From 4722330d68581d9ac20c419b1a4d2c8bf5137506 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 22:07:03 +0200 Subject: [PATCH 01/38] gnu: nss-pam-ldapd: Update to 0.9.11. * gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.11. [inputs]: Replace python-2 with python. --- gnu/packages/openldap.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index b84a417ff5..b355665da0 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -112,14 +112,14 @@ (define-public nss-pam-ldapd (package (name "nss-pam-ldapd") - (version "0.9.10") + (version "0.9.11") (source (origin (method url-fetch) (uri (string-append "https://arthurdejong.org/nss-pam-ldapd/" "nss-pam-ldapd-" version ".tar.gz")) (sha256 (base32 - "1cqamcr6qpgwxijlr6kg7jspjamjra8w0haan0qssn0yxn95d7c0")))) + "1dna3r0q6sjhhlkhcp8x2zkslrd4y7701kk6fl5r940sdph1pmyh")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -146,7 +146,7 @@ `(("linux-pam" ,linux-pam) ("openldap" ,openldap) ("mit-krb5" ,mit-krb5) - ("python" ,python-2))) + ("python" ,python))) (home-page "https://arthurdejong.org/nss-pam-ldapd") (synopsis "NSS and PAM modules for LDAP") (description "nss-pam-ldapd provides a @dfn{Name Service Switch} (NSS) From 45d04b2a7d01f693020149853e1d810cf92205a4 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Sun, 6 Oct 2019 22:02:25 +0200 Subject: [PATCH 02/38] gnu: emacs-helm: Update to 3.5.0. * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.5.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 442115882d..bfcfb98d1e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6621,7 +6621,7 @@ ack, ag, helm and pt.") (define-public emacs-helm (package (name "emacs-helm") - (version "3.3") + (version "3.5.0") (source (origin (method git-fetch) @@ -6630,7 +6630,7 @@ ack, ag, helm and pt.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0fqhw7r9fcsja5d3pgbipw7pkw9nj534faav6hi45413hc3gyv92")))) + (base32 "07bijcnfkv60l3swasxv53x32l6glds05mxnbb3xbnmkgm1pm9if")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-async" ,emacs-async) From cb2197508a62210b8bdb132b6f96aebba637e6b3 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Sun, 6 Oct 2019 22:02:46 +0200 Subject: [PATCH 03/38] gnu: Add emacs-helm-org. * gnu/packages/emacs-xyz.scm (emacs-helm-org): New variable. --- gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index bfcfb98d1e..cc16a5d04f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6647,6 +6647,31 @@ considered to be its successor. Helm sets out to clean up the legacy code in not tied in the trap of backward compatibility.") (license license:gpl3+))) +(define-public emacs-helm-org + (let ((commit "542dda7bc9a3b9dfb439e4f8a1e5f60cfb6cc256") + (revision "1")) + (package + (name "emacs-helm-org") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-helm/helm-org.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xa32w80icrykpyfb89fhb0s4l7ysi0sc7f7lfwqz5najwbgqipl")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-helm" ,emacs-helm))) + (home-page "https://github.com/emacs-helm/helm-org") + (synopsis "Helm interface to the Silver Searcher") + (description + "This package provides a frontend for grepping tools like ag and ack, +as well as features for editing search results.") + (license license:gpl3+)))) + (define-public emacs-helm-swoop (package (name "emacs-helm-swoop") From d050fdf4c6309cf5e0bfad3806cac51e3fefaa1b Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Sun, 6 Oct 2019 22:02:56 +0200 Subject: [PATCH 04/38] gnu: emacs-helm-ag: Fix version. * gnu/packages/emacs-xyz.scm (emacs-helm-ag): Fix version. --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cc16a5d04f..5be5b4be45 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6700,7 +6700,7 @@ for search-based navigation of buffers.") (revision "1")) (package (name "emacs-helm-ag") - (version "0.58") + (version (git-version "0.58" revision commit)) (source (origin (method git-fetch) From 122c1b3ce7718e956db0c6ce7e1058362dd7bb1c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:03:27 +0200 Subject: [PATCH 05/38] gnu: r-biomart: Update to 2.40.5. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5ec600598b..93a458b133 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7658,13 +7658,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.4") + (version "2.40.5") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0dj51qkxm7bh24b3bs1di7lic6zgi7g5gf9iqkqhrwkbm7sqvn0v")))) + "1kjvxnkpsx3j2hji3cg3ka2gv8a9mg117lzzxyqjb7qa4zw7dipx")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) From 94638cbe77f070645dbbeb983e1e8db8917c1be9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:03:39 +0200 Subject: [PATCH 06/38] gnu: r-rsamtools: Update to 2.0.2. * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 93a458b133..e4cfa0cad3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7742,13 +7742,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0wzp5vsmqs7h44r7lcw8fnz5x9bcdcfiqq8d3h62wwibyk2lg0w1")))) + "188k5g40lbli7dxr96hldyvg9r9hmlbh2fp0qs5nnd12b8zbf338")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) From 33651044c6e4989d2e3546a772963b2b3a8b0703 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:03:49 +0200 Subject: [PATCH 07/38] gnu: r-seurat: Update to 3.1.1. * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1. [propagated-inputs]: Add r-httr. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e4cfa0cad3..f2f67f36b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9465,13 +9465,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.1.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0icxndnnkkmmr9hhd01dv3w8pih7x9r0rlp3fq9pk3qajp9gmlyq")))) + "084lr2fjdksshsmv1ww82bgn3a9mml7kswsidjrs89snabgvn360")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -9484,6 +9484,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-ggridges" ,r-ggridges) + ("r-httr" ,r-httr) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) From 82acc94fbfc5cfb1257f0a75ae9997262d90fef6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:04:11 +0200 Subject: [PATCH 08/38] gnu: r-htmltools: Update to 0.4.0. * gnu/packages/cran.scm (r-htmltools): Update to 0.4.0. [arguments]: Remove field. [propagated-inputs]: Add r-rlang. --- gnu/packages/cran.scm | 21 ++++----------------- 1 file changed, 4 insertions(+), 17 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1f35356e05..1e153b1284 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -525,31 +525,18 @@ directory.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.3.6") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4")))) + "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v")))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; See https://github.com/rstudio/htmltools/pull/68 - ;; The resource files are in the store and have mode 444. After - ;; copying the files R fails to remove them again because it doesn't - ;; have write access to them. - (add-after 'unpack 'copy-files-without-mode - (lambda _ - (substitute* "R/html_dependency.R" - (("file.copy\\(from, to, " prefix) - (string-append prefix - "copy.mode = FALSE, "))) - #t))))) (propagated-inputs `(("r-digest" ,r-digest) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang))) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description From ff743445975ba67fc827c415e686b0ec2a0a7baf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:20 +0200 Subject: [PATCH 09/38] gnu: r-htmlwidgets: Update to 1.5. * gnu/packages/cran.scm (r-htmlwidgets): Update to 1.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1e153b1284..902a9975a8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -546,13 +546,13 @@ directory.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.3") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i")))) + "1h2sj5h9vcssb73nz63gmw5bajs73m9q807fsypvr621gb1s124i")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) From b7e7c320a27e013cd0bfd949f1825924c005278e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:26 +0200 Subject: [PATCH 10/38] gnu: r-maptools: Update to 0.9-8. * gnu/packages/cran.scm (r-maptools): Update to 0.9-8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 902a9975a8..500379bdae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5326,14 +5326,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "0.9-5") + (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax")))) + "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) From ab99236eba6d7f932b50652c80eb41946c0a92ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:31 +0200 Subject: [PATCH 11/38] gnu: r-later: Update to 1.0.0. * gnu/packages/cran.scm (r-later): Update to 1.0.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 500379bdae..384a0afa5c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5354,14 +5354,14 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "0.8.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb")))) + "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) From 2e6ccd6c2d94313ba37c6d48042a052ff9b0f829 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:37 +0200 Subject: [PATCH 12/38] gnu: r-promises: Update to 1.1.0. * gnu/packages/cran.scm (r-promises): Update to 1.1.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 384a0afa5c..b1e0847622 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5377,14 +5377,14 @@ time after the current time, after the R execution stack has emptied.") (define-public r-promises (package (name "r-promises") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "promises" version)) (sha256 (base32 - "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2")))) + "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8")))) (build-system r-build-system) (propagated-inputs `(("r-later" ,r-later) From 770321180fda2e9359842761699a5439047bdf94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:42 +0200 Subject: [PATCH 13/38] gnu: r-hdf5r: Update to 1.3.0. * gnu/packages/cran.scm (r-hdf5r): Update to 1.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b1e0847622..6073804398 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5847,14 +5847,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq")))) + "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) From 9b112f403059aadb268b8844c84fe08a5747f8c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:49 +0200 Subject: [PATCH 14/38] gnu: r-rcppparallel: Update to 4.4.4. * gnu/packages/cran.scm (r-rcppparallel): Update to 4.4.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6073804398..7a856df734 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8947,14 +8947,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "4.4.3") + (version "4.4.4") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s")))) + "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "http://rcppcore.github.io/RcppParallel") From f817005bfeb904810e102c3f675036ff34857229 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:54 +0200 Subject: [PATCH 15/38] gnu: r-gargle: Update to 0.4.0. * gnu/packages/cran.scm (r-gargle): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7a856df734..8754f83f72 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10304,14 +10304,14 @@ and manipulating sets of ontological terms.") (define-public r-gargle (package (name "r-gargle") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 - "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v")))) + "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx")))) (build-system r-build-system) (propagated-inputs `(("r-fs" ,r-fs) From 07d0645b6bc0d191dcf3d635159a8951ad395e0b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:06:59 +0200 Subject: [PATCH 16/38] gnu: r-backports: Update to 1.1.5. * gnu/packages/statistics.scm (r-backports): Update to 1.1.5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0c98e61cbc..3c69901a0a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2119,14 +2119,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.4") + (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "00zz969vc2gfi5p9q65pzghq2bxm3p9zqgwqswkyz9rgybz5wjzf")))) + "0k19w68b2aihyj5mflw3732gkkzs78sssqdns960pdw3yfnkiv33")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") From 1c2e573302421bf7c130afcac4c9207f63222333 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:07:04 +0200 Subject: [PATCH 17/38] gnu: r-regioner: Update to 1.16.5. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7ca6788dd8..9d6f5bb2ad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1192,14 +1192,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.16.4") + (version "1.16.5") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760")))) + "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs From eb796f53efd5332b401a5756429b8710664ee930 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:07:09 +0200 Subject: [PATCH 18/38] gnu: r-mixomics: Update to 6.8.5. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9d6f5bb2ad..9de3deedea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5343,14 +5343,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.8.4") + (version "6.8.5") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg")))) + "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs From 326746e14ce792710d41c24ad6994d1ac432d1b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 6 Oct 2019 23:07:16 +0200 Subject: [PATCH 19/38] gnu: r-variancepartition: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.14.1. [propagated-inputs]: Add r-biocparallel. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9de3deedea..7b0405427c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6010,19 +6010,20 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1ycapwb2mq57xibrzzjz9zwxqz4nwz9f3n5gskhlr5vcs7irkjd6")))) + "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) + ("r-biocparallel" ,r-biocparallel) ("r-colorramps" ,r-colorramps) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) From b44271350b897aff8cd90b5e77b3c40b0bf6e3dc Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Mon, 7 Oct 2019 01:43:37 +0200 Subject: [PATCH 20/38] gnu: emacs-deadgrep: Update to 0.8-2.3fc7ca1. * gnu/packages/emacs-xyz.scm (emacs-deadgrep): Update to 0.8-2.3fc7ca1. --- gnu/packages/emacs-xyz.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5be5b4be45..85931912d4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -15107,10 +15107,8 @@ accept and reject GitHub pull requests.") (license license:gpl3+)))) (define-public emacs-deadgrep - ;; We prefer a newer commit (four commits newer than release) because of a - ;; bugfix for globbing. - (let ((commit "329119c65126f7917d3910bc584f4191ba8f21ac") - (revision "1")) + (let ((commit "3fc7ca1f58e190f0c80da455a0e40187e673020e") + (revision "2")) (package (name "emacs-deadgrep") (version (git-version "0.8" revision commit)) @@ -15123,7 +15121,7 @@ accept and reject GitHub pull requests.") (file-name (git-file-name name version)) (sha256 (base32 - "0fxf7gq9sjfkgpdfqx10w3l3nd4rwa8kv9plyxk1fqacb3s5m6ai")))) + "016gwqxd9aqzjw3hqv3vdf8cs6la8r65g6azg5rlmjqwfx3vsaha")))) (build-system emacs-build-system) (inputs `(("emacs-dash" ,emacs-dash) From 47467ce75ab8c4ea24b9c8bf21d7e1041b8e603e Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Sun, 6 Oct 2019 07:31:25 +0200 Subject: [PATCH 21/38] gnu: Add emacs-peg. * gnu/packages/emacs-xyz.scm (emacs-peg): New variable. --- gnu/packages/emacs-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 85931912d4..95cb9951de 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11715,6 +11715,26 @@ tables of contents.") timestamps by providing a @code{ts} struct.") (license license:gpl3+)))) +(define-public emacs-peg + (package + (name "emacs-peg") + (version "0.6") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacsmirror/peg") + (commit version))) + (sha256 + (base32 + "0kjz7ch4bn0m4v9zgqyqcrsasnqc5c5drv2hp22j7rnbb7ny0q3n")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (home-page "https://github.com/emacsmirror/peg/") + (synopsis "Parsing Expression Grammars in Elisp") + (description "This package provides a macro that parses the current buffer +according to a parsing expression grammar.") + (license license:gpl3+))) + (define-public emacs-org-ql (package (name "emacs-org-ql") From 3f68853557ba57918c99cca5aad1c2d3daee8f54 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Mon, 7 Oct 2019 05:15:55 +0200 Subject: [PATCH 22/38] gnu: emacs-evil-traces: Update to 0.0.1-2.1931e3e. * gnu/packages/emacs-xyz.scm (emacs-evil-traces): Update to 0.0.1-2.1931e3e. --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 95cb9951de..7959f283f7 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -18204,8 +18204,8 @@ corresponding Evil keys.") (license license:expat)))) (define-public emacs-evil-traces - (let ((commit "b41b7432b8110378c199a3d25af464083777f453") - (revision "1")) + (let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3") + (revision "2")) (package (name "emacs-evil-traces") (version (git-version "0.0.1" revision commit)) @@ -18217,7 +18217,7 @@ corresponding Evil keys.") (file-name (git-file-name name version)) (sha256 (base32 - "0a15f2saynz9fws1h5s7py3cshsk4xs1kwgwj1m5rsin36g0j6hc")))) + "12p9lfxscs182vbd4dy0m5gacs3d4kyprbz5yndpwvl8g2qsqplz")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil))) From 4f2a3fbe8872f02e5186d354444da2dbee6b7c5f Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Mon, 7 Oct 2019 08:20:50 +0200 Subject: [PATCH 23/38] gnu: emacs-evil-nerd-commenter: Update to 3.3.8. * gnu/packages/emacs-xyz.scm (emacs-evil-nerd-commenter): Update to 3.3.8. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7959f283f7..5f8b3952fd 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7292,7 +7292,7 @@ pasting into and from @code{tmux} paste buffers.") (define-public emacs-evil-nerd-commenter (package (name "emacs-evil-nerd-commenter") - (version "3.3.7") + (version "3.3.8") (source (origin (method git-fetch) @@ -7302,7 +7302,7 @@ pasting into and from @code{tmux} paste buffers.") (file-name (git-file-name name version)) (sha256 (base32 - "1r8shfdddys9vqvrxf7s6z83ydqx9xhqs9sa7klbsajryqcp50b7")))) + "0qd5a89mzvdyhd8lm13iwp220vzpd6dajwx54frlc5bzsxdmg6vc")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil))) (arguments From 4261a9d162f723347981dfc6e72c8938343681a5 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Mon, 7 Oct 2019 10:21:19 +0300 Subject: [PATCH 24/38] gnu: emacs-mbsync: Update to 0.1.2-4.b62491c. * gnu/packages/emacs-xyz.scm (emacs-mbsync): Update to 0.1.2-4.b62491c. --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5f8b3952fd..e87fa2ad11 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12654,8 +12654,8 @@ key again.") (license license:gpl3+))) (define-public emacs-mbsync - (let ((commit "8f80c267cab1acb0d5bdd5b0059f5d1790d499ff") - (revision "3")) + (let ((commit "b62491c0e0d89eb9c66261a16d7ac81231c9c453") + (revision "4")) (package (name "emacs-mbsync") (version (git-version "0.1.2" revision commit)) @@ -12668,7 +12668,7 @@ key again.") (file-name (git-file-name name version)) (sha256 (base32 - "1dwlpcczsa6b7bwv5149by0qmk8v2y7bjad02k4fy25yxznqzci9")))) + "1zlih37mkqjn2czl12zn7lgxxljvrwhqqpbksj9c91zn0f0rm3mz")))) (build-system emacs-build-system) (home-page "https://github.com/dimitri/mbsync-el") (synopsis "Interface to mbsync for Emacs") From d3e22bcc1141cd33dde7017f51058f18d428917c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 7 Oct 2019 09:50:51 +0200 Subject: [PATCH 25/38] gnu: icedtea-7: Support non-Intel systems. This is a followup to 1b6f99ea538d767099596860017e67755c1ac42f. * gnu/packages/java.scm (icedtea-7)[arguments]: In 'install-libjvm' phase, match armhf and aarch64. [supported-systems]: New field. --- gnu/packages/java.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 3b7404973a..452180eead 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1377,11 +1377,17 @@ bootstrapping purposes.") (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((lib-path (string-append (assoc-ref outputs "out") "/lib/" + ;; See 'INSTALL_ARCH_DIR' in + ;; 'configure'. ,(match (%current-system) ("i686-linux" "i386") ("x86_64-linux" - "amd64"))))) + "amd64") + ("armhf-linux" + "arm") + ("aarch64-linux" + "aarch64"))))) (symlink (string-append lib-path "/server/libjvm.so") (string-append lib-path "/libjvm.so"))) #t)) @@ -1529,6 +1535,10 @@ bootstrapping purposes.") (description "This package provides the Java development kit OpenJDK built with the IcedTea build harness.") + + ;; 'configure' lists "mips" and "mipsel", but not "mips64el'. + (supported-systems (delete "mips64el-linux" %supported-systems)) + ;; IcedTea is released under the GPL2 + Classpath exception, which is the ;; same license as both GNU Classpath and OpenJDK. (license license:gpl2+)))) From 7b6a8e23b0de18262a42e44432f955517d71d796 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 7 Oct 2019 11:18:45 +0300 Subject: [PATCH 26/38] gnu: aria2: Update to 1.35.0. * gnu/packages/bittorrent.scm (aria2): Update to 1.35.0. [source]: Use new upstream uri. Remove patch. * gnu/packages/patches/aria2-CVE-2019-3500.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bittorrent.scm | 13 ++--- .../patches/aria2-CVE-2019-3500.patch | 55 ------------------- 3 files changed, 6 insertions(+), 63 deletions(-) delete mode 100644 gnu/packages/patches/aria2-CVE-2019-3500.patch diff --git a/gnu/local.mk b/gnu/local.mk index 54ae09f619..ffe697c2e1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -695,7 +695,6 @@ dist_patch_DATA = \ %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \ %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch \ %D%/packages/patches/apr-skip-getservbyname-test.patch \ - %D%/packages/patches/aria2-CVE-2019-3500.patch \ %D%/packages/patches/aspell-default-dict-dir.patch \ %D%/packages/patches/ath9k-htc-firmware-binutils.patch \ %D%/packages/patches/ath9k-htc-firmware-gcc.patch \ diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm index 50b63048e4..da01848ec7 100644 --- a/gnu/packages/bittorrent.scm +++ b/gnu/packages/bittorrent.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès ;;; Copyright © 2016, 2017, 2018, 2019 Leo Famulari -;;; Copyright © 2016, 2017, 2018 Efraim Flashner +;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner ;;; Copyright © 2016 Tomáš Čech ;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2017 Jelle Licht @@ -262,16 +262,15 @@ maintained upstream.") (define-public aria2 (package (name "aria2") - (version "1.34.0") + (version "1.35.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/tatsuhiro-t/aria2/" - "releases/download/release-" version "/" - name "-" version ".tar.xz")) - (patches (search-patches "aria2-CVE-2019-3500.patch")) + (uri (string-append "https://github.com/aria2/aria2/releases/" + "download/release-" version + "/aria2-" version ".tar.xz")) (sha256 (base32 - "18vpgr430vxlwbcc3598rr1srfmwypls6wp1m4wf21hncc1ahi1s")))) + "1zbxc517d97lb96f15xcy4l7b66grxrp3h2ids2jiwkaip87yaqy")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--enable-libaria2" diff --git a/gnu/packages/patches/aria2-CVE-2019-3500.patch b/gnu/packages/patches/aria2-CVE-2019-3500.patch deleted file mode 100644 index 891c9047ba..0000000000 --- a/gnu/packages/patches/aria2-CVE-2019-3500.patch +++ /dev/null @@ -1,55 +0,0 @@ -Fix CVE-2019-3500: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2019-3500 -https://github.com/aria2/aria2/issues/1329 - -Patch copied from upstream source repository: - -https://github.com/aria2/aria2/commit/37368130ca7de5491a75fd18a20c5c5cc641824a - -From 37368130ca7de5491a75fd18a20c5c5cc641824a Mon Sep 17 00:00:00 2001 -From: Tatsuhiro Tsujikawa -Date: Sat, 5 Jan 2019 09:32:40 +0900 -Subject: [PATCH] Mask headers - ---- - src/HttpConnection.cc | 18 ++++++++++++------ - 1 file changed, 12 insertions(+), 6 deletions(-) - -diff --git a/src/HttpConnection.cc b/src/HttpConnection.cc -index 77cb9d27a..be5b97723 100644 ---- a/src/HttpConnection.cc -+++ b/src/HttpConnection.cc -@@ -102,11 +102,17 @@ std::string HttpConnection::eraseConfidentialInfo(const std::string& request) - std::string result; - std::string line; - while (getline(istr, line)) { -- if (util::startsWith(line, "Authorization: Basic")) { -- result += "Authorization: Basic ********\n"; -+ if (util::istartsWith(line, "Authorization: ")) { -+ result += "Authorization: \n"; - } -- else if (util::startsWith(line, "Proxy-Authorization: Basic")) { -- result += "Proxy-Authorization: Basic ********\n"; -+ else if (util::istartsWith(line, "Proxy-Authorization: ")) { -+ result += "Proxy-Authorization: \n"; -+ } -+ else if (util::istartsWith(line, "Cookie: ")) { -+ result += "Cookie: \n"; -+ } -+ else if (util::istartsWith(line, "Set-Cookie: ")) { -+ result += "Set-Cookie: \n"; - } - else { - result += line; -@@ -154,8 +160,8 @@ std::unique_ptr HttpConnection::receiveResponse() - const auto& proc = outstandingHttpRequests_.front()->getHttpHeaderProcessor(); - if (proc->parse(socketRecvBuffer_->getBuffer(), - socketRecvBuffer_->getBufferLength())) { -- A2_LOG_INFO( -- fmt(MSG_RECEIVE_RESPONSE, cuid_, proc->getHeaderString().c_str())); -+ A2_LOG_INFO(fmt(MSG_RECEIVE_RESPONSE, cuid_, -+ eraseConfidentialInfo(proc->getHeaderString()).c_str())); - auto result = proc->getResult(); - if (result->getStatusCode() / 100 == 1) { - socketRecvBuffer_->drain(proc->getLastBytesProcessed()); From 048d21a8733f4173705ed59a22a03caddb876fe1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 7 Oct 2019 10:38:22 +0200 Subject: [PATCH 27/38] gnu: icedtea-7: Avoid massive rebuild. Reported by Efraim Flashner. * gnu/packages/java.scm (icedtea-7)[arguments]: Change 'lib-path' definition in 'install-libjvm' to avoid the rebuilds that commit 1b6f99ea538d767099596860017e67755c1ac42f would otherwise entail. --- gnu/packages/java.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 452180eead..1f5e39d9c6 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1376,18 +1376,17 @@ bootstrapping purposes.") (add-after 'install 'install-libjvm (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((lib-path (string-append (assoc-ref outputs "out") - "/lib/" ;; See 'INSTALL_ARCH_DIR' in ;; 'configure'. ,(match (%current-system) ("i686-linux" - "i386") + "/lib/i386") ("x86_64-linux" - "amd64") + "/lib/amd64") ("armhf-linux" - "arm") + "/lib/arm") ("aarch64-linux" - "aarch64"))))) + "/lib/aarch64"))))) (symlink (string-append lib-path "/server/libjvm.so") (string-append lib-path "/libjvm.so"))) #t)) From 7d82e920717f08bceb42bb570d786dff233171e1 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Sun, 6 Oct 2019 06:07:15 +0000 Subject: [PATCH 28/38] gnu: linux-libre: Update to 5.3.4. * gnu/packages/linux (linux-libre-5.3-version): Update to 5.3.4. (deblob-scripts-5.3): Update to 5.3.4. --- gnu/packages/linux.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 21cd4a205f..910aeed6ff 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -184,9 +184,9 @@ defconfig. Return the appropriate make target if applicable, otherwise return (define deblob-scripts-5.3 (linux-libre-deblob-scripts - "5.3.1" + "5.3.4" (base32 "15n09zq38d69y1wl28s3nasf3377qp2yil5b887zpqrm00dif7i4") - (base32 "1av9ykv714cnl0clls8rhwa8rwflz6ivg17gharj1x650qp6vnw3"))) + (base32 "0nrimraf46nf6y1hwkg29fyl0a83wnj0mwq54ggxvffn9gk5h9pa"))) (define deblob-scripts-5.2 (linux-libre-deblob-scripts @@ -358,10 +358,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." "linux-" version ".tar.xz")) (sha256 hash))) -(define-public linux-libre-5.3-version "5.3.2") +(define-public linux-libre-5.3-version "5.3.4") (define-public linux-libre-5.3-pristine-source (let ((version linux-libre-5.3-version) - (hash (base32 "0szw21mpp94gp3zn2fgllbv6fdjjf20njgrcjay7vjmm7farq7rn"))) + (hash (base32 "0vi4bgcr921z5l6fbcrcgmhaji5gl2avpmp7njna6v0f7sxism0r"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.3))) From 85747bab82f529a476a5468f0c0f48b8ba047594 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:45:53 +0200 Subject: [PATCH 29/38] gnu: sbcl-optima: Fix version number * gnu/packages/lisp.scm (sbcl-optima)[version]: It's actually 1.0. --- gnu/packages/lisp.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index ed3efc7bdb..c358aa6465 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -6388,7 +6388,7 @@ the return type of a function.") (package (name "sbcl-optima") (build-system asdf-build-system/sbcl) - (version (git-version "0.1" revision commit)) + (version (git-version "1.0" revision commit)) (home-page "https://github.com/m2ym/optima") (source (origin From 7baaf7f3587961255d429087e5d18d35275a176d Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:46:36 +0200 Subject: [PATCH 30/38] gnu: Add cl-fare-quasiquote. * gnu/packages/lisp.scm (cl-fare-quasiquote): New variable. --- gnu/packages/lisp.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index c358aa6465..c1ea8cc37b 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -6451,6 +6451,9 @@ quasiquote is enable matching of quasiquoted patterns, using Optima or Trivia.") (license license:expat))) +(define-public cl-fare-quasiquote + (sbcl-package->cl-source-package sbcl-fare-quasiquote)) + (define-public sbcl-fare-quasiquote-readtable (package (inherit sbcl-fare-quasiquote) From 06e2da719ea95a9d48ad86002ab183c5114ff2b1 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:46:55 +0200 Subject: [PATCH 31/38] gnu: Add fare-quasiquote-optima. * gnu/packages/lisp.scm (cl-fare-quasiquote-optima, sbcl-fare-quasiquote-optima): New variables. --- gnu/packages/lisp.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index c1ea8cc37b..4d3b4fbcbc 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -6454,6 +6454,26 @@ Trivia.") (define-public cl-fare-quasiquote (sbcl-package->cl-source-package sbcl-fare-quasiquote)) +(define-public sbcl-fare-quasiquote-optima + (package + (inherit sbcl-fare-quasiquote) + (name "sbcl-fare-quasiquote-optima") + (inputs + `(("optima" ,sbcl-optima) + ("fare-quasiquote" ,sbcl-fare-quasiquote))) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-requirement + (lambda _ + (substitute* "fare-quasiquote-optima.asd" + (("\\(:version \"optima\" \"1\\.0\"\\)") + "\"optima\"")) + #t))))))) + +(define-public cl-fare-quasiquote-optima + (sbcl-package->cl-source-package sbcl-fare-quasiquote-optima)) + (define-public sbcl-fare-quasiquote-readtable (package (inherit sbcl-fare-quasiquote) From 7b9cb9c01c097f66c0b617ad4e7462ee72a349c9 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:47:46 +0200 Subject: [PATCH 32/38] gnu: Add cl-fare-quasiquote-readtable. * gnu/packages/lisp.scm (cl-fare-quasiquote-readtable): New variable. --- gnu/packages/lisp.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 4d3b4fbcbc..b2cd4dd352 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -6487,6 +6487,9 @@ Trivia. This package uses fare-quasiquote with named-readtable."))) +(define-public cl-fare-quasiquote-readtable + (sbcl-package->cl-source-package sbcl-fare-quasiquote-readtable)) + (define-public sbcl-trivia.level0 (let ((commit "902e0c65602bbfe96ae82e679330b3771ddc7603") (revision "1")) From 6fdb5b79478d0c6087a1b05cd092ec87f7435c72 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:48:00 +0200 Subject: [PATCH 33/38] gnu: Add cl-fare-quasiquote-extras. * gnu/packages/lisp.scm (cl-fare-quasiquote-extras): New variable. --- gnu/packages/lisp.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index b2cd4dd352..0ca815fb2e 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -6490,6 +6490,19 @@ This package uses fare-quasiquote with named-readtable."))) (define-public cl-fare-quasiquote-readtable (sbcl-package->cl-source-package sbcl-fare-quasiquote-readtable)) +;; TODO: Add support for component-less system in asdf-build-system/sbcl. +(define-public cl-fare-quasiquote-extras + (package + (inherit cl-fare-quasiquote) + (name "cl-fare-quasiquote-extras") + (build-system asdf-build-system/source) + (propagated-inputs + `(("fare-quasiquote" ,cl-fare-quasiquote) + ("fare-quasiquote-optima" ,cl-fare-quasiquote-optima) + ("fare-quasiquote-readtable" ,cl-fare-quasiquote-readtable))) + (description "This library combines @code{fare-quasiquote-readtable} and +@code{fare-quasiquote-optima}."))) + (define-public sbcl-trivia.level0 (let ((commit "902e0c65602bbfe96ae82e679330b3771ddc7603") (revision "1")) From 3658db3fd73d3e04e81e5a3b03d2c395312e833a Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:48:23 +0200 Subject: [PATCH 34/38] gnu: Add string-case. * gnu/packages/lisp.scm (cl-string-case, ecl-string-case, sbcl-string-case): New variables. --- gnu/packages/lisp.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 0ca815fb2e..debe568347 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -7527,3 +7527,33 @@ of C+GObject libraries without the need of writing dedicated bindings.") (define-public cl-gobject-introspection (sbcl-package->cl-source-package sbcl-cl-gobject-introspection)) + +(define-public sbcl-string-case + (let ((commit "718c761e33749e297cd2809c7ba3ade1985c49f7") + (revision "0")) + (package + (name "sbcl-string-case") + (version (git-version "0.0.2" revision commit)) + (home-page "https://github.com/pkhuong/string-case") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1n5i3yh0h5s636rcnwn7jwqy3rjflikra04lymimhpcshhjsk0md")))) + (build-system asdf-build-system/sbcl) + (synopsis "Efficient string= case in Common Lisp") + (description + "@code{string-case} is a Common Lisp macro that generates specialised decision +trees to dispatch on string equality.") + (license license:bsd-3)))) + +(define-public cl-string-case + (sbcl-package->cl-source-package sbcl-string-case)) + +(define-public ecl-string-case + (sbcl-package->ecl-package sbcl-string-case)) From 003a714e7e1f458b84e60b7480149a59b034312c Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:48:52 +0200 Subject: [PATCH 35/38] gnu: Add global-vars. * gnu/packages/lisp.scm (cl-global-vars, ecl-global-vars, sbcl-global-vars): New variables. --- gnu/packages/lisp.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index debe568347..88261d5f8e 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -7557,3 +7557,40 @@ trees to dispatch on string equality.") (define-public ecl-string-case (sbcl-package->ecl-package sbcl-string-case)) + +(define-public sbcl-global-vars + (let ((commit "c749f32c9b606a1457daa47d59630708ac0c266e") + (revision "0")) + (package + (name "sbcl-global-vars") + (version (git-version "1.0.0" revision commit)) + (home-page "https://github.com/lmj/global-vars") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "06m3xc8l3pgsapl8fvsi9wf6y46zs75cp9zn7zh6dc65v4s5wz3d")))) + (build-system asdf-build-system/sbcl) + (synopsis "Efficient global variables in Common Lisp") + (description + "In Common Lisp, a special variable that is never dynamically bound +typically serves as a stand-in for a global variable. The @code{global-vars} +library provides true global variables that are implemented by some compilers. +An attempt to rebind a global variable properly results in a compiler error. +That is, a global variable cannot be dynamically bound. + +Global variables therefore allow us to communicate an intended usage that +differs from special variables. Global variables are also more efficient than +special variables, especially in the presence of threads.") + (license license:expat)))) + +(define-public cl-global-vars + (sbcl-package->cl-source-package sbcl-global-vars)) + +(define-public ecl-global-vars + (sbcl-package->ecl-package sbcl-global-vars)) From c6dd9cf7ffd968520e78c438f7064935c40e139d Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:49:42 +0200 Subject: [PATCH 36/38] gnu: Add trivial-file-size. * gnu/packages/lisp.scm (cl-trivial-file-size, ecl-trivial-file-size, sbcl-trivial-file-size): New variables. --- gnu/packages/lisp.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 88261d5f8e..031d172c39 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -7594,3 +7594,41 @@ special variables, especially in the presence of threads.") (define-public ecl-global-vars (sbcl-package->ecl-package sbcl-global-vars)) + +(define-public sbcl-trivial-file-size + (let ((commit "1c1d672a01a446ba0391dbb4ffc40be3b0476f23") + (revision "0")) + (package + (name "sbcl-trivial-file-size") + (version (git-version "0.0.0" revision commit)) + (home-page "https://github.com/ruricolist/trivial-file-size") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17pp86c9zs4y7i1sh7q9gbfw9iqv6655k7fz8qbj9ly1ypgxp4qs")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (synopsis "Size of a file in bytes in Common Lisp") + (description + "The canonical way to determine the size of a file in bytes, using Common Lisp, +is to open the file with an element type of (unsigned-byte 8) and then +calculate the length of the stream. This is less than ideal. In most cases +it is better to get the size of the file from its metadata, using a system +call. + +This library exports a single function, file-size-in-octets. It returns the +size of a file in bytes, using system calls when possible.") + (license license:expat)))) + +(define-public cl-trivial-file-size + (sbcl-package->cl-source-package sbcl-trivial-file-size)) + +(define-public ecl-trivial-file-size + (sbcl-package->ecl-package sbcl-trivial-file-size)) From fa4bbd9f3427994b3041ec6834500a864dbbe238 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 7 Oct 2019 13:50:07 +0200 Subject: [PATCH 37/38] gnu: Add trivial-macroexpand-all. * gnu/packages/lisp.scm (cl-trivial-macroexpand-all, ecl-trivial-macroexpand-all, sbcl-trivial-macroexpand-all): New variables. --- gnu/packages/lisp.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 031d172c39..84597e4e73 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -7632,3 +7632,35 @@ size of a file in bytes, using system calls when possible.") (define-public ecl-trivial-file-size (sbcl-package->ecl-package sbcl-trivial-file-size)) + +(define-public sbcl-trivial-macroexpand-all + (let ((commit "933270ac7107477de1bc92c1fd641fe646a7a8a9") + (revision "0")) + (package + (name "sbcl-trivial-macroexpand-all") + (version (git-version "0.0.0" revision commit)) + (home-page "https://github.com/cbaggers/trivial-macroexpand-all") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "191hnn4b5j4i3crydmlzbm231kj0h7l8zj6mzj69r1npbzkas4bd")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (synopsis "Portable macroexpand-all for Common Lisp") + (description + "This library provides a macroexpand-all function that calls the +implementation specific equivalent.") + (license license:unlicense)))) + +(define-public cl-trivial-macroexpand-all + (sbcl-package->cl-source-package sbcl-trivial-macroexpand-all)) + +(define-public ecl-trivial-macroexpand-all + (sbcl-package->ecl-package sbcl-trivial-macroexpand-all)) From fa984fa678f98ddc72cc89c6f6dc50ba4aff2487 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 7 Oct 2019 16:32:03 +0200 Subject: [PATCH 38/38] gnu: jack-2: Update to 1.9.13. * gnu/packages/audio.scm (jack-2): Update to 1.9.13. [arguments]: Don't build with python-2. [inputs]: Replace python2-dbus with python-dbus. --- gnu/packages/audio.scm | 42 ++++++++++++++++++++---------------------- 1 file changed, 20 insertions(+), 22 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 6eb61583f7..afa02c1239 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1532,7 +1532,7 @@ synchronous execution of all clients, and low latency operation.") (define-public jack-2 (package (inherit jack-1) (name "jack2") - (version "1.9.12") + (version "1.9.13") (source (origin (method url-fetch) (uri (string-append "https://github.com/jackaudio/jack2/releases/" @@ -1541,40 +1541,38 @@ synchronous execution of all clients, and low latency operation.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0crf4y9a5j9miw8r5ji4l3w5w0y2frrf7xyfsfdgacnw6vwy5vyy")))) + "1d1d403jn4366mqig6g8ghr8057b3rn7gs26b5p3rkal34j20qw2")))) (build-system waf-build-system) (arguments - `(#:python ,python-2 - #:tests? #f ; no check target + `(#:tests? #f ; no check target #:configure-flags '("--dbus" "--alsa") #:phases (modify-phases %standard-phases - (add-before - 'configure 'set-linkflags - (lambda _ - ;; Add $libdir to the RUNPATH of all the binaries. - (substitute* "wscript" - ((".*CFLAGS.*-Wall.*" m) - (string-append m - " conf.env.append_unique('LINKFLAGS'," - "'-Wl,-rpath=" %output "/lib')\n"))) - #t)) + (add-before 'configure 'set-linkflags + (lambda _ + ;; Add $libdir to the RUNPATH of all the binaries. + (substitute* "wscript" + ((".*CFLAGS.*-Wall.*" m) + (string-append m + " conf.env.append_unique('LINKFLAGS'," + "'-Wl,-rpath=" %output "/lib')\n"))) + #t)) (add-after 'install 'wrap-python-scripts - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'jack_control' runs with the correct PYTHONPATH. - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PYTHONPATH"))) - (wrap-program (string-append out "/bin/jack_control") - `("PYTHONPATH" ":" prefix (,path)))) - #t))))) + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Make sure 'jack_control' runs with the correct PYTHONPATH. + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out "/bin/jack_control") + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) (inputs `(("alsa-lib" ,alsa-lib) ("dbus" ,dbus) ("expat" ,expat) ("libsamplerate" ,libsamplerate) ("opus" ,opus) - ("python2-dbus" ,python2-dbus) + ("python-dbus" ,python-dbus) ("readline" ,readline))) (native-inputs `(("pkg-config" ,pkg-config)))