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2019-09-02swh: Add hooks for rate limiting handling.Ludovic Courtès
* 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.
2019-09-02tests: 'with-http-server' accepts multiple responses.Ludovic Courtès
* 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.
2019-09-02doc: Explain that "guix import" and "guix refresh" may need GnuPG.Ludovic Courtès
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.
2019-09-02gnu: Add rust-heapsize-plugin, rust-language-tags.Efraim Flashner
* gnu/packages/crates-io.scm (rust-heapsize-plugin, rust-language-tags): New variables.
2019-09-02gnu: Add rust-heapsize-0.3.Efraim Flashner
* gnu/packages/crates-io.scm (rust-heapsize-0.3): New variable.
2019-09-02gnu: Add rust-owning-ref.Efraim Flashner
* gnu/packages/crates-io.scm (rust-owning-ref): New variable.
2019-09-02gnu: Add rust-scoped-threadpool.Efraim Flashner
* gnu/packages/crates-io.scm (rust-scoped-threadpool): New variable.
2019-09-02gnu: Add rust-redox-syscall, rust-thread-id.Efraim Flashner
* gnu/packages/crates-io.scm (rust-redox-syscall, rust-thread-id): New variables.
2019-09-02import: cran: Only use the git import with what looks like a URL.Ricardo Wurmus
* guix/import/cran.scm (fetch-description): Abort if the argument does not look like a URL.
2019-09-02import: cran: Retry failed git imports on Bioconductor.Ricardo Wurmus
* guix/import/cran.scm (cran->guix-package): Retry failed git imports on Bioconductor.
2019-09-02gnu: r-ldblock: Update to 1.14.2.Ricardo Wurmus
* 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.
2019-09-02gnu: r-mixomics: Update to 6.8.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.2.
2019-09-02gnu: r-fgsea: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.10.1.
2019-09-02gnu: r-seurat: Update to 3.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.0. [propagated-inputs]: Add r-leiden, r-rcppannoy, and r-uwot.
2019-09-02gnu: r-rtracklayer: Update to 1.44.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.3.
2019-09-02gnu: r-biomart: Update to 2.40.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.4.
2019-09-02gnu: r-annotationdbi: Update to 1.46.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.1.
2019-09-02gnu: r-iranges: Update to 2.18.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.2.
2019-09-02gnu: r-pbapply: Update to 1.4-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-pbapply): Update to 1.4-2.
2019-09-02gnu: r-rmarkdown: Update to 1.15.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.15.
2019-09-02gnu: r-hms: Update to 0.5.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hms): Update to 0.5.1.
2019-09-02gnu: r-whisker: Update to 0.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-whisker): Update to 0.4.
2019-09-02gnu: r-chron: Update to 2.3-54.Ricardo Wurmus
* gnu/packages/statistics.scm (r-chron): Update to 2.3-54.
2019-09-02gnu: Add r-leiden.Ricardo Wurmus
* gnu/packages/cran.scm (r-leiden): New variable.
2019-09-02gnu: r-umap: Update to 0.2.3.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-umap): Update to 0.2.3.1. [propagated-inputs]: Add r-openssl.
2019-09-02gnu: r-enrichr: Update to 2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-enrichr): Update to 2.1.
2019-09-02gnu: r-dalex: Update to 0.4.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-dalex): Update to 0.4.7.
2019-09-02gnu: r-ggforce: Update to 0.3.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggforce): Update to 0.3.1.
2019-09-02gnu: r-bookdown: Update to 0.13.Ricardo Wurmus
* gnu/packages/cran.scm (r-bookdown): Update to 0.13.
2019-09-02gnu: r-tdthap: Update to 1.1-11.Ricardo Wurmus
* gnu/packages/cran.scm (r-tdthap): Update to 1.1-11.
2019-09-02gnu: r-units: Update to 0.6-4.Ricardo Wurmus
* gnu/packages/cran.scm (r-units): Update to 0.6-4.
2019-09-02gnu: r-wgaim: Update to 2.0-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-wgaim): Update to 2.0-0. [propagated-inputs]: Remove r-lattice; add r-ggplot2.
2019-09-02gnu: r-apcluster: Update to 1.4.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-apcluster): Update to 1.4.8.
2019-09-02gnu: r-lavaan: Update to 0.6-5.Ricardo Wurmus
* gnu/packages/cran.scm (r-lavaan): Update to 0.6-5.
2019-09-02gnu: r-ggextra: Update to 0.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggextra): Update to 0.9. [propagated-inputs]: Add r-r6.
2019-09-02gnu: r-fields: Update to 9.8-6.Ricardo Wurmus
* gnu/packages/cran.scm (r-fields): Update to 9.8-6.
2019-09-02gnu: r-rgl: Update to 0.100.30.Ricardo Wurmus
* gnu/packages/cran.scm (r-rgl): Update to 0.100.30.
2019-09-02gnu: r-afex: Update to 0.25-1.Ricardo Wurmus
* gnu/packages/cran.scm (r-afex): Update to 0.25-1.
2019-09-02gnu: r-summarytools: Update to 0.9.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-summarytools): Update to 0.9.4.
2019-09-02gnu: r-coin: Update to 1.3-1.Ricardo Wurmus
* gnu/packages/cran.scm (r-coin): Update to 1.3-1.
2019-09-02gnu: r-libcoin: Update to 1.0-5.Ricardo Wurmus
* gnu/packages/cran.scm (r-libcoin): Update to 1.0-5.
2019-09-02gnu: r-magick: Update to 2.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-magick): Update to 2.2.
2019-09-02gnu: r-raster: Update to 3.0-2.Ricardo Wurmus
* gnu/packages/cran.scm (r-raster): Update to 3.0-2.
2019-09-02gnu: r-zip: Update to 2.0.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-zip): Update to 2.0.4.
2019-09-02gnu: r-arules: Update to 1.6-4.Ricardo Wurmus
* gnu/packages/cran.scm (r-arules): Update to 1.6-4.
2019-09-02gnu: r-radiant-data: Update to 1.0.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-radiant-data): Update to 1.0.6.
2019-09-02gnu: r-xfun: Update to 0.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-xfun): Update to 0.9.
2019-09-02gnu: r-seriation: Update to 1.2-8.Ricardo Wurmus
* gnu/packages/cran.scm (r-seriation): Update to 1.2-8.
2019-09-02gnu: r-dtw: Update to 1.21-3.Ricardo Wurmus
* gnu/packages/cran.scm (r-dtw): Update to 1.21-3.
2019-09-02gnu: r-geometry: Update to 0.4.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-geometry): Update to 0.4.3.
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