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1 | ;;; GNU Guix --- Functional package management for GNU |
2 | ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> | |
ed6094fc | 3 | ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com> |
cb7e4867 RW |
4 | ;;; |
5 | ;;; This file is part of GNU Guix. | |
6 | ;;; | |
7 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
8 | ;;; under the terms of the GNU General Public License as published by | |
9 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
10 | ;;; your option) any later version. | |
11 | ;;; | |
12 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
13 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
15 | ;;; GNU General Public License for more details. | |
16 | ;;; | |
17 | ;;; You should have received a copy of the GNU General Public License | |
18 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
19 | ||
20 | (define-module (gnu packages statistics) | |
21 | #:use-module ((guix licenses) #:prefix license:) | |
22 | #:use-module (guix packages) | |
23 | #:use-module (guix download) | |
24 | #:use-module (guix utils) | |
25 | #:use-module (guix build-system gnu) | |
b12636e6 | 26 | #:use-module (guix build-system r) |
9bc08aa0 | 27 | #:use-module (guix build-system python) |
cb7e4867 RW |
28 | #:use-module (gnu packages) |
29 | #:use-module (gnu packages compression) | |
30 | #:use-module (gnu packages gcc) | |
31 | #:use-module (gnu packages gtk) | |
32 | #:use-module (gnu packages icu4c) | |
33 | #:use-module (gnu packages image) | |
34 | #:use-module (gnu packages java) | |
35 | #:use-module (gnu packages maths) | |
36 | #:use-module (gnu packages pcre) | |
37 | #:use-module (gnu packages perl) | |
38 | #:use-module (gnu packages pkg-config) | |
9bc08aa0 | 39 | #:use-module (gnu packages python) |
cb7e4867 | 40 | #:use-module (gnu packages readline) |
035711f1 | 41 | #:use-module (gnu packages ssh) |
cb7e4867 RW |
42 | #:use-module (gnu packages texlive) |
43 | #:use-module (gnu packages texinfo) | |
035711f1 | 44 | #:use-module (gnu packages tls) |
ce0614dd | 45 | #:use-module (gnu packages base) |
6140747f | 46 | #:use-module (gnu packages web) |
67a167fd | 47 | #:use-module (gnu packages xml) |
9bc08aa0 RW |
48 | #:use-module (gnu packages xorg) |
49 | #:use-module (gnu packages zip) | |
50 | #:use-module (srfi srfi-1)) | |
cb7e4867 RW |
51 | |
52 | (define-public r | |
53 | (package | |
54 | (name "r") | |
62de2545 | 55 | (version "3.2.2") |
cb7e4867 RW |
56 | (source (origin |
57 | (method url-fetch) | |
58 | (uri (string-append "mirror://cran/src/base/R-" | |
59 | (version-prefix version 1) "/R-" | |
60 | version ".tar.gz")) | |
61 | (sha256 | |
62 | (base32 | |
62de2545 | 63 | "07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw")))) |
cb7e4867 RW |
64 | (build-system gnu-build-system) |
65 | (arguments | |
ff2b1c17 RW |
66 | `(#:make-flags |
67 | (list (string-append "LDFLAGS=-Wl,-rpath=" | |
68 | (assoc-ref %outputs "out") | |
69 | "/lib/R/lib")) | |
70 | #:phases | |
f4f4ced8 RW |
71 | (modify-phases %standard-phases |
72 | (add-before | |
73 | 'configure 'set-default-pager | |
74 | ;; Set default pager to "cat", because otherwise it is "false", | |
75 | ;; making "help()" print nothing at all. | |
76 | (lambda _ (setenv "PAGER" "cat") #t)) | |
77 | (add-before | |
78 | 'check 'set-timezone | |
79 | ;; Some tests require the timezone to be set. | |
af23b6e9 RW |
80 | (lambda _ (setenv "TZ" "UTC") #t)) |
81 | (add-after 'build 'make-info | |
82 | (lambda _ (zero? (system* "make" "info")))) | |
83 | (add-after 'build 'install-info | |
84 | (lambda _ (zero? (system* "make" "install-info"))))) | |
cb7e4867 | 85 | #:configure-flags |
b05d1c68 | 86 | '("--with-blas=openblas" |
cb7e4867 RW |
87 | "--with-lapack" |
88 | "--with-cairo" | |
89 | "--with-libpng" | |
90 | "--with-jpeglib" | |
91 | "--with-libtiff" | |
92 | "--with-ICU" | |
93 | "--enable-R-shlib" | |
94 | "--enable-BLAS-shlib" | |
95 | "--with-system-zlib" | |
96 | "--with-system-bzlib" | |
97 | "--with-system-pcre" | |
98 | "--with-system-tre" | |
99 | "--with-system-xz"))) | |
5e9738b7 RW |
100 | ;; R has some support for Java. When the JDK is available at configure |
101 | ;; time environment variables pointing to the JDK will be recorded under | |
102 | ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R | |
103 | ;; CMD javareconf". "R CMD javareconf" appears to only be used to update | |
104 | ;; the recorded environment variables in $R_HOME/etc. Refer to | |
105 | ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support | |
106 | ;; for additional information. | |
107 | ||
108 | ;; As the JDK is a rather large input with only very limited effects on R, | |
109 | ;; we decided to drop it. | |
cb7e4867 RW |
110 | (native-inputs |
111 | `(("bzip2" ,bzip2) | |
112 | ("perl" ,perl) | |
113 | ("pkg-config" ,pkg-config) | |
cb7e4867 RW |
114 | ("texinfo" ,texinfo) ; for building HTML manuals |
115 | ("which" ,which) ; for tests/Examples/base-Ex.R | |
116 | ("xz" ,xz))) | |
117 | (inputs | |
b05d1c68 | 118 | `(("openblas" ,openblas) |
cb7e4867 | 119 | ("cairo" ,cairo) |
19afbea1 | 120 | ("gfortran" ,gfortran) |
cb7e4867 | 121 | ("icu4c" ,icu4c) |
cb7e4867 RW |
122 | ("lapack" ,lapack) |
123 | ("libjpeg" ,libjpeg) | |
124 | ("libpng" ,libpng) | |
125 | ("libtiff" ,libtiff) | |
126 | ("libxt" ,libxt) | |
127 | ("pcre" ,pcre) | |
128 | ("readline" ,readline) | |
129 | ("zlib" ,zlib))) | |
12a9f4af RW |
130 | (native-search-paths |
131 | (list (search-path-specification | |
132 | (variable "R_LIBS_SITE") | |
133 | (files (list "site-library/"))))) | |
cb7e4867 RW |
134 | (home-page "http://www.r-project.org/") |
135 | (synopsis "Environment for statistical computing and graphics") | |
136 | (description | |
137 | "R is a language and environment for statistical computing and graphics. | |
138 | It provides a variety of statistical techniques, such as linear and nonlinear | |
139 | modeling, classical statistical tests, time-series analysis, classification | |
140 | and clustering. It also provides robust support for producing | |
141 | publication-quality data plots. A large amount of 3rd-party packages are | |
142 | available, greatly increasing its breadth and scope.") | |
143 | (license license:gpl3+))) | |
b12636e6 RW |
144 | |
145 | (define-public r-colorspace | |
146 | (package | |
147 | (name "r-colorspace") | |
148 | (version "1.2-6") | |
149 | (source | |
150 | (origin | |
151 | (method url-fetch) | |
9cda3622 | 152 | (uri (cran-uri "colorspace" version)) |
b12636e6 RW |
153 | (sha256 |
154 | (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds")))) | |
155 | (build-system r-build-system) | |
156 | (home-page "http://cran.r-project.org/web/packages/colorspace") | |
157 | (synopsis "Color space manipulation") | |
158 | (description | |
159 | "This package carries out a mapping between assorted color spaces | |
160 | including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar | |
161 | CIELAB. Qualitative, sequential, and diverging color palettes based on HCL | |
162 | colors are provided.") | |
163 | (license license:bsd-3))) | |
3587effb RW |
164 | |
165 | (define-public r-dichromat | |
166 | (package | |
167 | (name "r-dichromat") | |
168 | (version "2.0-0") | |
169 | (source | |
170 | (origin | |
171 | (method url-fetch) | |
9cda3622 | 172 | (uri (cran-uri "dichromat" version)) |
3587effb RW |
173 | (sha256 |
174 | (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i")))) | |
175 | (build-system r-build-system) | |
176 | (home-page "http://cran.r-project.org/web/packages/dichromat") | |
177 | (synopsis "Color schemes for dichromats") | |
178 | (description | |
179 | "Dichromat collapses red-green or green-blue distinctions to simulate the | |
180 | effects of different types of color-blindness.") | |
181 | (license license:gpl2+))) | |
177f38c7 RW |
182 | |
183 | (define-public r-digest | |
184 | (package | |
185 | (name "r-digest") | |
186 | (version "0.6.8") | |
187 | (source | |
188 | (origin | |
189 | (method url-fetch) | |
9cda3622 | 190 | (uri (cran-uri "digest" version)) |
177f38c7 RW |
191 | (sha256 |
192 | (base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih")))) | |
193 | (build-system r-build-system) | |
194 | (home-page "http://dirk.eddelbuettel.com/code/digest.html") | |
195 | (synopsis "Create cryptographic hash digests of R objects") | |
196 | (description | |
197 | "This package contains an implementation of a function 'digest()' for the | |
198 | creation of hash digests of arbitrary R objects (using the md5, sha-1, | |
199 | sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison | |
200 | of R language objects, as well as a function 'hmac()' to create hash-based | |
201 | message authentication code. | |
202 | ||
203 | Please note that this package is not meant to be deployed for cryptographic | |
204 | purposes for which more comprehensive (and widely tested) libraries such as | |
205 | OpenSSL should be used.") | |
206 | (license license:gpl2+))) | |
112bb3c0 RW |
207 | |
208 | (define-public r-gtable | |
209 | (package | |
210 | (name "r-gtable") | |
211 | (version "0.1.2") | |
212 | (source | |
213 | (origin | |
214 | (method url-fetch) | |
9cda3622 | 215 | (uri (cran-uri "gtable" version)) |
112bb3c0 RW |
216 | (sha256 |
217 | (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh")))) | |
218 | (build-system r-build-system) | |
219 | (home-page "https://cran.r-project.org/web/packages/gtable") | |
220 | (synopsis "R library to arrange grobs in tables") | |
221 | (description | |
222 | "Gtable is a collection of tools to make it easier to work with | |
223 | \"tables\" of grobs.") | |
224 | (license license:gpl2+))) | |
b7eee9fc RW |
225 | |
226 | (define-public r-labeling | |
227 | (package | |
228 | (name "r-labeling") | |
229 | (version "0.3") | |
230 | (source | |
231 | (origin | |
232 | (method url-fetch) | |
9cda3622 | 233 | (uri (cran-uri "labeling" version)) |
b7eee9fc RW |
234 | (sha256 |
235 | (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d")))) | |
236 | (build-system r-build-system) | |
237 | (home-page "http://cran.r-project.org/web/packages/labeling") | |
238 | (synopsis "Axis labeling algorithms") | |
239 | (description "The labeling package provides a range of axis labeling | |
240 | algorithms.") | |
241 | (license license:expat))) | |
d69c4b04 RW |
242 | |
243 | (define-public r-magrittr | |
244 | (package | |
245 | (name "r-magrittr") | |
246 | (version "1.5") | |
247 | (source | |
248 | (origin | |
249 | (method url-fetch) | |
9cda3622 | 250 | (uri (cran-uri "magrittr" version)) |
d69c4b04 RW |
251 | (sha256 |
252 | (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05")))) | |
253 | (build-system r-build-system) | |
254 | (home-page "http://cran.r-project.org/web/packages/magrittr/index.html") | |
255 | (synopsis "A forward-pipe operator for R") | |
256 | (description | |
257 | "Magrittr provides a mechanism for chaining commands with a new | |
258 | forward-pipe operator, %>%. This operator will forward a value, or the result | |
259 | of an expression, into the next function call/expression. There is flexible | |
260 | support for the type of right-hand side expressions. For more information, | |
261 | see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") | |
262 | (license license:expat))) | |
44373339 RW |
263 | |
264 | (define-public r-munsell | |
265 | (package | |
266 | (name "r-munsell") | |
267 | (version "0.4.2") | |
268 | (source | |
269 | (origin | |
270 | (method url-fetch) | |
9cda3622 | 271 | (uri (cran-uri "munsell" version)) |
44373339 RW |
272 | (sha256 |
273 | (base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4")))) | |
274 | (build-system r-build-system) | |
275 | (propagated-inputs | |
276 | `(("r-colorspace" ,r-colorspace))) | |
277 | (home-page "http://cran.r-project.org/web/packages/munsell") | |
278 | (synopsis "Munsell colour system") | |
279 | (description | |
280 | "The Munsell package contains Functions for exploring and using the | |
281 | Munsell colour system.") | |
282 | (license license:expat))) | |
ea69e2f8 RW |
283 | |
284 | (define-public r-rcpp | |
285 | (package | |
286 | (name "r-rcpp") | |
287 | (version "0.12.0") | |
288 | (source | |
289 | (origin | |
290 | (method url-fetch) | |
9cda3622 | 291 | (uri (cran-uri "Rcpp" version)) |
ea69e2f8 RW |
292 | (sha256 |
293 | (base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38")))) | |
294 | (build-system r-build-system) | |
295 | (home-page "http://www.rcpp.org") | |
296 | (synopsis "Seamless R and C++ Integration") | |
297 | (description | |
298 | "The Rcpp package provides R functions as well as C++ classes which offer | |
299 | a seamless integration of R and C++. Many R data types and objects can be | |
300 | mapped back and forth to C++ equivalents which facilitates both writing of new | |
301 | code as well as easier integration of third-party libraries. Documentation | |
302 | about Rcpp is provided by several vignettes included in this package, via the | |
303 | 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel | |
304 | and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see | |
305 | 'citation(\"Rcpp\")' for details on these last two.") | |
306 | (license license:gpl2+))) | |
7e10056b RW |
307 | |
308 | (define-public r-plyr | |
309 | (package | |
310 | (name "r-plyr") | |
311 | (version "1.8.3") | |
312 | (source | |
313 | (origin | |
314 | (method url-fetch) | |
9cda3622 | 315 | (uri (cran-uri "plyr" version)) |
7e10056b RW |
316 | (sha256 |
317 | (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk")))) | |
318 | (build-system r-build-system) | |
319 | (native-inputs `(("r-rcpp" ,r-rcpp))) | |
320 | (home-page "http://had.co.nz/plyr") | |
321 | (synopsis "Tools for Splitting, Applying and Combining Data") | |
322 | (description | |
323 | "Plyr is a set of tools that solves a common set of problems: you need to | |
324 | break a big problem down into manageable pieces, operate on each piece and | |
325 | then put all the pieces back together. For example, you might want to fit a | |
326 | model to each spatial location or time point in your study, summarise data by | |
327 | panels or collapse high-dimensional arrays to simpler summary statistics.") | |
328 | (license license:expat))) | |
9a4d8968 RW |
329 | |
330 | (define-public r-proto | |
331 | (package | |
332 | (name "r-proto") | |
333 | (version "0.3-10") | |
334 | (source | |
335 | (origin | |
336 | (method url-fetch) | |
9cda3622 | 337 | (uri (cran-uri "proto" version)) |
9a4d8968 RW |
338 | (sha256 |
339 | (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh")))) | |
340 | (build-system r-build-system) | |
341 | (home-page "http://r-proto.googlecode.com") | |
342 | (synopsis "Prototype object-based programming") | |
343 | (description | |
344 | "Proto is an object oriented system using object-based, also called | |
345 | prototype-based, rather than class-based object oriented ideas.") | |
346 | (license license:gpl2+))) | |
a45ba127 RW |
347 | |
348 | (define-public r-rcolorbrewer | |
349 | (package | |
350 | (name "r-rcolorbrewer") | |
351 | (version "1.1-2") | |
352 | (source | |
353 | (origin | |
354 | (method url-fetch) | |
9cda3622 | 355 | (uri (cran-uri "RColorBrewer" version)) |
a45ba127 RW |
356 | (sha256 |
357 | (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk")))) | |
358 | (build-system r-build-system) | |
359 | (home-page "http://cran.r-project.org/web/packages/RColorBrewer") | |
360 | (synopsis "ColorBrewer palettes") | |
361 | (description | |
362 | "This package provides color schemes for maps (and other graphics) | |
363 | designed by Cynthia Brewer as described at http://colorbrewer2.org") | |
364 | ;; Includes code licensed under bsd-4 | |
365 | (license license:asl2.0))) | |
4dca98dc RW |
366 | |
367 | (define-public r-stringi | |
368 | (package | |
369 | (name "r-stringi") | |
370 | (version "0.5-5") | |
371 | (source | |
372 | (origin | |
373 | (method url-fetch) | |
9cda3622 | 374 | (uri (cran-uri "stringi" version)) |
4dca98dc RW |
375 | (sha256 |
376 | (base32 | |
377 | "183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw")))) | |
378 | (build-system r-build-system) | |
379 | (inputs `(("icu4c" ,icu4c))) | |
380 | (native-inputs `(("pkg-config" ,pkg-config))) | |
381 | (home-page "http://stringi.rexamine.com/") | |
382 | (synopsis "Character string processing facilities") | |
383 | (description | |
384 | "This package allows for fast, correct, consistent, portable, as well as | |
385 | convenient character string/text processing in every locale and any native | |
386 | encoding. Owing to the use of the ICU library, the package provides R users | |
387 | with platform-independent functions known to Java, Perl, Python, PHP, and Ruby | |
388 | programmers. Among available features there are: pattern searching | |
389 | (e.g. via regular expressions), random string generation, string collation, | |
390 | transliteration, concatenation, date-time formatting and parsing, etc.") | |
391 | (license license:bsd-3))) | |
d5cd5c15 RW |
392 | |
393 | (define-public r-stringr | |
394 | (package | |
395 | (name "r-stringr") | |
396 | (version "1.0.0") | |
397 | (source | |
398 | (origin | |
399 | (method url-fetch) | |
9cda3622 | 400 | (uri (cran-uri "stringr" version)) |
d5cd5c15 RW |
401 | (sha256 |
402 | (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq")))) | |
403 | (build-system r-build-system) | |
404 | (propagated-inputs | |
405 | `(("r-magrittr" ,r-magrittr) | |
406 | ("r-stringi" ,r-stringi))) | |
718a2bde | 407 | (home-page "https://github.com/hadley/stringr") |
d5cd5c15 RW |
408 | (synopsis "Simple, consistent wrappers for common string operations") |
409 | (description | |
410 | "Stringr is a consistent, simple and easy to use set of wrappers around | |
411 | the fantastic 'stringi' package. All function and argument names (and | |
412 | positions) are consistent, all functions deal with \"NA\"'s and zero length | |
413 | vectors in the same way, and the output from one function is easy to feed into | |
414 | the input of another.") | |
415 | (license license:gpl2+))) | |
9ca731ba RW |
416 | |
417 | (define-public r-reshape2 | |
418 | (package | |
419 | (name "r-reshape2") | |
420 | (version "1.4.1") | |
421 | (source | |
422 | (origin | |
423 | (method url-fetch) | |
9cda3622 | 424 | (uri (cran-uri "reshape2" version)) |
9ca731ba RW |
425 | (sha256 |
426 | (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v")))) | |
427 | (build-system r-build-system) | |
428 | (propagated-inputs | |
429 | `(("r-plyr" ,r-plyr) | |
430 | ("r-rcpp" ,r-rcpp) | |
431 | ("r-stringr" ,r-stringr))) | |
432 | (home-page "https://github.com/hadley/reshape") | |
433 | (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package") | |
434 | (description | |
435 | "Reshape2 is an R library to flexibly restructure and aggregate data | |
436 | using just two functions: melt and dcast (or acast).") | |
437 | (license license:expat))) | |
a11ee478 RW |
438 | |
439 | (define-public r-scales | |
440 | (package | |
441 | (name "r-scales") | |
91781b74 | 442 | (version "0.3.0") |
a11ee478 RW |
443 | (source |
444 | (origin | |
445 | (method url-fetch) | |
9cda3622 | 446 | (uri (cran-uri "scales" version)) |
a11ee478 | 447 | (sha256 |
91781b74 | 448 | (base32 "1kkgpqzb0a6lnpblhcprr4qzyfk5lhicdv4639xs5cq16n7bkqgl")))) |
a11ee478 RW |
449 | (build-system r-build-system) |
450 | (propagated-inputs | |
451 | `(("r-dichromat" ,r-dichromat) | |
452 | ("r-labeling" ,r-labeling) | |
453 | ("r-munsell" ,r-munsell) | |
454 | ("r-plyr" ,r-plyr) | |
455 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
456 | ("r-rcpp" ,r-rcpp))) | |
457 | (home-page "https://github.com/hadley/scales") | |
458 | (synopsis "Scale functions for visualization") | |
459 | (description | |
460 | "This package provides graphical scales that map data to aesthetics, and | |
461 | provides methods for automatically determining breaks and labels for axes and | |
462 | legends.") | |
463 | (license license:expat))) | |
d11b808f RW |
464 | |
465 | (define-public r-ggplot2 | |
466 | (package | |
467 | (name "r-ggplot2") | |
468 | (version "1.0.1") | |
469 | (source | |
470 | (origin | |
471 | (method url-fetch) | |
9cda3622 | 472 | (uri (cran-uri "ggplot2" version)) |
d11b808f RW |
473 | (sha256 |
474 | (base32 "0794kjqi3lrxb33lr1mykd58959hlgkhdn259vj8fxrh65mqw920")))) | |
475 | (build-system r-build-system) | |
476 | (propagated-inputs | |
477 | `(("r-digest" ,r-digest) | |
478 | ("r-gtable" ,r-gtable) | |
479 | ("r-plyr" ,r-plyr) | |
480 | ("r-proto" ,r-proto) | |
481 | ("r-reshape2" ,r-reshape2) | |
482 | ("r-scales" ,r-scales))) | |
483 | (home-page "http://ggplot2.org") | |
484 | (synopsis "An implementation of the grammar of graphics") | |
485 | (description | |
486 | "Ggplot2 is an implementation of the grammar of graphics in R. It | |
487 | combines the advantages of both base and lattice graphics: conditioning and | |
488 | shared axes are handled automatically, and you can still build up a plot step | |
489 | by step from multiple data sources. It also implements a sophisticated | |
490 | multidimensional conditioning system and a consistent interface to map data to | |
491 | aesthetic attributes.") | |
492 | (license license:gpl2+))) | |
ed6094fc VVP |
493 | |
494 | (define-public r-assertthat | |
495 | (package | |
496 | (name "r-assertthat") | |
497 | (version "0.1") | |
498 | (source (origin | |
499 | (method url-fetch) | |
9cda3622 | 500 | (uri (cran-uri "assertthat" version)) |
ed6094fc VVP |
501 | (sha256 |
502 | (base32 | |
503 | "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk")))) | |
504 | (build-system r-build-system) | |
505 | (home-page "https://github.com/hadley/assertthat") | |
506 | (synopsis "Easy pre and post assertions") | |
507 | (description | |
508 | "Assertthat is an extension to stopifnot() that makes it easy to declare | |
509 | the pre and post conditions that your code should satisfy, while also | |
510 | producing friendly error messages so that your users know what they've done | |
511 | wrong.") | |
512 | (license license:gpl3+))) | |
6af48134 VVP |
513 | |
514 | (define-public r-lazyeval | |
515 | (package | |
516 | (name "r-lazyeval") | |
517 | (version "0.1.10") | |
518 | (source (origin | |
519 | (method url-fetch) | |
9cda3622 | 520 | (uri (cran-uri "lazyeval" version)) |
6af48134 VVP |
521 | (sha256 |
522 | (base32 | |
523 | "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh")))) | |
524 | (build-system r-build-system) | |
525 | (home-page "https://github.com/hadley/lazyeval") | |
526 | (synopsis "Lazy (non-standard) evaluation in R") | |
527 | (description | |
528 | "This package provides the tools necessary to do non-standard | |
529 | evaluation (NSE) in R.") | |
530 | (license license:gpl3+))) | |
8ea6b30f VVP |
531 | |
532 | (define-public r-dbi | |
533 | (package | |
534 | (name "r-dbi") | |
535 | (version "0.3.1") | |
536 | (source (origin | |
537 | (method url-fetch) | |
9cda3622 | 538 | (uri (cran-uri "DBI" version)) |
8ea6b30f VVP |
539 | (sha256 |
540 | (base32 | |
541 | "0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw")))) | |
542 | (build-system r-build-system) | |
543 | (home-page "https://github.com/rstats-db/DBI") | |
544 | (synopsis "R database interface") | |
545 | (description | |
546 | "The DBI package provides a database interface (DBI) definition for | |
547 | communication between R and relational database management systems. All | |
548 | classes in this package are virtual and need to be extended by the various | |
549 | R/DBMS implementations.") | |
550 | (license license:lgpl2.0+))) | |
675c9f44 VVP |
551 | |
552 | (define-public r-bh | |
553 | (package | |
554 | (name "r-bh") | |
555 | (version "1.58.0-1") | |
556 | (source (origin | |
557 | (method url-fetch) | |
558 | (uri (cran-uri "BH" version)) | |
559 | (sha256 | |
560 | (base32 | |
561 | "17rnwyw9ib2pvm60iixzkbz7ff4fslpifp1nlx4czp42hy67kqpf")))) | |
562 | (build-system r-build-system) | |
563 | (home-page "https://github.com/eddelbuettel/bh") | |
564 | (synopsis "R package providing subset of Boost headers") | |
565 | (description | |
566 | "This package aims to provide the most useful subset of Boost libraries | |
567 | for template use among CRAN packages.") | |
568 | (license license:boost1.0))) | |
256ccc92 VVP |
569 | |
570 | (define-public r-evaluate | |
571 | (package | |
572 | (name "r-evaluate") | |
573 | (version "0.8") | |
574 | (source (origin | |
575 | (method url-fetch) | |
576 | (uri (cran-uri "evaluate" version)) | |
577 | (sha256 | |
578 | (base32 | |
579 | "137gc35jlizhqnx19mxim3llrkm403abj8ghb2b7v5ls9rvd40pq")))) | |
580 | (build-system r-build-system) | |
581 | (propagated-inputs | |
582 | `(("r-stringr" ,r-stringr))) | |
583 | (home-page "https://github.com/hadley/evaluate") | |
584 | (synopsis "Parsing and evaluation tools for R") | |
585 | (description | |
586 | "This package provides tools that allow you to recreate the parsing, | |
587 | evaluation and display of R code, with enough information that you can | |
588 | accurately recreate what happens at the command line. The tools can easily be | |
589 | adapted for other output formats, such as HTML or LaTeX.") | |
590 | (license license:gpl3+))) | |
c5bf3abe VVP |
591 | |
592 | (define-public r-formatr | |
593 | (package | |
594 | (name "r-formatr") | |
595 | (version "1.2.1") | |
596 | (source (origin | |
597 | (method url-fetch) | |
598 | (uri (cran-uri "formatR" version)) | |
599 | (sha256 | |
600 | (base32 | |
601 | "0f4cv2zv5wayyqx99ybfyl0p83kgjvnsv8dhcwa4s49kw6jsx1lr")))) | |
602 | (build-system r-build-system) | |
603 | (home-page "http://yihui.name/formatR") | |
604 | (synopsis "Format R code automatically") | |
605 | (description | |
606 | "This package provides a function to format R source code. Spaces and | |
607 | indent will be added to the code automatically, and comments will be preserved | |
608 | under certain conditions, so that R code will be more human-readable and tidy. | |
609 | There is also a Shiny app as a user interface in this package.") | |
610 | (license license:gpl3+))) | |
ad3f005b VVP |
611 | |
612 | (define-public r-highr | |
613 | (package | |
614 | (name "r-highr") | |
615 | (version "0.5.1") | |
616 | (source (origin | |
617 | (method url-fetch) | |
618 | (uri (cran-uri "highr" version)) | |
619 | (sha256 | |
620 | (base32 | |
621 | "11hyawzhaw3ph5y5xphi7alx6df1d0i6wh0a2n5m4sxxhdrzswnb")))) | |
622 | (build-system r-build-system) | |
623 | (home-page "https://github.com/yihui/highr") | |
624 | (synopsis "Syntax highlighting for R source code") | |
625 | (description | |
626 | "This package provides syntax highlighting for R source code. Currently | |
627 | it supports LaTeX and HTML output. Source code of other languages is | |
628 | supported via Andre Simon's highlight package.") | |
629 | (license license:gpl3+))) | |
acbb40fa VVP |
630 | |
631 | (define-public r-mime | |
632 | (package | |
633 | (name "r-mime") | |
634 | (version "0.4") | |
635 | (source (origin | |
636 | (method url-fetch) | |
637 | (uri (cran-uri "mime" version)) | |
638 | (sha256 | |
639 | (base32 | |
640 | "145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p")))) | |
641 | (build-system r-build-system) | |
642 | (home-page "https://github.com/yihui/mime") | |
643 | (synopsis "R package to map filenames to MIME types") | |
644 | (description | |
645 | "This package guesses the MIME type from a filename extension using the | |
646 | data derived from /etc/mime.types in UNIX-type systems.") | |
647 | (license license:gpl2))) | |
3f8ac353 VVP |
648 | |
649 | (define-public r-markdown | |
650 | (package | |
651 | (name "r-markdown") | |
652 | (version "0.7.7") | |
653 | (source (origin | |
654 | (method url-fetch) | |
655 | (uri (cran-uri "markdown" version)) | |
656 | (sha256 | |
657 | (base32 | |
658 | "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb")))) | |
659 | (build-system r-build-system) | |
660 | ;; Skip check phase because the tests require the r-knitr package to be | |
661 | ;; installed. This prevents installation failures. Knitr normally | |
662 | ;; shouldn't be available since r-markdown is a dependency of the r-knitr | |
663 | ;; package. | |
664 | (arguments `(#:tests? #f)) | |
665 | (propagated-inputs | |
666 | `(("r-mime" ,r-mime))) | |
667 | (home-page "https://github.com/rstudio/markdown") | |
668 | (synopsis "Markdown rendering for R") | |
669 | (description | |
670 | "This package provides R bindings to the Sundown Markdown rendering | |
671 | library (https://github.com/vmg/sundown). Markdown is a plain-text formatting | |
672 | syntax that can be converted to XHTML or other formats.") | |
673 | (license license:gpl2))) | |
ea3a8095 VVP |
674 | |
675 | (define-public r-yaml | |
676 | (package | |
677 | (name "r-yaml") | |
678 | (version "2.1.13") | |
679 | (source (origin | |
680 | (method url-fetch) | |
681 | (uri (cran-uri "yaml" version)) | |
682 | (sha256 | |
683 | (base32 | |
684 | "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6")))) | |
685 | (build-system r-build-system) | |
686 | (home-page "https://cran.r-project.org/web/packages/yaml/") | |
687 | (synopsis "Methods to convert R data to YAML and back") | |
688 | (description | |
689 | "This package implements the libyaml YAML 1.1 parser and | |
690 | emitter (http://pyyaml.org/wiki/LibYAML) for R.") | |
691 | (license license:bsd-3))) | |
213656b9 VVP |
692 | |
693 | (define-public r-knitr | |
694 | (package | |
695 | (name "r-knitr") | |
696 | (version "1.11") | |
697 | (source (origin | |
698 | (method url-fetch) | |
699 | (uri (cran-uri "knitr" version)) | |
700 | (sha256 | |
701 | (base32 | |
702 | "1ikjla0hnpjfkdbydqhhqypc0aiizbi4nyn8c694sdk9ca4jasdd")))) | |
703 | (build-system r-build-system) | |
704 | (propagated-inputs | |
705 | `(("r-evaluate" ,r-evaluate) | |
706 | ("r-digest" ,r-digest) | |
707 | ("r-formatr" ,r-formatr) | |
708 | ("r-highr" ,r-highr) | |
709 | ("r-markdown" ,r-markdown) | |
710 | ("r-stringr" ,r-stringr) | |
711 | ("r-yaml" ,r-yaml))) | |
712 | (home-page "http://yihui.name/knitr/") | |
713 | (synopsis "General-purpose package for dynamic report generation in R") | |
714 | (description | |
715 | "This package provides a general-purpose tool for dynamic report | |
716 | generation in R using Literate Programming techniques.") | |
717 | ;; The code is released under any version of the GPL. As it is used by | |
718 | ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+ | |
719 | ;; here. | |
720 | (license license:gpl2+))) | |
4f0e8484 VVP |
721 | |
722 | (define-public r-microbenchmark | |
723 | (package | |
724 | (name "r-microbenchmark") | |
725 | (version "1.4-2") | |
726 | (source (origin | |
727 | (method url-fetch) | |
728 | (uri (cran-uri "microbenchmark" version)) | |
729 | (sha256 | |
730 | (base32 | |
731 | "05yxvdnkxr2ll94h6f2m5sn3gg7vrlm9nbdxgmj2g8cp8gfxpfkg")))) | |
732 | (build-system r-build-system) | |
733 | (propagated-inputs | |
734 | `(("r-ggplot2" ,r-ggplot2))) | |
735 | (home-page "https://cran.r-project.org/web/packages/microbenchmark/") | |
736 | (synopsis "Accurate timing functions for R") | |
737 | (description | |
738 | "This package provides infrastructure to accurately measure and compare | |
739 | the execution time of R expressions.") | |
740 | (license license:bsd-2))) | |
1cf1cbb0 VVP |
741 | |
742 | (define-public r-codetools | |
743 | (package | |
744 | (name "r-codetools") | |
745 | (version "0.2-14") | |
746 | (source (origin | |
747 | (method url-fetch) | |
748 | (uri (cran-uri "codetools" version)) | |
749 | (sha256 | |
750 | (base32 | |
751 | "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397")))) | |
752 | (build-system r-build-system) | |
753 | (home-page "https://cran.r-project.org/web/packages/codetools/index.html") | |
754 | (synopsis "Code analysis tools for R") | |
755 | (description "This package provides code analysis tools for R.") | |
756 | (license license:gpl3+))) | |
0661b4db VVP |
757 | |
758 | (define-public r-pryr | |
759 | (package | |
760 | (name "r-pryr") | |
761 | (version "0.1.2") | |
762 | (source (origin | |
763 | (method url-fetch) | |
764 | (uri (cran-uri "pryr" version)) | |
765 | (sha256 | |
766 | (base32 | |
767 | "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5")))) | |
768 | (build-system r-build-system) | |
769 | (propagated-inputs | |
770 | `(("r-stringr" ,r-stringr) | |
771 | ("r-codetools" ,r-codetools))) | |
772 | (native-inputs | |
773 | `(("r-rcpp" ,r-rcpp))) | |
774 | (home-page "https://github.com/hadley/pryr") | |
775 | (synopsis "Tools for computing on the R language") | |
776 | (description | |
777 | "This package provides useful tools to pry back the covers of R and | |
778 | understand the language at a deeper level.") | |
779 | (license license:gpl2))) | |
b668a95c VVP |
780 | |
781 | (define-public r-memoise | |
782 | (package | |
783 | (name "r-memoise") | |
784 | (version "0.2.1") | |
785 | (source (origin | |
786 | (method url-fetch) | |
787 | (uri (cran-uri "memoise" version)) | |
788 | (sha256 | |
789 | (base32 | |
790 | "19wm4b3kq6xva43kga3xydnl7ybl5mq7b4y2fczgzzjz63jd75y4")))) | |
791 | (build-system r-build-system) | |
792 | (propagated-inputs | |
793 | `(("r-digest" ,r-digest))) | |
794 | (home-page "http://github.com/hadley/memoise") | |
795 | (synopsis "Memoise functions for R") | |
796 | (description | |
797 | "This R package allows to cache the results of a function so that when | |
798 | you call it again with the same arguments it returns the pre-computed value.") | |
799 | (license license:expat))) | |
834f7ff3 VVP |
800 | |
801 | (define-public r-crayon | |
802 | (package | |
803 | (name "r-crayon") | |
804 | (version "1.3.1") | |
805 | (source (origin | |
806 | (method url-fetch) | |
807 | (uri (cran-uri "crayon" version)) | |
808 | (sha256 | |
809 | (base32 | |
810 | "0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm")))) | |
811 | (build-system r-build-system) | |
812 | (propagated-inputs | |
813 | `(("r-memoise" ,r-memoise))) | |
814 | (home-page "https://github.com/gaborcsardi/crayon") | |
815 | (synopsis "Colored terminal output for R") | |
816 | (description | |
817 | "Colored terminal output on terminals that support ANSI color and | |
818 | highlight codes. It also works in Emacs ESS. ANSI color support is | |
819 | automatically detected. Colors and highlighting can be combined and nested. | |
820 | New styles can also be created easily. This package was inspired by the | |
821 | \"chalk\" JavaScript project.") | |
822 | (license license:expat))) | |
5b9789a6 VVP |
823 | |
824 | (define-public r-testthat | |
825 | (package | |
826 | (name "r-testthat") | |
827 | (version "0.10.0") | |
828 | (source (origin | |
829 | (method url-fetch) | |
830 | (uri (cran-uri "testthat" version)) | |
831 | (sha256 | |
832 | (base32 | |
833 | "0b3akwcx5mv9dmi8vssbk91hr3yrrdxd2fm6zhr31fnyz8kjx4pw")))) | |
834 | (build-system r-build-system) | |
835 | (propagated-inputs | |
836 | `(("r-digest" ,r-digest) | |
837 | ("r-crayon" ,r-crayon))) | |
838 | (home-page "https://github.com/hadley/testthat") | |
839 | (synopsis "Unit testing for R") | |
840 | (description | |
841 | "This package provides a unit testing system for R designed to be fun, | |
842 | flexible and easy to set up.") | |
843 | (license license:expat))) | |
ffd4b478 VVP |
844 | |
845 | (define-public r-r6 | |
846 | (package | |
847 | (name "r-r6") | |
848 | (version "2.1.1") | |
849 | (source (origin | |
850 | (method url-fetch) | |
851 | (uri (cran-uri "R6" version)) | |
852 | (sha256 | |
853 | (base32 | |
854 | "16qq35bgxgswf989yvsqkb6fv7srpf8n8dv2s2c0z9n6zgmwq66m")))) | |
855 | (build-system r-build-system) | |
856 | (propagated-inputs | |
857 | `(("r-knitr" ,r-knitr) | |
858 | ("r-microbenchmark" ,r-microbenchmark) | |
859 | ("r-pryr" ,r-pryr) | |
860 | ("r-testthat" ,r-testthat) | |
861 | ("r-ggplot2" ,r-ggplot2) | |
862 | ("r-scales" ,r-scales))) | |
863 | (home-page "https://github.com/wch/R6/") | |
864 | (synopsis "Classes with reference semantics in R") | |
865 | (description | |
866 | "The R6 package allows the creation of classes with reference semantics, | |
867 | similar to R's built-in reference classes. Compared to reference classes, R6 | |
868 | classes are simpler and lighter-weight, and they are not built on S4 classes | |
869 | so they do not require the methods package. These classes allow public and | |
870 | private members, and they support inheritance, even when the classes are | |
871 | defined in different packages.") | |
872 | (license license:expat))) | |
2a3a8ae7 VVP |
873 | |
874 | (define-public r-dplyr | |
875 | (package | |
876 | (name "r-dplyr") | |
877 | (version "0.4.3") | |
878 | (source (origin | |
879 | (method url-fetch) | |
880 | (uri (cran-uri "dplyr" version)) | |
881 | (sha256 | |
882 | (base32 | |
883 | "1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc")))) | |
884 | (build-system r-build-system) | |
885 | (propagated-inputs | |
886 | `(("r-assertthat" ,r-assertthat) | |
887 | ("r-r6" ,r-r6) | |
888 | ("r-magrittr" ,r-magrittr) | |
889 | ("r-lazyeval" ,r-lazyeval) | |
890 | ("r-dbi" ,r-dbi))) | |
891 | (native-inputs | |
892 | `(("r-rcpp" ,r-rcpp) | |
893 | ("r-bh" ,r-bh))) | |
894 | (home-page "https://github.com/hadley/dplyr") | |
895 | (synopsis "Tools for working with data frames in R") | |
896 | (description | |
897 | "dplyr is the next iteration of plyr. It is focussed on tools for | |
898 | working with data frames. It has three main goals: 1) identify the most | |
899 | important data manipulation tools needed for data analysis and make them easy | |
900 | to use in R; 2) provide fast performance for in-memory data by writing key | |
901 | pieces of code in C++; 3) use the same code interface to work with data no | |
902 | matter where it is stored, whether in a data frame, a data table or | |
903 | database.") | |
904 | (license license:expat))) | |
91312ebe VVP |
905 | |
906 | (define-public r-chron | |
907 | (package | |
908 | (name "r-chron") | |
909 | (version "2.3-47") | |
910 | (source (origin | |
911 | (method url-fetch) | |
912 | (uri (cran-uri "chron" version)) | |
913 | (sha256 | |
914 | (base32 | |
915 | "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s")))) | |
916 | (build-system r-build-system) | |
917 | (home-page "http://cran.r-project.org/web/packages/chron") | |
918 | (synopsis "Chronological R objects which can handle dates and times") | |
919 | (description | |
920 | "This package provides chronological R objects which can handle dates and | |
921 | times.") | |
922 | (license license:gpl2))) | |
0e4e03f8 VVP |
923 | |
924 | (define-public r-data.table | |
925 | (package | |
926 | (name "r-data.table") | |
927 | (version "1.9.6") | |
928 | (source (origin | |
929 | (method url-fetch) | |
930 | (uri (cran-uri "data.table" version)) | |
931 | (sha256 | |
932 | (base32 | |
933 | "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g")))) | |
934 | (build-system r-build-system) | |
935 | (propagated-inputs | |
936 | `(("r-chron" ,r-chron))) | |
937 | (home-page "https://github.com/Rdatatable/data.table/wiki") | |
938 | (synopsis "Enhanced version of data.frame R object") | |
939 | (description | |
940 | "The R data.table package provides functions for fast aggregation of | |
941 | large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of | |
942 | columns by group, column listing and fast file reading.") | |
943 | (license license:gpl2+))) | |
9bc08aa0 RW |
944 | |
945 | (define-public python-patsy | |
946 | (package | |
947 | (name "python-patsy") | |
948 | (version "0.4.0") | |
949 | (source (origin | |
950 | (method url-fetch) | |
951 | (uri (string-append "https://pypi.python.org/packages/source/" | |
952 | "p/patsy/patsy-" version ".zip")) | |
953 | (sha256 | |
954 | (base32 | |
955 | "1kbs996xc2haxalmhd19rr1wh5fa4gbbxf81czkf5w4kam7h7wz4")))) | |
956 | (build-system python-build-system) | |
957 | (arguments | |
958 | `(#:phases | |
959 | (modify-phases %standard-phases | |
960 | (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))) | |
961 | (add-after 'unpack 'prevent-generation-of-egg-archive | |
962 | (lambda _ | |
963 | (substitute* "setup.py" | |
964 | (("from setuptools import setup") | |
965 | "from distutils.core import setup")) | |
966 | #t))))) | |
967 | (propagated-inputs | |
968 | `(("python-numpy" ,python-numpy) | |
969 | ("python-scipy" ,python-scipy) | |
970 | ("python-six" ,python-six))) | |
971 | (native-inputs | |
972 | `(("python-nose" ,python-nose) | |
973 | ("unzip" ,unzip))) | |
974 | (home-page "https://github.com/pydata/patsy") | |
975 | (synopsis "Describe statistical models and build design matrices") | |
976 | (description | |
977 | "Patsy is a Python package for describing statistical models and for | |
978 | building design matrices.") | |
979 | ;; The majority of the code is distributed under BSD-2. The module | |
980 | ;; patsy.compat contains code derived from the Python standard library, | |
981 | ;; and is covered by the PSFL. | |
982 | (license (list license:bsd-2 license:psfl)))) | |
983 | ||
984 | (define-public python2-patsy | |
985 | (let ((patsy (package-with-python2 python-patsy))) | |
986 | (package (inherit patsy) | |
987 | (native-inputs | |
988 | `(("python2-setuptools" ,python2-setuptools) | |
989 | ,@(package-native-inputs patsy))) | |
990 | (propagated-inputs | |
991 | `(("python2-numpy" ,python2-numpy) | |
992 | ("python2-scipy" ,python2-scipy) | |
993 | ,@(alist-delete "python-numpy" | |
994 | (alist-delete "python-scipy" | |
995 | (package-propagated-inputs patsy)))))))) | |
37fdba7e RW |
996 | |
997 | (define-public python-statsmodels | |
998 | (package | |
999 | (name "python-statsmodels") | |
1000 | (version "0.6.1") | |
1001 | (source | |
1002 | (origin | |
1003 | (method url-fetch) | |
1004 | (uri (string-append "https://pypi.python.org/packages/source/" | |
1005 | "s/statsmodels/statsmodels-" version ".tar.gz")) | |
1006 | (sha256 | |
1007 | (base32 | |
1008 | "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy")))) | |
1009 | (build-system python-build-system) | |
1010 | (arguments | |
1011 | `(#:phases | |
1012 | (modify-phases %standard-phases | |
1013 | ;; tests must be run after installation | |
1014 | (delete 'check) | |
1015 | (add-after 'unpack 'set-matplotlib-backend-to-agg | |
1016 | (lambda _ | |
1017 | ;; Set the matplotlib backend to Agg to avoid problems using the | |
1018 | ;; GTK backend without a display. | |
1019 | (substitute* (find-files "statsmodels/graphics/tests" "\\.py") | |
1020 | (("import matplotlib\\.pyplot as plt" line) | |
1021 | (string-append "import matplotlib;matplotlib.use('Agg');" | |
1022 | line))) | |
1023 | #t)) | |
1024 | (add-after 'install 'check | |
1025 | (lambda _ | |
1026 | (with-directory-excursion "/tmp" | |
1027 | (zero? (system* "nosetests" | |
1028 | "--stop" | |
1029 | "-v" "statsmodels")))))))) | |
1030 | (propagated-inputs | |
1031 | `(("python-numpy" ,python-numpy) | |
1032 | ("python-scipy" ,python-scipy) | |
1033 | ("python-pandas" ,python-pandas) | |
1034 | ("python-patsy" ,python-patsy) | |
1035 | ("python-matplotlib" ,python-matplotlib))) | |
1036 | (native-inputs | |
1037 | `(("python-cython" ,python-cython) | |
1038 | ("python-nose" ,python-nose) | |
1039 | ("python-sphinx" ,python-sphinx))) | |
1040 | (home-page "http://statsmodels.sourceforge.net/") | |
1041 | (synopsis "Statistical modeling and econometrics in Python") | |
1042 | (description | |
1043 | "Statsmodels is a Python package that provides a complement to scipy for | |
1044 | statistical computations including descriptive statistics and estimation and | |
1045 | inference for statistical models.") | |
1046 | (license license:bsd-3))) | |
1047 | ||
1048 | (define-public python2-statsmodels | |
1049 | (let ((stats (package-with-python2 python-statsmodels))) | |
1050 | (package (inherit stats) | |
1051 | (propagated-inputs | |
1052 | `(("python2-numpy" ,python2-numpy) | |
1053 | ("python2-scipy" ,python2-scipy) | |
1054 | ("python2-pandas" ,python2-pandas) | |
1055 | ("python2-patsy" ,python2-patsy) | |
1056 | ("python2-matplotlib" ,python2-matplotlib))) | |
1057 | (native-inputs | |
1058 | `(("python2-setuptools" ,python2-setuptools) | |
1059 | ,@(package-native-inputs stats)))))) | |
67a167fd RW |
1060 | |
1061 | (define-public r-xml2 | |
1062 | (package | |
1063 | (name "r-xml2") | |
1064 | (version "0.1.2") | |
1065 | (source | |
1066 | (origin | |
1067 | (method url-fetch) | |
1068 | (uri (cran-uri "xml2" version)) | |
1069 | (sha256 | |
1070 | (base32 | |
1071 | "0jjilz36h7vbdbkpvjnja1vgjf6d1imql3z4glqn2m2b74w5qm4c")))) | |
1072 | (build-system r-build-system) | |
1073 | (inputs | |
1074 | `(("libxml2" ,libxml2))) | |
1075 | (propagated-inputs | |
1076 | `(("r-rcpp" ,r-rcpp) | |
1077 | ("r-bh" ,r-bh))) | |
1078 | (home-page "https://github.com/hadley/xml2") | |
1079 | (synopsis "Parse XML with R") | |
1080 | (description | |
1081 | "This package provides a simple, consistent interface to working with XML | |
1082 | files in R. It is built on top of the libxml2 C library.") | |
1083 | (license license:gpl2+))) | |
6140747f RW |
1084 | |
1085 | (define-public r-rversions | |
1086 | (package | |
1087 | (name "r-rversions") | |
1088 | (version "1.0.2") | |
1089 | (source (origin | |
1090 | (method url-fetch) | |
1091 | (uri (cran-uri "rversions" version)) | |
1092 | (sha256 | |
1093 | (base32 | |
1094 | "0xmi461g1rf5ngb7r1sri798jn6icld1xq25wj9jii2ca8j8xv68")))) | |
1095 | (build-system r-build-system) | |
1096 | (propagated-inputs | |
1097 | `(("r-curl" ,r-curl) | |
1098 | ("r-xml2" ,r-xml2))) | |
1099 | (home-page "https://github.com/metacran/rversions") | |
1100 | (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") | |
1101 | (description | |
1102 | "This package provides functions to query the main R repository to find | |
1103 | the versions that @code{r-release} and @code{r-oldrel} refer to, and also all | |
1104 | previous R versions and their release dates.") | |
1105 | (license license:expat))) | |
1a77eccd RW |
1106 | |
1107 | (define-public r-whisker | |
1108 | (package | |
1109 | (name "r-whisker") | |
1110 | (version "0.3-2") | |
1111 | (source (origin | |
1112 | (method url-fetch) | |
1113 | (uri (cran-uri "whisker" version)) | |
1114 | (sha256 | |
1115 | (base32 | |
1116 | "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28")))) | |
1117 | (build-system r-build-system) | |
1118 | (home-page "http://github.com/edwindj/whisker") | |
1119 | (synopsis "Logicless mustache templating for R") | |
1120 | (description | |
1121 | "This package provides logicless templating, with a syntax that is not | |
1122 | limited to R.") | |
1123 | (license license:gpl3+))) | |
13d083af RW |
1124 | |
1125 | (define-public r-brew | |
1126 | (package | |
1127 | (name "r-brew") | |
1128 | (version "1.0-6") | |
1129 | (source (origin | |
1130 | (method url-fetch) | |
1131 | (uri (cran-uri "brew" version)) | |
1132 | (sha256 | |
1133 | (base32 | |
1134 | "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp")))) | |
1135 | (build-system r-build-system) | |
1136 | (home-page "http://cran.r-project.org/web/packages/brew") | |
1137 | (synopsis "Templating framework for report generation") | |
1138 | (description | |
1139 | "The brew package implements a templating framework for mixing text and R | |
1140 | code for report generation. The template syntax is similar to PHP, Ruby's erb | |
1141 | module, Java Server Pages, and Python's psp module.") | |
1142 | (license license:gpl2+))) | |
167c9882 RW |
1143 | |
1144 | (define-public r-roxygen2 | |
1145 | (package | |
1146 | (name "r-roxygen2") | |
1147 | (version "5.0.0") | |
1148 | (source (origin | |
1149 | (method url-fetch) | |
1150 | (uri (cran-uri "roxygen2" version)) | |
1151 | (sha256 | |
1152 | (base32 | |
1153 | "0xjdphjs7l1v71lylmqgp76cbcxzvm9z1a40jgkdwvz072nn08vr")))) | |
1154 | (build-system r-build-system) | |
1155 | (propagated-inputs | |
1156 | `(("r-brew" ,r-brew) | |
1157 | ("r-digest" ,r-digest) | |
1158 | ("r-rcpp" ,r-rcpp) | |
1159 | ("r-stringi" ,r-stringi) | |
1160 | ("r-stringr" ,r-stringr))) | |
1161 | (home-page "https://github.com/klutometis/roxygen") | |
1162 | (synopsis "In-source documentation system for R") | |
1163 | (description | |
1164 | "Roxygen2 is a Doxygen-like in-source documentation system for Rd, | |
1165 | collation, and NAMESPACE files.") | |
1166 | (license license:gpl2+))) | |
681e03c1 RW |
1167 | |
1168 | (define-public r-httr | |
1169 | (package | |
1170 | (name "r-httr") | |
1171 | (version "1.0.0") | |
1172 | (source (origin | |
1173 | (method url-fetch) | |
1174 | (uri (cran-uri "httr" version)) | |
1175 | (sha256 | |
1176 | (base32 | |
1177 | "1yprw8p4g8026jhravgg1hdwj1g51cpdgycyr5a58jwm4i5f79cq")))) | |
1178 | (build-system r-build-system) | |
1179 | (propagated-inputs | |
1180 | `(("r-curl" ,r-curl) | |
1181 | ("r-digest" ,r-digest) | |
1182 | ("r-jsonlite" ,r-jsonlite) | |
1183 | ("r-mime" ,r-mime) | |
1184 | ("r-r6" ,r-r6) | |
1185 | ("r-stringr" ,r-stringr))) | |
1186 | (home-page "https://github.com/hadley/httr") | |
1187 | (synopsis "Tools for working with URLs and HTTP") | |
1188 | (description | |
1189 | "The aim of httr is to provide a wrapper for RCurl customised to the | |
1190 | demands of modern web APIs. It provides useful tools for working with HTTP | |
1191 | organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration | |
1192 | functions make it easy to control additional request components.") | |
1193 | (license license:expat))) | |
035711f1 RW |
1194 | |
1195 | (define-public r-git2r | |
1196 | (package | |
1197 | (name "r-git2r") | |
1198 | (version "0.11.0") | |
1199 | (source (origin | |
1200 | (method url-fetch) | |
1201 | (uri (cran-uri "git2r" version)) | |
1202 | (sha256 | |
1203 | (base32 | |
1204 | "1h5ag8sm512jsn2sp4yhiqspc7hjq5y8z0kqz24sdznxa3b7rpn9")))) | |
1205 | (build-system r-build-system) | |
1206 | ;; This R package contains modified sources of libgit2. This modified | |
1207 | ;; version of libgit2 is built as the package is built. Hence libgit2 is | |
1208 | ;; not among the inputs of this package. | |
1209 | (inputs | |
1210 | `(("libssh2" ,libssh2) | |
1211 | ("openssl" ,openssl) | |
1212 | ("zlib" ,zlib))) | |
1213 | (home-page "https://github.com/ropensci/git2r") | |
1214 | (synopsis "Access Git repositories with R") | |
1215 | (description | |
1216 | "This package provides an R interface to the libgit2 library, which is a | |
1217 | pure C implementation of the Git core methods.") | |
1218 | ;; GPLv2 only with linking exception. | |
1219 | (license license:gpl2))) | |
81a4228b RW |
1220 | |
1221 | (define-public r-rstudioapi | |
1222 | (package | |
1223 | (name "r-rstudioapi") | |
1224 | (version "0.3.1") | |
1225 | (source (origin | |
1226 | (method url-fetch) | |
1227 | (uri (cran-uri "rstudioapi" version)) | |
1228 | (sha256 | |
1229 | (base32 | |
1230 | "0q7671d924nzqsqhs8d9p7l907bcam56wjwm7vvz44xgj0saj8bs")))) | |
1231 | (build-system r-build-system) | |
1232 | (home-page "http://cran.r-project.org/web/packages/rstudioapi") | |
1233 | (synopsis "Safely access the RStudio API") | |
1234 | (description | |
1235 | "This package provides functions to access the RStudio API and provide | |
1236 | informative error messages when it's not available.") | |
1237 | (license license:expat))) | |
d6e21589 RW |
1238 | |
1239 | (define-public r-devtools | |
1240 | (package | |
1241 | (name "r-devtools") | |
1242 | (version "1.9.1") | |
1243 | (source (origin | |
1244 | (method url-fetch) | |
1245 | (uri (cran-uri "devtools" version)) | |
1246 | (sha256 | |
1247 | (base32 | |
1248 | "10ycx3kkiz5x8nmgw31d9wa5hhlx2fhda2nqzxfrczqpz1jik6ci")))) | |
1249 | (build-system r-build-system) | |
1250 | (propagated-inputs | |
1251 | `(("r-curl" ,r-curl) | |
1252 | ("r-digest" ,r-digest) | |
1253 | ("r-evaluate" ,r-evaluate) | |
1254 | ("r-git2r" ,r-git2r) | |
1255 | ("r-httr" ,r-httr) | |
1256 | ("r-jsonlite" ,r-jsonlite) | |
1257 | ("r-memoise" ,r-memoise) | |
1258 | ("r-roxygen2" ,r-roxygen2) | |
1259 | ("r-rstudioapi" ,r-rstudioapi) | |
1260 | ("r-rversions" ,r-rversions) | |
1261 | ("r-whisker" ,r-whisker))) | |
1262 | (home-page "https://github.com/hadley/devtools") | |
1263 | (synopsis "Tools to make developing R packages easier") | |
1264 | (description "The devtools package is a collection of package development | |
1265 | tools to simplify the devolpment of R packages.") | |
1266 | (license license:gpl2+))) |