/packages/statistics.scm
914 +++ b/gnu/packages/statistics.scm
915 @@ -284,6 +284,26 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
916 ;; Either of the two versions can be picked.
917 (license (list license:gpl2 license:gpl3))))
918
919 +(define-public r-cluster
920 + (package
921 + (name "r-cluster")
922 + (version "2.0.5")
923 + (source
924 + (origin
925 + (method url-fetch)
926 + (uri (cran-uri "cluster" version))
927 + (sha256
928 + (base32
929 + "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
930 + (build-system r-build-system)
931 + (home-page "http://cran.r-project.org/web/packages/cluster")
932 + (synopsis "Methods for cluster analysis")
933 + (description
934 + "This package provides methods for cluster analysis. It is a much
935 +extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
936 +Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
937 + (license license:gpl2+)))
938 +
939 (define-public r-bit
940 (package
941 (name "r-bit")
942 --
943 2.12.0
944
945
946
947
948
949 \ 3
950 \a
951 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:16 +0000
952 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:16 2017
953 Received: from localhost ([127.0.0.1]:54744 helo=debbugs.gnu.org)
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955 (envelope-from <debbugs-submit-bounces@debbugs.gnu.org>)
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957 for submit@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:16 -0400
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964 Tue, 14 Mar 2017 02:03:11 -0700 (PDT)
965 From: Ricardo Wurmus <rekado@example.com>
966 To: 26095@debbugs.gnu.org
967 Subject: [PATCH 04/17] gnu: Add r-cluster.
968 Date: Tue, 14 Mar 2017 10:02:43 +0100
969 Message-Id: <20170314090256.7695-4-rekado@example.com>
970 X-Mailer: git-send-email 2.12.0
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973 <20170314090256.7695-1-rekado@example.com>
974 X-Spam-Score: 1.0 (+)
975 X-Debbugs-Envelope-To: 26095
976 Cc: Ricardo Wurmus <rekado@example.com>
977 X-BeenThere: debbugs-submit@debbugs.gnu.org
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991
992 * gnu/packages/statistics.scm (r-cluster): New variable.
993 ---
994 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
995 1 file changed, 20 insertions(+)
996
997 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
998 index 9199c0b9e..1492dccfb 100644
999 --- a/gnu/packages/statistics.scm
1000 +++ b/gnu/packages/statistics.scm
1001 @@ -284,6 +284,26 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
1002 ;; Either of the two versions can be picked.
1003 (license (list license:gpl2 license:gpl3))))
1004
1005 +(define-public r-cluster
1006 + (package
1007 + (name "r-cluster")
1008 + (version "2.0.5")
1009 + (source
1010 + (origin
1011 + (method url-fetch)
1012 + (uri (cran-uri "cluster" version))
1013 + (sha256
1014 + (base32
1015 + "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
1016 + (build-system r-build-system)
1017 + (home-page "http://cran.r-project.org/web/packages/cluster")
1018 + (synopsis "Methods for cluster analysis")
1019 + (description
1020 + "This package provides methods for cluster analysis. It is a much
1021 +extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
1022 +Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
1023 + (license license:gpl2+)))
1024 +
1025 (define-public r-bit
1026 (package
1027 (name "r-bit")
1028 --
1029 2.12.0
1030
1031
1032
1033
1034
1035 \ 3
1036 \ 6
1037 <!-- request_addr: guix-patches@gnu.org -->
1038 <!-- time:1489482243 -->
1039 <strong>Information forwarded</strong>
1040 to <code>guix-patches@gnu.org</code>:<br>
1041 <code>bug#26095</code>; Package <code>guix-patches</code>.
1042 \ 3
1043 \ 2
1044 guix-patches@gnu.org
1045 \ 5
1046 X-Loop: help-debbugs@gnu.org
1047 Subject: bug#26095: [PATCH 05/17] gnu: Add r-codetools.
1048 Resent-From: Ricardo Wurmus <rekado@example.com>
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1080 <20170314090256.7695-1-rekado@example.com>
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1096
1097 * gnu/packages/statistics.scm (r-codetools): New variable.
1098 ---
1099 gnu/packages/statistics.scm | 18 ++++++++++++++++++
1100 1 file changed, 18 insertions(+)
1101
1102 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1103 index 1492dccfb..cbf5c14b1 100644
1104 --- a/gnu/packages/statistics.scm
1105 +++ b/gnu/packages/statistics.scm
1106 @@ -304,6 +304,24 @@ extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
1107 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
1108 (license license:gpl2+)))
1109
1110 +(define-public r-codetools
1111 + (package
1112 + (name "r-codetools")
1113 + (version "0.2-15")
1114 + (source
1115 + (origin
1116 + (method url-fetch)
1117 + (uri (cran-uri "codetools" version))
1118 + (sha256
1119 + (base32
1120 + "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
1121 + (build-system r-build-system)
1122 + (home-page "http://cran.r-project.org/web/packages/codetools")
1123 + (synopsis "Code analysis tools for R")
1124 + (description "This package provides code analysis tools for R.")
1125 + ;; Any version of the GPL.
1126 + (license (list license:gpl2+ license:gpl3+))))
1127 +
1128 (define-public r-bit
1129 (package
1130 (name "r-bit")
1131 --
1132 2.12.0
1133
1134
1135
1136
1137
1138 \ 3
1139 \a
1140 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:19 +0000
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1153 Tue, 14 Mar 2017 02:03:13 -0700 (PDT)
1154 From: Ricardo Wurmus <rekado@example.com>
1155 To: 26095@debbugs.gnu.org
1156 Subject: [PATCH 05/17] gnu: Add r-codetools.
1157 Date: Tue, 14 Mar 2017 10:02:44 +0100
1158 Message-Id: <20170314090256.7695-5-rekado@example.com>
1159 X-Mailer: git-send-email 2.12.0
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1180
1181 * gnu/packages/statistics.scm (r-codetools): New variable.
1182 ---
1183 gnu/packages/statistics.scm | 18 ++++++++++++++++++
1184 1 file changed, 18 insertions(+)
1185
1186 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1187 index 1492dccfb..cbf5c14b1 100644
1188 --- a/gnu/packages/statistics.scm
1189 +++ b/gnu/packages/statistics.scm
1190 @@ -304,6 +304,24 @@ extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
1191 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
1192 (license license:gpl2+)))
1193
1194 +(define-public r-codetools
1195 + (package
1196 + (name "r-codetools")
1197 + (version "0.2-15")
1198 + (source
1199 + (origin
1200 + (method url-fetch)
1201 + (uri (cran-uri "codetools" version))
1202 + (sha256
1203 + (base32
1204 + "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
1205 + (build-system r-build-system)
1206 + (home-page "http://cran.r-project.org/web/packages/codetools")
1207 + (synopsis "Code analysis tools for R")
1208 + (description "This package provides code analysis tools for R.")
1209 + ;; Any version of the GPL.
1210 + (license (list license:gpl2+ license:gpl3+))))
1211 +
1212 (define-public r-bit
1213 (package
1214 (name "r-bit")
1215 --
1216 2.12.0
1217
1218
1219
1220
1221
1222 \ 3
1223 \ 6
1224 <!-- request_addr: guix-patches@gnu.org -->
1225 <!-- time:1489482243 -->
1226 <strong>Information forwarded</strong>
1227 to <code>guix-patches@gnu.org</code>:<br>
1228 <code>bug#26095</code>; Package <code>guix-patches</code>.
1229 \ 3
1230 \ 2
1231 guix-patches@gnu.org
1232 \ 5
1233 X-Loop: help-debbugs@gnu.org
1234 Subject: bug#26095: [PATCH 06/17] gnu: Add r-foreign.
1235 Resent-From: Ricardo Wurmus <rekado@example.com>
1236 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
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1262 Date: Tue, 14 Mar 2017 10:02:45 +0100
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1283
1284 * gnu/packages/statistics.scm (r-foreign): New variable.
1285 ---
1286 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
1287 1 file changed, 20 insertions(+)
1288
1289 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1290 index cbf5c14b1..2317b37c3 100644
1291 --- a/gnu/packages/statistics.scm
1292 +++ b/gnu/packages/statistics.scm
1293 @@ -322,6 +322,26 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
1294 ;; Any version of the GPL.
1295 (license (list license:gpl2+ license:gpl3+))))
1296
1297 +(define-public r-foreign
1298 + (package
1299 + (name "r-foreign")
1300 + (version "0.8-67")
1301 + (source
1302 + (origin
1303 + (method url-fetch)
1304 + (uri (cran-uri "foreign" version))
1305 + (sha256
1306 + (base32
1307 + "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd"))))
1308 + (build-system r-build-system)
1309 + (home-page "http://cran.r-project.org/web/packages/foreign")
1310 + (synopsis "Read data stored by other statistics software")
1311 + (description
1312 + "This package provides functions for reading and writing data stored by
1313 +some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
1314 +for reading and writing some dBase files.")
1315 + (license license:gpl2+)))
1316 +
1317 (define-public r-bit
1318 (package
1319 (name "r-bit")
1320 --
1321 2.12.0
1322
1323
1324
1325
1326
1327 \ 3
1328 \a
1329 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:24 +0000
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1343 From: Ricardo Wurmus <rekado@example.com>
1344 To: 26095@debbugs.gnu.org
1345 Subject: [PATCH 06/17] gnu: Add r-foreign.
1346 Date: Tue, 14 Mar 2017 10:02:45 +0100
1347 Message-Id: <20170314090256.7695-6-rekado@example.com>
1348 X-Mailer: git-send-email 2.12.0
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1368 X-Spam-Score: 1.0 (+)
1369
1370 * gnu/packages/statistics.scm (r-foreign): New variable.
1371 ---
1372 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
1373 1 file changed, 20 insertions(+)
1374
1375 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1376 index cbf5c14b1..2317b37c3 100644
1377 --- a/gnu/packages/statistics.scm
1378 +++ b/gnu/packages/statistics.scm
1379 @@ -322,6 +322,26 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
1380 ;; Any version of the GPL.
1381 (license (list license:gpl2+ license:gpl3+))))
1382
1383 +(define-public r-foreign
1384 + (package
1385 + (name "r-foreign")
1386 + (version "0.8-67")
1387 + (source
1388 + (origin
1389 + (method url-fetch)
1390 + (uri (cran-uri "foreign" version))
1391 + (sha256
1392 + (base32
1393 + "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd"))))
1394 + (build-system r-build-system)
1395 + (home-page "http://cran.r-project.org/web/packages/foreign")
1396 + (synopsis "Read data stored by other statistics software")
1397 + (description
1398 + "This package provides functions for reading and writing data stored by
1399 +some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
1400 +for reading and writing some dBase files.")
1401 + (license license:gpl2+)))
1402 +
1403 (define-public r-bit
1404 (package
1405 (name "r-bit")
1406 --
1407 2.12.0
1408
1409
1410
1411
1412
1413 \ 3
1414 \ 6
1415 <!-- request_addr: guix-patches@gnu.org -->
1416 <!-- time:1489482244 -->
1417 <strong>Information forwarded</strong>
1418 to <code>guix-patches@gnu.org</code>:<br>
1419 <code>bug#26095</code>; Package <code>guix-patches</code>.
1420 \ 3
1421 \ 2
1422 guix-patches@gnu.org
1423 \ 5
1424 X-Loop: help-debbugs@gnu.org
1425 Subject: bug#26095: [PATCH 07/17] gnu: Add r-kernsmooth.
1426 Resent-From: Ricardo Wurmus <rekado@example.com>
1427 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
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1452 From: Ricardo Wurmus <rekado@example.com>
1453 Date: Tue, 14 Mar 2017 10:02:46 +0100
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1474
1475 * gnu/packages/statistics.scm (r-kernsmooth): New variable.
1476 ---
1477 gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1478 1 file changed, 22 insertions(+)
1479
1480 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1481 index 2317b37c3..0b092ed15 100644
1482 --- a/gnu/packages/statistics.scm
1483 +++ b/gnu/packages/statistics.scm
1484 @@ -342,6 +342,28 @@ some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
1485 for reading and writing some dBase files.")
1486 (license license:gpl2+)))
1487
1488 +(define-public r-kernsmooth
1489 + (package
1490 + (name "r-kernsmooth")
1491 + (version "2.23-15")
1492 + (source
1493 + (origin
1494 + (method url-fetch)
1495 + (uri (cran-uri "KernSmooth" version))
1496 + (sha256
1497 + (base32
1498 + "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
1499 + (properties `((upstream-name . "KernSmooth")))
1500 + (build-system r-build-system)
1501 + (home-page "http://cran.r-project.org/web/packages/KernSmooth")
1502 + (synopsis "Functions for kernel smoothing")
1503 + (description
1504 + "This package provides functions for kernel smoothing (and density
1505 +estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
1506 +\"Kernel Smoothing\".")
1507 + ;; Unlimited distribution
1508 + (license (license:non-copyleft "file://LICENCE.note"))))
1509 +
1510 (define-public r-bit
1511 (package
1512 (name "r-bit")
1513 --
1514 2.12.0
1515
1516
1517
1518
1519
1520 \ 3
1521 \a
1522 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:24 +0000
1523 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:24 2017
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1532 for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:23 -0400
1533 Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by
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1535 Tue, 14 Mar 2017 02:03:19 -0700 (PDT)
1536 From: Ricardo Wurmus <rekado@example.com>
1537 To: 26095@debbugs.gnu.org
1538 Subject: [PATCH 07/17] gnu: Add r-kernsmooth.
1539 Date: Tue, 14 Mar 2017 10:02:46 +0100
1540 Message-Id: <20170314090256.7695-7-rekado@example.com>
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1547 Cc: Ricardo Wurmus <rekado@example.com>
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1562
1563 * gnu/packages/statistics.scm (r-kernsmooth): New variable.
1564 ---
1565 gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1566 1 file changed, 22 insertions(+)
1567
1568 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1569 index 2317b37c3..0b092ed15 100644
1570 --- a/gnu/packages/statistics.scm
1571 +++ b/gnu/packages/statistics.scm
1572 @@ -342,6 +342,28 @@ some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
1573 for reading and writing some dBase files.")
1574 (license license:gpl2+)))
1575
1576 +(define-public r-kernsmooth
1577 + (package
1578 + (name "r-kernsmooth")
1579 + (version "2.23-15")
1580 + (source
1581 + (origin
1582 + (method url-fetch)
1583 + (uri (cran-uri "KernSmooth" version))
1584 + (sha256
1585 + (base32
1586 + "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
1587 + (properties `((upstream-name . "KernSmooth")))
1588 + (build-system r-build-system)
1589 + (home-page "http://cran.r-project.org/web/packages/KernSmooth")
1590 + (synopsis "Functions for kernel smoothing")
1591 + (description
1592 + "This package provides functions for kernel smoothing (and density
1593 +estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
1594 +\"Kernel Smoothing\".")
1595 + ;; Unlimited distribution
1596 + (license (license:non-copyleft "file://LICENCE.note"))))
1597 +
1598 (define-public r-bit
1599 (package
1600 (name "r-bit")
1601 --
1602 2.12.0
1603
1604
1605
1606
1607
1608 \ 3
1609 \ 6
1610 <!-- request_addr: guix-patches@gnu.org -->
1611 <!-- time:1489482244 -->
1612 <strong>Information forwarded</strong>
1613 to <code>guix-patches@gnu.org</code>:<br>
1614 <code>bug#26095</code>; Package <code>guix-patches</code>.
1615 \ 3
1616 \ 2
1617 guix-patches@gnu.org
1618 \ 5
1619 X-Loop: help-debbugs@gnu.org
1620 Subject: bug#26095: [PATCH 08/17] gnu: r-lattice: Move to other recommended R packages.
1621 Resent-From: Ricardo Wurmus <rekado@example.com>
1622 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
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1647 From: Ricardo Wurmus <rekado@example.com>
1648 Date: Tue, 14 Mar 2017 10:02:47 +0100
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1669
1670 * gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
1671 packages.
1672 ---
1673 gnu/packages/statistics.scm | 40 ++++++++++++++++++++--------------------
1674 1 file changed, 20 insertions(+), 20 deletions(-)
1675
1676 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1677 index 0b092ed15..0fa3be42c 100644
1678 --- a/gnu/packages/statistics.scm
1679 +++ b/gnu/packages/statistics.scm
1680 @@ -364,6 +364,26 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
1681 ;; Unlimited distribution
1682 (license (license:non-copyleft "file://LICENCE.note"))))
1683
1684 +(define-public r-lattice
1685 + (package
1686 + (name "r-lattice")
1687 + (version "0.20-34")
1688 + (source (origin
1689 + (method url-fetch)
1690 + (uri (cran-uri "lattice" version))
1691 + (sha256
1692 + (base32
1693 + "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
1694 + (build-system r-build-system)
1695 + (home-page "http://lattice.r-forge.r-project.org/")
1696 + (synopsis "High-level data visualization system")
1697 + (description
1698 + "The lattice package provides a powerful and elegant high-level data
1699 +visualization system inspired by Trellis graphics, with an emphasis on
1700 +multivariate data. Lattice is sufficient for typical graphics needs, and is
1701 +also flexible enough to handle most nonstandard requirements.")
1702 + (license license:gpl2+)))
1703 +
1704 (define-public r-bit
1705 (package
1706 (name "r-bit")
1707 @@ -2171,26 +2191,6 @@ scaling functions for R.")
1708 "This package provides an integration of base and grid graphics for R.")
1709 (license license:gpl2+)))
1710
1711 -(define-public r-lattice
1712 - (package
1713 - (name "r-lattice")
1714 - (version "0.20-34")
1715 - (source (origin
1716 - (method url-fetch)
1717 - (uri (cran-uri "lattice" version))
1718 - (sha256
1719 - (base32
1720 - "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
1721 - (build-system r-build-system)
1722 - (home-page "http://lattice.r-forge.r-project.org/")
1723 - (synopsis "High-level data visualization system")
1724 - (description
1725 - "The lattice package provides a powerful and elegant high-level data
1726 -visualization system inspired by Trellis graphics, with an emphasis on
1727 -multivariate data. Lattice is sufficient for typical graphics needs, and is
1728 -also flexible enough to handle most nonstandard requirements.")
1729 - (license license:gpl2+)))
1730 -
1731 (define-public r-latticeextra
1732 (package
1733 (name "r-latticeextra")
1734 --
1735 2.12.0
1736
1737
1738
1739
1740
1741 \ 3
1742 \a
1743 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:28 +0000
1744 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:28 2017
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1756 Tue, 14 Mar 2017 02:03:22 -0700 (PDT)
1757 From: Ricardo Wurmus <rekado@example.com>
1758 To: 26095@debbugs.gnu.org
1759 Subject: [PATCH 08/17] gnu: r-lattice: Move to other recommended R packages.
1760 Date: Tue, 14 Mar 2017 10:02:47 +0100
1761 Message-Id: <20170314090256.7695-8-rekado@example.com>
1762 X-Mailer: git-send-email 2.12.0
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1783
1784 * gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
1785 packages.
1786 ---
1787 gnu/packages/statistics.scm | 40 ++++++++++++++++++++--------------------
1788 1 file changed, 20 insertions(+), 20 deletions(-)
1789
1790 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1791 index 0b092ed15..0fa3be42c 100644
1792 --- a/gnu/packages/statistics.scm
1793 +++ b/gnu/packages/statistics.scm
1794 @@ -364,6 +364,26 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
1795 ;; Unlimited distribution
1796 (license (license:non-copyleft "file://LICENCE.note"))))
1797
1798 +(define-public r-lattice
1799 + (package
1800 + (name "r-lattice")
1801 + (version "0.20-34")
1802 + (source (origin
1803 + (method url-fetch)
1804 + (uri (cran-uri "lattice" version))
1805 + (sha256
1806 + (base32
1807 + "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
1808 + (build-system r-build-system)
1809 + (home-page "http://lattice.r-forge.r-project.org/")
1810 + (synopsis "High-level data visualization system")
1811 + (description
1812 + "The lattice package provides a powerful and elegant high-level data
1813 +visualization system inspired by Trellis graphics, with an emphasis on
1814 +multivariate data. Lattice is sufficient for typical graphics needs, and is
1815 +also flexible enough to handle most nonstandard requirements.")
1816 + (license license:gpl2+)))
1817 +
1818 (define-public r-bit
1819 (package
1820 (name "r-bit")
1821 @@ -2171,26 +2191,6 @@ scaling functions for R.")
1822 "This package provides an integration of base and grid graphics for R.")
1823 (license license:gpl2+)))
1824
1825 -(define-public r-lattice
1826 - (package
1827 - (name "r-lattice")
1828 - (version "0.20-34")
1829 - (source (origin
1830 - (method url-fetch)
1831 - (uri (cran-uri "lattice" version))
1832 - (sha256
1833 - (base32
1834 - "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
1835 - (build-system r-build-system)
1836 - (home-page "http://lattice.r-forge.r-project.org/")
1837 - (synopsis "High-level data visualization system")
1838 - (description
1839 - "The lattice package provides a powerful and elegant high-level data
1840 -visualization system inspired by Trellis graphics, with an emphasis on
1841 -multivariate data. Lattice is sufficient for typical graphics needs, and is
1842 -also flexible enough to handle most nonstandard requirements.")
1843 - (license license:gpl2+)))
1844 -
1845 (define-public r-latticeextra
1846 (package
1847 (name "r-latticeextra")
1848 --
1849 2.12.0
1850
1851
1852
1853
1854
1855 \ 3
1856 \ 6
1857 <!-- request_addr: guix-patches@gnu.org -->
1858 <!-- time:1489482245 -->
1859 <strong>Information forwarded</strong>
1860 to <code>guix-patches@gnu.org</code>:<br>
1861 <code>bug#26095</code>; Package <code>guix-patches</code>.
1862 \ 3
1863 \ 2
1864 guix-patches@gnu.org
1865 \ 5
1866 X-Loop: help-debbugs@gnu.org
1867 Subject: bug#26095: [PATCH 09/17] gnu: r-matrix: Move to set of recommended R packages.
1868 Resent-From: Ricardo Wurmus <rekado@example.com>
1869 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
1870 Resent-CC: guix-patches@gnu.org
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1894 From: Ricardo Wurmus <rekado@example.com>
1895 Date: Tue, 14 Mar 2017 10:02:48 +0100
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1916
1917 * gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
1918 packages.
1919 ---
1920 gnu/packages/statistics.scm | 44 ++++++++++++++++++++++----------------------
1921 1 file changed, 22 insertions(+), 22 deletions(-)
1922
1923 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
1924 index 0fa3be42c..23d6c9392 100644
1925 --- a/gnu/packages/statistics.scm
1926 +++ b/gnu/packages/statistics.scm
1927 @@ -384,6 +384,28 @@ multivariate data. Lattice is sufficient for typical graphics needs, and is
1928 also flexible enough to handle most nonstandard requirements.")
1929 (license license:gpl2+)))
1930
1931 +(define-public r-matrix
1932 + (package
1933 + (name "r-matrix")
1934 + (version "1.2-7.1")
1935 + (source
1936 + (origin
1937 + (method url-fetch)
1938 + (uri (cran-uri "Matrix" version))
1939 + (sha256
1940 + (base32
1941 + "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
1942 + (properties `((upstream-name . "Matrix")))
1943 + (build-system r-build-system)
1944 + (propagated-inputs
1945 + `(("r-lattice" ,r-lattice)))
1946 + (home-page "http://Matrix.R-forge.R-project.org/")
1947 + (synopsis "Sparse and dense matrix classes and methods")
1948 + (description
1949 + "This package provides classes and methods for dense and sparse matrices
1950 +and operations on them using LAPACK and SuiteSparse.")
1951 + (license license:gpl2+)))
1952 +
1953 (define-public r-bit
1954 (package
1955 (name "r-bit")
1956 @@ -623,28 +645,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1957 'citation(\"Rcpp\")' for details on these last two.")
1958 (license license:gpl2+)))
1959
1960 -(define-public r-matrix
1961 - (package
1962 - (name "r-matrix")
1963 - (version "1.2-7.1")
1964 - (source
1965 - (origin
1966 - (method url-fetch)
1967 - (uri (cran-uri "Matrix" version))
1968 - (sha256
1969 - (base32
1970 - "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
1971 - (properties `((upstream-name . "Matrix")))
1972 - (build-system r-build-system)
1973 - (propagated-inputs
1974 - `(("r-lattice" ,r-lattice)))
1975 - (home-page "http://Matrix.R-forge.R-project.org/")
1976 - (synopsis "Sparse and dense matrix classes and methods")
1977 - (description
1978 - "This package provides classes and methods for dense and sparse matrices
1979 -and operations on them using LAPACK and SuiteSparse.")
1980 - (license license:gpl2+)))
1981 -
1982 (define-public r-mgcv
1983 (package
1984 (name "r-mgcv")
1985 --
1986 2.12.0
1987
1988
1989
1990
1991
1992 \ 3
1993 \a
1994 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:31 +0000
1995 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:31 2017
1996 Received: from localhost ([127.0.0.1]:54759 helo=debbugs.gnu.org)
1997 by debbugs.gnu.org with esmtp (Exim 4.84_2)
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1999 id 1cniMc-0002s9-Om
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2004 for 26095@debbugs.gnu.org; Tue, 14 Mar 2017 05:03:28 -0400
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2007 Tue, 14 Mar 2017 02:03:25 -0700 (PDT)
2008 From: Ricardo Wurmus <rekado@example.com>
2009 To: 26095@debbugs.gnu.org
2010 Subject: [PATCH 09/17] gnu: r-matrix: Move to set of recommended R packages.
2011 Date: Tue, 14 Mar 2017 10:02:48 +0100
2012 Message-Id: <20170314090256.7695-9-rekado@example.com>
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2016 <20170314090256.7695-1-rekado@example.com>
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2034
2035 * gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
2036 packages.
2037 ---
2038 gnu/packages/statistics.scm | 44 ++++++++++++++++++++++----------------------
2039 1 file changed, 22 insertions(+), 22 deletions(-)
2040
2041 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2042 index 0fa3be42c..23d6c9392 100644
2043 --- a/gnu/packages/statistics.scm
2044 +++ b/gnu/packages/statistics.scm
2045 @@ -384,6 +384,28 @@ multivariate data. Lattice is sufficient for typical graphics needs, and is
2046 also flexible enough to handle most nonstandard requirements.")
2047 (license license:gpl2+)))
2048
2049 +(define-public r-matrix
2050 + (package
2051 + (name "r-matrix")
2052 + (version "1.2-7.1")
2053 + (source
2054 + (origin
2055 + (method url-fetch)
2056 + (uri (cran-uri "Matrix" version))
2057 + (sha256
2058 + (base32
2059 + "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
2060 + (properties `((upstream-name . "Matrix")))
2061 + (build-system r-build-system)
2062 + (propagated-inputs
2063 + `(("r-lattice" ,r-lattice)))
2064 + (home-page "http://Matrix.R-forge.R-project.org/")
2065 + (synopsis "Sparse and dense matrix classes and methods")
2066 + (description
2067 + "This package provides classes and methods for dense and sparse matrices
2068 +and operations on them using LAPACK and SuiteSparse.")
2069 + (license license:gpl2+)))
2070 +
2071 (define-public r-bit
2072 (package
2073 (name "r-bit")
2074 @@ -623,28 +645,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2075 'citation(\"Rcpp\")' for details on these last two.")
2076 (license license:gpl2+)))
2077
2078 -(define-public r-matrix
2079 - (package
2080 - (name "r-matrix")
2081 - (version "1.2-7.1")
2082 - (source
2083 - (origin
2084 - (method url-fetch)
2085 - (uri (cran-uri "Matrix" version))
2086 - (sha256
2087 - (base32
2088 - "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
2089 - (properties `((upstream-name . "Matrix")))
2090 - (build-system r-build-system)
2091 - (propagated-inputs
2092 - `(("r-lattice" ,r-lattice)))
2093 - (home-page "http://Matrix.R-forge.R-project.org/")
2094 - (synopsis "Sparse and dense matrix classes and methods")
2095 - (description
2096 - "This package provides classes and methods for dense and sparse matrices
2097 -and operations on them using LAPACK and SuiteSparse.")
2098 - (license license:gpl2+)))
2099 -
2100 (define-public r-mgcv
2101 (package
2102 (name "r-mgcv")
2103 --
2104 2.12.0
2105
2106
2107
2108
2109
2110 \ 3
2111 \ 6
2112 <!-- request_addr: guix-patches@gnu.org -->
2113 <!-- time:1489482245 -->
2114 <strong>Information forwarded</strong>
2115 to <code>guix-patches@gnu.org</code>:<br>
2116 <code>bug#26095</code>; Package <code>guix-patches</code>.
2117 \ 3
2118 \ 2
2119 guix-patches@gnu.org
2120 \ 5
2121 X-Loop: help-debbugs@gnu.org
2122 Subject: bug#26095: [PATCH 10/17] gnu: Add r-nlme.
2123 Resent-From: Ricardo Wurmus <rekado@example.com>
2124 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
2125 Resent-CC: guix-patches@gnu.org
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2149 From: Ricardo Wurmus <rekado@example.com>
2150 Date: Tue, 14 Mar 2017 10:02:49 +0100
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2171
2172 * gnu/packages/statistics.scm (r-nlme): New variable.
2173 ---
2174 gnu/packages/statistics.scm | 23 +++++++++++++++++++++++
2175 1 file changed, 23 insertions(+)
2176
2177 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2178 index 23d6c9392..c072bcbcb 100644
2179 --- a/gnu/packages/statistics.scm
2180 +++ b/gnu/packages/statistics.scm
2181 @@ -406,6 +406,29 @@ also flexible enough to handle most nonstandard requirements.")
2182 and operations on them using LAPACK and SuiteSparse.")
2183 (license license:gpl2+)))
2184
2185 +(define-public r-nlme
2186 + (package
2187 + (name "r-nlme")
2188 + (version "3.1-131")
2189 + (source
2190 + (origin
2191 + (method url-fetch)
2192 + (uri (cran-uri "nlme" version))
2193 + (sha256
2194 + (base32
2195 + "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
2196 + (build-system r-build-system)
2197 + (propagated-inputs
2198 + `(("r-lattice" ,r-lattice)))
2199 + (native-inputs
2200 + `(("gfortran" ,gfortran)))
2201 + (home-page "http://cran.r-project.org/web/packages/nlme")
2202 + (synopsis "Linear and nonlinear mixed effects models")
2203 + (description
2204 + "This package provides tools to fit and compare Gaussian linear and
2205 +nonlinear mixed-effects models.")
2206 + (license license:gpl2+)))
2207 +
2208 (define-public r-bit
2209 (package
2210 (name "r-bit")
2211 --
2212 2.12.0
2213
2214
2215
2216
2217
2218 \ 3
2219 \a
2220 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:32 +0000
2221 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:32 2017
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2234 From: Ricardo Wurmus <rekado@example.com>
2235 To: 26095@debbugs.gnu.org
2236 Subject: [PATCH 10/17] gnu: Add r-nlme.
2237 Date: Tue, 14 Mar 2017 10:02:49 +0100
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2260
2261 * gnu/packages/statistics.scm (r-nlme): New variable.
2262 ---
2263 gnu/packages/statistics.scm | 23 +++++++++++++++++++++++
2264 1 file changed, 23 insertions(+)
2265
2266 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2267 index 23d6c9392..c072bcbcb 100644
2268 --- a/gnu/packages/statistics.scm
2269 +++ b/gnu/packages/statistics.scm
2270 @@ -406,6 +406,29 @@ also flexible enough to handle most nonstandard requirements.")
2271 and operations on them using LAPACK and SuiteSparse.")
2272 (license license:gpl2+)))
2273
2274 +(define-public r-nlme
2275 + (package
2276 + (name "r-nlme")
2277 + (version "3.1-131")
2278 + (source
2279 + (origin
2280 + (method url-fetch)
2281 + (uri (cran-uri "nlme" version))
2282 + (sha256
2283 + (base32
2284 + "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
2285 + (build-system r-build-system)
2286 + (propagated-inputs
2287 + `(("r-lattice" ,r-lattice)))
2288 + (native-inputs
2289 + `(("gfortran" ,gfortran)))
2290 + (home-page "http://cran.r-project.org/web/packages/nlme")
2291 + (synopsis "Linear and nonlinear mixed effects models")
2292 + (description
2293 + "This package provides tools to fit and compare Gaussian linear and
2294 +nonlinear mixed-effects models.")
2295 + (license license:gpl2+)))
2296 +
2297 (define-public r-bit
2298 (package
2299 (name "r-bit")
2300 --
2301 2.12.0
2302
2303
2304
2305
2306
2307 \ 3
2308 \ 6
2309 <!-- request_addr: guix-patches@gnu.org -->
2310 <!-- time:1489482246 -->
2311 <strong>Information forwarded</strong>
2312 to <code>guix-patches@gnu.org</code>:<br>
2313 <code>bug#26095</code>; Package <code>guix-patches</code>.
2314 \ 3
2315 \ 2
2316 guix-patches@gnu.org
2317 \ 5
2318 X-Loop: help-debbugs@gnu.org
2319 Subject: bug#26095: [PATCH 11/17] gnu: r-mgcv: Move to set of recommended R packages.
2320 Resent-From: Ricardo Wurmus <rekado@example.com>
2321 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
2322 Resent-CC: guix-patches@gnu.org
2323 Resent-Date: Tue, 14 Mar 2017 09:04:06 +0000
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2326 X-GNU-PR-Message: followup 26095
2327 X-GNU-PR-Package: guix-patches
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2329 To: 26095@debbugs.gnu.org
2330 Cc: Ricardo Wurmus <rekado@example.com>
2331 Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948221511080
2332 (code B ref 26095); Tue, 14 Mar 2017 09:04:06 +0000
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2346 From: Ricardo Wurmus <rekado@example.com>
2347 Date: Tue, 14 Mar 2017 10:02:50 +0100
2348 Message-Id: <20170314090256.7695-11-rekado@example.com>
2349 X-Mailer: git-send-email 2.12.0
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2351 References: <87h92w1cu0.fsf@example.com>
2352 <20170314090256.7695-1-rekado@example.com>
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2368
2369 * gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
2370 packages.
2371 ---
2372 gnu/packages/statistics.scm | 45 ++++++++++++++++++++++++---------------------
2373 1 file changed, 24 insertions(+), 21 deletions(-)
2374
2375 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2376 index c072bcbcb..e5237d509 100644
2377 --- a/gnu/packages/statistics.scm
2378 +++ b/gnu/packages/statistics.scm
2379 @@ -429,6 +429,30 @@ and operations on them using LAPACK and SuiteSparse.")
2380 nonlinear mixed-effects models.")
2381 (license license:gpl2+)))
2382
2383 +(define-public r-mgcv
2384 + (package
2385 + (name "r-mgcv")
2386 + (version "1.8-16")
2387 + (source
2388 + (origin
2389 + (method url-fetch)
2390 + (uri (cran-uri "mgcv" version))
2391 + (sha256
2392 + (base32
2393 + "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
2394 + (build-system r-build-system)
2395 + (propagated-inputs
2396 + `(("r-matrix" ,r-matrix)
2397 + ("r-nlme" ,r-nlme)))
2398 + (home-page "http://cran.r-project.org/web/packages/mgcv")
2399 + (synopsis "Mixed generalised additive model computation")
2400 + (description
2401 + "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
2402 +parameter estimation by GCV, REML or UBRE/AIC. The library includes a
2403 +@code{gam()} function, a wide variety of smoothers, JAGS support and
2404 +distributions beyond the exponential family.")
2405 + (license license:gpl2+)))
2406 +
2407 (define-public r-bit
2408 (package
2409 (name "r-bit")
2410 @@ -668,27 +692,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2411 'citation(\"Rcpp\")' for details on these last two.")
2412 (license license:gpl2+)))
2413
2414 -(define-public r-mgcv
2415 - (package
2416 - (name "r-mgcv")
2417 - (version "1.8-16")
2418 - (source
2419 - (origin
2420 - (method url-fetch)
2421 - (uri (cran-uri "mgcv" version))
2422 - (sha256
2423 - (base32
2424 - "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
2425 - (build-system r-build-system)
2426 - (home-page "http://cran.r-project.org/web/packages/mgcv")
2427 - (synopsis "Mixed generalised additive model computation")
2428 - (description
2429 - "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
2430 -parameter estimation by GCV, REML or UBRE/AIC. The library includes a
2431 -@code{gam()} function, a wide variety of smoothers, JAGS support and
2432 -distributions beyond the exponential family.")
2433 - (license license:gpl2+)))
2434 -
2435 (define-public r-permute
2436 (package
2437 (name "r-permute")
2438 --
2439 2.12.0
2440
2441
2442
2443
2444
2445 \ 3
2446 \a
2447 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:35 +0000
2448 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:35 2017
2449 Received: from localhost ([127.0.0.1]:54765 helo=debbugs.gnu.org)
2450 by debbugs.gnu.org with esmtp (Exim 4.84_2)
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2460 Tue, 14 Mar 2017 02:03:31 -0700 (PDT)
2461 From: Ricardo Wurmus <rekado@example.com>
2462 To: 26095@debbugs.gnu.org
2463 Subject: [PATCH 11/17] gnu: r-mgcv: Move to set of recommended R packages.
2464 Date: Tue, 14 Mar 2017 10:02:50 +0100
2465 Message-Id: <20170314090256.7695-11-rekado@example.com>
2466 X-Mailer: git-send-email 2.12.0
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2468 References: <87h92w1cu0.fsf@example.com>
2469 <20170314090256.7695-1-rekado@example.com>
2470 X-Spam-Score: 1.0 (+)
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2472 Cc: Ricardo Wurmus <rekado@example.com>
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2487
2488 * gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
2489 packages.
2490 ---
2491 gnu/packages/statistics.scm | 45 ++++++++++++++++++++++++---------------------
2492 1 file changed, 24 insertions(+), 21 deletions(-)
2493
2494 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2495 index c072bcbcb..e5237d509 100644
2496 --- a/gnu/packages/statistics.scm
2497 +++ b/gnu/packages/statistics.scm
2498 @@ -429,6 +429,30 @@ and operations on them using LAPACK and SuiteSparse.")
2499 nonlinear mixed-effects models.")
2500 (license license:gpl2+)))
2501
2502 +(define-public r-mgcv
2503 + (package
2504 + (name "r-mgcv")
2505 + (version "1.8-16")
2506 + (source
2507 + (origin
2508 + (method url-fetch)
2509 + (uri (cran-uri "mgcv" version))
2510 + (sha256
2511 + (base32
2512 + "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
2513 + (build-system r-build-system)
2514 + (propagated-inputs
2515 + `(("r-matrix" ,r-matrix)
2516 + ("r-nlme" ,r-nlme)))
2517 + (home-page "http://cran.r-project.org/web/packages/mgcv")
2518 + (synopsis "Mixed generalised additive model computation")
2519 + (description
2520 + "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
2521 +parameter estimation by GCV, REML or UBRE/AIC. The library includes a
2522 +@code{gam()} function, a wide variety of smoothers, JAGS support and
2523 +distributions beyond the exponential family.")
2524 + (license license:gpl2+)))
2525 +
2526 (define-public r-bit
2527 (package
2528 (name "r-bit")
2529 @@ -668,27 +692,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2530 'citation(\"Rcpp\")' for details on these last two.")
2531 (license license:gpl2+)))
2532
2533 -(define-public r-mgcv
2534 - (package
2535 - (name "r-mgcv")
2536 - (version "1.8-16")
2537 - (source
2538 - (origin
2539 - (method url-fetch)
2540 - (uri (cran-uri "mgcv" version))
2541 - (sha256
2542 - (base32
2543 - "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
2544 - (build-system r-build-system)
2545 - (home-page "http://cran.r-project.org/web/packages/mgcv")
2546 - (synopsis "Mixed generalised additive model computation")
2547 - (description
2548 - "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
2549 -parameter estimation by GCV, REML or UBRE/AIC. The library includes a
2550 -@code{gam()} function, a wide variety of smoothers, JAGS support and
2551 -distributions beyond the exponential family.")
2552 - (license license:gpl2+)))
2553 -
2554 (define-public r-permute
2555 (package
2556 (name "r-permute")
2557 --
2558 2.12.0
2559
2560
2561
2562
2563
2564 \ 3
2565 \ 6
2566 <!-- request_addr: guix-patches@gnu.org -->
2567 <!-- time:1489482246 -->
2568 <strong>Information forwarded</strong>
2569 to <code>guix-patches@gnu.org</code>:<br>
2570 <code>bug#26095</code>; Package <code>guix-patches</code>.
2571 \ 3
2572 \ 2
2573 guix-patches@gnu.org
2574 \ 5
2575 X-Loop: help-debbugs@gnu.org
2576 Subject: bug#26095: [PATCH 12/17] gnu: r-nnet: Move to set of recommended R packages.
2577 Resent-From: Ricardo Wurmus <rekado@example.com>
2578 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
2579 Resent-CC: guix-patches@gnu.org
2580 Resent-Date: Tue, 14 Mar 2017 09:04:06 +0000
2581 Resent-Message-ID: <handler.26095.B26095.148948221911098@debbugs.gnu.org>
2582 Resent-Sender: help-debbugs@gnu.org
2583 X-GNU-PR-Message: followup 26095
2584 X-GNU-PR-Package: guix-patches
2585 X-GNU-PR-Keywords:
2586 To: 26095@debbugs.gnu.org
2587 Cc: Ricardo Wurmus <rekado@example.com>
2588 Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948221911098
2589 (code B ref 26095); Tue, 14 Mar 2017 09:04:06 +0000
2590 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:39 +0000
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2602 Tue, 14 Mar 2017 02:03:33 -0700 (PDT)
2603 From: Ricardo Wurmus <rekado@example.com>
2604 Date: Tue, 14 Mar 2017 10:02:51 +0100
2605 Message-Id: <20170314090256.7695-12-rekado@example.com>
2606 X-Mailer: git-send-email 2.12.0
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2608 References: <87h92w1cu0.fsf@example.com>
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2625
2626 * gnu/packages/machine-learning.scm (r-nnet): Move from here...
2627 * gnu/packages/statistics.scm (r-nnet): ...to here because the other
2628 recommended R packages are here.
2629 ---
2630 gnu/packages/machine-learning.scm | 19 -------------------
2631 gnu/packages/statistics.scm | 19 +++++++++++++++++++
2632 2 files changed, 19 insertions(+), 19 deletions(-)
2633
2634 diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
2635 index 7bad833b3..73c78744f 100644
2636 --- a/gnu/packages/machine-learning.scm
2637 +++ b/gnu/packages/machine-learning.scm
2638 @@ -460,25 +460,6 @@ adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
2639 geometric models.")
2640 (license license:lgpl3+)))
2641
2642 -(define-public r-nnet
2643 - (package
2644 - (name "r-nnet")
2645 - (version "7.3-12")
2646 - (source
2647 - (origin
2648 - (method url-fetch)
2649 - (uri (cran-uri "nnet" version))
2650 - (sha256
2651 - (base32
2652 - "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
2653 - (build-system r-build-system)
2654 - (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
2655 - (synopsis "Feed-forward neural networks and multinomial log-linear models")
2656 - (description
2657 - "This package provides functions for feed-forward neural networks with a
2658 -single hidden layer, and for multinomial log-linear models.")
2659 - (license (list license:gpl2+ license:gpl3+))))
2660 -
2661 (define-public r-kernlab
2662 (package
2663 (name "r-kernlab")
2664 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2665 index e5237d509..29cf32a60 100644
2666 --- a/gnu/packages/statistics.scm
2667 +++ b/gnu/packages/statistics.scm
2668 @@ -453,6 +453,25 @@ parameter estimation by GCV, REML or UBRE/AIC. The library includes a
2669 distributions beyond the exponential family.")
2670 (license license:gpl2+)))
2671
2672 +(define-public r-nnet
2673 + (package
2674 + (name "r-nnet")
2675 + (version "7.3-12")
2676 + (source
2677 + (origin
2678 + (method url-fetch)
2679 + (uri (cran-uri "nnet" version))
2680 + (sha256
2681 + (base32
2682 + "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
2683 + (build-system r-build-system)
2684 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
2685 + (synopsis "Feed-forward neural networks and multinomial log-linear models")
2686 + (description
2687 + "This package provides functions for feed-forward neural networks with a
2688 +single hidden layer, and for multinomial log-linear models.")
2689 + (license (list license:gpl2+ license:gpl3+))))
2690 +
2691 (define-public r-bit
2692 (package
2693 (name "r-bit")
2694 --
2695 2.12.0
2696
2697
2698
2699
2700
2701 \ 3
2702 \a
2703 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:39 +0000
2704 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:38 2017
2705 Received: from localhost ([127.0.0.1]:54768 helo=debbugs.gnu.org)
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2716 Tue, 14 Mar 2017 02:03:33 -0700 (PDT)
2717 From: Ricardo Wurmus <rekado@example.com>
2718 To: 26095@debbugs.gnu.org
2719 Subject: [PATCH 12/17] gnu: r-nnet: Move to set of recommended R packages.
2720 Date: Tue, 14 Mar 2017 10:02:51 +0100
2721 Message-Id: <20170314090256.7695-12-rekado@example.com>
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2739 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
2740 Errors-To: debbugs-submit-bounces@debbugs.gnu.org
2741 Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
2742 X-Spam-Score: 1.0 (+)
2743
2744 * gnu/packages/machine-learning.scm (r-nnet): Move from here...
2745 * gnu/packages/statistics.scm (r-nnet): ...to here because the other
2746 recommended R packages are here.
2747 ---
2748 gnu/packages/machine-learning.scm | 19 -------------------
2749 gnu/packages/statistics.scm | 19 +++++++++++++++++++
2750 2 files changed, 19 insertions(+), 19 deletions(-)
2751
2752 diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
2753 index 7bad833b3..73c78744f 100644
2754 --- a/gnu/packages/machine-learning.scm
2755 +++ b/gnu/packages/machine-learning.scm
2756 @@ -460,25 +460,6 @@ adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
2757 geometric models.")
2758 (license license:lgpl3+)))
2759
2760 -(define-public r-nnet
2761 - (package
2762 - (name "r-nnet")
2763 - (version "7.3-12")
2764 - (source
2765 - (origin
2766 - (method url-fetch)
2767 - (uri (cran-uri "nnet" version))
2768 - (sha256
2769 - (base32
2770 - "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
2771 - (build-system r-build-system)
2772 - (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
2773 - (synopsis "Feed-forward neural networks and multinomial log-linear models")
2774 - (description
2775 - "This package provides functions for feed-forward neural networks with a
2776 -single hidden layer, and for multinomial log-linear models.")
2777 - (license (list license:gpl2+ license:gpl3+))))
2778 -
2779 (define-public r-kernlab
2780 (package
2781 (name "r-kernlab")
2782 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2783 index e5237d509..29cf32a60 100644
2784 --- a/gnu/packages/statistics.scm
2785 +++ b/gnu/packages/statistics.scm
2786 @@ -453,6 +453,25 @@ parameter estimation by GCV, REML or UBRE/AIC. The library includes a
2787 distributions beyond the exponential family.")
2788 (license license:gpl2+)))
2789
2790 +(define-public r-nnet
2791 + (package
2792 + (name "r-nnet")
2793 + (version "7.3-12")
2794 + (source
2795 + (origin
2796 + (method url-fetch)
2797 + (uri (cran-uri "nnet" version))
2798 + (sha256
2799 + (base32
2800 + "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
2801 + (build-system r-build-system)
2802 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
2803 + (synopsis "Feed-forward neural networks and multinomial log-linear models")
2804 + (description
2805 + "This package provides functions for feed-forward neural networks with a
2806 +single hidden layer, and for multinomial log-linear models.")
2807 + (license (list license:gpl2+ license:gpl3+))))
2808 +
2809 (define-public r-bit
2810 (package
2811 (name "r-bit")
2812 --
2813 2.12.0
2814
2815
2816
2817
2818
2819 \ 3
2820 \ 6
2821 <!-- request_addr: guix-patches@gnu.org -->
2822 <!-- time:1489482247 -->
2823 <strong>Information forwarded</strong>
2824 to <code>guix-patches@gnu.org</code>:<br>
2825 <code>bug#26095</code>; Package <code>guix-patches</code>.
2826 \ 3
2827 \ 2
2828 guix-patches@gnu.org
2829 \ 5
2830 X-Loop: help-debbugs@gnu.org
2831 Subject: bug#26095: [PATCH 13/17] gnu: r-rpart: Move to the set of recommended packages.
2832 Resent-From: Ricardo Wurmus <rekado@example.com>
2833 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
2834 Resent-CC: guix-patches@gnu.org
2835 Resent-Date: Tue, 14 Mar 2017 09:04:07 +0000
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2841 To: 26095@debbugs.gnu.org
2842 Cc: Ricardo Wurmus <rekado@example.com>
2843 Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948222211116
2844 (code B ref 26095); Tue, 14 Mar 2017 09:04:07 +0000
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2858 From: Ricardo Wurmus <rekado@example.com>
2859 Date: Tue, 14 Mar 2017 10:02:52 +0100
2860 Message-Id: <20170314090256.7695-13-rekado@example.com>
2861 X-Mailer: git-send-email 2.12.0
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2863 References: <87h92w1cu0.fsf@example.com>
2864 <20170314090256.7695-1-rekado@example.com>
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2880
2881 * gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
2882 packages.
2883 ---
2884 gnu/packages/statistics.scm | 38 +++++++++++++++++++-------------------
2885 1 file changed, 19 insertions(+), 19 deletions(-)
2886
2887 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
2888 index 29cf32a60..8780027d3 100644
2889 --- a/gnu/packages/statistics.scm
2890 +++ b/gnu/packages/statistics.scm
2891 @@ -472,6 +472,25 @@ distributions beyond the exponential family.")
2892 single hidden layer, and for multinomial log-linear models.")
2893 (license (list license:gpl2+ license:gpl3+))))
2894
2895 +(define-public r-rpart
2896 + (package
2897 + (name "r-rpart")
2898 + (version "4.1-10")
2899 + (source
2900 + (origin
2901 + (method url-fetch)
2902 + (uri (cran-uri "rpart" version))
2903 + (sha256
2904 + (base32
2905 + "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
2906 + (build-system r-build-system)
2907 + (home-page "http://cran.r-project.org/web/packages/rpart")
2908 + (synopsis "Recursive partitioning and regression trees")
2909 + (description
2910 + "This package provides recursive partitioning functions for
2911 +classification, regression and survival trees.")
2912 + (license (list license:gpl2+ license:gpl3+))))
2913 +
2914 (define-public r-bit
2915 (package
2916 (name "r-bit")
2917 @@ -3644,25 +3663,6 @@ following problems:
2918 @end enumerate\n")
2919 (license license:gpl3+)))
2920
2921 -(define-public r-rpart
2922 - (package
2923 - (name "r-rpart")
2924 - (version "4.1-10")
2925 - (source
2926 - (origin
2927 - (method url-fetch)
2928 - (uri (cran-uri "rpart" version))
2929 - (sha256
2930 - (base32
2931 - "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
2932 - (build-system r-build-system)
2933 - (home-page "http://cran.r-project.org/web/packages/rpart")
2934 - (synopsis "Recursive partitioning and regression trees")
2935 - (description
2936 - "This package provides recursive partitioning functions for
2937 -classification, regression and survival trees.")
2938 - (license (list license:gpl2+ license:gpl3+))))
2939 -
2940 (define-public r-survival
2941 (package
2942 (name "r-survival")
2943 --
2944 2.12.0
2945
2946
2947
2948
2949
2950 \ 3
2951 \a
2952 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:42 +0000
2953 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:42 2017
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2965 Tue, 14 Mar 2017 02:03:36 -0700 (PDT)
2966 From: Ricardo Wurmus <rekado@example.com>
2967 To: 26095@debbugs.gnu.org
2968 Subject: [PATCH 13/17] gnu: r-rpart: Move to the set of recommended packages.
2969 Date: Tue, 14 Mar 2017 10:02:52 +0100
2970 Message-Id: <20170314090256.7695-13-rekado@example.com>
2971 X-Mailer: git-send-email 2.12.0
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2974 <20170314090256.7695-1-rekado@example.com>
2975 X-Spam-Score: 1.0 (+)
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2990 Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
2991 X-Spam-Score: 1.0 (+)
2992
2993 * gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
2994 packages.
2995 ---
2996 gnu/packages/statistics.scm | 38 +++++++++++++++++++-------------------
2997 1 file changed, 19 insertions(+), 19 deletions(-)
2998
2999 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
3000 index 29cf32a60..8780027d3 100644
3001 --- a/gnu/packages/statistics.scm
3002 +++ b/gnu/packages/statistics.scm
3003 @@ -472,6 +472,25 @@ distributions beyond the exponential family.")
3004 single hidden layer, and for multinomial log-linear models.")
3005 (license (list license:gpl2+ license:gpl3+))))
3006
3007 +(define-public r-rpart
3008 + (package
3009 + (name "r-rpart")
3010 + (version "4.1-10")
3011 + (source
3012 + (origin
3013 + (method url-fetch)
3014 + (uri (cran-uri "rpart" version))
3015 + (sha256
3016 + (base32
3017 + "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
3018 + (build-system r-build-system)
3019 + (home-page "http://cran.r-project.org/web/packages/rpart")
3020 + (synopsis "Recursive partitioning and regression trees")
3021 + (description
3022 + "This package provides recursive partitioning functions for
3023 +classification, regression and survival trees.")
3024 + (license (list license:gpl2+ license:gpl3+))))
3025 +
3026 (define-public r-bit
3027 (package
3028 (name "r-bit")
3029 @@ -3644,25 +3663,6 @@ following problems:
3030 @end enumerate\n")
3031 (license license:gpl3+)))
3032
3033 -(define-public r-rpart
3034 - (package
3035 - (name "r-rpart")
3036 - (version "4.1-10")
3037 - (source
3038 - (origin
3039 - (method url-fetch)
3040 - (uri (cran-uri "rpart" version))
3041 - (sha256
3042 - (base32
3043 - "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
3044 - (build-system r-build-system)
3045 - (home-page "http://cran.r-project.org/web/packages/rpart")
3046 - (synopsis "Recursive partitioning and regression trees")
3047 - (description
3048 - "This package provides recursive partitioning functions for
3049 -classification, regression and survival trees.")
3050 - (license (list license:gpl2+ license:gpl3+))))
3051 -
3052 (define-public r-survival
3053 (package
3054 (name "r-survival")
3055 --
3056 2.12.0
3057
3058
3059
3060
3061
3062 \ 3
3063 \ 6
3064 <!-- request_addr: guix-patches@gnu.org -->
3065 <!-- time:1489482247 -->
3066 <strong>Information forwarded</strong>
3067 to <code>guix-patches@gnu.org</code>:<br>
3068 <code>bug#26095</code>; Package <code>guix-patches</code>.
3069 \ 3
3070 \ 2
3071 guix-patches@gnu.org
3072 \ 5
3073 X-Loop: help-debbugs@gnu.org
3074 Subject: bug#26095: [PATCH 14/17] gnu: Add r-spatial.
3075 Resent-From: Ricardo Wurmus <rekado@example.com>
3076 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
3077 Resent-CC: guix-patches@gnu.org
3078 Resent-Date: Tue, 14 Mar 2017 09:04:07 +0000
3079 Resent-Message-ID: <handler.26095.B26095.148948222511130@debbugs.gnu.org>
3080 Resent-Sender: help-debbugs@gnu.org
3081 X-GNU-PR-Message: followup 26095
3082 X-GNU-PR-Package: guix-patches
3083 X-GNU-PR-Keywords:
3084 To: 26095@debbugs.gnu.org
3085 Cc: Ricardo Wurmus <rekado@example.com>
3086 Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948222511130
3087 (code B ref 26095); Tue, 14 Mar 2017 09:04:07 +0000
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3100 Tue, 14 Mar 2017 02:03:39 -0700 (PDT)
3101 From: Ricardo Wurmus <rekado@example.com>
3102 Date: Tue, 14 Mar 2017 10:02:53 +0100
3103 Message-Id: <20170314090256.7695-14-rekado@example.com>
3104 X-Mailer: git-send-email 2.12.0
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3106 References: <87h92w1cu0.fsf@example.com>
3107 <20170314090256.7695-1-rekado@example.com>
3108 X-Spam-Score: 1.0 (+)
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3112 List-Id: <debbugs-submit.debbugs.gnu.org>
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3123
3124 * gnu/packages/statistics.scm (r-spatial): New variable.
3125 ---
3126 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
3127 1 file changed, 20 insertions(+)
3128
3129 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
3130 index 8780027d3..b338efcda 100644
3131 --- a/gnu/packages/statistics.scm
3132 +++ b/gnu/packages/statistics.scm
3133 @@ -491,6 +491,26 @@ single hidden layer, and for multinomial log-linear models.")
3134 classification, regression and survival trees.")
3135 (license (list license:gpl2+ license:gpl3+))))
3136
3137 +(define-public r-spatial
3138 + (package
3139 + (name "r-spatial")
3140 + (version "7.3-11")
3141 + (source
3142 + (origin
3143 + (method url-fetch)
3144 + (uri (cran-uri "spatial" version))
3145 + (sha256
3146 + (base32
3147 + "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
3148 + (build-system r-build-system)
3149 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
3150 + (synopsis "Functions for kriging and point pattern analysis")
3151 + (description
3152 + "This package provides functions for kriging and point pattern
3153 +analysis.")
3154 + ;; Either version may be picked.
3155 + (license (list license:gpl2 license:gpl3))))
3156 +
3157 (define-public r-bit
3158 (package
3159 (name "r-bit")
3160 --
3161 2.12.0
3162
3163
3164
3165
3166
3167 \ 3
3168 \a
3169 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:45 +0000
3170 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:45 2017
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3182 Tue, 14 Mar 2017 02:03:39 -0700 (PDT)
3183 From: Ricardo Wurmus <rekado@example.com>
3184 To: 26095@debbugs.gnu.org
3185 Subject: [PATCH 14/17] gnu: Add r-spatial.
3186 Date: Tue, 14 Mar 2017 10:02:53 +0100
3187 Message-Id: <20170314090256.7695-14-rekado@example.com>
3188 X-Mailer: git-send-email 2.12.0
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3204 List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>,
3205 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
3206 Errors-To: debbugs-submit-bounces@debbugs.gnu.org
3207 Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
3208 X-Spam-Score: 1.0 (+)
3209
3210 * gnu/packages/statistics.scm (r-spatial): New variable.
3211 ---
3212 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
3213 1 file changed, 20 insertions(+)
3214
3215 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
3216 index 8780027d3..b338efcda 100644
3217 --- a/gnu/packages/statistics.scm
3218 +++ b/gnu/packages/statistics.scm
3219 @@ -491,6 +491,26 @@ single hidden layer, and for multinomial log-linear models.")
3220 classification, regression and survival trees.")
3221 (license (list license:gpl2+ license:gpl3+))))
3222
3223 +(define-public r-spatial
3224 + (package
3225 + (name "r-spatial")
3226 + (version "7.3-11")
3227 + (source
3228 + (origin
3229 + (method url-fetch)
3230 + (uri (cran-uri "spatial" version))
3231 + (sha256
3232 + (base32
3233 + "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
3234 + (build-system r-build-system)
3235 + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
3236 + (synopsis "Functions for kriging and point pattern analysis")
3237 + (description
3238 + "This package provides functions for kriging and point pattern
3239 +analysis.")
3240 + ;; Either version may be picked.
3241 + (license (list license:gpl2 license:gpl3))))
3242 +
3243 (define-public r-bit
3244 (package
3245 (name "r-bit")
3246 --
3247 2.12.0
3248
3249
3250
3251
3252
3253 \ 3
3254 \ 6
3255 <!-- request_addr: guix-patches@gnu.org -->
3256 <!-- time:1489482248 -->
3257 <strong>Information forwarded</strong>
3258 to <code>guix-patches@gnu.org</code>:<br>
3259 <code>bug#26095</code>; Package <code>guix-patches</code>.
3260 \ 3
3261 \ 2
3262 guix-patches@gnu.org
3263 \ 5
3264 X-Loop: help-debbugs@gnu.org
3265 Subject: bug#26095: [PATCH 15/17] gnu: r-survival: Move to set of recommended R packages.
3266 Resent-From: Ricardo Wurmus <rekado@example.com>
3267 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
3268 Resent-CC: guix-patches@gnu.org
3269 Resent-Date: Tue, 14 Mar 2017 09:04:08 +0000
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3273 X-GNU-PR-Package: guix-patches
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3275 To: 26095@debbugs.gnu.org
3276 Cc: Ricardo Wurmus <rekado@example.com>
3277 Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948222911148
3278 (code B ref 26095); Tue, 14 Mar 2017 09:04:08 +0000
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3292 From: Ricardo Wurmus <rekado@example.com>
3293 Date: Tue, 14 Mar 2017 10:02:54 +0100
3294 Message-Id: <20170314090256.7695-15-rekado@example.com>
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3310 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
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3314
3315 * gnu/packages/statistics.scm (r-survival): Move up to set of recommended R
3316 packages.
3317 ---
3318 gnu/packages/statistics.scm | 42 ++++++++++++++++++++++--------------------
3319 1 file changed, 22 insertions(+), 20 deletions(-)
3320
3321 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
3322 index b338efcda..c836409b6 100644
3323 --- a/gnu/packages/statistics.scm
3324 +++ b/gnu/packages/statistics.scm
3325 @@ -511,6 +511,28 @@ analysis.")
3326 ;; Either version may be picked.
3327 (license (list license:gpl2 license:gpl3))))
3328
3329 +(define-public r-survival
3330 + (package
3331 + (name "r-survival")
3332 + (version "2.40-1")
3333 + (source
3334 + (origin
3335 + (method url-fetch)
3336 + (uri (cran-uri "survival" version))
3337 + (sha256
3338 + (base32
3339 + "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
3340 + (build-system r-build-system)
3341 + (propagated-inputs
3342 + `(("r-matrix" ,r-matrix)))
3343 + (home-page "https://github.com/therneau/survival")
3344 + (synopsis "Survival analysis")
3345 + (description
3346 + "This package contains the core survival analysis routines, including
3347 +definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
3348 +curves, Cox models, and parametric accelerated failure time models.")
3349 + (license license:lgpl2.0+)))
3350 +
3351 (define-public r-bit
3352 (package
3353 (name "r-bit")
3354 @@ -3683,26 +3705,6 @@ following problems:
3355 @end enumerate\n")
3356 (license license:gpl3+)))
3357
3358 -(define-public r-survival
3359 - (package
3360 - (name "r-survival")
3361 - (version "2.40-1")
3362 - (source
3363 - (origin
3364 - (method url-fetch)
3365 - (uri (cran-uri "survival" version))
3366 - (sha256
3367 - (base32
3368 - "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
3369 - (build-system r-build-system)
3370 - (home-page "https://github.com/therneau/survival")
3371 - (synopsis "Survival analysis")
3372 - (description
3373 - "This package contains the core survival analysis routines, including
3374 -definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
3375 -curves, Cox models, and parametric accelerated failure time models.")
3376 - (license license:lgpl2.0+)))
3377 -
3378 (define-public r-base64
3379 (package
3380 (name "r-base64")
3381 --
3382 2.12.0
3383
3384
3385
3386
3387
3388 \ 3
3389 \a
3390 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:03:49 +0000
3391 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 05:03:49 2017
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3403 Tue, 14 Mar 2017 02:03:42 -0700 (PDT)
3404 From: Ricardo Wurmus <rekado@example.com>
3405 To: 26095@debbugs.gnu.org
3406 Subject: [PATCH 15/17] gnu: r-survival: Move to set of recommended R packages.
3407 Date: Tue, 14 Mar 2017 10:02:54 +0100
3408 Message-Id: <20170314090256.7695-15-rekado@example.com>
3409 X-Mailer: git-send-email 2.12.0
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3412 <20170314090256.7695-1-rekado@example.com>
3413 X-Spam-Score: 1.0 (+)
3414 X-Debbugs-Envelope-To: 26095
3415 Cc: Ricardo Wurmus <rekado@example.com>
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3430
3431 * gnu/packages/statistics.scm (r-survival): Move up to set of recommended R
3432 packages.
3433 ---
3434 gnu/packages/statistics.scm | 42 ++++++++++++++++++++++--------------------
3435 1 file changed, 22 insertions(+), 20 deletions(-)
3436
3437 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
3438 index b338efcda..c836409b6 100644
3439 --- a/gnu/packages/statistics.scm
3440 +++ b/gnu/packages/statistics.scm
3441 @@ -511,6 +511,28 @@ analysis.")
3442 ;; Either version may be picked.
3443 (license (list license:gpl2 license:gpl3))))
3444
3445 +(define-public r-survival
3446 + (package
3447 + (name "r-survival")
3448 + (version "2.40-1")
3449 + (source
3450 + (origin
3451 + (method url-fetch)
3452 + (uri (cran-uri "survival" version))
3453 + (sha256
3454 + (base32
3455 + "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
3456 + (build-system r-build-system)
3457 + (propagated-inputs
3458 + `(("r-matrix" ,r-matrix)))
3459 + (home-page "https://github.com/therneau/survival")
3460 + (synopsis "Survival analysis")
3461 + (description
3462 + "This package contains the core survival analysis routines, including
3463 +definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
3464 +curves, Cox models, and parametric accelerated failure time models.")
3465 + (license license:lgpl2.0+)))
3466 +
3467 (define-public r-bit
3468 (package
3469 (name "r-bit")
3470 @@ -3683,26 +3705,6 @@ following problems:
3471 @end enumerate\n")
3472 (license license:gpl3+)))
3473
3474 -(define-public r-survival
3475 - (package
3476 - (name "r-survival")
3477 - (version "2.40-1")
3478 - (source
3479 - (origin
3480 - (method url-fetch)
3481 - (uri (cran-uri "survival" version))
3482 - (sha256
3483 - (base32
3484 - "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
3485 - (build-system r-build-system)
3486 - (home-page "https://github.com/therneau/survival")
3487 - (synopsis "Survival analysis")
3488 - (description
3489 - "This package contains the core survival analysis routines, including
3490 -definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
3491 -curves, Cox models, and parametric accelerated failure time models.")
3492 - (license license:lgpl2.0+)))
3493 -
3494 (define-public r-base64
3495 (package
3496 (name "r-base64")
3497 --
3498 2.12.0
3499
3500
3501
3502
3503
3504 \ 3
3505 \ 6
3506 <!-- request_addr: guix-patches@gnu.org -->
3507 <!-- time:1489482248 -->
3508 <strong>Information forwarded</strong>
3509 to <code>guix-patches@gnu.org</code>:<br>
3510 <code>bug#26095</code>; Package <code>guix-patches</code>.
3511 \ 3
3512 \ 2
3513 guix-patches@gnu.org
3514 \ 5
3515 X-Loop: help-debbugs@gnu.org
3516 Subject: bug#26095: [PATCH 16/17] gnu: r: Do not build recommended packages.
3517 Resent-From: Ricardo Wurmus <rekado@example.com>
3518 Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
3519 Resent-CC: guix-patches@gnu.org
3520 Resent-Date: Tue, 14 Mar 2017 09:04:08 +0000
3521 Resent-Message-ID: <handler.26095.B26095.148948224111182@debbugs.gnu.org>
3522 Resent-Sender: help-debbugs@gnu.org
3523 X-GNU-PR-Message: followup 26095
3524 X-GNU-PR-Package: guix-patches
3525 X-GNU-PR-Keywords:
3526 To: 26095@debbugs.gnu.org
3527 Cc: Ricardo Wurmus <rekado@example.com>
3528 Received: via spool by 26095-submit@debbugs.gnu.org id=B26095.148948224111182
3529 (code B ref 26095); Tue, 14 Mar 2017 09:04:08 +0000
3530 Received: (at 26095) by debbugs.gnu.org; 14 Mar 2017 09:04:01 +0000
3531 Received: from localhost ([127.0.0.1]:54780 helo=debbugs.gnu.org)
3532 by debbugs.gnu.org with esmtp (Exim 4.84_2)
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3542 Tue, 14 Mar 2017 02:03:45 -0700 (PDT)
3543 From: Ricardo Wurmus <rekado@example.com>
3544 Date: Tue, 14 Mar 2017 10:02:55 +0100
3545 Message-Id: <20170314090256.7695-16-rekado@example.com>
3546 X-Mailer: git-send-email 2.12.0
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3548 References: <87h92w1cu0.fsf@example.com>
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3565
3566 * gnu/packages/statistics.scm (r)[arguments]: Rename phase
3567 "build-recommended-packages-reproducibly" to "build-reproducibly"; add
3568 configure flag "--without-recommended-packages".
3569 * guix/import/cran.scm (default-r-packages): Remove recommended packages.
3570 * gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
3571 and r-nlme.
3572 (r-vegan)[propagated-inputs]: Add r-mass.
3573 (r-genefilter)[propagated-inputs]: Add r-survival.
3574 (r-grohmm)[propagated-inputs]: Add r-mass.
3575 (r-bioccheck)[propagated-inputs]: Add r-codetools.
3576 (r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
3577 (r-topgo)[propagated-inputs]: Add r-lattice.
3578 (r-sva)[propagated-inputs]: Add r-mgcv.
3579 (r-raremetals2)[propagated-inputs]: Add r-mass.
3580 (r-vsn)[propagated-inputs]: Add r-lattice.
3581 (r-pcamethods)[propagated-inputs]: Add r-mass.
3582 * gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
3583 (r-locfit)[propagated-inputs]: Add r-lattice.
3584 (r-coda)[propagated-inputs]: Add r-lattice.
3585 (r-irlba)[propagated-inputs]: Add r-matrix.
3586 (r-glmnet)[propagated-inputs]: Add r-matrix.
3587 (r-e1071)[propagated-inputs]: Add r-class.
3588 (r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
3589 (r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
3590 r-rpart.
3591 (r-zoo)[propagated-inputs]: Add r-lattice.
3592 (r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
3593 (r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
3594 (r-prabclus)[propagated-inputs]: Add r-mass.
3595 (r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
3596 (r-rcppeigen)[propagated-inputs]: Add r-matrix.
3597 (r-matrixmodels)[propagated-inputs]: Add r-matrix.
3598 (r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
3599 (r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
3600 (r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
3601 (r-tclust)[propagated-inputs]: Add r-cluster.
3602 ---
3603 gnu/packages/bioinformatics.scm | 21 +++++++++--
3604 gnu/packages/statistics.scm | 83 ++++++++++++++++++++++++++++++-----------
3605 guix/import/cran.scm | 18 +--------
3606 3 files changed, 80 insertions(+), 42 deletions(-)
3607
3608 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
3609 index 770bea7e3..daef0f6de 100644
3610 --- a/gnu/packages/bioinformatics.scm
3611 +++ b/gnu/packages/bioinformatics.scm
3612 @@ -108,6 +108,9 @@
3613 (base32
3614 "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk"))))
3615 (build-system r-build-system)
3616 + (propagated-inputs
3617 + `(("r-lattice" ,r-lattice)
3618 + ("r-nlme" ,r-nlme)))
3619 (home-page "http://ape-package.ird.fr/")
3620 (synopsis "Analyses of phylogenetics and evolution")
3621 (description
3622 @@ -5344,6 +5347,7 @@ information as possible.")
3623 (propagated-inputs
3624 `(("r-cluster" ,r-cluster)
3625 ("r-lattice" ,r-lattice)
3626 + ("r-mass" ,r-mass)
3627 ("r-mgcv" ,r-mgcv)
3628 ("r-permute" ,r-permute)))
3629 (home-page "https://cran.r-project.org/web/packages/vegan")
3630 @@ -5425,7 +5429,8 @@ microarrays.")
3631 `(("r-annotate" ,r-annotate)
3632 ("r-annotationdbi" ,r-annotationdbi)
3633 ("r-biobase" ,r-biobase)
3634 - ("r-s4vectors" ,r-s4vectors)))
3635 + ("r-s4vectors" ,r-s4vectors)
3636 + ("r-survival" ,r-survival)))
3637 (home-page "http://bioconductor.org/packages/genefilter")
3638 (synopsis "Filter genes from high-throughput experiments")
3639 (description
3640 @@ -5723,6 +5728,7 @@ annotation infrastructure.")
3641 ("r-genomicalignments" ,r-genomicalignments)
3642 ("r-genomicranges" ,r-genomicranges)
3643 ("r-iranges" ,r-iranges)
3644 + ("r-mass" ,r-mass)
3645 ("r-rtracklayer" ,r-rtracklayer)
3646 ("r-s4vectors" ,r-s4vectors)))
3647 (home-page "https://github.com/Kraus-Lab/groHMM")
3648 @@ -6122,7 +6128,8 @@ functionality.")
3649 (native-inputs
3650 `(("which" ,which)))
3651 (propagated-inputs
3652 - `(("r-graph" ,r-graph)
3653 + `(("r-codetools" ,r-codetools)
3654 + ("r-graph" ,r-graph)
3655 ("r-knitr" ,r-knitr)
3656 ("r-httr" ,r-httr)
3657 ("r-optparse" ,r-optparse)
3658 @@ -6650,6 +6657,7 @@ files.")
3659 ("r-genomeinfodb" ,r-genomeinfodb)
3660 ("r-genomicranges" ,r-genomicranges)
3661 ("r-iranges" ,r-iranges)
3662 + ("r-matrix" ,r-matrix)
3663 ("r-s4vectors" ,r-s4vectors)))
3664 (home-page "http://bioconductor.org/packages/SummarizedExperiment")
3665 (synopsis "Container for representing genomic ranges by sample")
3666 @@ -6841,8 +6849,9 @@ information about the latest version of the Gene Ontologies.")
3667 ("r-biobase" ,r-biobase)
3668 ("r-biocgenerics" ,r-biocgenerics)
3669 ("r-go-db" ,r-go-db)
3670 - ("r-matrixstats" ,r-matrixstats)
3671 ("r-graph" ,r-graph)
3672 + ("r-lattice" ,r-lattice)
3673 + ("r-matrixstats" ,r-matrixstats)
3674 ("r-sparsem" ,r-sparsem)))
3675 (home-page "http://bioconductor.org/packages/topGO")
3676 (synopsis "Enrichment analysis for gene ontology")
3677 @@ -8234,7 +8243,8 @@ number detection tools.")
3678 "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
3679 (build-system r-build-system)
3680 (propagated-inputs
3681 - `(("r-genefilter" ,r-genefilter)))
3682 + `(("r-genefilter" ,r-genefilter)
3683 + ("r-mgcv" ,r-mgcv)))
3684 (home-page "http://bioconductor.org/packages/sva")
3685 (synopsis "Surrogate variable analysis")
3686 (description
3687 @@ -8286,6 +8296,7 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
3688 (propagated-inputs
3689 `(("r-seqminer" ,r-seqminer)
3690 ("r-mvtnorm" ,r-mvtnorm)
3691 + ("r-mass" ,r-mass)
3692 ("r-compquadform" ,r-compquadform)
3693 ("r-getopt" ,r-getopt)))
3694 (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
3695 @@ -8444,6 +8455,7 @@ analysis.")
3696 `(("r-affy" ,r-affy)
3697 ("r-biobase" ,r-biobase)
3698 ("r-ggplot2" ,r-ggplot2)
3699 + ("r-lattice" ,r-lattice)
3700 ("r-limma" ,r-limma)))
3701 (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
3702 (synopsis "Variance stabilization and calibration for microarray data")
3703 @@ -8507,6 +8519,7 @@ specific parser.")
3704 (propagated-inputs
3705 `(("r-biobase" ,r-biobase)
3706 ("r-biocgenerics" ,r-biocgenerics)
3707 + ("r-mass" ,r-mass)
3708 ("r-rcpp" ,r-rcpp)))
3709 (home-page "https://github.com/hredestig/pcamethods")
3710 (synopsis "Collection of PCA methods")
3711 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
3712 index c836409b6..b8abbf62d 100644
3713 --- a/gnu/packages/statistics.scm
3714 +++ b/gnu/packages/statistics.scm
3715 @@ -99,6 +99,9 @@ can be imported from spreadsheets, text files and database sources and it can
3716 be output in text, PostScript, PDF or HTML.")
3717 (license license:gpl3+)))
3718
3719 +;; Update this package together with the set of recommended packages: r-boot,
3720 +;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
3721 +;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
3722 (define-public r
3723 (package
3724 (name "r")
3725 @@ -128,12 +131,8 @@ be output in text, PostScript, PDF or HTML.")
3726 (substitute* "src/scripts/R.sh.in"
3727 (("uname") uname-bin)))
3728 #t))
3729 - (add-after 'unpack 'build-recommended-packages-reproducibly
3730 + (add-after 'unpack 'build-reproducibly
3731 (lambda _
3732 - (substitute* "src/library/Recommended/Makefile.in"
3733 - (("INSTALL_OPTS =(.*)" line rest )
3734 - (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01"
3735 - rest)))
3736 ;; Ensure that gzipped files are reproducible
3737 (substitute* '("src/library/grDevices/Makefile.in"
3738 "doc/manual/Makefile.in")
3739 @@ -162,7 +161,12 @@ be output in text, PostScript, PDF or HTML.")
3740 (add-after 'build 'install-info
3741 (lambda _ (zero? (system* "make" "install-info")))))
3742 #:configure-flags
3743 - '("--with-cairo"
3744 + '(;; Do not build the recommended packages. The build system creates
3745 + ;; random temporary directories and embeds their names in some
3746 + ;; package files. We build these packages with the r-build-system
3747 + ;; instead.
3748 + "--without-recommended-packages"
3749 + "--with-cairo"
3750 "--with-blas=-lopenblas"
3751 "--with-libpng"
3752 "--with-jpeglib"
3753 @@ -991,6 +995,7 @@ legends.")
3754 ("r-gtable" ,r-gtable)
3755 ("r-plyr" ,r-plyr)
3756 ("r-lazyeval" ,r-lazyeval)
3757 + ("r-mass" ,r-mass)
3758 ("r-tibble" ,r-tibble)
3759 ("r-reshape2" ,r-reshape2)
3760 ("r-scales" ,r-scales)
3761 @@ -1611,6 +1616,8 @@ side.")
3762 (base32
3763 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
3764 (build-system r-build-system)
3765 + (propagated-inputs
3766 + `(("r-lattice" ,r-lattice)))
3767 (home-page "http://cran.r-project.org/web/packages/locfit")
3768 (synopsis "Local regression, likelihood and density estimation")
3769 (description
3770 @@ -1788,6 +1795,8 @@ inference for statistical models.")
3771 (base32
3772 "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
3773 (build-system r-build-system)
3774 + (propagated-inputs
3775 + `(("r-lattice" ,r-lattice)))
3776 (home-page "http://cran.r-project.org/web/packages/coda")
3777 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
3778 (description "This package provides functions for summarizing and plotting
3779 @@ -2936,6 +2945,8 @@ flexible than the orphaned \"base64\" package.")
3780 (base32
3781 "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si"))))
3782 (build-system r-build-system)
3783 + (propagated-inputs
3784 + `(("r-matrix" ,r-matrix)))
3785 (home-page "http://cran.r-project.org/web/packages/irlba")
3786 (synopsis "Methods for eigendecomposition of large matrices")
3787 (description
3788 @@ -2956,10 +2967,11 @@ analysis of large sparse or dense matrices.")
3789 (base32
3790 "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c"))))
3791 (build-system r-build-system)
3792 - (inputs
3793 - `(("gfortran" ,gfortran)))
3794 + (inputs
3795 + `(("gfortran" ,gfortran)))
3796 (propagated-inputs
3797 - `(("r-foreach" ,r-foreach)))
3798 + `(("r-foreach" ,r-foreach)
3799 + ("r-matrix" ,r-matrix)))
3800 (home-page "http://www.jstatsoft.org/v33/i01")
3801 (synopsis "Lasso and elastic-net regularized generalized linear models")
3802 (description
3803 @@ -3077,6 +3089,8 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3804 (base32
3805 "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h"))))
3806 (build-system r-build-system)
3807 + (propagated-inputs
3808 + `(("r-class" ,r-class)))
3809 (home-page "http://cran.r-project.org/web/packages/e1071")
3810 (synopsis "Miscellaneous functions for probability theory")
3811 (description
3812 @@ -3688,6 +3702,9 @@ from within R.")
3813 (("if isnan\\(lambda\\) \\{")
3814 "if (isnan(lambda)) {"))
3815 #t)))))
3816 + (propagated-inputs
3817 + `(("r-lattice" ,r-lattice)