all messages for Guix-related lists mirrored at yhetil.org
 help / color / mirror / code / Atom feed
blob 11843703ac84c08b18d89e4948f5439d23a7fa46 46206 bytes (raw)
name: guix/import/cran.scm 	 # note: path name is non-authoritative(*)

   1
   2
   3
   4
   5
   6
   7
   8
   9
  10
  11
  12
  13
  14
  15
  16
  17
  18
  19
  20
  21
  22
  23
  24
  25
  26
  27
  28
  29
  30
  31
  32
  33
  34
  35
  36
  37
  38
  39
  40
  41
  42
  43
  44
  45
  46
  47
  48
  49
  50
  51
  52
  53
  54
  55
  56
  57
  58
  59
  60
  61
  62
  63
  64
  65
  66
  67
  68
  69
  70
  71
  72
  73
  74
  75
  76
  77
  78
  79
  80
  81
  82
  83
  84
  85
  86
  87
  88
  89
  90
  91
  92
  93
  94
  95
  96
  97
  98
  99
 100
 101
 102
 103
 104
 105
 106
 107
 108
 109
 110
 111
 112
 113
 114
 115
 116
 117
 118
 119
 120
 121
 122
 123
 124
 125
 126
 127
 128
 129
 130
 131
 132
 133
 134
 135
 136
 137
 138
 139
 140
 141
 142
 143
 144
 145
 146
 147
 148
 149
 150
 151
 152
 153
 154
 155
 156
 157
 158
 159
 160
 161
 162
 163
 164
 165
 166
 167
 168
 169
 170
 171
 172
 173
 174
 175
 176
 177
 178
 179
 180
 181
 182
 183
 184
 185
 186
 187
 188
 189
 190
 191
 192
 193
 194
 195
 196
 197
 198
 199
 200
 201
 202
 203
 204
 205
 206
 207
 208
 209
 210
 211
 212
 213
 214
 215
 216
 217
 218
 219
 220
 221
 222
 223
 224
 225
 226
 227
 228
 229
 230
 231
 232
 233
 234
 235
 236
 237
 238
 239
 240
 241
 242
 243
 244
 245
 246
 247
 248
 249
 250
 251
 252
 253
 254
 255
 256
 257
 258
 259
 260
 261
 262
 263
 264
 265
 266
 267
 268
 269
 270
 271
 272
 273
 274
 275
 276
 277
 278
 279
 280
 281
 282
 283
 284
 285
 286
 287
 288
 289
 290
 291
 292
 293
 294
 295
 296
 297
 298
 299
 300
 301
 302
 303
 304
 305
 306
 307
 308
 309
 310
 311
 312
 313
 314
 315
 316
 317
 318
 319
 320
 321
 322
 323
 324
 325
 326
 327
 328
 329
 330
 331
 332
 333
 334
 335
 336
 337
 338
 339
 340
 341
 342
 343
 344
 345
 346
 347
 348
 349
 350
 351
 352
 353
 354
 355
 356
 357
 358
 359
 360
 361
 362
 363
 364
 365
 366
 367
 368
 369
 370
 371
 372
 373
 374
 375
 376
 377
 378
 379
 380
 381
 382
 383
 384
 385
 386
 387
 388
 389
 390
 391
 392
 393
 394
 395
 396
 397
 398
 399
 400
 401
 402
 403
 404
 405
 406
 407
 408
 409
 410
 411
 412
 413
 414
 415
 416
 417
 418
 419
 420
 421
 422
 423
 424
 425
 426
 427
 428
 429
 430
 431
 432
 433
 434
 435
 436
 437
 438
 439
 440
 441
 442
 443
 444
 445
 446
 447
 448
 449
 450
 451
 452
 453
 454
 455
 456
 457
 458
 459
 460
 461
 462
 463
 464
 465
 466
 467
 468
 469
 470
 471
 472
 473
 474
 475
 476
 477
 478
 479
 480
 481
 482
 483
 484
 485
 486
 487
 488
 489
 490
 491
 492
 493
 494
 495
 496
 497
 498
 499
 500
 501
 502
 503
 504
 505
 506
 507
 508
 509
 510
 511
 512
 513
 514
 515
 516
 517
 518
 519
 520
 521
 522
 523
 524
 525
 526
 527
 528
 529
 530
 531
 532
 533
 534
 535
 536
 537
 538
 539
 540
 541
 542
 543
 544
 545
 546
 547
 548
 549
 550
 551
 552
 553
 554
 555
 556
 557
 558
 559
 560
 561
 562
 563
 564
 565
 566
 567
 568
 569
 570
 571
 572
 573
 574
 575
 576
 577
 578
 579
 580
 581
 582
 583
 584
 585
 586
 587
 588
 589
 590
 591
 592
 593
 594
 595
 596
 597
 598
 599
 600
 601
 602
 603
 604
 605
 606
 607
 608
 609
 610
 611
 612
 613
 614
 615
 616
 617
 618
 619
 620
 621
 622
 623
 624
 625
 626
 627
 628
 629
 630
 631
 632
 633
 634
 635
 636
 637
 638
 639
 640
 641
 642
 643
 644
 645
 646
 647
 648
 649
 650
 651
 652
 653
 654
 655
 656
 657
 658
 659
 660
 661
 662
 663
 664
 665
 666
 667
 668
 669
 670
 671
 672
 673
 674
 675
 676
 677
 678
 679
 680
 681
 682
 683
 684
 685
 686
 687
 688
 689
 690
 691
 692
 693
 694
 695
 696
 697
 698
 699
 700
 701
 702
 703
 704
 705
 706
 707
 708
 709
 710
 711
 712
 713
 714
 715
 716
 717
 718
 719
 720
 721
 722
 723
 724
 725
 726
 727
 728
 729
 730
 731
 732
 733
 734
 735
 736
 737
 738
 739
 740
 741
 742
 743
 744
 745
 746
 747
 748
 749
 750
 751
 752
 753
 754
 755
 756
 757
 758
 759
 760
 761
 762
 763
 764
 765
 766
 767
 768
 769
 770
 771
 772
 773
 774
 775
 776
 777
 778
 779
 780
 781
 782
 783
 784
 785
 786
 787
 788
 789
 790
 791
 792
 793
 794
 795
 796
 797
 798
 799
 800
 801
 802
 803
 804
 805
 806
 807
 808
 809
 810
 811
 812
 813
 814
 815
 816
 817
 818
 819
 820
 821
 822
 823
 824
 825
 826
 827
 828
 829
 830
 831
 832
 833
 834
 835
 836
 837
 838
 839
 840
 841
 842
 843
 844
 845
 846
 847
 848
 849
 850
 851
 852
 853
 854
 855
 856
 857
 858
 859
 860
 861
 862
 863
 864
 865
 866
 867
 868
 869
 870
 871
 872
 873
 874
 875
 876
 877
 878
 879
 880
 881
 882
 883
 884
 885
 886
 887
 888
 889
 890
 891
 892
 893
 894
 895
 896
 897
 898
 899
 900
 901
 902
 903
 904
 905
 906
 907
 908
 909
 910
 911
 912
 913
 914
 915
 916
 917
 918
 919
 920
 921
 922
 923
 924
 925
 926
 927
 928
 929
 930
 931
 932
 933
 934
 935
 936
 937
 938
 939
 940
 941
 942
 943
 944
 945
 946
 947
 948
 949
 950
 951
 952
 953
 954
 955
 956
 957
 958
 959
 960
 961
 962
 963
 964
 965
 966
 967
 968
 969
 970
 971
 972
 973
 974
 975
 976
 977
 978
 979
 980
 981
 982
 983
 984
 985
 986
 987
 988
 989
 990
 991
 992
 993
 994
 995
 996
 997
 998
 999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
 
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015-2017, 2019-2021, 2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2024 Herman Rimm <herman@rimm.ee>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (guix import cran)
  #:use-module (ice-9 ftw)
  #:use-module (ice-9 match)
  #:use-module (ice-9 regex)
  #:use-module (ice-9 popen)
  #:use-module ((ice-9 rdelim) #:select (read-string read-line))
  #:use-module (srfi srfi-1)
  #:use-module (srfi srfi-2)
  #:use-module (srfi srfi-26)
  #:use-module (srfi srfi-34)
  #:use-module (srfi srfi-35)
  #:use-module (srfi srfi-71)
  #:use-module (web uri)
  #:use-module (guix memoization)
  #:use-module (guix http-client)
  #:use-module (guix diagnostics)
  #:use-module (guix hash)
  #:use-module (guix i18n)
  #:use-module (guix store)
  #:use-module (guix base32)
  #:use-module ((guix download) #:select (download-to-store))
  #:use-module (guix import utils)
  #:use-module ((guix build utils)
                #:select (find-files
                          delete-file-recursively
                          with-directory-excursion))
  #:use-module (guix utils)
  #:use-module (guix git)
  #:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
  #:use-module (guix upstream)
  #:use-module (guix packages)
  #:use-module (guix sets)
  #:export (%input-style

            %bioconductor-version
            download
            fetch-description

            cran->guix-package
            bioconductor->guix-package
            cran-recursive-import
            %cran-updater
            %bioconductor-updater
            %bioconductor-version

            cran-package?
            bioconductor-package?
            bioconductor-data-package?
            bioconductor-experiment-package?

            description->alist
            description->package))

;;; Commentary:
;;;
;;; Generate a package declaration template for the latest version of an R
;;; package on CRAN, using the DESCRIPTION file downloaded from
;;; cran.r-project.org.
;;;
;;; Code:

(define %input-style
  (make-parameter 'variable)) ; or 'specification

(define (string->licenses license-string license-prefix)
  (let ((licenses
         (map string-trim-both
              (string-tokenize license-string
                               (char-set-complement (char-set #\|))))))
    (string->license licenses license-prefix)))

(define (string->license license-string license-prefix)
  (let ((prefix license-prefix))
    (match license-string
      ("AGPL-3" (prefix 'agpl3))
      ("AGPL (>= 3)" (prefix 'agpl3+))
      ("Artistic-2.0" (prefix 'artistic2.0))
      ((or "Apache License 2.0"
           "Apache License (== 2.0)"
           "Apache License (>= 2.0)")
       (prefix 'asl2.0))
      ("BSD_2_clause" (prefix 'bsd-2))
      ("BSD_2_clause + file LICENSE" (prefix 'bsd-2))
      ("BSD_3_clause" (prefix 'bsd-3))
      ("BSD_3_clause + file LICENSE" (prefix 'bsd-3))
      ("CC0" (prefix 'cc0))
      ("CC BY-SA 4.0" (prefix 'cc-by-sa4.0))
      ("CeCILL" (prefix 'cecill))
      ((or "GPL"
           "GNU General Public License")
       `(list ,(prefix 'gpl2+) ,(prefix 'gpl3+)))
      ((or "GPL (>= 2)"
           "GPL (>= 2.0)")
       (prefix 'gpl2+))
      ((or "GPL (> 2)"
           "GPL (>= 3)"
           "GPL (>= 3.0)"
           "GPL (>=3)"
           "GNU General Public License (>= 3)")
       (prefix 'gpl3+))
      ((or "GPL-2"
           "GNU General Public License version 2")
       (prefix 'gpl2))
      ((or "GPL-3"
           "GNU General Public License version 3")
       (prefix 'gpl3))
      ((or "GNU Lesser General Public License"
           "LGPL")
       (prefix 'lgpl2.0+))
      ("LGPL-2" (prefix 'lgpl2.0))
      ("LGPL-2.1" (prefix 'lgpl2.1))
      ("LGPL-3" (prefix 'lgpl3))
      ((or "LGPL (>= 2)"
           "LGPL (>= 2.0)")
       (prefix 'lgpl2.0+))
      ("LGPL (>= 2.1)" (prefix 'lgpl2.1+))
      ("LGPL (>= 3)" (prefix 'lgpl3+))
      ("MIT" (prefix 'expat))
      ("MIT + file LICENSE" (prefix 'expat))
      ("file LICENSE"
       `(,(prefix 'fsdg-compatible) "file://LICENSE"))
      ((x) (string->license x license-prefix))
      ((lst ...) `(list ,@(map (cut string->license <> license-prefix) lst)))
      (unknown `(,(prefix 'fsdg-compatible) ,unknown)))))

(define (description->alist description)
  "Convert a DESCRIPTION string into an alist."
  (let ((lines (string-split description #\newline))
        (parse (lambda (line acc)
                 (if (string-null? line) acc
                     ;; Keys usually start with a capital letter and end with
                     ;; ":".  There are some exceptions, unfortunately (such
                     ;; as "biocViews").  There are no blanks in a key.
                     (if (string-match "^[A-Za-z][^ :]+:( |\n|$)" line)
                         ;; New key/value pair
                         (let* ((pos   (string-index line #\:))
                                (key   (string-take line pos))
                                (value (string-drop line (+ 1 pos))))
                           (cons (cons key
                                       (string-trim-both value))
                                 acc))
                         ;; This is a continuation of the previous pair
                         (match-let ((((key . value) . rest) acc))
                           (cons (cons key (string-join
                                            (list value
                                                  (string-trim-both line))))
                                 rest)))))))
    (fold parse '() lines)))

(define* (maybe-inputs package-inputs #:optional (input-type 'inputs))
  "Given a list of PACKAGE-INPUTS, tries to generate the TYPE field of a
package definition."
  (define (format-input input)
    (case (%input-style)
      ((specification)
       `(specification->package ,(upstream-input-downstream-name input)))
      (else
       ((compose string->symbol
                  upstream-input-downstream-name)
        input))))

  (define (upstream-input-name<? i1 i2)
    (string-ci<? (upstream-input-name i1)
                 (upstream-input-name i2)))

  (maybe-list-field input-type
    (map format-input (sort package-inputs upstream-input-name<?))))

(define %cran-url "https://cloud.r-project.org/web/packages/")
(define %cran-canonical-url "https://cran.r-project.org/package=")
(define %bioconductor-url "https://bioconductor.org/packages/")

;; The latest Bioconductor release is 3.20.  Bioconductor packages should be
;; updated together.
(define %bioconductor-version "3.20")

(define* (bioconductor-packages-list-url #:optional type)
  (string-append "https://bioconductor.org/packages/"
                 %bioconductor-version
                 (match type
                   ('annotation "/data/annotation")
                   ('experiment "/data/experiment")
                   (_ "/bioc"))
                 "/src/contrib/PACKAGES"))

(define* (bioconductor-packages-list #:optional type)
  "Return the latest version of package NAME for the current bioconductor
release."
  (let ((url (string->uri (bioconductor-packages-list-url type))))
    (guard (c ((http-get-error? c)
               (warning (G_ "failed to retrieve list of packages \
from ~a: ~a (~a)~%")
                        (uri->string (http-get-error-uri c))
                        (http-get-error-code c)
                        (http-get-error-reason c))
               #f))
      ;; Split the big list on empty lines, then turn each chunk into an
      ;; alist of attributes.
      (map (lambda (chunk)
             (description->alist (string-join chunk "\n")))
           (let* ((port  (http-fetch/cached url))
                  (lines (read-lines port)))
             (close-port port)
             (chunk-lines lines))))))

(define* (latest-bioconductor-package-version name #:optional type)
  "Return the version string corresponding to the latest release of the
bioconductor package NAME, or #F if the package is unknown."
  (and=> (find (lambda (meta)
                 (string=? (assoc-ref meta "Package") name))
               (bioconductor-packages-list type))
         (cut assoc-ref <> "Version")))

;; Little helper to download URLs only once.
(define download
  (memoize
   (lambda* (url #:key method (ref '()))
     (with-store store
       (cond
        ((eq? method 'git)
         (latest-repository-commit store url #:ref ref))
        ((eq? method 'hg)
         (call-with-temporary-directory
          (lambda (dir)
            (unless (zero? (system* "hg" "clone" url dir))
              (leave (G_ "~A: hg download failed~%") url))
            (with-directory-excursion dir
              (let* ((port (open-pipe* OPEN_READ "hg" "id" "--id"))
                     (changeset (string-trim-right (read-string port))))
                (close-pipe port)
                (for-each delete-file-recursively
                          (find-files dir "^\\.hg$" #:directories? #t))
                (let ((store-directory
                       (add-to-store store (basename url) #t "sha256" dir)))
                  (values store-directory changeset)))))))
        (else
         (match url
           ((? string?)
            (download-to-store store url))
           ((urls ...)
            ;; Try all the URLs.  A use case where this is useful is when one
            ;; of the URLs is the /Archive CRAN URL.
            (any (cut download-to-store store <>) urls)))))))))

(define* (fetch-description-from-tarball url #:key (download download))
  "Fetch the tarball at URL, extra its 'DESCRIPTION' file, parse it, and
return the resulting alist."
  (match (download url)
    (#f #f)
    (tarball
     (call-with-temporary-directory
      (lambda (dir)
        (parameterize ((current-error-port (%make-void-port "rw+"))
                       (current-output-port (%make-void-port "rw+")))
          (and (zero? (system* "tar" "--wildcards" "-x"
                               "--strip-components=1"
                               "-C" dir
                               "-f" tarball "*/DESCRIPTION"))
               (description->alist
                (call-with-input-file (string-append dir "/DESCRIPTION")
                  read-string)))))))))

(define* (fetch-description repository name #:optional version replacement-download)
  "Return an alist of the contents of the DESCRIPTION file for the R package
NAME at VERSION in the given REPOSITORY, or #f in case of failure.  NAME is
case-sensitive."
  (case repository
    ((cran)
     (guard (c ((http-get-error? c)
                (warning (G_ "failed to retrieve package information \
from ~a: ~a (~a)~%")
                         (uri->string (http-get-error-uri c))
                         (http-get-error-code c)
                         (http-get-error-reason c))
                #f))
       ;; When VERSION is true, we have to download the tarball to get at its
       ;; 'DESCRIPTION' file; only the latest one is directly accessible over
       ;; HTTP.
       (if version
           (let ((urls (list (string-append "mirror://cran/src/contrib/"
                                            name "_" version ".tar.gz")
                             (string-append "mirror://cran/src/contrib/Archive/"
                                            name "/"
                                            name "_" version ".tar.gz"))))
             (fetch-description-from-tarball
              urls #:download (or replacement-download
                                  download)))
           (let* ((url    (string-append %cran-url name "/DESCRIPTION"))
                  (port   (http-fetch url))
                  (result (description->alist (read-string port))))
             (close-port port)
             result))))
    ((bioconductor)
     ;; Currently, the bioconductor project does not offer a way to access a
     ;; package's DESCRIPTION file over HTTP, so we determine the version,
     ;; download the source tarball, and then extract the DESCRIPTION file.
     (and-let* ((type    (or
                          (and (latest-bioconductor-package-version name) #t)
                          (and (latest-bioconductor-package-version name 'annotation) 'annotation)
                          (and (latest-bioconductor-package-version name 'experiment) 'experiment)))
                ;; TODO: Honor VERSION.
                (version (latest-bioconductor-package-version name type))
                (url     (bioconductor-uri name version type))
                (meta    (fetch-description-from-tarball
                          url #:download (or replacement-download
                                             download))))
       (if (boolean? type)
           meta
           (cons `(bioconductor-type . ,type) meta))))
    ((git)
     (and (string-prefix? "http" name)
          ;; Download the git repository at "NAME"
          (call-with-values
              (lambda () (download name #:method 'git))
            (lambda (dir commit)
              (and=> (description->alist (with-input-from-file
                                             (string-append dir "/DESCRIPTION") read-string))
                     (lambda (meta)
                       (cons* `(git . ,name)
                              `(git-commit . ,commit)
                              meta)))))))
    ((hg)
     (and (string-prefix? "http" name)
          ;; Download the mercurial repository at "NAME"
          (call-with-values
              (lambda () (download name #:method 'hg))
            (lambda (dir changeset)
              (and=> (description->alist (with-input-from-file
                                             (string-append dir "/DESCRIPTION") read-string))
                     (lambda (meta)
                       (cons* `(hg . ,name)
                              `(hg-changeset . ,changeset)
                              meta)))))))))

(define (listify meta field)
  "Look up FIELD in the alist META.  If FIELD contains a comma-separated
string, turn it into a list and strip off parenthetic expressions.  Return the
empty list when the FIELD cannot be found."
  (let ((value (assoc-ref meta field)))
    (if (not value)
        '()
        ;; Strip off parentheses
        (let ((items (string-split (regexp-substitute/global
                                    #f "( *\\([^\\)]+\\)) *"
                                    value 'pre 'post)
                                   #\,)))
          (remove (lambda (item)
                    (or (string-null? item)
                        ;; When there is whitespace inside of items it is
                        ;; probably because this was not an actual list to
                        ;; begin with.
                        (string-any char-set:whitespace item)))
                  (map string-trim-both items))))))

;; Trick Guile 3 so that it keeps the 'listify' binding accessible *and*
;; private even though this module is declarative.
(set! listify listify)

(define default-r-packages
  (list "base"
        "compiler"
        "datasets"
        "grDevices"
        "graphics"
        "grid"
        "methods"
        "parallel"
        "splines"
        "stats"
        "stats4"
        "tcltk"
        "tools"
        "translations"
        "utils"))

;; The field for system dependencies is often abused to specify non-package
;; dependencies (such as c++11).  This list is used to ignore them.
(define invalid-packages
  (list "build-essential"
        "c++"
        "c++11"
        "c++14"
        "c++17"
        "c99"
        "getopt::long"
        "gnu"
        "posix.1-2001"
        "linux"
        "libR"
        "none"
        "rtools"
        "unix"
        "use_c17"
        "windows"
        "xcode"
        "xquartz"))

(define (transform-sysname sysname)
  "Return a Guix package name for the common package name SYSNAME."
  (match sysname
    ("booktabs" "texlive-booktabs")
    ("bowtie2" "bowtie")
    ("cat" "coreutils")
    ("java" "openjdk")
    ("exiftool" "perl-image-exiftool")
    ("fftw3" "fftw")
    ("freetype2" "freetype")
    ("gettext" "gnu-gettext")
    ("gmake" "gnu-make")
    ("h5py" "python-h5py")
    ("hmmer3" "hmmer")
    ("leidenalg" "python-leidenalg")
    ("libarchive-devel" "libarchive")
    ("libarchive_dev" "libarchive")
    ("libbz2" "bzip2")
    ("libexpat" "expat")
    ("libjpeg" "libjpeg-turbo")
    ("liblz4" "lz4")
    ("liblzma" "xz")
    ("libssl-dev" "openssl")
    ("libssl_dev" "openssl")
    ("libzstd" "zstd")
    ("libxml2-devel" "libxml2")
    ("libxml2-dev" "libxml2")
    ("libz" "zlib")
    ("libz-dev" "zlib")
    ("mariadb-devel" "mariadb")
    ("mysql56_dev" "mariadb")
    ("nodejs" "node")
    ("numpy" "python-numpy")
    ("openssl-devel" "openssl")
    ("openssl@1.1" "openssl-1.1")
    ("packaging" "python-packaging")
    ("pandas" "python-pandas")
    ("pandoc-citeproc" "pandoc")
    ("python3" "python-3")
    ("pytorch" "python-pytorch")
    ("scikit-learn" "python-scikit-learn")
    ("scipy" "python-scipy")
    ("sklearn" "python-scikit-learn")
    ("sqlite3" "sqlite")
    ("svn" "subversion")
    ("tcl/tk" "tcl")
    ("udunits-2" "udunits")
    ("whoami" "coreutils")
    ("x11" "libx11")
    ("xml2" "libxml2")
    ("zlib-devel" "zlib")
    ("zlib1g-dev" "zlib")
    (_ sysname)))

(define cran-guix-name (cut guix-name "r-" <>))

(define (directory-needs-fortran? dir)
  "Check if the directory DIR contains Fortran source files."
  (match (find-files dir "\\.f(90|95)?$")
    (() #f)
    (_ #t)))

(define (directory-needs-esbuild? dir)
  "Check if the directory DIR contains minified JavaScript files and thus
needs a JavaScript compiler."
  (match (find-files dir "\\.min.js$")
    (() #f)
    (_ #t)))

(define (files-match-pattern? directory regexp . file-patterns)
  "Return #T if any of the files matching FILE-PATTERNS in the DIRECTORY match
the given REGEXP."
  (let ((pattern (make-regexp regexp)))
    (any (lambda (file)
           (call-with-input-file file
             (lambda (port)
               (let loop ()
                 (let ((line (read-line port)))
                   (cond
                    ((eof-object? line) #f)
                    ((regexp-exec pattern line) #t)
                    (else (loop))))))))
         (apply find-files directory file-patterns))))

(define packages-for-matches
  '(("-lcrypto"    . "openssl")
    ("-lcurl"      . "curl")
    ("-lgit2"      . "libgit2")
    ("-lpcre"      . "pcre2")
    ("-lssh"       . "openssh")
    ("-lssl"       . "openssl")
    ("-ltbb"       . "tbb")
    ("-lz"         . "zlib")
    ("gsl-config"  . "gsl")
    ("xml2-config" . "libxml2")
    ("CURL_LIBS"   . "curl")))

(define libraries-pattern
  (make-regexp
   (string-append "("
                  (string-join
                   (map (compose regexp-quote first) packages-for-matches) "|")
                  ")")))

(define (needed-libraries-in-directory dir)
  "Return a list of package names that correspond to libraries that are
referenced in build system files."
  (set->list
   (fold
    (lambda (file packages)
      (call-with-input-file file
        (lambda (port)
          (let loop ((packages packages))
            (let ((line (read-line port)))
              (cond
               ((eof-object? line) packages)
               (else
                (loop
                 (fold (lambda (match acc)
                         (or (and=> (assoc-ref packages-for-matches
                                               (match:substring match))
                                    (cut set-insert <> acc))
                             acc))
                       packages
                       (list-matches libraries-pattern line))))))))))
    (set)
    (find-files dir "(Makevars(.in.*)?|configure.*)"))))

;; A pattern matching package imports.  It detects uses of "library" or
;; "require", capturing the first argument; it also detects direct access of
;; namespaces via "::" or ":::", capturing the namespace.
(define import-pattern
  (make-regexp
   (string-append
    ;; Ignore leading spaces, but don't capture commented expressions.
    "(^ *"
    ;; Quiet imports
    "(suppressPackageStartupMessages\\()?"
    ;; the actual import statement.
    "(require|library)\\(\"?([^, \")]+)"
    ;; Or perhaps...
    "|"
    ;; ...direct namespace access.
    " *([A-Za-z0-9]+):::?"
    ")")))

(define (needed-test-inputs-in-directory dir)
  "Return a set of R package names that are found in library import
statements in files in the directory DIR."
  (if (getenv "GUIX_CRAN_IGNORE_TEST_INPUTS")
      (set)
      (match (scandir dir (negate (cute member <> '("." ".."))))
        ((package-directory-name . rest)
         (let* ((test-directories
                 (filter file-exists?
                         (list (string-append dir "/" package-directory-name "/tests")
                               (string-append dir "/" package-directory-name "/Tests")
                               (string-append dir "/" package-directory-name "/inst/unitTests")
                               (string-append dir "/" package-directory-name "/inst/UnitTests"))))
                (imported-packages
                 (fold (lambda (file packages)
                         (call-with-input-file file
                           (lambda (port)
                             (let loop ((packages packages))
                               (let ((line (read-line port)))
                                 (cond
                                  ((eof-object? line) packages)
                                  (else
                                   (loop
                                    (fold (lambda (match acc)
                                            (let ((imported (or (match:substring match 4)
                                                                (match:substring match 5))))
                                              (if (or (not imported)
                                                      (string=? imported package-directory-name)
                                                      (member imported default-r-packages))
                                                  acc
                                                  (set-insert imported acc))))
                                          packages
                                          (list-matches import-pattern line))))))))))
                       (set)
                       (append-map (lambda (directory)
                                     (find-files directory "\\.(R|Rmd)"))
                                   test-directories))))

           ;; Special case for BiocGenerics + RUnit.
           (if (any (lambda (directory)
                      (files-match-pattern? directory "BiocGenerics:::testPackage"
                                            "\\.R"))
                    test-directories)
               (set-insert "RUnit"
                           (set-insert "BiocGenerics" imported-packages))
               imported-packages)))
        (_ (set)))))

(define (needed-vignettes-inputs-in-directory dir)
  "Return a set of R package names that are found in library import statements
in vignette files in the directory DIR."
  (if (getenv "GUIX_CRAN_IGNORE_VIGNETTE_INPUTS")
      (set)
      (match (scandir dir (negate (cute member <> '("." ".."))))
        ((package-directory-name . rest)
         (let ((vignettes-directories
                (filter file-exists?
                        (list (string-append dir "/" package-directory-name "/vignettes")))))
           (fold (lambda (file packages)
                   (call-with-input-file file
                     (lambda (port)
                       (let loop ((packages packages))
                         (let ((line (read-line port)))
                           (cond
                            ((eof-object? line) packages)
                            (else
                             (loop
                              (fold (lambda (match acc)
                                      (let ((imported (match:substring match 4)))
                                        (if (or (not imported)
                                                (string=? imported package-directory-name)
                                                (member imported default-r-packages))
                                            acc
                                            (set-insert imported acc))))
                                    packages
                                    (list-matches import-pattern line))))))))))
                 (set)
                 (append-map (lambda (directory)
                               (find-files directory "\\.Rnw"))
                             vignettes-directories))))
        (_ (set)))))

(define (directory-needs-pkg-config? dir)
  "Return #T if any of the Makevars files in the src directory DIR reference
the pkg-config tool."
  (files-match-pattern? dir "pkg-config"
                        "(Makevars.*|configure.*)"))

(define (source-dir->dependencies dir)
  "Guess dependencies of R package source in DIR and return a list of
<upstream-input> corresponding to the dependencies guessed from source files
in DIR."
  (define (native name)
    (upstream-input
     (name name)
     (downstream-name name)
     (type 'native)))

  (append (map (lambda (name)
                 (upstream-input
                  (name name)
                  (downstream-name name)))
               (needed-libraries-in-directory dir))
          (map (lambda (name)
                 (upstream-input
                  (name name)
                  (downstream-name (cran-guix-name name))
                  (type 'native)))
               (set->list
                (set-union (needed-test-inputs-in-directory dir)
                           (needed-vignettes-inputs-in-directory dir))))
          (if (directory-needs-esbuild? dir)
              (list (native "esbuild"))
              '())
          (if (directory-needs-pkg-config? dir)
              (list (native "pkg-config"))
              '())
          (if (directory-needs-fortran? dir)
              (list (native "gfortran"))
              '())))

(define (source->dependencies source tarball?)
  "SOURCE-DIR->DEPENDENCIES, but for directories and tarballs as indicated
by TARBALL?"
  (if tarball?
    (call-with-temporary-directory
     (lambda (dir)
       (parameterize ((current-error-port (%make-void-port "rw+")))
         (system* "tar" "xf" source "-C" dir))
       (source-dir->dependencies dir)))
    (source-dir->dependencies source)))

(define (vignette-builders meta)
  (map (lambda (name)
         (upstream-input
          (name name)
          (downstream-name (cran-guix-name name))
          (type 'native)))
       (listify meta "VignetteBuilder")))

(define (uri-helper repository)
  (match repository
    ('cran         cran-uri)
    ('bioconductor bioconductor-uri)
    ('git          #f)
    ('hg           #f)))

(define (cran-package-source-url meta repository)
  "Return the URL of the source code referred to by META, a package in
REPOSITORY."
  (case repository
    ((git) (assoc-ref meta 'git))
    ((hg)  (assoc-ref meta 'hg))
    (else
     (match (apply (uri-helper repository)
                   (assoc-ref meta "Package")
                   (assoc-ref meta "Version")
                   (case repository
                     ((bioconductor)
                      (list (assoc-ref meta 'bioconductor-type)))
                     (else '())))
       ((urls ...) urls)
       ((? string? url) url)
       (_ #f)))))

(define (cran-package-propagated-inputs meta)
  "Return the list of <upstream-input> derived from dependency information in
META."
  (filter-map (lambda (name)
                (and (not (member name
                                  (append default-r-packages invalid-packages)))
                     (upstream-input
                      (name name)
                      (downstream-name (cran-guix-name name))
                      (type 'propagated))))
              (lset-union equal?
                          (listify meta "Imports")
                          (listify meta "LinkingTo")
                          (delete "R" (listify meta "Depends")))))

(define* (cran-package-inputs meta repository
                              #:key (download-source download))
  "Return the list of <upstream-input> corresponding to all the dependencies
of META, a package in REPOSITORY."
  (let* ((url    (cran-package-source-url meta repository))
         (name   (assoc-ref meta "Package"))
         (source (apply download-source url
                        (cond
                         ((assoc-ref meta 'git) '(#:method git))
                         ((assoc-ref meta 'hg) '(#:method hg))
                         (else '()))))
         (tarball? (not (or (assoc-ref meta 'git)
                            (assoc-ref meta 'hg))))
         (compare-upstream-inputs
          (lambda (input1 input2)
            (string<? (upstream-input-downstream-name input1)
                      (upstream-input-downstream-name input2))))
         (upstream-inputs-equal?
          (lambda (input1 input2)
            (string=? (upstream-input-downstream-name input1)
                      (upstream-input-downstream-name input2))))
         (r-inputs
          (append (cran-package-propagated-inputs meta)
                  (vignette-builders meta)))
         (source-derived-inputs
          ;; Only keep new inputs
          (lset-difference upstream-inputs-equal?
                           (source->dependencies source tarball?)
                           r-inputs))
         (system-inputs
          (filter-map (lambda (name)
                        (and (not (member name invalid-packages))
                             (upstream-input
                              (name name)
                              (downstream-name
                               (transform-sysname name)))))
                      (map string-downcase
                           (listify meta "SystemRequirements")))))
    (sort (filter
           ;; Prevent tight cycles.
           (lambda (input)
             ((negate string=?) name (upstream-input-name input)))
           (append source-derived-inputs
                   system-inputs
                   r-inputs))
          compare-upstream-inputs)))

(define (phases-for-inputs input-names)
  "Generate a list of build phases based on the provided INPUT-NAMES, a list
of package names for all input packages."
  (let ((rules
         (list (lambda ()
                 (and (any (lambda (name)
                             (member name
                                     '("styler"
                                       "ExperimentHub"
                                       "R.cache"
                                       "R.rsp")))
                           input-names)
                      '(add-after 'unpack 'set-HOME
                         (lambda _ (setenv "HOME" "/tmp")))))
               (lambda ()
                 (and (member "esbuild" input-names)
                      '(add-after 'unpack 'process-javascript
                         (lambda* (#:key inputs #:allow-other-keys)
                           (with-directory-excursion "inst/"
                             (for-each (match-lambda
                                         ((source . target)
                                          (minify source #:target target)))
                                       '())))))))))
    (fold (lambda (rule phases)
            (let ((new-phase (rule)))
              (if new-phase (cons new-phase phases) phases)))
          (list)
          rules)))

(define (maybe-arguments inputs)
  "Generate a list for the arguments field that can be spliced into a package
S-expression."
  (let ((input-names (map upstream-input-name inputs))
        (esbuild-modules '(#:modules
                           '((guix build r-build-system)
                             (guix build minify-build-system)
                             (guix build utils)
                             (ice-9 match))
                           #:imported-modules
                           `(,@%r-build-system-modules
                             (guix build minify-build-system)))))
    (match (phases-for-inputs input-names)
      (() '())
      (phases
       `((arguments
          (list
           ,@(if (member "esbuild" input-names)
                 esbuild-modules '())
           #:phases
           '(modify-phases %standard-phases
              ,@phases))))))))

(define* (description->package repository meta #:key (license-prefix identity)
                               (download-source download))
  "Return the `package' s-expression for an R package published on REPOSITORY
from the alist META, which was derived from the R package's DESCRIPTION file."
  (let* ((base-url   (case repository
                       ((cran)         %cran-url)
                       ((bioconductor) %bioconductor-url)
                       ((git)          #f)
                       ((hg)           #f)))
         (canonical-url-base (case repository
                               ((cran)         %cran-canonical-url)
                               ((bioconductor) %bioconductor-url)
                               ((git)          #f)))
         (name       (assoc-ref meta "Package"))
         (synopsis   (assoc-ref meta "Title"))
         (version    (assoc-ref meta "Version"))
         (license    (and=> (assoc-ref meta "License")
                            (cut string->licenses <> license-prefix)))
         ;; Some packages have multiple home pages.  Some have none.
         (home-page  (case repository
                       ((git) (assoc-ref meta 'git))
                       ((hg)  (assoc-ref meta 'hg))
                       (else (match (listify meta "URL")
                               ((url rest ...) url)
                               (_ (string-append canonical-url-base name))))))
         (source-url (cran-package-source-url meta repository))
         (git?       (if (assoc-ref meta 'git) #true #false))
         (hg?        (if (assoc-ref meta 'hg) #true #false))
         (source     (apply download-source source-url
                            (cond
                             (git? '(#:method git))
                             (hg? '(#:method hg))
                             (else '()))))
         (uri-helper (uri-helper repository))
         (inputs     (cran-package-inputs meta repository
                                          #:download-source download-source))
         (package
           `(package
              (name ,(cran-guix-name name))
              (version ,(cond
                         (git?
                          `(git-version ,version revision commit))
                         (hg?
                          `(string-append ,version "-" revision "." changeset))
                         (else version)))
              (source (origin
                        (method ,(cond
                                  (git? 'git-fetch)
                                  (hg?  'hg-fetch)
                                  (else 'url-fetch)))
                        (uri ,(cond
                               (git?
                                `(git-reference
                                  (url ,(assoc-ref meta 'git))
                                  (commit commit)))
                               (hg?
                                `(hg-reference
                                  (url ,(assoc-ref meta 'hg))
                                  (changeset changeset)))
                               (else
                                `(,(procedure-name uri-helper) ,name version
                                  ,@(or (and=> (assoc-ref meta 'bioconductor-type)
                                               (lambda (type)
                                                 (list (list 'quote type))))
                                        '())))))
                        ,@(cond
                           (git?
                            '((file-name (git-file-name name version))))
                           (hg?
                            '((file-name (string-append name "-" version "-checkout"))))
                           (else '()))
                        (sha256
                         (base32
                          ,(bytevector->nix-base32-string
                            (file-hash* source #:recursive? (or git? hg?)))))))
              ,@(if (not (and git? hg?
                              (equal? (string-append "r-" name)
                                      (cran-guix-name name))))
                    `((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
                    '())
              (build-system r-build-system)
              ,@(maybe-arguments inputs)
              ,@(maybe-inputs (filter (upstream-input-type-predicate 'regular)
                                      inputs)
                              'inputs)
              ,@(maybe-inputs (filter (upstream-input-type-predicate
                                       'propagated)
                                      inputs)
                              'propagated-inputs)
              ,@(maybe-inputs (filter (upstream-input-type-predicate 'native)
                                      inputs)
                              'native-inputs)

              (home-page ,(if (string-null? home-page)
                              (string-append base-url name)
                              home-page))
              (synopsis ,(beautify-synopsis synopsis))
              (description ,(beautify-description (or (assoc-ref meta "Description")
                                                      "")))
              (license ,license))))
    (values
     (cond
      (git?
       `(let ((commit ,(assoc-ref meta 'git-commit))
              (revision "1"))
          ,package))
      (hg?
       `(let ((changeset ,(assoc-ref meta 'hg-changeset))
              (revision "1"))
          ,package))
      (else package))
     (filter-map (lambda (input)
                   (and (string-prefix? "r-"
                                        (upstream-input-downstream-name input))
                        (upstream-input-name input)))
                 inputs))))

(define cran->guix-package
  (memoize
   (lambda* (package-name #:key (repo 'cran) version (license-prefix identity)
                          (fetch-description fetch-description)
                          (download-source download)
                          #:allow-other-keys)
     "Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
s-expression corresponding to that package, or #f on failure."
     (let ((description (fetch-description repo package-name version)))
       (if description
           (description->package repo description
                                 #:license-prefix license-prefix
                                 #:download-source download-source)
           (case repo
             ((git)
              ;; Retry import from Bioconductor
              (cran->guix-package package-name #:repo 'bioconductor
                                  #:license-prefix license-prefix))
             ((hg)
              ;; Retry import from Bioconductor
              (cran->guix-package package-name #:repo 'bioconductor
                                  #:license-prefix license-prefix))
             ((bioconductor)
              ;; Retry import from CRAN
              (cran->guix-package package-name #:repo 'cran
                                  #:license-prefix license-prefix))
             (else
              (values #f '()))))))))

(define* (cran-recursive-import package-name #:key (repo 'cran) version
                                (license-prefix identity))
  (recursive-import package-name
                    #:version version
                    #:repo repo
                    #:repo->guix-package cran->guix-package
                    #:guix-name cran-guix-name
                    #:license-prefix license-prefix))

\f
;;;
;;; Updater.
;;;

(define (package->upstream-name package)
  "Return the upstream name of the PACKAGE."
  (let* ((properties (package-properties package))
         (upstream-name (and=> properties
                               (cut assoc-ref <> 'upstream-name))))
    (if upstream-name
        upstream-name
        (match (package-source package)
          ((? origin? origin)
           (match (origin-uri origin)
             ((or (? string? url) (url _ ...))
              (let ((end   (string-rindex url #\_))
                    (start (string-rindex url #\/)))
                ;; The URL ends on
                ;; (string-append "/" name "_" version ".tar.gz")
                (and start end (substring url (+ start 1) end))))
             (_ #f)))
          (_ #f)))))

(define* (latest-cran-release pkg #:key (version #f))
  "Return an <upstream-source> for the latest release of the package PKG."
  (when version
    (error
     (formatted-message
      (G_ "~a provides only the latest version of each package, sorry.")
      "CRAN")))

  (define upstream-name
    (package->upstream-name pkg))

  (define meta
    (fetch-description 'cran upstream-name))

  (and meta
       (let ((version (assoc-ref meta "Version")))
         ;; CRAN does not provide signatures.
         (upstream-source
          (package (package-name pkg))
          (version version)
          (urls (cran-uri upstream-name version))
          (inputs (cran-package-inputs meta 'cran))))))

(define* (latest-bioconductor-release pkg #:key (version #f))
  "Return an <upstream-source> for the latest release of the package PKG."
  (when version
    (error
     (formatted-message
      (G_ "~a provides only the latest version of each package, sorry.")
      "bioconductor.org")))

  (define upstream-name
    (package->upstream-name pkg))

  (define type
    (cond
     ((bioconductor-data-package? pkg)
      'annotation)
     ((bioconductor-experiment-package? pkg)
      'experiment)
     ((bioconductor-package? pkg)
      #true)
     (else #false)))

  (define latest-version
    (latest-bioconductor-package-version upstream-name type))

  (and latest-version
       ;; Bioconductor does not provide signatures.
       (upstream-source
        (package (package-name pkg))
        (version latest-version)
        (urls (bioconductor-uri upstream-name latest-version type))
        (inputs
         (let ((meta (fetch-description 'bioconductor upstream-name)))
           (cran-package-inputs meta 'bioconductor))))))

(define (cran-package? package)
  "Return true if PACKAGE is an R package from CRAN."
  (and (string-prefix? "r-" (package-name package))
       ;; Check if the upstream name can be extracted from package uri.
       (package->upstream-name package)
       ;; Check if package uri(s) are prefixed by "mirror://cran".
       ((url-predicate (cut string-prefix? "mirror://cran" <>)) package)))

(define (bioconductor-package? package)
  "Return true if PACKAGE is an R package from Bioconductor."
  (let ((predicate (lambda (uri)
                     (and (string-prefix? "https://bioconductor.org" uri)
                          ;; Data packages are neither listed in SVN nor on
                          ;; the Github mirror, so we have to exclude them
                          ;; from the set of bioconductor packages that can be
                          ;; updated automatically.
                          (not (string-contains uri "/data/annotation/"))
                          ;; Experiment packages are in a separate repository.
                          (not (string-contains uri "/data/experiment/"))))))
    (and (string-prefix? "r-" (package-name package))
         ((url-predicate predicate) package))))

(define (bioconductor-data-package? package)
  "Return true if PACKAGE is an R data package from Bioconductor."
  (let ((predicate (lambda (uri)
                     (and (string-prefix? "https://bioconductor.org" uri)
                          (string-contains uri "/data/annotation/")))))
    (and (string-prefix? "r-" (package-name package))
         ((url-predicate predicate) package))))

(define (bioconductor-experiment-package? package)
  "Return true if PACKAGE is an R experiment package from Bioconductor."
  (let ((predicate (lambda (uri)
                     (and (string-prefix? "https://bioconductor.org" uri)
                          (string-contains uri "/data/experiment/")))))
    (and (string-prefix? "r-" (package-name package))
         ((url-predicate predicate) package))))

(define %cran-updater
  (upstream-updater
   (name 'cran)
   (description "Updater for CRAN packages")
   (pred cran-package?)
   (import latest-cran-release)))

(define %bioconductor-updater
  (upstream-updater
   (name 'bioconductor)
   (description "Updater for Bioconductor packages")
   (pred (lambda (pkg)
           (or (bioconductor-package? pkg)
               (bioconductor-data-package? pkg)
               (bioconductor-experiment-package? pkg))))
   (import latest-bioconductor-release)))

;;; cran.scm ends here

debug log:

solving 11843703ac ...
found 11843703ac in https://yhetil.org/guix/ffca10726eee00287a2f7470651c867486fae72a.1733774143.git.herman@rimm.ee/
found fe69cb87f7 in https://git.savannah.gnu.org/cgit/guix.git
preparing index
index prepared:
100644 fe69cb87f7c78102f18737fbdd232fd8d9fc4f9a	guix/import/cran.scm

applying [1/1] https://yhetil.org/guix/ffca10726eee00287a2f7470651c867486fae72a.1733774143.git.herman@rimm.ee/
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index fe69cb87f7..11843703ac 100644

Checking patch guix/import/cran.scm...
Applied patch guix/import/cran.scm cleanly.

index at:
100644 11843703ac84c08b18d89e4948f5439d23a7fa46	guix/import/cran.scm

(*) Git path names are given by the tree(s) the blob belongs to.
    Blobs themselves have no identifier aside from the hash of its contents.^

Code repositories for project(s) associated with this external index

	https://git.savannah.gnu.org/cgit/guix.git

This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.