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47525 Commits

Author SHA1 Message Date
Kei Kebreau b888396d70
gnu: gcl: Enable tests. 
* gnu/packages/lisp.scm (gcl)[arguments]: Remove #:tests? flag and set the
  #:test-target to "ansi-tests/test_results".
 2019-09-02 13:46:06 -04:00
Pierre Neidhardt cc16f90a07
gnu: Add cl-hooks. 
* gnu/packages/lisp.scm (cl-hooks, ecl-cl-hooks, sbcl-cl-hooks): New variables.
 2019-09-02 17:09:28 +02:00
Pierre Neidhardt 0b2396b6c6
gnu: sbcl-fiveam: Update to 1.4.1. 
* gnu/packages/lisp.scm (sbcl-fiveam): Update to 1.4.1.
 2019-09-02 17:09:28 +02:00
Pierre Neidhardt 0403d01f01
gnu: Add net.didierverna.asdf-flv. 
* gnu/packages/lisp.scm (cl-net.didierverna.asdf-flv,
  ecl-net.didierverna.asdf-flv, sbcl-net.didierverna.asdf-flv): New variables.
 2019-09-02 17:09:28 +02:00
Ludovic Courtès 55549c7b9b
lint: Add 'archival' checker. 
* guix/lint.scm (check-archival): New procedure.
(%network-dependent-checkers): Add 'archival' checker.
* tests/lint.scm ("archival: missing content")
("archival: content available")
("archival: missing revision")
("archival: revision available")
("archival: rate limit reached"): New tests.
* doc/guix.texi (Invoking guix lint): Document it.
 2019-09-02 15:25:01 +02:00
Ludovic Courtès d370cc7319
swh: Make 'commit-id?' public. 
* guix/swh.scm (commit-id?): Make public.
 2019-09-02 15:25:01 +02:00
Ludovic Courtès ba1c1853a7
swh: Add hooks for rate limiting handling. 
* guix/swh.scm (%allow-request?, %save-rate-limit-reset-time)
(%general-rate-limit-reset-time): New variables.
(request-rate-limit-reached?, update-rate-limit-reset-time!): New
procedures.
(call): Call '%allow-request?'.  Change 'swh-error' protocol to pass
METHOD in addition to URL.
* tests/swh.scm ("rate limit reached")
("%allow-request? and request-rate-limit-reached?"): New tests.
 2019-09-02 15:25:01 +02:00
Ludovic Courtès 9323ab550f
tests: 'with-http-server' accepts multiple responses. 
* guix/tests/http.scm (call-with-http-server): Replace 'code' and 'data'
parameters with 'responses+data'.  Compute RESPONSES as a function of
that.  Remove #:headers parameter.
[http-write]: Quit only when RESPONSES is empty.
[server-body]: Get the response and data from RESPONSES, and set it to
point to the rest.
(with-http-server): Adjust accordingly.
* tests/derivations.scm ("'download' built-in builder")
("'download' built-in builder, invalid hash")
("'download' built-in builder, not found")
("'download' built-in builder, check mode"): Adjust to new
'with-http-server' interface.
* tests/lint.scm ("home-page: 200")
("home-page: 200 but short length")
("home-page: 404", "home-page: 301, invalid"):
("home-page: 301 -> 200", "home-page: 301 -> 404")
("source: 200", "source: 200 but short length")
("source: 404", "source: 404 and 200")
("source: 301 -> 200", "source: 301 -> 404"):
("github-url", github-url): Likewise.
* tests/swh.scm (with-json-result)
("lookup-origin, not found"): Likewise.
 2019-09-02 15:25:01 +02:00
Ludovic Courtès d34e9114e6
doc: Explain that "guix import" and "guix refresh" may need GnuPG. 
Fixes <https://bugs.gnu.org/36051>.
Reported by Jesse Gibbons <jgibbons2357@gmail.com>.

* doc/guix.texi (Invoking guix import, Invoking guix refresh): Mention
that GnuPG must be installed.
 2019-09-02 15:25:00 +02:00
Efraim Flashner eb98d5a83c
gnu: Add rust-heapsize-plugin, rust-language-tags. 
* gnu/packages/crates-io.scm (rust-heapsize-plugin, rust-language-tags):
New variables.
 2019-09-02 15:54:59 +03:00
Efraim Flashner 7439498366
gnu: Add rust-heapsize-0.3. 
* gnu/packages/crates-io.scm (rust-heapsize-0.3): New variable.
 2019-09-02 15:54:59 +03:00
Efraim Flashner bb41995dc7
gnu: Add rust-owning-ref. 
* gnu/packages/crates-io.scm (rust-owning-ref): New variable.
 2019-09-02 15:54:59 +03:00
Efraim Flashner 44b6397a58
gnu: Add rust-scoped-threadpool. 
* gnu/packages/crates-io.scm (rust-scoped-threadpool): New variable.
 2019-09-02 15:54:58 +03:00
Efraim Flashner 76ee4446fd
gnu: Add rust-redox-syscall, rust-thread-id. 
* gnu/packages/crates-io.scm (rust-redox-syscall, rust-thread-id): New
variables.
 2019-09-02 15:54:58 +03:00
Ricardo Wurmus 8786fec485
import: cran: Only use the git import with what looks like a URL. 
* guix/import/cran.scm (fetch-description): Abort if the argument does not
look like a URL.
 2019-09-02 14:46:04 +02:00
Ricardo Wurmus c7358ac4fc
import: cran: Retry failed git imports on Bioconductor. 
* guix/import/cran.scm (cran->guix-package): Retry failed git imports on
Bioconductor.
 2019-09-02 14:45:17 +02:00
Ricardo Wurmus e107ccea84
gnu: r-ldblock: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.2.
[propagated-inputs]: Remove r-erma; add r-ensdb-hsapiens-v75, r-ensembldb, and
r-httr.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus b58b4410e2
gnu: r-mixomics: Update to 6.8.2. 
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.2.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 9b275285e9
gnu: r-fgsea: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.10.1.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 32fcd898f0
gnu: r-seurat: Update to 3.1.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.0.
[propagated-inputs]: Add r-leiden, r-rcppannoy, and r-uwot.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 91addfe05c
gnu: r-rtracklayer: Update to 1.44.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.3.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 2c7a32c2ac
gnu: r-biomart: Update to 2.40.4. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.4.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus e5bc6fce19
gnu: r-annotationdbi: Update to 1.46.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.1.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus aea33b475b
gnu: r-iranges: Update to 2.18.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.2.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus df0f876ee4
gnu: r-pbapply: Update to 1.4-2. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.4-2.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 21890aad50
gnu: r-rmarkdown: Update to 1.15. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.15.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus a1a7afc06c
gnu: r-hms: Update to 0.5.1. 
* gnu/packages/statistics.scm (r-hms): Update to 0.5.1.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus b21620bb47
gnu: r-whisker: Update to 0.4. 
* gnu/packages/statistics.scm (r-whisker): Update to 0.4.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 560f7c949a
gnu: r-chron: Update to 2.3-54. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-54.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 8e28535d0b
gnu: Add r-leiden. 
* gnu/packages/cran.scm (r-leiden): New variable.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 8bcd6c953a
gnu: r-umap: Update to 0.2.3.1. 
* gnu/packages/cran.scm (r-umap): Update to 0.2.3.1.
[propagated-inputs]: Add r-openssl.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus 7a90573fd0
gnu: r-enrichr: Update to 2.1. 
* gnu/packages/cran.scm (r-enrichr): Update to 2.1.
 2019-09-02 14:40:56 +02:00
Ricardo Wurmus d64ac92f6c
gnu: r-dalex: Update to 0.4.7. 
* gnu/packages/cran.scm (r-dalex): Update to 0.4.7.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 466e68b4b2
gnu: r-ggforce: Update to 0.3.1. 
* gnu/packages/cran.scm (r-ggforce): Update to 0.3.1.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus e768b33936
gnu: r-bookdown: Update to 0.13. 
* gnu/packages/cran.scm (r-bookdown): Update to 0.13.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 87b4381584
gnu: r-tdthap: Update to 1.1-11. 
* gnu/packages/cran.scm (r-tdthap): Update to 1.1-11.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus dfe4c8c405
gnu: r-units: Update to 0.6-4. 
* gnu/packages/cran.scm (r-units): Update to 0.6-4.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 5feaa77591
gnu: r-wgaim: Update to 2.0-0. 
* gnu/packages/cran.scm (r-wgaim): Update to 2.0-0.
[propagated-inputs]: Remove r-lattice; add r-ggplot2.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 530404083a
gnu: r-apcluster: Update to 1.4.8. 
* gnu/packages/cran.scm (r-apcluster): Update to 1.4.8.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 553742fa98
gnu: r-lavaan: Update to 0.6-5. 
* gnu/packages/cran.scm (r-lavaan): Update to 0.6-5.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus e31eb738f7
gnu: r-ggextra: Update to 0.9. 
* gnu/packages/cran.scm (r-ggextra): Update to 0.9.
[propagated-inputs]: Add r-r6.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 6c81cc885d
gnu: r-fields: Update to 9.8-6. 
* gnu/packages/cran.scm (r-fields): Update to 9.8-6.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 4f1c668d31
gnu: r-rgl: Update to 0.100.30. 
* gnu/packages/cran.scm (r-rgl): Update to 0.100.30.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 0eb284350e
gnu: r-afex: Update to 0.25-1. 
* gnu/packages/cran.scm (r-afex): Update to 0.25-1.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 084ea3481b
gnu: r-summarytools: Update to 0.9.4. 
* gnu/packages/cran.scm (r-summarytools): Update to 0.9.4.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 1656a4259b
gnu: r-coin: Update to 1.3-1. 
* gnu/packages/cran.scm (r-coin): Update to 1.3-1.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus a13f81dde7
gnu: r-libcoin: Update to 1.0-5. 
* gnu/packages/cran.scm (r-libcoin): Update to 1.0-5.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 9c2d978041
gnu: r-magick: Update to 2.2. 
* gnu/packages/cran.scm (r-magick): Update to 2.2.
 2019-09-02 14:40:55 +02:00
Ricardo Wurmus 761f4764f9
gnu: r-raster: Update to 3.0-2. 
* gnu/packages/cran.scm (r-raster): Update to 3.0-2.
 2019-09-02 14:40:54 +02:00
Ricardo Wurmus 59fd6915c8
gnu: r-zip: Update to 2.0.4. 
* gnu/packages/cran.scm (r-zip): Update to 2.0.4.
 2019-09-02 14:40:54 +02:00