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Ludovic Courtès 73b08ad1a3
utils: 'edit-expression' copies part of the original source map. 
* guix/utils.scm (source-location-key/stamp): New procedure.
(go-to-location): Use it.
(move-source-location-map!): New procedure.
(edit-expression): Call it.
 2021-07-11 00:49:15 +02:00
Ludovic Courtès f05433f208
utils: 'edit-expression' modifies the file only if necessary. 
* guix/utils.scm (edit-expression): Check whether STR* equals STR.
 2021-07-11 00:49:15 +02:00
Ludovic Courtès ef1432f064
utils: Add 'go-to-location' with source location caching. 
* guix/utils.scm (%source-location-map): New variable.
(go-to-location): New procedure.
(edit-expression): Use it instead of custom loop.
* guix/packages.scm (package-field-location)[goto]: Remove.
Use 'go-to-location' instead of 'goto'.
 2021-07-11 00:49:15 +02:00
Ludovic Courtès 4dcc606766
utils: 'edit-expression' no longer leaks file ports. 
* guix/utils.scm (edit-expression): Use 'call-with-input-file' to make
sure IN gets closed.
 2021-07-11 00:49:14 +02:00
Ludovic Courtès 2f73ea3487
gnu: Change inputs of core packages to plain lists. 
This is transparent: the resulting derivations are unchanged.

* gnu/packages/base.scm (grep, sed, tar, patch, diffutils, glibc/hurd-headers)
(coreutils, gnu-make, make-glibc-utf8-locales): Change input fields to
plain package lists and use 'modify-inputs'.
* gnu/packages/guile.scm (guile-1.8, guile-json-1, guile-json-3)
(guile-gdbm-ffi, guile-sqlite3, guile-bytestructures)
(guile-git, guile-zlib, guile-lzlib, guile-zstd, guile-next): Likewise.
* gnu/packages/mes.scm (nyacc-0.86, nyacc-0.99)
(nyacc, nyacc-1.00.2, mes-0.19, mes, m2-planet): Likewise.
 2021-07-11 00:49:14 +02:00
Ludovic Courtès 04b2f3dd80
packages: Add 'modify-inputs'. 
* guix/packages.scm (inputs-sans-labels, replace-input): New procedures.
(prepend, replace, modify-inputs): New macros.
* doc/guix.texi (Defining Package Variants): Document 'modify-inputs'.
* dir-locals.el: Add 'modify-inputs' and its keywords.
 2021-07-11 00:49:14 +02:00
Ludovic Courtès ba32f63638
packages: Add 'lookup-package-input' & co. 
* guix/packages.scm (lookup-input, lookup-package-input)
(lookup-package-native-input, lookup-package-propagated-input)
(lookup-package-direct-input): New procedures.
* doc/guix.texi (package Reference): Document them.
 2021-07-11 00:49:14 +02:00
Ludovic Courtès b7f1b4c1d0
lint: Add 'input-labels' checker. 
* guix/lint.scm (check-input-labels): New procedure.
(%local-checkers): Add 'input-labels' checker.
* tests/lint.scm ("input labels: no warnings")
("input labels: one warning"): New tests.
* doc/guix.texi (Invoking guix lint): Mention it.
 2021-07-11 00:49:14 +02:00
Ludovic Courtès 8524349f78
packages: Allow inputs to be plain package lists. 
* guix/packages.scm (add-input-label, sanitize-inputs): New procedures.
(<package>)[inputs, propagated-inputs, native-inputs]: Add 'sanitize' property.
* doc/guix.texi (Defining Packages, package Reference):
(Defining Package Variants): Adjust examples accordingly.
* tests/packages.scm ("transaction-upgrade-entry, zero upgrades, propagated inputs")
("transaction-upgrade-entry, grafts")
("package-transitive-inputs")
("package-transitive-supported-systems")
("package-closure")
("supported-package?")
("package-derivation, inputs deduplicated")
("package-transitive-native-search-paths")
("package-grafts, indirect grafts")
("package-grafts, indirect grafts, propagated inputs")
("package-grafts, same replacement twice")
("package-grafts, dependency on several outputs")
("replacement also grafted")
("package->bag, sensitivity to %current-target-system")
("package->bag, propagated inputs")
("package->bag, sensitivity to %current-system")
("package-input-rewriting/spec, identity")
("package-input-rewriting, identity"): Use the label-less input style.
 2021-07-11 00:49:14 +02:00
Ludovic Courtès 8be1632199
records: Support field sanitizers. 
* guix/records.scm (make-syntactic-constructor): Add #:sanitizers.
[field-sanitizer]: New procedure.
[wrap-field-value]: Honor F's sanitizer.
(define-record-type*)[field-sanitizer]: New procedure.
Pass #:sanitizer to 'make-syntactic-constructor'.
* tests/records.scm ("define-record-type* & sanitize")
("define-record-type* & sanitize & thunked"): New tests.
 2021-07-11 00:49:14 +02:00
Ludovic Courtès 2a3cd4ee35
environment: Adjust to earlier 'gcc-bootstrap' search paths changes. 
This is a followup to fe6775f52b.

* tests/guix-environment.sh: Expect C_INCLUDE_PATH rather than CPATH in
environment containing 'gcc-bootstrap'.
 2021-07-11 00:46:54 +02:00
Ludovic Courtès 152b167cfa
pack: Adjust test to earlier <compressor> changes. 
This is a followup to 5a0997ef7f, which
broke the "self-contained tarball" test.

* tests/pack.scm (%gzip-compressor): Add 'list' in third field.
 2021-07-11 00:39:56 +02:00
Ricardo Wurmus 6db1afed3d
gnu: r-car: Update to 3.0-11. 
* gnu/packages/statistics.scm (r-car): Update to 3.0-11.
 2021-07-10 21:35:36 +02:00
Ricardo Wurmus 762b1de334
gnu: r-lme4: Update to 1.1-27.1. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-27.1.
 2021-07-10 21:35:36 +02:00
Ricardo Wurmus c7e86b9af6
gnu: r-quantreg: Update to 5.86. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.86.
 2021-07-10 21:35:36 +02:00
Ricardo Wurmus 4e7bf05978
gnu: r-plotly: Update to 4.9.4.1. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.9.4.1.
 2021-07-10 21:35:36 +02:00
Ricardo Wurmus 85738e4566
gnu: r-mvtnorm: Update to 1.1-2. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.1-2.
 2021-07-10 21:35:36 +02:00
Ricardo Wurmus 3a68bf166d
gnu: r-glmnet: Update to 4.1-2. 
* gnu/packages/statistics.scm (r-glmnet): Update to 4.1-2.
 2021-07-10 21:35:36 +02:00
Ricardo Wurmus 01d2ac1b7b
gnu: r-rmarkdown: Update to 2.9. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.9.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 47ffcaf1d6
gnu: r-devtools: Update to 2.4.2. 
* gnu/packages/statistics.scm (r-devtools): Update to 2.4.2.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 88d0cc0e77
gnu: r-ade4: Update to 1.7-17. 
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-17.
[propagated-inputs]: Remove r-progress.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus b5912cdea5
gnu: r-dplyr: Update to 1.0.7. 
* gnu/packages/statistics.scm (r-dplyr): Update to 1.0.7.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 7dd5f33d31
gnu: r-testthat: Update to 3.0.4. 
* gnu/packages/statistics.scm (r-testthat): Update to 3.0.4.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 756449c642
gnu: r-mime: Update to 0.11. 
* gnu/packages/statistics.scm (r-mime): Update to 0.11.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus c4b65d50e3
gnu: r-ggplot2: Update to 3.3.5. 
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.5.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 7ca365a304
gnu: r-vroom: Update to 1.5.2. 
* gnu/packages/cran.scm (r-vroom): Update to 1.5.2.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 15507dc5ab
gnu: r-btm: Update to 0.3.6. 
* gnu/packages/cran.scm (r-btm): Update to 0.3.6.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 05334f818d
gnu: r-eyelinker: Update to 0.2.1. 
* gnu/packages/cran.scm (r-eyelinker): Update to 0.2.1.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 76ea5b92ed
gnu: r-stars: Update to 0.5-3. 
* gnu/packages/cran.scm (r-stars): Update to 0.5-3.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 9e7cae489b
gnu: r-ragg: Update to 1.1.3. 
* gnu/packages/cran.scm (r-ragg): Update to 1.1.3.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus fb034eee87
gnu: r-textshaping: Update to 0.3.5. 
* gnu/packages/cran.scm (r-textshaping): Update to 0.3.5.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 494d72e956
gnu: r-mlr3misc: Update to 0.9.2. 
* gnu/packages/cran.scm (r-mlr3misc): Update to 0.9.2.
 2021-07-10 21:35:35 +02:00
Ricardo Wurmus 59355a551a
gnu: r-diversitree: Update to 0.9-16. 
* gnu/packages/cran.scm (r-diversitree): Update to 0.9-16.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 53bff86803
gnu: r-slider: Update to 0.2.2. 
* gnu/packages/cran.scm (r-slider): Update to 0.2.2.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 10bbb68d30
gnu: r-cpp11: Update to 0.3.1. 
* gnu/packages/cran.scm (r-cpp11): Update to 0.3.1.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 933986d42f
gnu: r-spatstat: Update to 2.2-0. 
* gnu/packages/cran.scm (r-spatstat): Update to 2.2-0.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 69eb17751b
gnu: r-spatstat-linnet: Update to 2.2-1. 
* gnu/packages/cran.scm (r-spatstat-linnet): Update to 2.2-1.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 86b4c08fd7
gnu: r-spatstat-core: Update to 2.2-0. 
* gnu/packages/cran.scm (r-spatstat-core): Update to 2.2-0.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus b29b3b4bc8
gnu: r-spatstat-geom: Update to 2.2-0. 
* gnu/packages/cran.scm (r-spatstat-geom): Update to 2.2-0.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus de77e21eed
gnu: r-spatstat-utils: Update to 2.2-0. 
* gnu/packages/cran.scm (r-spatstat-utils): Update to 2.2-0.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus c13d544d67
gnu: r-rismed: Update to 2.3.0. 
* gnu/packages/cran.scm (r-rismed): Update to 2.3.0.
[propagated-inputs]: Add r-httr and r-xml2.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 8afab27a97
gnu: r-optimx: Update to 2021-6.12. 
* gnu/packages/cran.scm (r-optimx): Update to 2021-6.12.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 43d1119db9
gnu: r-zvcv: Update to 2.1.1. 
* gnu/packages/cran.scm (r-zvcv): Update to 2.1.1.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 91bb4f5228
gnu: r-tam: Update to 3.7-16. 
* gnu/packages/cran.scm (r-tam): Update to 3.7-16.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 6f9530ca13
gnu: r-openmx: Update to 2.19.6. 
* gnu/packages/cran.scm (r-openmx): Update to 2.19.6.
[propagated-inputs]: Add r-rcppparallel.
 2021-07-10 21:35:34 +02:00
Ricardo Wurmus 85c613434c
gnu: r-regsem: Update to 1.8.0. 
* gnu/packages/cran.scm (r-regsem): Update to 1.8.0.
 2021-07-10 21:35:33 +02:00
Ricardo Wurmus 7668566ed6
gnu: r-semtools: Update to 0.5-5. 
* gnu/packages/cran.scm (r-semtools): Update to 0.5-5.
[propagated-inputs]: Add r-pbivnorm.
 2021-07-10 21:35:33 +02:00
Ricardo Wurmus 026bd0b219
gnu: r-matrixcalc: Update to 1.0-4. 
* gnu/packages/cran.scm (r-matrixcalc): Update to 1.0-4.
 2021-07-10 21:35:33 +02:00
Ricardo Wurmus ed5f29921d
gnu: r-icge: Update to 0.4.1. 
* gnu/packages/cran.scm (r-icge): Update to 0.4.1.
[propagated-inputs]: Add r-fastcluster.
 2021-07-10 21:35:33 +02:00
Ricardo Wurmus f1d6a1fe0f
gnu: r-imager: Update to 0.42.10. 
* gnu/packages/cran.scm (r-imager): Update to 0.42.10.
 2021-07-10 21:35:33 +02:00