diff --git a/gnu/local.mk b/gnu/local.mk index 898d22f639..39b8e009b2 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -693,7 +693,6 @@ 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/aspell-gcc-compat.patch \ %D%/packages/patches/ath9k-htc-firmware-binutils.patch \ diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index f1a45bc1ca..49ec474ffd 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1536,7 +1536,7 @@ (define-public jack-1 (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/" @@ -1545,40 +1545,38 @@ (define-public jack-2 (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))) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7ca6788dd8..7b0405427c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1192,14 +1192,14 @@ (define-public r-hpar (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 @@ -5343,14 +5343,14 @@ (define-public r-flowsom (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 @@ -6010,19 +6010,20 @@ (define-public r-wavetiling (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) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5261e346d1..a573ef682f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7647,13 +7647,13 @@ (define-public r-annotationdbi (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) @@ -7731,13 +7731,13 @@ (define-public r-biostrings (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) @@ -9454,13 +9454,13 @@ (define-public r-msnid (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 @@ -9473,6 +9473,7 @@ (define-public r-seurat ("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) diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm index adb377f25f..70f80398fa 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 @@ (define-public transmission-remote-cli (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/cran.scm b/gnu/packages/cran.scm index 1f35356e05..8754f83f72 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -525,31 +525,18 @@ (define-public r-servr (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 @@ -559,13 +546,13 @@ (define-public r-htmltools (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) @@ -5339,14 +5326,14 @@ (define-public r-rio (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) @@ -5367,14 +5354,14 @@ (define-public r-maptools (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) @@ -5390,14 +5377,14 @@ (define-public r-later (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) @@ -5860,14 +5847,14 @@ (define-public r-nbclust (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) @@ -8960,14 +8947,14 @@ (define-public r-rcpphnsw (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") @@ -10317,14 +10304,14 @@ (define-public r-ontologyindex (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) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 23ec3555cf..1b9ae73966 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6621,7 +6621,7 @@ (define-public emacs-wgrep (define-public emacs-helm (package (name "emacs-helm") - (version "3.3") + (version "3.5.0") (source (origin (method git-fetch) @@ -6630,7 +6630,7 @@ (define-public emacs-helm (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) @@ -6647,6 +6647,31 @@ (define-public emacs-helm 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") @@ -6675,7 +6700,7 @@ (define-public emacs-helm-ag (revision "1")) (package (name "emacs-helm-ag") - (version "0.58") + (version (git-version "0.58" revision commit)) (source (origin (method git-fetch) @@ -7267,7 +7292,7 @@ (define-public emacs-evil-expat (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) @@ -7277,7 +7302,7 @@ (define-public emacs-evil-nerd-commenter (file-name (git-file-name name version)) (sha256 (base32 - "1r8shfdddys9vqvrxf7s6z83ydqx9xhqs9sa7klbsajryqcp50b7")))) + "0qd5a89mzvdyhd8lm13iwp220vzpd6dajwx54frlc5bzsxdmg6vc")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil))) (arguments @@ -11690,6 +11715,26 @@ (define-public emacs-ts 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") @@ -12609,8 +12654,8 @@ (define-public emacs-beginend (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)) @@ -12623,7 +12668,7 @@ (define-public emacs-mbsync (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") @@ -15082,10 +15127,8 @@ (define-public emacs-github-review (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)) @@ -15098,7 +15141,7 @@ (define-public emacs-deadgrep (file-name (git-file-name name version)) (sha256 (base32 - "0fxf7gq9sjfkgpdfqx10w3l3nd4rwa8kv9plyxk1fqacb3s5m6ai")))) + "016gwqxd9aqzjw3hqv3vdf8cs6la8r65g6azg5rlmjqwfx3vsaha")))) (build-system emacs-build-system) (inputs `(("emacs-dash" ,emacs-dash) @@ -18161,8 +18204,8 @@ (define-public emacs-evil-cleverparens (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)) @@ -18174,7 +18217,7 @@ (define-public emacs-evil-traces (file-name (git-file-name name version)) (sha256 (base32 - "0a15f2saynz9fws1h5s7py3cshsk4xs1kwgwj1m5rsin36g0j6hc")))) + "12p9lfxscs182vbd4dy0m5gacs3d4kyprbz5yndpwvl8g2qsqplz")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil))) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 495e6bbd3a..d9ea5526b8 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1406,12 +1406,17 @@ (define-public icedtea-7 (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" + "/lib/arm") + ("aarch64-linux" + "/lib/aarch64"))))) (symlink (string-append lib-path "/server/libjvm.so") (string-append lib-path "/libjvm.so"))) #t)) @@ -1559,6 +1564,10 @@ (define (import-cert cert) (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+)))) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e1fc4a983a..63ce0c62ae 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -183,9 +183,9 @@ (define (linux-libre-deblob-scripts version (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 @@ -357,10 +357,10 @@ (define (%upstream-linux-source version hash) "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))) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index ed3efc7bdb..84597e4e73 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -6388,7 +6388,7 @@ (define-public sbcl-optima (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 @@ -6451,6 +6451,29 @@ (define-public sbcl-fare-quasiquote Trivia.") (license license:expat))) +(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) @@ -6464,6 +6487,22 @@ (define-public sbcl-fare-quasiquote-readtable 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")) @@ -7488,3 +7527,140 @@ (define-public sbcl-cl-gobject-introspection (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)) + +(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)) + +(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)) + +(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)) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index 2f80920ed4..7abe9ab6f0 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -112,14 +112,14 @@ (define-public openldap (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 @@ (define-public nss-pam-ldapd `(("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) 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()); 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 @@ (define-public r-whisker (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")