From 2dfa90721d71b373d85498b6e11d50ba19623b0c Mon Sep 17 00:00:00 2001 From: ng0 Date: Sun, 23 Oct 2016 16:14:53 +0000 Subject: gnu: weechat: Update to 1.6. * gnu/packages/irc.scm (weechat): Update to 1.6. Signed-off-by: Leo Famulari --- gnu/packages/irc.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index db398de530..bda56f9dc7 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2014 Kevin Lemonnier ;;; Copyright © 2015 Ludovic Courtès ;;; Copyright © 2015, 2016 Efraim Flashner -;;; Copyright © 2016 ng0 +;;; Copyright © 2016 ng0 ;;; ;;; This file is part of GNU Guix. ;;; @@ -139,14 +139,14 @@ SILC and ICB protocols via plugins.") (define-public weechat (package (name "weechat") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (string-append "http://weechat.org/files/src/weechat-" version ".tar.gz")) (sha256 (base32 - "0w87w4wy61x705ama8h36z9mgdj2gmmzdfrsxvwyh2m2as2max1i")) + "0lyqrymdjdvkzg8510l46c4zw8mjagnmri2i6m9y9qz0c1sfaq9h")) (patches (search-patches "weechat-python.patch")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) -- cgit v1.3 From d6465efaa9ebe9b464371b16a8cb7cdbe429a421 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 19 Oct 2016 10:20:04 +0530 Subject: gnu: gajim: License is "version 3 only". * gnu/packages/messaging.scm (gajim)[license]: Change to GPL3. Signed-off-by: Leo Famulari --- gnu/packages/messaging.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 0089da1112..37bbed75e5 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -504,7 +504,7 @@ Among its features are: a tabbed chat window and single window modes; support for group chat (with Multi-User Chat protocol), invitation, chat to group chat transformation; audio and video conferences; file transfer; TLS, GPG and end-to-end encryption support; XML console.") - (license license:gpl3+))) + (license license:gpl3))) (define-public prosody (package -- cgit v1.3 From 0f6b6cb996e3e28b2075bd5cb40940cfeb3eba78 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 20 Oct 2016 16:32:37 +0530 Subject: gnu: gajim: Update to 0.16.6. * gnu/packages/messaging.scm (gajim): Update to 0.16.6. Signed-off-by: Leo Famulari --- gnu/packages/messaging.scm | 43 ++++++++++++++++++------------------------- 1 file changed, 18 insertions(+), 25 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 37bbed75e5..66cf231cfb 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -452,7 +452,7 @@ was initially a fork of xmpppy, but is using non-blocking sockets.") (define-public gajim (package (name "gajim") - (version "0.16.5") + (version "0.16.6") (source (origin (method url-fetch) (uri (string-append "https://gajim.org/downloads/" @@ -460,34 +460,27 @@ was initially a fork of xmpppy, but is using non-blocking sockets.") "/gajim-" version ".tar.bz2")) (sha256 (base32 - "14fhcqnkqygh91132dnf1idayj4r3iqbwb44sd3mxv20n6ribh55")))) + "1p3qwzy07f0wkika9yigyiq167l2k6wn12flqa7x55z4ihbysmqk")))) (build-system gnu-build-system) (arguments - `(;; The only check done by gajim-0.16.x is to check that the - ;; translations are up-to-date, and in 0.16.5 they are not, so - ;; "make check" fails. Therefore, we disable tests for now. - ;; - ;; XXX TODO Try re-enabling tests in gajim-0.16.6 or later. - ;; - #:tests? #f - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'install 'wrap-program - (lambda* (#:key outputs #:allow-other-keys) - ;; Make sure all Python scripts run with the correct PYTHONPATH. - (let ((out (assoc-ref outputs "out")) - (path (getenv "PYTHONPATH"))) - (for-each (lambda (name) - (let ((file (string-append out "/bin/" name))) - ;; Wrapping destroys identification of intended - ;; application, so we need to override "APP". - (substitute* file - (("APP=`basename \\$0`") - (string-append "APP=" name))) - (wrap-program file - `("PYTHONPATH" ":" prefix (,path))))) - '("gajim" "gajim-remote" "gajim-history-manager"))) - #t))))) + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure all Python scripts run with the correct PYTHONPATH. + (let ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (for-each (lambda (name) + (let ((file (string-append out "/bin/" name))) + ;; Wrapping destroys identification of intended + ;; application, so we need to override "APP". + (substitute* file + (("APP=`basename \\$0`") + (string-append "APP=" name))) + (wrap-program file + `("PYTHONPATH" ":" prefix (,path))))) + '("gajim" "gajim-remote" "gajim-history-manager"))) + #t))))) (native-inputs `(("intltool" ,intltool))) (propagated-inputs -- cgit v1.3 From 8e3017cc65c1a326df50085f014df26784580f5c Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sun, 23 Oct 2016 10:41:37 -0400 Subject: gnu: windowmaker: Update to 0.95.7. * gnu/packages/gnustep.scm (windowmaker): Update to 0.95.7. --- gnu/packages/gnustep.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm index 6c522866c9..f49b25492e 100644 --- a/gnu/packages/gnustep.scm +++ b/gnu/packages/gnustep.scm @@ -35,7 +35,7 @@ (define-public windowmaker (package (name "windowmaker") - (version "0.95.6") + (version "0.95.7") (source (origin (method url-fetch) (uri (string-append @@ -43,7 +43,7 @@ version ".tar.gz")) (sha256 (base32 - "1i3dw1yagsa3rs9x2na2ynqlgmbahayws0kz4vl00fla6550nns3")))) + "1acph0nq6fsb452sl7j7a7kcc87zqqaw7qms1p8ijar19dn4hbc4")))) (build-system gnu-build-system) (arguments '(#:phases (alist-cons-before -- cgit v1.3 From 02cfea6627e385f6a0e566d810f3593c74bbc029 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 23 Oct 2016 18:07:30 -0400 Subject: gnu: musl: Fix CVE-2016-8859. * gnu/packages/patches/musl-CVE-2016-8859.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/musl.scm (musl)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/musl.scm | 1 + gnu/packages/patches/musl-CVE-2016-8859.patch | 81 +++++++++++++++++++++++++++ 3 files changed, 83 insertions(+) create mode 100644 gnu/packages/patches/musl-CVE-2016-8859.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index df9f8fc4a2..0d400e93e4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -712,6 +712,7 @@ dist_patch_DATA = \ %D%/packages/patches/mupdf-CVE-2016-6265.patch \ %D%/packages/patches/mupdf-CVE-2016-6525.patch \ %D%/packages/patches/mupen64plus-ui-console-notice.patch \ + %D%/packages/patches/musl-CVE-2016-8859.patch \ %D%/packages/patches/mutt-store-references.patch \ %D%/packages/patches/nasm-no-ps-pdf.patch \ %D%/packages/patches/net-tools-bitrot.patch \ diff --git a/gnu/packages/musl.scm b/gnu/packages/musl.scm index a96185a561..321290872e 100644 --- a/gnu/packages/musl.scm +++ b/gnu/packages/musl.scm @@ -32,6 +32,7 @@ (method url-fetch) (uri (string-append "http://www.musl-libc.org/releases/" name "-" version ".tar.gz")) + (patches (search-patches "musl-CVE-2016-8859.patch")) (sha256 (base32 "1ymhxkskivzph0q34zadwfglc5gyahqajm7chqqn2zraxv3lgr4p")))) diff --git a/gnu/packages/patches/musl-CVE-2016-8859.patch b/gnu/packages/patches/musl-CVE-2016-8859.patch new file mode 100644 index 0000000000..7bb5b892dd --- /dev/null +++ b/gnu/packages/patches/musl-CVE-2016-8859.patch @@ -0,0 +1,81 @@ +Fix CVE-2016-8859: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8859 + +Patch copied from upstream source repository: + +http://git.musl-libc.org/cgit/musl/commit/?id=c3edc06d1e1360f3570db9155d6b318ae0d0f0f7 + +From c3edc06d1e1360f3570db9155d6b318ae0d0f0f7 Mon Sep 17 00:00:00 2001 +From: Rich Felker +Date: Thu, 6 Oct 2016 18:34:58 -0400 +Subject: [PATCH] fix missing integer overflow checks in regexec buffer size + computations + +most of the possible overflows were already ruled out in practice by +regcomp having already succeeded performing larger allocations. +however at least the num_states*num_tags multiplication can clearly +overflow in practice. for safety, check them all, and use the proper +type, size_t, rather than int. + +also improve comments, use calloc in place of malloc+memset, and +remove bogus casts. +--- + src/regex/regexec.c | 23 ++++++++++++++++++----- + 1 file changed, 18 insertions(+), 5 deletions(-) + +diff --git a/src/regex/regexec.c b/src/regex/regexec.c +index 16c5d0a..dd52319 100644 +--- a/src/regex/regexec.c ++++ b/src/regex/regexec.c +@@ -34,6 +34,7 @@ + #include + #include + #include ++#include + + #include + +@@ -206,11 +207,24 @@ tre_tnfa_run_parallel(const tre_tnfa_t *tnfa, const void *string, + + /* Allocate memory for temporary data required for matching. This needs to + be done for every matching operation to be thread safe. This allocates +- everything in a single large block from the stack frame using alloca() +- or with malloc() if alloca is unavailable. */ ++ everything in a single large block with calloc(). */ + { +- int tbytes, rbytes, pbytes, xbytes, total_bytes; ++ size_t tbytes, rbytes, pbytes, xbytes, total_bytes; + char *tmp_buf; ++ ++ /* Ensure that tbytes and xbytes*num_states cannot overflow, and that ++ * they don't contribute more than 1/8 of SIZE_MAX to total_bytes. */ ++ if (num_tags > SIZE_MAX/(8 * sizeof(int) * tnfa->num_states)) ++ goto error_exit; ++ ++ /* Likewise check rbytes. */ ++ if (tnfa->num_states+1 > SIZE_MAX/(8 * sizeof(*reach_next))) ++ goto error_exit; ++ ++ /* Likewise check pbytes. */ ++ if (tnfa->num_states > SIZE_MAX/(8 * sizeof(*reach_pos))) ++ goto error_exit; ++ + /* Compute the length of the block we need. */ + tbytes = sizeof(*tmp_tags) * num_tags; + rbytes = sizeof(*reach_next) * (tnfa->num_states + 1); +@@ -221,10 +235,9 @@ tre_tnfa_run_parallel(const tre_tnfa_t *tnfa, const void *string, + + (rbytes + xbytes * tnfa->num_states) * 2 + tbytes + pbytes; + + /* Allocate the memory. */ +- buf = xmalloc((unsigned)total_bytes); ++ buf = calloc(total_bytes, 1); + if (buf == NULL) + return REG_ESPACE; +- memset(buf, 0, (size_t)total_bytes); + + /* Get the various pointers within tmp_buf (properly aligned). */ + tmp_tags = (void *)buf; +-- +2.10.1 + -- cgit v1.3 From bd1b1e0517b046a6ad6d48633d43c644edea7424 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Mon, 24 Oct 2016 19:12:59 +0800 Subject: gnu: gnumeric: Use 'glib-or-gtk-build-system'. Reported by Pjotr Prins . * gnu/packages/gnome.scm (gnumeric)[build-systems]: Switch to GLIB-OR-GTK-BUILD-SYSTEM. --- gnu/packages/gnome.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 5f4fc8275f..1bd0caccb3 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1598,7 +1598,7 @@ Hints specification (EWMH).") (sha256 (base32 "1rvadlgikklwb6rccqc3rlhqv3m9qx27rchm7znxr062fn7fgb68")))) - (build-system gnu-build-system) + (build-system glib-or-gtk-build-system) (arguments `(;; The gnumeric developers don't worry much about failing tests. ;; See https://bugzilla.gnome.org/show_bug.cgi?id=732387 -- cgit v1.3 From 9c798f9036d2d3f90e567052efb06b269c08ed14 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 18 Oct 2016 08:04:54 +0000 Subject: gnu: Add whois. * gnu/packages/networking.scm (whois): New variable. Signed-off-by: Marius Bakke --- gnu/packages/networking.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 52bd0c4cf6..ac8867352d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages gettext) #:use-module (gnu packages gnupg) #:use-module (gnu packages gtk) + #:use-module (gnu packages libidn) #:use-module (gnu packages linux) #:use-module (gnu packages lua) #:use-module (gnu packages mit-krb5) @@ -424,6 +425,44 @@ and up to 1 Mbit/s downstream.") ;; src/md5.[ch] is released under the zlib license (license (list license:isc license:zlib)))) +(define-public whois + (package + (name "whois") + (version "5.2.12") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://debian/pool/main/w/whois/" + name "_" version ".tar.xz")) + (sha256 + (base32 + "1wfdyqi64l5x56j259jrrlbh19b7q7i6r83a8q8rjzcqp0kl0vdj")))) + (build-system gnu-build-system) + ;; TODO: unbundle mkpasswd binary + its po files. + (arguments + `(#:tests? #f ; Does not exist + #:make-flags (list "CC=gcc" + (string-append "prefix=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) ; No configure + (add-before 'build 'setenv + (lambda _ + (setenv "HAVE_ICONV" "1") + (setenv "HAVE_LIBIDN" "1")))))) + (inputs + `(("libidn" ,libidn))) + (native-inputs + `(("gettext" ,gnu-gettext) + ("perl" ,perl))) + (synopsis "Improved whois client") + (description "This whois client is intelligent and can +automatically select the appropriate whois server for most queries. +Because of historical reasons this also includes a tool called mkpasswd +which can be used to encrypt a password with @code{crypt(3)}.") + (home-page "https://github.com/rfc1036/whois") + (license license:gpl2+))) + (define-public wireshark (package (name "wireshark") -- cgit v1.3 From c201b28bfa4c8a60a765770e53a5bd0fe85a2f44 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Mon, 24 Oct 2016 13:24:11 -0400 Subject: gnu: red-eclipse: Update to 1.5.6. * gnu/packages/games.scm (red-eclipse): Update to 1.5.6. [arguments]: Adjust phases. --- gnu/packages/games.scm | 70 +++++++++++++++++++++++++------------------------- 1 file changed, 35 insertions(+), 35 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 8cd487659e..365cf5b4b1 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -2158,42 +2158,42 @@ http://lavachat.symlynx.com/unix/") (define-public red-eclipse (let ((data-sources - '(("acerspyro" "0s6q56i5marpm67lx70g5109lir5d6r45y45i8kbz6arc1spa7pp") - ("actors" "0jclmciz64i81ngxwbag8x5m8wvxkhraa9c7plix566y6rh28fv1") - ("appleflap" "1iz5igzdksamldhy0zh4vdjkxqhmg5c0n5g64pd3kan6h8vlbkq4") - ("blendbrush" "1hz3x5npp25dixcadp020xyahmd1i3ihs4cdf77iy84i9njbp7bv") - ("caustics" "05sbj46lrc6lkf7j6ls6jwc21n0qzxvfhfy9j7hdw482p9gvz54h") - ("crosshairs" "05vfxc6vm91dyf1kzig550fglgydp9szl9135q677lk4g60w5dfh") - ("elyvisions" "0fzdbxc40ggqmv4v1llx6sys2gjc6l1nxsbi5scpxqvm86dbddi9") - ("fonts" "0sbvnd96aip49dy1ja01s36p8fwwczibpic7myfw1frs110m0zgr") - ("freezurbern" "0k60dzzq42mfq360qf7bsf4alhy6k5gjfaidg2i1wsz5zssgmqwn") - ("john" "1ln9v8vfm0ggavvdyl438cy4mizzm1i87r9msx1sbja30q8f57c1") - ("jojo" "0cdgl82s4bm6qlv07fsq5l7anbywvvw13d0mng831yn6scf0hxb1") - ("jwin" "0yg5vriffyckgfjmi4487sw07hsp44b3gfw90f0v4jsgbjjm2v20") - ("luckystrike" "0f82caq09znsr9m08qnlbh3jl9j5w0ysga0b7d5ayqr5lpqxfk9k") - ("maps" "14m23h3mip12anhx7i9k5xlapwkjbw4n0l7lj1b7dfcimf71gjll") - ("mayhem" "0dxrr6craqi7ag724qfj9y0lb0pmwyrfpap02cndmjbbacdya0ra") - ("mikeplus64" "040giyrk3hdd26sxhdx37q4mk923g5v3jbrinq1fw2yfvsl6n1cs") - ("misc" "07xfs9hngshg27rl2vf65nyxilgnak3534h8msaan0fjgmzvlk0q") - ("nobiax" "1n3nghi5426r2zav4rsfih8gn37sfa85absvhdwhir8wycsvbkh6") - ("particles" "0yj0nykal3fgxx50278xl2zn2bfz09wbrjcvng56aa6hhfiwp8gd") - ("philipk" "1m3krkxq9hsknbmxg1g5sgnpcv7c8c2q7zpbizw2wb3dir8snvcj") - ("projectiles" "05swvalja7vzqc3dlk136n5b5kdzn3a8il6bg1h12alcaa0k9rba") - ("props" "1cqi6gw5s4z5pj06x6kiiilh4if0hm1yrbqys5dln23mcvw8f0ny") - ("skyboxes" "1mm6xl89b0l98l2h3qn99id7svmpwr940bydgjbcrvlx21yqdric") - ("sounds" "03q7jazf0chszyiaa9cxirbwdnckcp5fl812sj42lv0z4sqz222l") - ("textures" "1caqyxa9xkrwpyhac65akdv1l7nqychgz7zfivasnskk2yy6jani") - ("torley" "1hp8lkzqmdqyq3jn9rains32diw11gg1w3dxxlln5pc041cd7vil") - ("trak" "0wlczjax33q0hz75lgc4qnxlm592pcxgnbkin5qrglv59nrxzxyr") - ("ulukai" "0dkn7qxf92sidhsy4sm4v5z54n449a2z2w9qax5cfgzs78kb5c34") - ("unnamed" "0p9mmfp0vplmswyxh8qab33phcl8lzmzh3mms4f7i587hppdg6db") - ("vanities" "1w23853lmvj4kx5cbxvb5dk598jiqz7ml2bm0qiy7idkf5mcd2lv") - ("vegetation" "0jw1ljhmv62fzvklid6i8syiacmrs075cp7r3gc069bg4fg47cpn") - ("weapons" "1p64ry1s4y7hkgm6i2rdk2x78368359wvx8v81gg179p3sjnjkww") - ("wicked" "1kmpy2n15lyh50rqjspyfg3qrc72jf0n3dx2y3ian7pjfp6ldxd9")))) + '(("acerspyro" "0hqwa3b65l8mz73mcdsvrwbc14mrx1qn52073p5zh69pqd0mlfi0") + ("actors" "0v87wifqwam5j6vsiidmcvw22i51h9h4skgwhi511mxkwryrp26h") + ("appleflap" "0bkh1v125dwd5jhb4rrc1sl0jdlbb2ib53ihbxa66x1p8l27aklw") + ("blendbrush" "1wh88fshsy492kjvadql2ik1q5pqgcj84jz0hc93ngag8xibxhfi") + ("caustics" "0pc5bnd4fmxh06cm3h8045wgiy894f9x5a943n28gymdyql7q4f6") + ("crosshairs" "1w9acqhxw5nm690862msl5jjbk8qlizxm1vv7p95lgm7q7pg0yxx") + ("elyvisions" "04q31lp5jm8b9crf81s6k1jvrn90i1ay3s6vk103iv8g4amsfhdx") + ("fonts" "1rsfk2d9xk0aaazvrcxk4z5n2cnys7pixadh521mv7zrxbx2d95x") + ("freezurbern" "0b2xg5x79yxanr30dhw3zr6dsc6x9w7v7aghbh9kp292j31l280m") + ("john" "07pgjg1rxl3bmwriy2yl3g63nnryjws8jl0ry1cza3p9wd59f8rz") + ("jojo" "0lkzd5pwfqan1gaaz22r5iz4z2nq8dkzycddwa0cxavmq8qmj281") + ("jwin" "0mnyp1inhabw56mw5wkhfd4k6z0lvyhr6cjj6hnj3bz2dip2y2zm") + ("luckystrike" "1d89xnvahmzlgm0bjh3zhf02vxx1q16b70x2cihbl05dic1v75pr") + ("maps" "19gy8kl7w2llsklym32hnlnd05z2dhq5dhdxhq5ss5na67skv5by") + ("mayhem" "1si2gnsf732ml8ygkhg27ckvic9wafqmkgq0ab1ifpfpy606sa8d") + ("mikeplus64" "0l48czyglbc0d4ack8xz9imarb6r4l29krq0mf3ld7yrxbc296vr") + ("misc" "0fri1l3i1s1pzvr7aah4a7d9h2i877c21x184z80v4jpqv4228f3") + ("nobiax" "1jv2yv2qj9qbxhaj1nd70v5142dpg074gkkh3bw2anchi8pzyhs8") + ("particles" "0gwj6m5197gpwddqb3pwlkaiafgfszqysaz2h1bx60qzh5crgsf9") + ("philipk" "0ngccscmvlgc2z96vira7phr87f65l4v7immbl697zmc5fda6k68") + ("projectiles" "1ig6dag5989rgwrhvmz7xz5q8gf5slgnda8h8zmiyhvrnal09hbp") + ("props" "0g3sgrlgmk9zrl67d9pa93hzb4xx3wwznfxa1h3wwilld0m7gzhx") + ("skyboxes" "0lvpzc741vkmy2rnra41ij91wq3pdl28xamy6vapq61mf44xmmvj") + ("sounds" "0jmvvixcx7kv34sxjs4x7vqsyhir6l5av6b3lm8m8rsfi0sdvqml") + ("textures" "1yx01k9yn2v1k79sa68wa51qw1zk03b8irkvxyd14ygibkicvgnb") + ("torley" "1286srp05nfjban6ca124njyil70gr7bm6aqn5p0vz0xr00l4dw5") + ("trak" "1079fg2cbm95psxic3r63i94z3cnbf04wlid2hqnw308s9l9q36c") + ("ulukai" "0yd80ivn51ya60m4cg4bw13wxgijkjagfgskdphy9adgsaqq9n7b") + ("unnamed" "0l21dhw7kbav59p7ysn6dr2sqzjivwxafml4023yznlhxx5fic4m") + ("vanities" "1aqi32lf7y64fv1y00mpixckjr9wj8p1prgyxjiv7s3hf5q7n2b3") + ("vegetation" "0253fdn5sxywrjb79krhvq2884almxpysn6dn0hi6ylpjzl78zrn") + ("weapons" "0y2zsx6g6k9izshgix9id3y01hsisd88mp5zrlm5x9v8y0sf6kf8") + ("wicked" "0ib0325dn6vzpx3p4cr6bhg9qhj8c5s20xyzy88xjc3y2pazbdvx")))) (package (name "red-eclipse") - (version "1.5.5") + (version "1.5.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/red-eclipse/base" @@ -2201,7 +2201,7 @@ http://lavachat.symlynx.com/unix/") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0xl3655876i8j5nixy0yp73s0yw9nwysj68fyhqs2agmvshryy96")))) + "1sv3xhng18sl655sd46lpmqbqz32h32s7nwz68bdr9z9w3iwkf66")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target -- cgit v1.3 From 405be8dceb41d18c9fefb3343e053fd7c0ce3321 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 Oct 2016 20:58:03 +0300 Subject: gnu: efl: Update to 1.18.2. * gnu/packages/enlightenment.scm (efl): Update to 1.18.2. --- gnu/packages/enlightenment.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index 99c5b394fe..625fdae6e9 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -56,7 +56,7 @@ (define-public efl (package (name "efl") - (version "1.18.1") + (version "1.18.2") (source (origin (method url-fetch) (uri (string-append @@ -64,7 +64,7 @@ version ".tar.xz")) (sha256 (base32 - "08njx6wd505as1vn0yp4mnmf6mb2v28jsipxxx4zhf78v18d2sqc")))) + "1vbvsrrpkvvrmvjavwnp5q77kw5i7vmbaj2vq5mnmrbzamvaybr9")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.3 From 8c00b83818acbbc3dfd406465e50439c3418afc5 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Mon, 26 Sep 2016 23:55:58 +0200 Subject: services: nginx: Virtual hosts are first-class configuration items. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/web.scm (): New record type. (config-domain-strings): New procedure. (config-index-strings): New procedure. (default-nginx-vhost-config): New procedure. (default-nginx-config): Add vhost support and temporary directories (nginx-activation): Create temporary directories (nginx-service): Add vhost-list key. * doc/guix.texi (Web Services): Document 'nginx-vhost-configuration'. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 50 +++++++++++++++++++++++++++- gnu/services/web.scm | 92 +++++++++++++++++++++++++++++++++++++++++++++++++--- 2 files changed, 137 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index 86b82c8c4a..1293b8bc1e 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -27,7 +27,8 @@ Copyright @copyright{} 2016 Chris Marusich@* Copyright @copyright{} 2016 Efraim Flashner@* Copyright @copyright{} 2016 John Darrington@* Copyright @copyright{} 2016 ng0@* -Copyright @copyright{} 2016 Jan Nieuwenhuizen +Copyright @copyright{} 2016 Jan Nieuwenhuizen@* +Copyright @copyright{} 2016 Julien Lepiller Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or @@ -10397,6 +10398,7 @@ The @code{(gnu services web)} module provides the following service: @deffn {Scheme Procedure} nginx-service [#:nginx nginx] @ [#:log-directory ``/var/log/nginx''] @ [#:run-directory ``/var/run/nginx''] @ + [#:vhost-list (list (nginx-vhost-configuration))] @ [#:config-file] Return a service that runs @var{nginx}, the nginx web server. @@ -10407,8 +10409,54 @@ files are written to @var{run-directory}. For proper operation, these arguments should match what is in @var{config-file} to ensure that the directories are created when the service is activated. +As an alternative to using a @var{config-file}, @var{vhost-list} can be +used to specify the list of @dfn{virtual hosts} required on the host. For +this to work, use the default value for @var{config-file}. + @end deffn +@deftp {Data Type} nginx-vhost-configuration +Data type representing the configuration of an nginx virtual host. +This type has the following parameters: + +@table @asis +@item @code{http-port} (default: @code{80}) +Nginx will listen for HTTP connection on this port. Set it at @code{#f} if +nginx should not listen for HTTP (non secure) connection for this +@dfn{virtual host}. + +@item @code{https-port} (default: @code{443}) +Nginx will listen for HTTPS connection on this port. Set it at @code{#f} if +nginx should not listen for HTTPS (secure) connection for this @dfn{virtual host}. + +Note that nginx can listen for HTTP and HTTPS connections in the same +@dfn{virtual host}. + +@item @code{server-name} (default: @code{(list 'default)}) +A list of server names this vhost represents. @code{'default} represents the +default vhost for connections matching no other vhost. + +@item @code{root} (default: @code{"/srv/http"}) +Root of the website nginx will serve. + +@item @code{index} (default: @code{(list "index.html")}) +Index files to look for when clients ask for a directory. If it cannot be found, +Nginx will send the list of files in the directory. + +@item @code{ssl-certificate} (default: @code{"/etc/nginx/cert.pem"}) +Where to find the certificate for secure connections. Set it to @code{#f} if +you don't have a certificate or you don't want to use HTTPS. + +@item @code{ssl-certificate-key} (default: @code{"/etc/nginx/key.pem"}) +Where to find the private key for secure connections. Set it to @code{#f} if +you don't have a key or you don't want to use HTTPS. + +@item @code{server-tokens?} (default: @code{#f}) +Whether the server should add its configuration to response. + +@end table +@end deftp + @node Network File System @subsubsection Network File System @cindex NFS diff --git a/gnu/services/web.scm b/gnu/services/web.scm index 0a2a09bbf5..59e1e54e04 100644 --- a/gnu/services/web.scm +++ b/gnu/services/web.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2015 David Thompson ;;; Copyright © 2015, 2016 Ludovic Courtès ;;; Copyright © 2016 ng0 +;;; Copyright © 2016 Julien Lepiller ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,6 +30,8 @@ #:use-module (ice-9 match) #:export (nginx-configuration nginx-configuration? + nginx-vhost-configuration + nginx-vhost-configuration? nginx-service nginx-service-type)) @@ -38,6 +41,26 @@ ;;; ;;; Code: +(define-record-type* + nginx-vhost-configuration make-nginx-vhost-configuration + nginx-vhost-configuration? + (http-port nginx-vhost-configuration-http-port + (default 80)) + (https-port nginx-vhost-configuration-https-port + (default 443)) + (server-name nginx-vhost-configuration-server-name + (default (list 'default))) + (root nginx-vhost-configuration-root + (default "/srv/http")) + (index nginx-vhost-configuration-index + (default (list "index.html"))) + (ssl-certificate nginx-vhost-configuration-ssl-certificate + (default "/etc/nginx/cert.pem")) + (ssl-certificate-key nginx-vhost-configuration-ssl-certificate-key + (default "/etc/nginx/key.pem")) + (server-tokens? nginx-vhost-configuration-server-tokens? + (default #f))) + (define-record-type* nginx-configuration make-nginx-configuration nginx-configuration? @@ -46,16 +69,70 @@ (run-directory nginx-configuration-run-directory) ;string (file nginx-configuration-file)) ;string | file-like -(define (default-nginx-config log-directory run-directory) +(define (config-domain-strings names) + "Return a string denoting the nginx config representation of NAMES, a list +of domain names." + (string-concatenate + (map (match-lambda + ('default "_") + ((? string? str) str)) + names))) + +(define (config-index-strings names) + "Return a string denoting the nginx config representation of NAMES, a list +of index files." + (string-concatenate + (map (match-lambda + ((? string? str) str)) + names))) + +(define (default-nginx-vhost-config vhost) + (string-append + " server {\n" + (if (nginx-vhost-configuration-http-port vhost) + (string-append " listen " + (number->string (nginx-vhost-configuration-http-port vhost)) + ";\n") + "") + (if (nginx-vhost-configuration-https-port vhost) + (string-append " listen " + (number->string (nginx-vhost-configuration-https-port vhost)) + " ssl;\n") + "") + " server_name " (config-domain-strings + (nginx-vhost-configuration-server-name vhost)) + ";\n" + (if (nginx-vhost-configuration-ssl-certificate vhost) + (string-append " ssl_certificate " + (nginx-vhost-configuration-ssl-certificate vhost) ";\n") + "") + (if (nginx-vhost-configuration-ssl-certificate-key vhost) + (string-append " ssl_certificate_key " + (nginx-vhost-configuration-ssl-certificate-key vhost) ";\n") + "") + " root " (nginx-vhost-configuration-root vhost) ";\n" + " index " (config-index-strings (nginx-vhost-configuration-index vhost)) ";\n" + " server_tokens " (if (nginx-vhost-configuration-server-tokens? vhost) + "on" "off") ";\n" + " }\n")) + +(define (default-nginx-config log-directory run-directory vhost-list) (plain-file "nginx.conf" (string-append "user nginx nginx;\n" "pid " run-directory "/pid;\n" "error_log " log-directory "/error.log info;\n" "http {\n" + " client_body_temp_path " run-directory "/client_body_temp;\n" + " proxy_temp_path " run-directory "/proxy_temp;\n" + " fastcgi_temp_path " run-directory "/fastcgi_temp;\n" + " uwsgi_temp_path " run-directory "/uwsgi_temp;\n" + " scgi_temp_path " run-directory "/scgi_temp;\n" " access_log " log-directory "/access.log;\n" - " root /var/www;\n" - " server {}\n" + (let ((http (map default-nginx-vhost-config vhost-list))) + (do ((http http (cdr http)) + (block "" (string-append (car http) "\n" block ))) + ((null? http) block))) "}\n" "events {}\n"))) @@ -79,6 +156,12 @@ (mkdir-p #$log-directory) (format #t "creating nginx run directory '~a'~%" #$run-directory) (mkdir-p #$run-directory) + (format #t "creating nginx temp directories '~a/{client_body,proxy,fastcgi,uwsgi,scgi}_temp'~%" #$run-directory) + (mkdir-p (string-append #$run-directory "/client_body_temp")) + (mkdir-p (string-append #$run-directory "/proxy_temp")) + (mkdir-p (string-append #$run-directory "/fastcgi_temp")) + (mkdir-p (string-append #$run-directory "/uwsgi_temp")) + (mkdir-p (string-append #$run-directory "/scgi_temp")) ;; Check configuration file syntax. (system* (string-append #$nginx "/sbin/nginx") "-c" #$config-file "-t"))))) @@ -114,8 +197,9 @@ (define* (nginx-service #:key (nginx nginx) (log-directory "/var/log/nginx") (run-directory "/var/run/nginx") + (vhost-list (list (nginx-vhost-configuration))) (config-file - (default-nginx-config log-directory run-directory))) + (default-nginx-config log-directory run-directory vhost-list))) "Return a service that runs NGINX, the nginx web server. The nginx daemon loads its runtime configuration from CONFIG-FILE, stores log -- cgit v1.3 From 3b5783fcd94a7e213b37e1d0008403fec68db70f Mon Sep 17 00:00:00 2001 From: Amirouche Date: Sun, 9 Oct 2016 12:31:20 +0200 Subject: gnu: Add guile-bytestructures MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile.scm (guile-bytestructures): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/guile.scm | 81 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 81 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index a6a7d69b30..f712514285 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2016 Eraim Flashner ;;; Copyright © 2016 Alex Kost ;;; Copyright © 2016 Adonay "adfeno" Felipe Nogueira +;;; Copyright © 2016 Amirouche ;;; ;;; This file is part of GNU Guix. ;;; @@ -1266,4 +1267,84 @@ is no support for parsing block and inline level HTML.") (define-public guile2.2-commonmark (package-for-guile-2.2 guile-commonmark)) +(define-public guile-bytestructures + (package + (name "guile-bytestructures") + (version "20160726.53127f6") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/TaylanUB/scheme-bytestructures") + (commit "53127f608caf64b34fa41c389b2743b546fbe9da"))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0l4nx1vp9fkrgrgwjiycj7nx6wfjfd39rqamv4pmq7issi8mrywq")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils) + (ice-9 match) + (ice-9 popen) + (ice-9 rdelim)) + (let* ((out (assoc-ref %outputs "out")) + (guile (assoc-ref %build-inputs "guile")) + (effective (read-line + (open-pipe* OPEN_READ + (string-append guile "/bin/guile") + "-c" "(display (effective-version))"))) + (module-dir (string-append out "/share/guile/site/" + effective)) + (source (assoc-ref %build-inputs "source")) + (doc (string-append out "/share/doc/scheme-bytestructures")) + (scm-files (filter (lambda (path) + (not (string-prefix? "bytestructures/r7" path))) + (with-directory-excursion source + (find-files "bytestructures" "\\.scm$")))) + (guild (string-append (assoc-ref %build-inputs "guile") + "/bin/guild"))) + ;; Make installation directories. + (mkdir-p doc) + + ;; Compile .scm files and install. + (chdir source) + (setenv "GUILE_AUTO_COMPILE" "0") + (for-each (lambda (file) + (let* ((dest-file (string-append module-dir "/" + file)) + (go-file (string-append module-dir "/" + (substring file 0 + (string-rindex file #\.)) + ".go"))) + ;; Install source module. + (mkdir-p (dirname dest-file)) + (copy-file file dest-file) + + ;; Install compiled module. + (mkdir-p (dirname go-file)) + (unless (zero? (system* guild "compile" + "-L" source + "-o" go-file + file)) + (error (format #f "Failed to compile ~s to ~s!" + file go-file))))) + scm-files) + + ;; Also copy over the README. + (install-file "README.md" doc) + #t)))) + (inputs + `(("guile" ,guile-2.0))) + (home-page "https://github.com/TaylanUB/scheme-bytestructures") + (synopsis "Structured access to bytevector contents for Guile") + (description + "Guile bytestructures offers a system imitating the type system +of the C programming language, to be used on bytevectors. C's type +system works on raw memory, and Guile works on bytevectors which are +an abstraction over raw memory. It's also more powerful than the C +type system, elevating types to first-class status.") + (license gpl3+))) + ;;; guile.scm ends here -- cgit v1.3 From d3c4f3bb00b9e04b7bdb2847f21e33292b103c21 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Fri, 30 Sep 2016 09:59:08 +0200 Subject: gnu: Add hdf-eos2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (hdf-eos2): New variable. * gnu/packages/patches/hdf-eos2-build-shared.patch: New file. * gnu/packages/patches/hdf-eos2-remove-gctp.patch: New file. * gnu/packages/patches/hdf-eos2-fortrantests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add patches. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 3 + gnu/packages/maths.scm | 35 +++ gnu/packages/patches/hdf-eos2-build-shared.patch | 25 ++ gnu/packages/patches/hdf-eos2-fortrantests.patch | 329 +++++++++++++++++++++++ gnu/packages/patches/hdf-eos2-remove-gctp.patch | 55 ++++ 5 files changed, 447 insertions(+) create mode 100644 gnu/packages/patches/hdf-eos2-build-shared.patch create mode 100644 gnu/packages/patches/hdf-eos2-fortrantests.patch create mode 100644 gnu/packages/patches/hdf-eos2-remove-gctp.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 0d400e93e4..3e900b14fb 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -590,6 +590,9 @@ dist_patch_DATA = \ %D%/packages/patches/hdf4-reproducibility.patch \ %D%/packages/patches/hdf4-shared-fortran.patch \ %D%/packages/patches/hdf5-config-date.patch \ + %D%/packages/patches/hdf-eos2-build-shared.patch \ + %D%/packages/patches/hdf-eos2-remove-gctp.patch \ + %D%/packages/patches/hdf-eos2-fortrantests.patch \ %D%/packages/patches/hdf-eos5-build-shared.patch \ %D%/packages/patches/hdf-eos5-remove-gctp.patch \ %D%/packages/patches/hdf-eos5-fix-szip.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d41a3f11bf..0cdf4f74b5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -544,6 +544,41 @@ extremely large and complex data collections.") (license (license:x11-style "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) +(define-public hdf-eos2 + (package + (name "hdf-eos2") + (version "19.1.0") + (source + (origin + (method url-fetch) + (uri "ftp://edhs1.gsfc.nasa.gov\ +/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z") + (sha256 + (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz")) + (patches (search-patches "hdf-eos2-remove-gctp.patch" + "hdf-eos2-build-shared.patch" + "hdf-eos2-fortrantests.patch")))) + (build-system gnu-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs + `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API + ("zlib" ,zlib) + ("libjpeg" ,libjpeg) + ("gctp" ,gctp))) + (arguments + `( #:configure-flags '("--enable-install-include" "--enable-shared" + "CC=h4cc -Df2cFortran" "LIBS=-lgctp") + #:parallel-tests? #f)) + (home-page "http://hdfeos.org/software/library.php#HDF-EOS2") + (synopsis "HDF4-based data format for NASA's Earth Observing System") + (description "HDF-EOS2 is a software library built on HDF4 which supports +the construction of data structures used in NASA's Earth Observing +System (Grid, Point and Swath).") + + ;; Source files carry a permissive license header. + (license (license:non-copyleft home-page)))) + (define-public hdf-eos5 (package (name "hdf-eos5") diff --git a/gnu/packages/patches/hdf-eos2-build-shared.patch b/gnu/packages/patches/hdf-eos2-build-shared.patch new file mode 100644 index 0000000000..71112e38c2 --- /dev/null +++ b/gnu/packages/patches/hdf-eos2-build-shared.patch @@ -0,0 +1,25 @@ +Changes necessary for shared library linking to succeed. + +diff --git a/src/Makefile.in b/src/Makefile.in +index 9534473..12411bf 100644 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -73,7 +73,7 @@ LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) \ + $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ + $(AM_CFLAGS) $(CFLAGS) + CCLD = $(CC) +-LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ ++LINK = HDF4_USE_SHLIB=yes $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ + $(AM_LDFLAGS) $(LDFLAGS) -o $@ + SOURCES = $(libhdfeos_la_SOURCES) + DIST_SOURCES = $(libhdfeos_la_SOURCES) +@@ -125,8 +125,6 @@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ + INSTALL_SCRIPT = @INSTALL_SCRIPT@ + INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ + +-# Set LDFLAGS to alow the HDF-EOS library to use extern variables from HDF4 +-LDFLAGS = -Wl,-single_module + LIBOBJS = @LIBOBJS@ + LIBS = @LIBS@ + LIBTOOL = @LIBTOOL@ + diff --git a/gnu/packages/patches/hdf-eos2-fortrantests.patch b/gnu/packages/patches/hdf-eos2-fortrantests.patch new file mode 100644 index 0000000000..adecc184cb --- /dev/null +++ b/gnu/packages/patches/hdf-eos2-fortrantests.patch @@ -0,0 +1,329 @@ +Fix multi-line string formatting in fortran test programs (reported upstream). + +diff --git a/samples/appendfield.f b/samples/appendfield.f +index 42c4b6b..58257f7 100644 +--- a/samples/appendfield.f ++++ b/samples/appendfield.f +@@ -22,8 +22,8 @@ c + inarray(i) = i + enddo + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer_o +- 1f_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + swid = swattach(swfid, "Swath1") + + +diff --git a/samples/definefields.f b/samples/definefields.f +index 89859e4..f3b3497 100644 +--- a/samples/definefields.f ++++ b/samples/definefields.f +@@ -24,8 +24,8 @@ c DFACC_RDWR accesscode in the open statement. The SWopen + c routine returns the swath fileid, swfid, which is used to + c identify the file in subsequent routines. + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + + c +diff --git a/samples/definegdflds.f b/samples/definegdflds.f +index 177422e..1b7fcf6 100644 +--- a/samples/definegdflds.f ++++ b/samples/definegdflds.f +@@ -21,8 +21,8 @@ + fillval1=-7.0 + fillval2=-9999.0 + +- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_ +- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + + gdid1 = gdattach(gdfid, "UTMGrid") +diff --git a/samples/definelevels.f b/samples/definelevels.f +index 2496d5f..64b2842 100644 +--- a/samples/definelevels.f ++++ b/samples/definelevels.f +@@ -32,8 +32,8 @@ c DFACC_RDWR access code in the open statement. The ptopen + c routine returns the point fileid, ptfid, which is used to + c identify the file in subsequent routines. + +- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"// ++ 1 "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + + c +diff --git a/samples/inquiregrid.f b/samples/inquiregrid.f +index 8110461..8ce71e4 100644 +--- a/samples/inquiregrid.f ++++ b/samples/inquiregrid.f +@@ -18,8 +18,8 @@ + + + +- gdfid = gdopen('GridFile_created_with_hadeos_sample_file_writer_ +- 1of_HDFEOS2_version_219_or_higher_release.hdf', DFACC_READ) ++ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) + + + if (gdfid .ne. -1) then +diff --git a/samples/inquireswath.f b/samples/inquireswath.f +index 899ee59..78c292b 100644 +--- a/samples/inquireswath.f ++++ b/samples/inquireswath.f +@@ -24,8 +24,8 @@ c + c Open the Swath File for read only access + c + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) + + + if (swfid .NE. -1) then +diff --git a/samples/readdimscalegrid.f b/samples/readdimscalegrid.f +index fed5540..a0bb48a 100644 +--- a/samples/readdimscalegrid.f ++++ b/samples/readdimscalegrid.f +@@ -34,8 +34,8 @@ + ! * id, gdfid, which is used to identify the file in subsequent routines. + ! */ + +- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_ +- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + ! /* + ! * If the grid file cannot be found, gdopen will return -1 for the file +diff --git a/samples/readdimscaleswath.f b/samples/readdimscaleswath.f +index 97b6264..1b61624 100644 +--- a/samples/readdimscaleswath.f ++++ b/samples/readdimscaleswath.f +@@ -33,8 +33,8 @@ + ! * id, swfid, which is used to identify the file in subsequent routines. + ! */ + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + ! /* + ! * If the swath file cannot be found, swopen will return -1 for the file +diff --git a/samples/readfields.f b/samples/readfields.f +index 873b30a..29d42f0 100644 +--- a/samples/readfields.f ++++ b/samples/readfields.f +@@ -21,8 +21,8 @@ c + c Open the HDF swath file, "SwathFile.hdf" + c + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) + + + if (swfid .NE. -1) then +diff --git a/samples/readgdflds.f b/samples/readgdflds.f +index e5fe85f..ff2bd86 100644 +--- a/samples/readgdflds.f ++++ b/samples/readgdflds.f +@@ -9,8 +9,8 @@ + integer DFNT_FLOAT32 + parameter (DFNT_FLOAT32=5) + +- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_ +- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + if (gdfid .ne. -1) then + +diff --git a/samples/readlevels.f b/samples/readlevels.f +index a7fd033..f349398 100644 +--- a/samples/readlevels.f ++++ b/samples/readlevels.f +@@ -36,8 +36,8 @@ c + c Open the HDF swath file, "PointFile.hdf". + c + +- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) ++ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"// ++ + "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) + + c + c Read Simple Point +@@ -47,6 +47,8 @@ c + status = ptlevinfo(ptid, 0, fldlist, fldtype, fldorder) + n = ptnrecs(ptid, 0) + ++ write(*,*) n ++ + do 5 i=1,n + recs(i) = i - 1 + 5 continue +diff --git a/samples/setupgrid.f b/samples/setupgrid.f +index be5408c..cf4bd04 100644 +--- a/samples/setupgrid.f ++++ b/samples/setupgrid.f +@@ -34,8 +34,8 @@ c code in the open statement. The GDopen routine returns the grid + c file id, gdfid, which is used to identify the file in subsequent + c routines in the library. + c +- gdfid = gdopen('GridFile_created_with_hadeos_sample_file_writer_of +- 1_HDFEOS2_version_219_or_higher_release.hdf',DFACC_CREATE) ++ gdfid = gdopen('GridFile_created_with_hadeos_sample_file_writer_"// ++ 1"of_HDFEOS2_version_219_or_higher_release.hdf',DFACC_CREATE) + + c + c Create UTM Grid +diff --git a/samples/setupswath.f b/samples/setupswath.f +index d0289d6..fbaa0bb 100644 +--- a/samples/setupswath.f ++++ b/samples/setupswath.f +@@ -22,8 +22,8 @@ c code in the open statement. The SWopen routine returns the swath + c file id, swfid, which is used to identify the file in subsequent + c routines in the library. + c +- swfid = swopen('SwathFile_created_with_hadeos_sample_file_writer_o +- 1f_HDFEOS2_version_219_or_higher_release.hdf',DFACC_CREATE) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf",DFACC_CREATE) + + c + c The first of these, SWcreate, creates the swath, "Swath1", within the +diff --git a/samples/subsetgrid.f b/samples/subsetgrid.f +index c57e541..087e5b1 100644 +--- a/samples/subsetgrid.f ++++ b/samples/subsetgrid.f +@@ -22,8 +22,8 @@ c + c Open the HDF grid file, "GridFile.hdf" + c + +- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_ +- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) ++ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) + + if (gdfid .NE. -1) then + +diff --git a/samples/subsetpoint.f b/samples/subsetpoint.f +index 9e72c5f..2e76d7d 100644 +--- a/samples/subsetpoint.f ++++ b/samples/subsetpoint.f +@@ -21,8 +21,8 @@ c + c Open the HDF point file, "PointFile.hdf" + c + +- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) ++ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"// ++ 1 "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) + + if (ptfid .NE. -1) then + +diff --git a/samples/subsetswath.f b/samples/subsetswath.f +index dcee609..9af8a46 100644 +--- a/samples/subsetswath.f ++++ b/samples/subsetswath.f +@@ -28,8 +28,8 @@ c + c Open the HDF swath file, "SwathFile.hdf" + c + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ) + + if (swfid .NE. -1) then + +diff --git a/samples/writedimscalegrid.f b/samples/writedimscalegrid.f +index 09688d8..42013fe 100644 +--- a/samples/writedimscalegrid.f ++++ b/samples/writedimscalegrid.f +@@ -29,8 +29,8 @@ + ! * id, gdfid, which is used to identify the file in subsequent routines. + ! */ + +- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_ +- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + ! /* + ! * If the grid file cannot be found, gdopen will return -1 for the file +diff --git a/samples/writedimscaleswath.f b/samples/writedimscaleswath.f +index 1151671..1a911a6 100644 +--- a/samples/writedimscaleswath.f ++++ b/samples/writedimscaleswath.f +@@ -31,8 +31,8 @@ + ! * id, swfid, which is used to identify the file in subsequent routines. + ! */ + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_write +- 1r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + ! /* + ! * If the swath file cannot be found, swopen will return -1 for the file +diff --git a/samples/writefields.f b/samples/writefields.f +index a743661..862b96c 100644 +--- a/samples/writefields.f ++++ b/samples/writefields.f +@@ -31,8 +31,8 @@ c + c Open the HDF swath file, "SwathFile.hdf" + c + +- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + + if (swfid .NE. -1) then +diff --git a/samples/writegdflds.f b/samples/writegdflds.f +index d1540b3..81aef75 100644 +--- a/samples/writegdflds.f ++++ b/samples/writegdflds.f +@@ -23,8 +23,8 @@ + enddo + + +- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_ +- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"// ++ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + if (gdfid .ne. -1) then + +diff --git a/samples/writelevels.f b/samples/writelevels.f +index 88e7780..cb40c9e 100644 +--- a/samples/writelevels.f ++++ b/samples/writelevels.f +@@ -32,8 +32,8 @@ c + c Open the HDF point file, "PointFile.hdf". + c + +- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer +- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) ++ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"// ++ + "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR) + + + c +-- +2.10.0 + diff --git a/gnu/packages/patches/hdf-eos2-remove-gctp.patch b/gnu/packages/patches/hdf-eos2-remove-gctp.patch new file mode 100644 index 0000000000..0776c0685e --- /dev/null +++ b/gnu/packages/patches/hdf-eos2-remove-gctp.patch @@ -0,0 +1,55 @@ +Don't build the GCTP bundled with the source and link with the +system's -lgctp instead. We also remove references to the +"testdrivers" directory, which is not distributed together with the +source, causing autoreconf to fail. + +diff --git a/Makefile.in b/Makefile.in +index d468af2..90428a7 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -206,7 +206,7 @@ LIBGCTP = $(top_builddir)/gctp/src/libGctp.la + @TESTDRIVERS_CONDITIONAL_TRUE@TESTDRIVERS = testdrivers + @INSTALL_INCLUDE_CONDITIONAL_FALSE@INCLUDE = + @INSTALL_INCLUDE_CONDITIONAL_TRUE@INCLUDE = include +-SUBDIRS = gctp src $(INCLUDE) samples $(TESTDRIVERS) ++SUBDIRS = src $(INCLUDE) samples $(TESTDRIVERS) + all: all-recursive + + .SUFFIXES: +diff --git a/include/Makefile.in b/include/Makefile.in +index 9938b23..afb7f40 100644 +--- a/include/Makefile.in ++++ b/include/Makefile.in +@@ -190,7 +190,7 @@ LIBGCTP = $(top_builddir)/gctp/src/libGctp.la + # Boilerplate include + + # Headers to install +-include_HEADERS = HE2_config.h HdfEosDef.h HDFEOSVersion.h cfortHdf.h ease.h ++include_HEADERS = HdfEosDef.h HDFEOSVersion.h cfortHdf.h ease.h + all: HE2_config.h + $(MAKE) $(AM_MAKEFLAGS) all-am + +diff --git a/samples/Makefile.in b/samples/Makefile.in +index 9da6e28..6a6186c 100644 +--- a/samples/Makefile.in ++++ b/samples/Makefile.in +@@ -108,7 +108,6 @@ AppendField_SOURCES = AppendField.c + AppendField_OBJECTS = AppendField.$(OBJEXT) + AppendField_LDADD = $(LDADD) + am__DEPENDENCIES_1 = $(top_builddir)/src/libhdfeos.la +-am__DEPENDENCIES_2 = $(top_builddir)/gctp/src/libGctp.la + AppendField_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_2) + DefineFields_SOURCES = DefineFields.c + DefineFields_OBJECTS = DefineFields.$(OBJEXT) +@@ -481,7 +480,7 @@ sharedstatedir = @sharedstatedir@ + sysconfdir = @sysconfdir@ + target_alias = @target_alias@ + LIBHDFEOS2 = $(top_builddir)/src/libhdfeos.la +-LIBGCTP = $(top_builddir)/gctp/src/libGctp.la ++LIBGCTP = + + # Boilerplate definitions file + +-- +2.10.0 + -- cgit v1.3 From d91025e3d0f7a30b38798bc4ef9c0f96d3f85db7 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Wed, 19 Oct 2016 11:44:33 +0200 Subject: gnu: Add coda. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (coda): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0cdf4f74b5..2928cb63a3 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -113,6 +113,37 @@ interactive dialogs to guide them.") (license license:gpl3+) (home-page "http://www.gnu.org/software/c-graph/"))) +(define-public coda + (package + (name "coda") + (version "2.17.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/stcorp/coda/releases/download/" + version "/coda-" version ".tar.gz")) + (sha256 + (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h")))) + (native-inputs + `(("fortran" ,gfortran) + ("python" ,python) + ("python-numpy" ,python-numpy))) + (inputs + `(("zlib" ,zlib) + ("hdf4" ,hdf4-alt) + ("hdf5" ,hdf5))) + (build-system gnu-build-system) + (arguments + '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"))) + (synopsis "A common interface to various earth observation data formats") + (description + "The Common Data Access toolbox (CODA) provides a set of interfaces for +reading remote sensing data from earth observation data files. It consists of +command line applications and interfaces to the C, Fortran, Python, and Java +programming languages.") + (home-page "https://stcorp.nl/coda") + (license license:gpl2+))) + (define-public units (package (name "units") -- cgit v1.3 From ffde82c9ecf99524220e463055f4f18c8c9e7a81 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 25 Oct 2016 00:58:26 +0200 Subject: system: grub: Use Guile-{RSVG,Cairo} instead of Inkscape + ImageMagick. Based on a suggestion by Andy Wingo at . * gnu/build/svg.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/system/grub.scm (svg->png): Add #:width and #:height. Rewrite to use (gnu build svg). (resize-image): Remove. (grub-background-image): Adjust accordingly. --- gnu/build/svg.scm | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++++ gnu/local.mk | 1 + gnu/system/grub.scm | 41 +++++++++++++++---------------- 3 files changed, 89 insertions(+), 22 deletions(-) create mode 100644 gnu/build/svg.scm (limited to 'gnu') diff --git a/gnu/build/svg.scm b/gnu/build/svg.scm new file mode 100644 index 0000000000..d9b909cd73 --- /dev/null +++ b/gnu/build/svg.scm @@ -0,0 +1,69 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Ludovic Courtès +;;; Copyright © 2015 Andy Wingo +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu build svg) + #:use-module (srfi srfi-11) + #:export (svg->png)) + +;; We need Guile-RSVG and Guile-Cairo. Load them lazily, at run time, to +;; allow compilation to proceed. +(module-use! (current-module) (resolve-interface '(rsvg))) +(module-use! (current-module) (resolve-interface '(cairo))) + +(define* (downscaled-surface surface + #:key + source-width source-height + width height) + "Return a new rendering context where SURFACE is scaled to WIDTH x HEIGHT." + (let ((cr (cairo-create (cairo-image-surface-create 'argb32 + width height)))) + (cairo-scale cr (/ width source-width) (/ height source-height)) + (cairo-set-source-surface cr surface 0 0) + (cairo-pattern-set-filter (cairo-get-source cr) 'best) + (cairo-rectangle cr 0 0 source-width source-height) + (cairo-fill cr) + cr)) + +(define* (svg->png in-svg out-png + #:key width height) + "Render the file at IN-SVG as a PNG file in OUT-PNG. When WIDTH and HEIGHT +are provided, use them as the dimensions of OUT-PNG; otherwise preserve the +dimensions of IN-SVG." + (define svg + (rsvg-handle-new-from-file in-svg)) + + (let-values (((origin-width origin-height) + (rsvg-handle-get-dimensions svg))) + (let* ((surf (cairo-image-surface-create 'argb32 + origin-width origin-height)) + (cr (cairo-create surf))) + (rsvg-handle-render-cairo svg cr) + (cairo-surface-flush surf) + (let ((cr (if (and width height + (not (= width origin-width)) + (not (= height origin-height))) + (downscaled-surface surf + #:source-width origin-width + #:source-height origin-height + #:width width + #:height height) + cr))) + (cairo-surface-write-to-png (cairo-get-target cr) out-png))))) + +;;; svg.scm ends here diff --git a/gnu/local.mk b/gnu/local.mk index 3e900b14fb..1cf81c1648 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -431,6 +431,7 @@ GNU_SYSTEM_MODULES = \ %D%/build/linux-initrd.scm \ %D%/build/linux-modules.scm \ %D%/build/marionette.scm \ + %D%/build/svg.scm \ %D%/build/vm.scm \ \ %D%/tests.scm \ diff --git a/gnu/system/grub.scm b/gnu/system/grub.scm index ead48f0e32..249b415ab4 100644 --- a/gnu/system/grub.scm +++ b/gnu/system/grub.scm @@ -27,9 +27,8 @@ #:use-module (gnu artwork) #:use-module (gnu system file-systems) #:autoload (gnu packages grub) (grub) - #:autoload (gnu packages inkscape) (inkscape) - #:autoload (gnu packages imagemagick) (imagemagick) #:autoload (gnu packages compression) (gzip) + #:autoload (gnu packages gtk) (guile-cairo guile-rsvg) #:use-module (ice-9 match) #:use-module (ice-9 regex) #:use-module (srfi srfi-1) @@ -132,25 +131,23 @@ object denoting a file name." ;;; Background image & themes. ;;; -(define (svg->png svg) - "Build a PNG from SVG." - ;; Don't use #:local-build? so that it's substitutable. +(define* (svg->png svg #:key width height) + "Build a PNG of HEIGHT x WIDTH from SVG." (gexp->derivation "grub-image.png" - #~(zero? - (system* (string-append #$inkscape "/bin/inkscape") - "--without-gui" - (string-append "--export-png=" #$output) - #$svg)))) - -(define (resize-image image width height) - "Resize IMAGE to WIDTHxHEIGHT." - ;; Don't use #:local-build? so that it's substitutable. - (let ((size (string-append (number->string width) - "x" (number->string height)))) - (gexp->derivation "grub-image.resized.png" - #~(zero? - (system* (string-append #$imagemagick "/bin/convert") - "-resize" #$size #$image #$output))))) + (with-imported-modules '((gnu build svg)) + #~(begin + ;; We need these two libraries. + (add-to-load-path (string-append #$guile-rsvg + "/share/guile/site/" + (effective-version))) + (add-to-load-path (string-append #$guile-cairo + "/share/guile/site/" + (effective-version))) + + (use-modules (gnu build svg)) + (svg->png #$svg #$output + #:width #$width + #:height #$height))))) (define* (grub-background-image config #:key (width 1024) (height 768)) "Return the GRUB background image defined in CONFIG with a ratio of @@ -160,8 +157,8 @@ WIDTH/HEIGHT, or #f if none was found." (= (grub-image-aspect-ratio image) ratio)) (grub-theme-images (grub-configuration-theme config))))) (if image - (mlet %store-monad ((png (svg->png (grub-image-file image)))) - (resize-image png width height)) + (svg->png (grub-image-file image) + #:width width #:height height) (with-monad %store-monad (return #f))))) -- cgit v1.3 From e9a19bde40a3c8488b30cc3dbc74ea84879decc0 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 24 Oct 2016 22:53:18 -0400 Subject: gnu: linux-libre@4.1: Update to 4.1.35. * gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.35. Remove patch. * gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/linux.scm | 9 +- .../patches/linux-libre-4.1-CVE-2016-5195.patch | 99 ---------------------- 3 files changed, 3 insertions(+), 106 deletions(-) delete mode 100644 gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 1cf81c1648..51849f42c7 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -684,7 +684,6 @@ dist_patch_DATA = \ %D%/packages/patches/libxv-CVE-2016-5407.patch \ %D%/packages/patches/libxvmc-CVE-2016-7953.patch \ %D%/packages/patches/libxslt-generated-ids.patch \ - %D%/packages/patches/linux-libre-4.1-CVE-2016-5195.patch \ %D%/packages/patches/lirc-localstatedir.patch \ %D%/packages/patches/llvm-for-extempore.patch \ %D%/packages/patches/lm-sensors-hwmon-attrs.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 616423aef7..c3c84f4a86 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -336,13 +336,10 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.1 - (make-linux-libre "4.1.34" - "0dajsb363p9lgga22ml8gp9k9lxd8mvrzxk9y3h9c6hpzfcmqdqr" + (make-linux-libre "4.1.35" + "05zvrld1digqwf9kqf5pxx0mxqmwpr5kamhnks6y4yfy7x7jynyk" %intel-compatible-systems - #:configuration-file kernel-config - #:patches (list %boot-logo-patch - (search-patch - "linux-libre-4.1-CVE-2016-5195.patch")))) + #:configuration-file kernel-config)) ;; Avoid rebuilding kernel variants when there is a minor version bump. (define %linux-libre-version "4.8.4") diff --git a/gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch b/gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch deleted file mode 100644 index 37a41f61e4..0000000000 --- a/gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch +++ /dev/null @@ -1,99 +0,0 @@ -Fix CVE-2016-5195, a.k.a. Dirty COW. -Backported to linux-libre-4.1.x by Mark H Weaver . - -From 18652320ea99913c95e7130d654be7f1da6b694f Mon Sep 17 00:00:00 2001 -From: Linus Torvalds -Date: Thu, 13 Oct 2016 13:07:36 -0700 -Subject: [PATCH] mm: remove gup_flags FOLL_WRITE games from __get_user_pages() - -commit 19be0eaffa3ac7d8eb6784ad9bdbc7d67ed8e619 upstream. - -This is an ancient bug that was actually attempted to be fixed once -(badly) by me eleven years ago in commit 4ceb5db9757a ("Fix -get_user_pages() race for write access") but that was then undone due to -problems on s390 by commit f33ea7f404e5 ("fix get_user_pages bug"). - -In the meantime, the s390 situation has long been fixed, and we can now -fix it by checking the pte_dirty() bit properly (and do it better). The -s390 dirty bit was implemented in abf09bed3cce ("s390/mm: implement -software dirty bits") which made it into v3.9. Earlier kernels will -have to look at the page state itself. - -Also, the VM has become more scalable, and what used a purely -theoretical race back then has become easier to trigger. - -To fix it, we introduce a new internal FOLL_COW flag to mark the "yes, -we already did a COW" rather than play racy games with FOLL_WRITE that -is very fundamental, and then use the pte dirty flag to validate that -the FOLL_COW flag is still valid. - -Reported-and-tested-by: Phil "not Paul" Oester -Acked-by: Hugh Dickins -Reviewed-by: Michal Hocko -Cc: Andy Lutomirski -Cc: Kees Cook -Cc: Oleg Nesterov -Cc: Willy Tarreau -Cc: Nick Piggin -Cc: Greg Thelen -Signed-off-by: Linus Torvalds -Signed-off-by: Greg Kroah-Hartman ---- - include/linux/mm.h | 1 + - mm/gup.c | 14 ++++++++++++-- - 2 files changed, 13 insertions(+), 2 deletions(-) - -diff --git a/include/linux/mm.h b/include/linux/mm.h -index 6b85ec6..7cadf0a 100644 ---- a/include/linux/mm.h -+++ b/include/linux/mm.h -@@ -2064,6 +2064,7 @@ static inline struct page *follow_page(struct vm_area_struct *vma, - #define FOLL_NUMA 0x200 /* force NUMA hinting page fault */ - #define FOLL_MIGRATION 0x400 /* wait for page to replace migration entry */ - #define FOLL_TRIED 0x800 /* a retry, previous pass started an IO */ -+#define FOLL_COW 0x4000 /* internal GUP flag */ - - typedef int (*pte_fn_t)(pte_t *pte, pgtable_t token, unsigned long addr, - void *data); -diff --git a/mm/gup.c b/mm/gup.c -index 6297f6b..e6de9e7 100644 ---- a/mm/gup.c -+++ b/mm/gup.c -@@ -32,6 +32,16 @@ static struct page *no_page_table(struct vm_area_struct *vma, - return NULL; - } - -+/* -+ * FOLL_FORCE can write to even unwritable pte's, but only -+ * after we've gone through a COW cycle and they are dirty. -+ */ -+static inline bool can_follow_write_pte(pte_t pte, unsigned int flags) -+{ -+ return pte_write(pte) || -+ ((flags & FOLL_FORCE) && (flags & FOLL_COW) && pte_dirty(pte)); -+} -+ - static struct page *follow_page_pte(struct vm_area_struct *vma, - unsigned long address, pmd_t *pmd, unsigned int flags) - { -@@ -66,7 +76,7 @@ retry: - } - if ((flags & FOLL_NUMA) && pte_protnone(pte)) - goto no_page; -- if ((flags & FOLL_WRITE) && !pte_write(pte)) { -+ if ((flags & FOLL_WRITE) && !can_follow_write_pte(pte, flags)) { - pte_unmap_unlock(ptep, ptl); - return NULL; - } -@@ -315,7 +325,7 @@ static int faultin_page(struct task_struct *tsk, struct vm_area_struct *vma, - * reCOWed by userspace write). - */ - if ((ret & VM_FAULT_WRITE) && !(vma->vm_flags & VM_WRITE)) -- *flags &= ~FOLL_WRITE; -+ *flags |= FOLL_COW; - return 0; - } - --- -2.10.1 - -- cgit v1.3 From 8ce84bf1f5705f5280e8bf8f150ec2e859b045ee Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 25 Oct 2016 13:56:23 +0200 Subject: svg: Autoload Guile-RSVG and Guile-Cairo. Fixes compilation by 'guix pull' where Guile-{RSVG,Cairo} are missing. Reported by Efraim Flashner. * gnu/build/svg.scm: Use 'module-autoload!' rather than 'module-use!'. --- gnu/build/svg.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/build/svg.scm b/gnu/build/svg.scm index d9b909cd73..f7e92a1a19 100644 --- a/gnu/build/svg.scm +++ b/gnu/build/svg.scm @@ -22,9 +22,11 @@ #:export (svg->png)) ;; We need Guile-RSVG and Guile-Cairo. Load them lazily, at run time, to -;; allow compilation to proceed. -(module-use! (current-module) (resolve-interface '(rsvg))) -(module-use! (current-module) (resolve-interface '(cairo))) +;; allow compilation to proceed. See also . +(module-autoload! (current-module) + '(rsvg) '(rsvg-handle-new-from-file)) +(module-autoload! (current-module) + '(cairo) '(cairo-image-surface-create)) (define* (downscaled-surface surface #:key -- cgit v1.3 From 4b12fe5caba259bbf32865001c94a1de14965c66 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 25 Oct 2016 10:56:46 +0200 Subject: gnu: coda: Remove bundled libraries. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (coda): Remove bundled libraries. [source]: Add patch and snippet to remove bundled zlib, pcre and expat. [inputs]: Add system zlib, pcre and expat. * gnu/packages/patches/coda-use-system-libs.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/maths.scm | 14 ++++++-- gnu/packages/patches/coda-use-system-libs.patch | 46 +++++++++++++++++++++++++ 3 files changed, 59 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/coda-use-system-libs.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 51849f42c7..4ffd37af91 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -484,6 +484,7 @@ dist_patch_DATA = \ %D%/packages/patches/clucene-pkgconfig.patch \ %D%/packages/patches/clx-remove-demo.patch \ %D%/packages/patches/cmake-fix-tests.patch \ + %D%/packages/patches/coda-use-system-libs.patch \ %D%/packages/patches/cpio-CVE-2016-2037.patch \ %D%/packages/patches/cpufrequtils-fix-aclocal.patch \ %D%/packages/patches/cracklib-CVE-2016-6318.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2928cb63a3..1b43bdabc7 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -123,18 +123,28 @@ interactive dialogs to guide them.") (uri (string-append "https://github.com/stcorp/coda/releases/download/" version "/coda-" version ".tar.gz")) (sha256 - (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h")))) + (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h")) + (patches (search-patches "coda-use-system-libs.patch")) + (modules '((guix build utils))) + (snippet + ;; Make sure we don't use the bundled software. + '(for-each (lambda (d) + (delete-file-recursively (string-append "libcoda/" d))) + '("zlib" "pcre" "expat"))))) (native-inputs `(("fortran" ,gfortran) ("python" ,python) ("python-numpy" ,python-numpy))) (inputs `(("zlib" ,zlib) + ("pcre" ,pcre) + ("expat" ,expat) ("hdf4" ,hdf4-alt) ("hdf5" ,hdf5))) (build-system gnu-build-system) (arguments - '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"))) + '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python" + "LIBS= -lz -lpcre -lexpat"))) (synopsis "A common interface to various earth observation data formats") (description "The Common Data Access toolbox (CODA) provides a set of interfaces for diff --git a/gnu/packages/patches/coda-use-system-libs.patch b/gnu/packages/patches/coda-use-system-libs.patch new file mode 100644 index 0000000000..fbf8441958 --- /dev/null +++ b/gnu/packages/patches/coda-use-system-libs.patch @@ -0,0 +1,46 @@ +Remove dependencies on bundled zlib, pcre and expat. + +diff --git a/Makefile.in b/Makefile.in +index 4360a26..80f9f59 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -210,8 +210,7 @@ coda_matlab_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ + @BUILD_MATLAB_TRUE@@SUBPACKAGE_MODE_FALSE@ -rpath \ + @BUILD_MATLAB_TRUE@@SUBPACKAGE_MODE_FALSE@ $(matlabmexexecdir) + am__DEPENDENCIES_1 = +-libcoda_la_DEPENDENCIES = @LTLIBOBJS@ libexpat_internal.la \ +- libpcre_internal.la libz_internal.la $(am__DEPENDENCIES_1) \ ++libcoda_la_DEPENDENCIES = @LTLIBOBJS@ $(am__DEPENDENCIES_1) \ + $(am__DEPENDENCIES_1) + am__libcoda_la_SOURCES_DIST = libcoda/coda-ascbin-cursor.c \ + libcoda/coda-ascbin.h libcoda/coda-ascii-cursor.c \ +@@ -306,8 +305,7 @@ libcoda_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ + $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ + $(libcoda_la_LDFLAGS) $(LDFLAGS) -o $@ + @SUBPACKAGE_MODE_FALSE@am_libcoda_la_rpath = -rpath $(libdir) +-am__DEPENDENCIES_2 = @LTLIBOBJS@ libexpat_internal.la \ +- libpcre_internal.la libz_internal.la $(am__DEPENDENCIES_1) \ ++am__DEPENDENCIES_2 = @LTLIBOBJS@ $(am__DEPENDENCIES_1) \ + $(am__DEPENDENCIES_1) + libcoda_internal_la_DEPENDENCIES = $(am__DEPENDENCIES_2) + am__libcoda_internal_la_SOURCES_DIST = libcoda/coda-ascbin-cursor.c \ +@@ -898,8 +896,8 @@ INSTALL_DATA_HOOK_TARGETS = $(am__append_1) + UNINSTALL_HOOK_TARGETS = + CLEAN_LOCAL_TARGETS = $(am__append_11) + ALL_LOCAL_TARGETS = +-@SUBPACKAGE_MODE_FALSE@noinst_LTLIBRARIES = libcoda_internal.la libexpat_internal.la libpcre_internal.la libz_internal.la +-@SUBPACKAGE_MODE_TRUE@noinst_LTLIBRARIES = libcoda_internal.la libexpat_internal.la libpcre_internal.la libz_internal.la ++@SUBPACKAGE_MODE_FALSE@noinst_LTLIBRARIES = libcoda_internal.la ++@SUBPACKAGE_MODE_TRUE@noinst_LTLIBRARIES = libcoda_internal.la + + # libraries (+ related files) + @SUBPACKAGE_MODE_FALSE@lib_LTLIBRARIES = libcoda.la +@@ -1048,7 +1046,7 @@ libcoda_hdf5_files = \ + + libcoda_la_CPPFLAGS = -Ilibcoda/expat -I$(srcdir)/libcoda/expat -Ilibcoda/pcre -I$(srcdir)/libcoda/pcre -Ilibcoda/zlib -I$(srcdir)/libcoda/zlib $(AM_CPPFLAGS) + libcoda_la_LDFLAGS = -no-undefined -version-info $(LIBCODA_CURRENT):$(LIBCODA_REVISION):$(LIBCODA_AGE) +-libcoda_la_LIBADD = @LTLIBOBJS@ libexpat_internal.la libpcre_internal.la libz_internal.la $(HDF4LIBS) $(HDF5LIBS) ++libcoda_la_LIBADD = @LTLIBOBJS@ $(HDF4LIBS) $(HDF5LIBS) + libcoda_internal_la_SOURCES = libcoda/coda-ascbin-cursor.c \ + libcoda/coda-ascbin.h libcoda/coda-ascii-cursor.c \ + libcoda/coda-ascii-internal.h libcoda/coda-ascii.c \ -- cgit v1.3 From 47a04fca999b91309d196afc9ebf4d8ac6f2083f Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Tue, 25 Oct 2016 12:49:52 -0400 Subject: gnu: mupdf: Fix CVE-2016-8674. * gnu/packages/patches/mupdf-CVE-2016-8674.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (mupdf): Use it. --- gnu/local.mk | 1 + gnu/packages/patches/mupdf-CVE-2016-8674.patch | 166 +++++++++++++++++++++++++ gnu/packages/pdf.scm | 3 +- 3 files changed, 169 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/mupdf-CVE-2016-8674.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 4ffd37af91..ff2d9767ab 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -715,6 +715,7 @@ dist_patch_DATA = \ %D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch \ %D%/packages/patches/mupdf-CVE-2016-6265.patch \ %D%/packages/patches/mupdf-CVE-2016-6525.patch \ + %D%/packages/patches/mupdf-CVE-2016-8674.patch \ %D%/packages/patches/mupen64plus-ui-console-notice.patch \ %D%/packages/patches/musl-CVE-2016-8859.patch \ %D%/packages/patches/mutt-store-references.patch \ diff --git a/gnu/packages/patches/mupdf-CVE-2016-8674.patch b/gnu/packages/patches/mupdf-CVE-2016-8674.patch new file mode 100644 index 0000000000..62e4a0237a --- /dev/null +++ b/gnu/packages/patches/mupdf-CVE-2016-8674.patch @@ -0,0 +1,166 @@ +Fix CVE-2016-8674 (use-after-free in pdf_to_num()). + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8674 +https://security-tracker.debian.org/tracker/CVE-2016-8674 + +Patch copied from upstream source repository: +http://git.ghostscript.com/?p=mupdf.git;h=1e03c06456d997435019fb3526fa2d4be7dbc6ec + +diff --git a/include/mupdf/pdf/document.h b/include/mupdf/pdf/document.h +index aabf05f..0078c4a 100644 +--- a/include/mupdf/pdf/document.h ++++ b/include/mupdf/pdf/document.h +@@ -269,6 +269,10 @@ struct pdf_document_s + fz_hash_table *images; + fz_hash_table *fonts; + } resources; ++ ++ int orphans_max; ++ int orphans_count; ++ pdf_obj **orphans; + }; + + /* +diff --git a/include/mupdf/pdf/object.h b/include/mupdf/pdf/object.h +index 5bc3dca..bf57455 100644 +--- a/include/mupdf/pdf/object.h ++++ b/include/mupdf/pdf/object.h +@@ -110,6 +110,7 @@ pdf_obj *pdf_dict_gets(fz_context *ctx, pdf_obj *dict, const char *key); + pdf_obj *pdf_dict_getsa(fz_context *ctx, pdf_obj *dict, const char *key, const char *abbrev); + void pdf_dict_put(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val); + void pdf_dict_put_drop(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val); ++void pdf_dict_get_put_drop(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val, pdf_obj **old_val); + void pdf_dict_puts(fz_context *ctx, pdf_obj *dict, const char *key, pdf_obj *val); + void pdf_dict_puts_drop(fz_context *ctx, pdf_obj *dict, const char *key, pdf_obj *val); + void pdf_dict_putp(fz_context *ctx, pdf_obj *dict, const char *path, pdf_obj *val); +diff --git a/source/pdf/pdf-object.c b/source/pdf/pdf-object.c +index b4e33f3..1c19ba4 100644 +--- a/source/pdf/pdf-object.c ++++ b/source/pdf/pdf-object.c +@@ -1265,11 +1265,14 @@ pdf_dict_geta(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *abbrev) + return pdf_dict_get(ctx, obj, abbrev); + } + +-void +-pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) ++static void ++pdf_dict_get_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val, pdf_obj **old_val) + { + int i; + ++ if (old_val) ++ *old_val = NULL; ++ + RESOLVE(obj); + if (!OBJ_IS_DICT(obj)) + fz_throw(ctx, FZ_ERROR_GENERIC, "not a dict (%s)", pdf_objkindstr(obj)); +@@ -1295,7 +1298,10 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) + { + pdf_obj *d = DICT(obj)->items[i].v; + DICT(obj)->items[i].v = pdf_keep_obj(ctx, val); +- pdf_drop_obj(ctx, d); ++ if (old_val) ++ *old_val = d; ++ else ++ pdf_drop_obj(ctx, d); + } + } + else +@@ -1316,10 +1322,27 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) + } + + void ++pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) ++{ ++ pdf_dict_get_put(ctx, obj, key, val, NULL); ++} ++ ++void + pdf_dict_put_drop(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) + { + fz_try(ctx) +- pdf_dict_put(ctx, obj, key, val); ++ pdf_dict_get_put(ctx, obj, key, val, NULL); ++ fz_always(ctx) ++ pdf_drop_obj(ctx, val); ++ fz_catch(ctx) ++ fz_rethrow(ctx); ++} ++ ++void ++pdf_dict_get_put_drop(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val, pdf_obj **old_val) ++{ ++ fz_try(ctx) ++ pdf_dict_get_put(ctx, obj, key, val, old_val); + fz_always(ctx) + pdf_drop_obj(ctx, val); + fz_catch(ctx) +diff --git a/source/pdf/pdf-repair.c b/source/pdf/pdf-repair.c +index 690bf15..167f609 100644 +--- a/source/pdf/pdf-repair.c ++++ b/source/pdf/pdf-repair.c +@@ -260,6 +260,27 @@ pdf_repair_obj_stm(fz_context *ctx, pdf_document *doc, int stm_num) + } + } + ++static void ++orphan_object(fz_context *ctx, pdf_document *doc, pdf_obj *obj) ++{ ++ if (doc->orphans_count == doc->orphans_max) ++ { ++ int new_max = (doc->orphans_max ? doc->orphans_max*2 : 32); ++ ++ fz_try(ctx) ++ { ++ doc->orphans = fz_resize_array(ctx, doc->orphans, new_max, sizeof(*doc->orphans)); ++ doc->orphans_max = new_max; ++ } ++ fz_catch(ctx) ++ { ++ pdf_drop_obj(ctx, obj); ++ fz_rethrow(ctx); ++ } ++ } ++ doc->orphans[doc->orphans_count++] = obj; ++} ++ + void + pdf_repair_xref(fz_context *ctx, pdf_document *doc) + { +@@ -528,12 +549,13 @@ pdf_repair_xref(fz_context *ctx, pdf_document *doc) + /* correct stream length for unencrypted documents */ + if (!encrypt && list[i].stm_len >= 0) + { ++ pdf_obj *old_obj = NULL; + dict = pdf_load_object(ctx, doc, list[i].num); + + length = pdf_new_int(ctx, doc, list[i].stm_len); +- pdf_dict_put(ctx, dict, PDF_NAME_Length, length); +- pdf_drop_obj(ctx, length); +- ++ pdf_dict_get_put_drop(ctx, dict, PDF_NAME_Length, length, &old_obj); ++ if (old_obj) ++ orphan_object(ctx, doc, old_obj); + pdf_drop_obj(ctx, dict); + } + } +diff --git a/source/pdf/pdf-xref.c b/source/pdf/pdf-xref.c +index 7d21775..0cf20d4 100644 +--- a/source/pdf/pdf-xref.c ++++ b/source/pdf/pdf-xref.c +@@ -1620,6 +1620,12 @@ pdf_drop_document_imp(fz_context *ctx, pdf_document *doc) + + pdf_drop_resource_tables(ctx, doc); + ++ for (i = 0; i < doc->orphans_count; i++) ++ { ++ pdf_drop_obj(ctx, doc->orphans[i]); ++ } ++ fz_free(ctx, doc->orphans); ++ + fz_free(ctx, doc); + } + fz_always(ctx) +-- +2.9.1 + diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 461472abe9..42547dff9b 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -489,7 +489,8 @@ extracting content or merging files.") "1k64pdapyj8a336jw3j61fhn0rp4q6az7d0dqp9r5n3d9rgwa5c0")) (patches (search-patches "mupdf-build-with-openjpeg-2.1.patch" "mupdf-CVE-2016-6265.patch" - "mupdf-CVE-2016-6525.patch")) + "mupdf-CVE-2016-6525.patch" + "mupdf-CVE-2016-8674.patch")) (modules '((guix build utils))) (snippet ;; Delete all the bundled libraries except for mujs, which is -- cgit v1.3 From 3de764f7a79f5018e459f9df9735e6b54f95bc50 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 Oct 2016 22:42:56 -0400 Subject: gnu: gtk+-2: Update to 2.24.31 [fixes CVE-2013-7447]. * gnu/packages/gtk.scm (gtk+-2): Update to 2.24.31. --- gnu/packages/gtk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index df79239951..386430fa56 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -566,7 +566,7 @@ is part of the GNOME accessibility project.") (define-public gtk+-2 (package (name "gtk+") - (version "2.24.30") + (version "2.24.31") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -574,7 +574,7 @@ is part of the GNOME accessibility project.") name "-" version ".tar.xz")) (sha256 (base32 - "0l6aqk86aw5w132ygy6hv6nlxvd1h6xg7c85qbm60p6mnv1ww58d")) + "0n26jm09n03nqbd00d2ij63xrby3vik56sk5yj6w1vy768kr5hb8")) (patches (search-patches "gtk2-respect-GUIX_GTK2_PATH.patch" "gtk2-respect-GUIX_GTK2_IM_MODULE_FILE.patch" "gtk2-theme-paths.patch")))) -- cgit v1.3 From 6c18c4f6031aad4f60db953a26917942c7401762 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 25 Oct 2016 22:08:20 -0400 Subject: gnu: elfutils: Update to 0.167. * gnu/packages/elf.scm (elfutils): Update to 0.167. --- gnu/packages/elf.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/elf.scm b/gnu/packages/elf.scm index 674b8ac7a1..35b644906b 100644 --- a/gnu/packages/elf.scm +++ b/gnu/packages/elf.scm @@ -30,7 +30,7 @@ (define-public elfutils (package (name "elfutils") - (version "0.166") + (version "0.167") (source (origin (method url-fetch) (uri (string-append @@ -38,7 +38,7 @@ version "/elfutils-" version ".tar.bz2")) (sha256 (base32 - "0c5s9klq1zyb0zkmrw636k97kz30p5ih8y8dpq8b4f54r0a6j19w")) + "0lv5fz2h7j9362l5apbg9jff7309ni385d3325ckavrbqj3h0c1z")) (patches (search-patches "elfutils-tests-ptrace.patch")))) (build-system gnu-build-system) -- cgit v1.3 From f9875807e89d7aa94428eb21374b5bcf42494c18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 25 Oct 2016 18:44:06 +0200 Subject: gnu: emacs-emms-player-mpv: Update to 0.0.10. * gnu/packages/emacs.scm (emacs-emms-player-mpv): Update to 0.0.10. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 10be825e68..2a275d0672 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -955,7 +955,7 @@ light user interface.") (define-public emacs-emms-player-mpv (package (name "emacs-emms-player-mpv") - (version "0.0.8") + (version "0.0.10") (source (origin (method url-fetch) @@ -964,7 +964,7 @@ light user interface.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "01wj410dpx25b3i8781i2j9c6nlvzvvphy9qgh7zfpmyz6a3wsm4")))) + "1q81fpmwr8hpdgq71vbdai2nml4yyqbmk4ffdyl4irlwph8gfjyq")))) (build-system emacs-build-system) (propagated-inputs `(("emms" ,emms))) -- cgit v1.3 From 557a4b8e61e42e1d2b9036705cbb419b81385569 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:42:02 +0200 Subject: gnu: Add r-kernsmooth. * gnu/packages/statistics.scm (r-kernsmooth): New variable. --- gnu/packages/statistics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 959251d84c..2a42153df6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3278,6 +3278,30 @@ conversion of R objects to LaTeX code, and recoding variables.") framework, with additional code inspection and report generation tools.") (license license:gpl2+))) +(define-public r-kernsmooth + (package + (name "r-kernsmooth") + (version "2.23-15") + (source + (origin + (method url-fetch) + (uri (cran-uri "KernSmooth" version)) + (sha256 + (base32 + "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) + (properties `((upstream-name . "KernSmooth"))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/KernSmooth") + (synopsis "Functions for kernel smoothing") + (description + "This package provides functions for kernel smoothing (and density +estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) +\"Kernel Smoothing\".") + ;; Unlimited use and distribution + (license (license:non-copyleft "file://LICENSE.note")))) + (define-public r-zoo (package (name "r-zoo") -- cgit v1.3 From 9beba74f660303ea780bd5f245ee0d4baf46524a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:43:40 +0200 Subject: gnu: r-annotate: Update to 1.52.0. * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d0b8056179..3926d37671 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5190,14 +5190,14 @@ data types as well.") (define-public r-annotate (package (name "r-annotate") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "00wnhbjp5i6a5vyvlq4f5hs8qngjxz7fm869kla1spmd0dp2ynsy")))) + "1fd2csq7dcs2gwndgwdx2nwkymz8gsmlnqqzv3p0vjjsvvq5n2a8")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.3 From 6faa2a48f0cf41f2500e231d74a3daa8cfc16f8b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:44:11 +0200 Subject: gnu: r-geneplotter: Update to 1.52.0. * gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3926d37671..3810f525cf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5216,14 +5216,14 @@ microarrays.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "0lvrywl0251g4y0h0qlgkbg4l83ja5544c85z1wj30qxiy77iqc2")))) + "1p6yvxi243irhjxwm97hp73abhwampj0myyf8z00ij166674pc7h")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit v1.3 From 1e66e71921374cd34f64d4173f38c34ca2bf02a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:44:45 +0200 Subject: gnu: r-genefilter: Update to 1.56.0. * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3810f525cf..02f5d8181c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5241,14 +5241,14 @@ microarrays.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.54.2") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1hmz6as0njvrsrdbgmk72jyclnnqvfdvp6kqv456h43ldq2ajfv5")))) + "1vzgciqd09csqcw9qync8blsv51ylrd86a65iadgyy6j26g01fwd")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.3 From e1db8dd813ea4290c700716e40d96c8cec6fda6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:45:17 +0200 Subject: gnu: r-deseq2: Update to 1.14.0. * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02f5d8181c..5c018bdef0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5267,14 +5267,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.12.4") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "12h77f0dpi5xaj7aqf50kkyn6lq9j7bcsly1r0ffmyfcszrp1sfx")))) + "0kq06jy4xg5ii3a9l62f17kirsfx0gsiwq6mhiy985cqzpdn893g")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (arguments -- cgit v1.3 From 55cd914c3d47e057cc5bc63b42bef6f4ad87582a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:46:01 +0200 Subject: gnu: r-annotationforge: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0. [propagated-inputs]: Add r-rcurl. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5c018bdef0..38ce2c099f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5312,14 +5312,14 @@ distribution.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1vkdd1qdv5g680ipw4vwjvn52xn66xpg6ngmwyknz77ckxnnpf4q")))) + "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5328,6 +5328,7 @@ distribution.") ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) + ("r-rcurl" ,r-rcurl) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) -- cgit v1.3 From 700c780dcf89b2a0eab67e1fd62119e9dcbd718b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:46:45 +0200 Subject: gnu: r-rbgl: Update to 1.50.0. * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38ce2c099f..478b6a0e60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5342,14 +5342,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.48.1") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "1k82zcbyfx3p9hc8r0hwq73krbhakjan8fgbfr6w8z2crfkv3zmz")))) + "1q14m8w6ih56v680kf3d9wh1qbgp7af33kz3cxafdf1vvzx9km08")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) -- cgit v1.3 From 558d02c3613af15e3a7768437d47f67dbaab4565 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:47:20 +0200 Subject: gnu: r-gseabase: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 478b6a0e60..d12d50792c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5363,14 +5363,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1mvgja8malrnbzfakzjl5mmi7g080kj8zgxwc5964hcmn33i937j")))) + "0l2x7yj7lfb0m2dmsav5ib026dikpgl4crdckrnj776yy08lgxpj")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From 816599c1e7cc9fa303aa49a8bef575b8e6ef7bc8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:47:57 +0200 Subject: gnu: r-category: Update to 2.40.0. * gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d12d50792c..bb88b757fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5390,14 +5390,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0c8px9ar589f3iqkbk9vfhwj30dpnxj81h8sfq20cl1cbmcx2a04")))) + "16ncwz7b4y48k0p3fvbrbmvf7nfz63li9ysgcl8kp9kl4hg7llng")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From ae6899b683f6f9b8f47d565e24887a8db59ec6a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:48:42 +0200 Subject: gnu: r-gostats: Update to 2.40.0. * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bb88b757fe..7c3599ce5a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5421,14 +5421,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.38.1") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1hhw6vqr8f3g4jzq0v8f2za0r1h117j5s6av87zxs41cv7dq1wb3")))) + "0g2czm94zhzx92z7y2r4mjfxhwml7bhab2db6820ks8nkw1zvr9n")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From b87b41a74d3020f75680cd6030d039b8c959cfc8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:49:20 +0200 Subject: gnu: r-shortread: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7c3599ce5a..e854d7f7bf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5451,14 +5451,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0qlxns4bhwfpafx3km2lnivgl2qyp7n4g1ardm6vrinpq8paxbjg")))) + "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit v1.3 From 1265d3877b78f35da0d1ace4e84276213bf83e59 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:49:51 +0200 Subject: gnu: r-systempiper: Update to 1.8.1. * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e854d7f7bf..5969a13f71 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5493,14 +5493,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.6.4") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0s2g46a5d5bvx45i3cgmib48wf8hrniyladhm0f7kgcbfx57248m")))) + "0hyi841w8fm2yzpm6lwqi3jz5kc8ny8dy5p29dxynzaw5bpjw56d")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From c9b5046a18fcdcb8d76b85baf2344d197452ae30 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:50:21 +0200 Subject: gnu: r-grohmm: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5969a13f71..0e7cbb3dfe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5539,14 +5539,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1l9mcyzyc548114ysb9r0q7hgzw3yy7gpiahrzkzj6hblc4f1jyp")))) + "0d91nyhqbi5hv3mgmr2z0g29wg2md26g0hyv5mgapmz20cd9zi4y")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From f0b297e17b48afa333fda717111126bef8da73ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:50:48 +0200 Subject: gnu: r-biocgenerics: Update to 0.20.0. * gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0e7cbb3dfe..48952a87c7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5853,13 +5853,13 @@ barplots or heatmaps.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.18.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1jjp48vbph09w5bmc7368gjjywsa1lmzfybpiwlypr60b51vlkp6")))) + "06szdz7dfs1iyv5zdl4fjzad18nnf1zf3wvglc6c6yd9mrqlf7vk")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit v1.3 From 5c7b04e0c37618d52c5845003764fd1dc2875649 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:51:18 +0200 Subject: gnu: r-biocinstaller: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 48952a87c7..7a9313459c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5873,13 +5873,13 @@ packages.") (define-public r-biocinstaller (package (name "r-biocinstaller") - (version "1.22.3") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocInstaller" version)) (sha256 (base32 - "02qkfq6f2b7v9klri6d1nv21r54bywv1zd5x47ka0jhhp946cqpr")))) + "0y1y5wmy6lzjqx3hdg15n91d417ccjj8dbvdkhmp99bs5aijwcpn")))) (properties `((upstream-name . "BiocInstaller"))) (build-system r-build-system) -- cgit v1.3 From 22c5d736af63ef55568d9a7f126ae2dded5eac08 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:51:50 +0200 Subject: gnu: r-dnacopy: Update to 1.48.0. * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a9313459c..6b4822c1a2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6033,13 +6033,13 @@ that accept short and long options.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0vwv2mndfjpcjp4sybg75abc7xnx8zyw8zjk717k6xh8c33ymcip")))) + "1idyvfvy7xx8k9vk00y4k3819qmip8iqm809j3vpxabmsn7r9zyh")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) -- cgit v1.3 From b120c5f3a2e290dde76399b0127884faa14dab01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:52:20 +0200 Subject: gnu: r-s4vectors: Update to 0.12.0. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6b4822c1a2..f09a6c125e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6055,13 +6055,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.10.3") + (version "0.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "09lrvy3d5q58hsgw9as4hyyx07k1vyy2zjn3xsvhyfd97yk6w6lv")))) + "0m0npc0vhmcwcxws7v2f8k4hvvrjvnlrsr94klxf4a8m4xw2xzzk")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.3 From 7f354dafb12461ec4d46144cc888289384f491c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:52:50 +0200 Subject: gnu: r-iranges: Update to 2.8.0. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f09a6c125e..44b565ac99 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6107,13 +6107,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "06pyam3bjjfw2m3l86rda503lsz2jcg645lcnhvrz6qi0nv359yg")))) + "0cdl1sfd3cvf93lnz91fdk64fbg1mnd5g958dwh1il8r358hqq3f")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.3 From dece310a2511d4f615d4a1b95418c27e9b69fea1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:53:16 +0200 Subject: gnu: r-genomeinfodb: Update to 1.10.0. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 44b565ac99..9bbe0d8b3e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6136,13 +6136,13 @@ possible.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.8.7") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1x96468bbjx7z3ikp1dgr2krnz9pwx86vmssfbfrsikaxfs4q829")))) + "0nhg4bk38gzvf3mvnbqgisbbhfv1kzjld27z1z9knnlkplkiyyyv")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.3 From 5e48005fa96d25214b8afb1bd61abbfa9cc243b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:53:46 +0200 Subject: gnu: r-edger: Update to 3.16.0. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit. --- gnu/packages/bioinformatics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9bbe0d8b3e..11810589ba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6162,17 +6162,18 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "14vrygy7rz5ngaap4kgkvr3j18y5l6m742n79h68plk6iqgmsskn")))) + "1qr20j55m35dwzqyzzmla69gk5bzff8v1v2qjh7yd3362wq1ch49")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma))) + `(("r-limma" ,r-limma) + ("r-locfit" ,r-locfit))) (home-page "http://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of -- cgit v1.3 From 37d96f1ddee6c25bb8b6a7c600c32454eabcdd82 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:54:23 +0200 Subject: gnu: r-variantannotation: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.0. [propagated-inputs]: Add r-biobase, r-biostrings, r-iranges, r-rtracklayer, r-s4vectors, r-xvector. --- gnu/packages/bioinformatics.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 11810589ba..058bbaeb73 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6188,27 +6188,33 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.18.7") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "002kif2c66wbcng953m3g1jys7w1lgz7hh3zsk4jlnhc20jdv1vj")))) + "1lwzfgahz8ipwli73kcfqb18y6adi129hap1gnycnj3980m54i8q")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-dbi" ,r-dbi) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) ("r-zlibbioc" ,r-zlibbioc))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/VariantAnnotation") -- cgit v1.3 From 753bc32b8eaaef2df1a0ca1971e1a3598601a554 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:55:26 +0200 Subject: gnu: r-limma: Update to 3.30.0. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 058bbaeb73..c8314f3f00 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6226,13 +6226,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.28.21") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1dvisifd2rr7s1rrsqj5vrv2qcg4la4yi2ajbn0zkk5z81ffxv9f")))) + "0d8wp7b7nymawf4czwsg27k4c61i4ij2lhv7phi6cb3hdd8c76yf")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.3 From 1d048589caf9f7d1bc76f6961efb7f3b192ec166 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:55:55 +0200 Subject: gnu: r-xvector: Update to 0.14.0. * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c8314f3f00..0762e430ba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6245,13 +6245,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.12.1") + (version "0.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1kydy9f5y0ihn2mbkamr1kh0g1d3g1k9d7s4i09qgw9ysr6j414v")))) + "09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit v1.3 From 92a740afac9aa8c89d0bf443df936d7e36c14c1b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:56:27 +0200 Subject: gnu: r-genomicranges: Update to 1.26.1. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1. [propagated-inputs]: Add r-iranges, r-s4vectors. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0762e430ba..e39e1a81a7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6281,19 +6281,21 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.24.3") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "098a34hfgb5z120v6wpl5nv8v61nm65yg6xq0j7i9bigvxr7apg2")))) + "039nxccg9i2an8q2wni79x8dr9p1fcfcqvih9hg9w243pczg2g3c")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) (home-page "http://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") -- cgit v1.3 From 464870caf789fc7f7dfa968d823c84f865f74762 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:57:08 +0200 Subject: gnu: r-biobase: Update to 2.34.0. * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e39e1a81a7..744fde31f3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6310,13 +6310,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0q4icv9n5rc2qfkv6k1wjhmfcpzcyr8f45m2z3xharbdv912kl1i")))) + "0js9j9wqls8f571ifl9ylllbb9a9hwf7b7drf2grwb1fl31ldazl")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit v1.3 From e45dc05781f0b7907ef59f731237a7ee4ef91053 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:57:44 +0200 Subject: gnu: r-annotationdbi: Update to 1.36.0. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 744fde31f3..e689409094 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6332,13 +6332,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.34.4") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1k3gfsjrivc7467vg0h705hh4dvzgdhknz62j7zmfxm67qk9r8rq")))) + "0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.3 From 94053331869a31ff04d18fbfbfbc157f4a1c80e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:58:13 +0200 Subject: gnu: r-biomart: Update to 2.30.0. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e689409094..967160abb8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6359,13 +6359,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1g0w6an9hkflgyhvq6pmrs92s93qarv23v636b9a4bz771wjvm5v")))) + "1x0flcghq71784q2l02j0g4f9jkmyb14f6i307n6c59d6ji7h7x6")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit v1.3 From 89559a124e6ace46c0182e7f60d006ae432f8d86 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:58:45 +0200 Subject: gnu: r-biocparallel: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 967160abb8..0e5e53eb63 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6389,13 +6389,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.6.6") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1l39zmvhjlvlczrk5wal4y2s4g0b2kmaczgq5biah9qn45y474mw")))) + "0vz23i14f7wjygr5d4y1hp8ki6l6igwcsjscfpr6dcigmknyi55c")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.3 From 47d39b6e7ad079f94547927fdd6a64921f1ff6de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:59:11 +0200 Subject: gnu: r-biostrings: Update to 2.42.0. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0e5e53eb63..f084c03ca2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6413,13 +6413,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.40.2") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "153rfws5sdha324p1nv7jp75ip6ny0f62jzhqcvs46l85h3i8zgh")))) + "08z8lkz3axa94wkf144a931ry6vf6cc25avi1ywr84ln2k5czz9f")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.3 From c0ccef41ae145fe8da7c8368073acbeb50973be1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 08:59:39 +0200 Subject: gnu: r-rsamtools: Update to 1.26.1. * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f084c03ca2..26c0c508d4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6439,13 +6439,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0w0drs8cpk8nlazq64ag7nm1w5jd1m8riialivm01hz5zcra7scb")))) + "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit v1.3 From 08da08d296f6b4dda51d083dc8f6ab9232f33214 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:00:08 +0200 Subject: gnu: r-summarizedexperiment: Update to 1.4.0. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.4.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 26c0c508d4..634ef243b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6483,13 +6483,13 @@ files.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.2.3") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0c43fsrha886sd0diislnlf8r5h5x7fbhphkzcm0rw3k2jz8wlyk")))) + "1kbj8sg2ik9f8d6g95wz0py62jldg01qy5rsdpg1cxw95nf7dzi3")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.3 From 4ab32f0cd66bff5693e9e0702e9d1f5609a6e6d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:00:36 +0200 Subject: gnu: r-genomicalignments: Update to 1.10.0. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 634ef243b0..e5b80780c6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6512,13 +6512,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.8.4") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1cccvalmm83ilk1kpq31ll8kdy9xclsr4pm4mlcc7bmp0rwkd2p2")))) + "11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit v1.3 From 6a45fd9aeace360072ca93c3dcd61a1e869cc6a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:01:11 +0200 Subject: gnu: r-rtracklayer: Update to 1.34.0. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e5b80780c6..fa6791a671 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6545,13 +6545,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.32.2") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "190767zpwc7maqjpy0x5bpkm0jp1vfawy9991fifw0mc634cjkga")))) + "0mix5k75j70mwplbdipqw71n8qic75ny6y8w2f5jj0pqg1k0327d")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.3 From b17aac083e153215defc4959155c8dddf329358e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:01:52 +0200 Subject: gnu: r-genomicfeatures: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa6791a671..b76eaa0336 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6590,13 +6590,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.24.5") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "17qpisdgqyjz2mnaiwc4dx7dg11pwq3mkvmkah9zn07g9rhh8f7p")))) + "0z8spi2knwzwi10c38vr7xlvi3ah9faj7m1lka880mmxkl9cai4k")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.3 From d1b1587cad1b5922d21b8821e582f14de83e1a11 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:02:32 +0200 Subject: gnu: r-go-db: Update to 3.4.0. * gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b76eaa0336..0987bffcb8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6631,7 +6631,7 @@ extracting the desired features in a convenient format.") (define-public r-go-db (package (name "r-go-db") - (version "3.3.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (string-append "http://www.bioconductor.org/packages/" @@ -6639,7 +6639,7 @@ extracting the desired features in a convenient format.") version ".tar.gz")) (sha256 (base32 - "0x2hkbhg9d8waw32hdn05887vv3zbs5aqff3mf5vfyzvl7xhgxy0")))) + "02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) -- cgit v1.3 From 3587b464fc10877d3d37253d1f0fb80773ce667e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:13:48 +0200 Subject: gnu: r-graph: Update to 1.52.0. * gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0987bffcb8..2f86c2e403 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6655,13 +6655,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-graph (package (name "r-graph") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0ys5s19m5r30rlr0fnx2h0z2qw7n2xrad4l2yfb1bbrk8dwyf4pi")))) + "0g3dk5vsdp489fmyg8mifczmzgqrjlakkkr8i96dj15gghp3l135")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit v1.3 From 30ec4de7389631a8d6751fbcaba3d4ca53ebf061 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:14:22 +0200 Subject: gnu: r-topgo: Update to 2.26.0. * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0. [propagated-inputs]: Add r-dbi. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2f86c2e403..fa88e1f296 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6674,18 +6674,19 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1p4vsl32qhjw15yv9ym01ni63gjg73jaghlf17wc4zfn3iaz2zar")))) + "0j6sgvam4lk9348ag6pypcbkv93x4fk0di8ivhr23mz2s2yqzwrx")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-dbi" ,r-dbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-go-db" ,r-go-db) -- cgit v1.3 From 3d74c044511767194010605e269f1a8801981e45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:14:54 +0200 Subject: gnu: r-bsgenome: Update to 1.42.0. * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa88e1f296..a74f588e76 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6706,13 +6706,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0zmlzlcwairka59is5wmkh6knh6j4d328z9fsw3v91fx6gavjl2n")))) + "0hxwc02h5mzhkrk60d1jmlsfjf0ai9jxdc0128kj1sg4r2k1q94y")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit v1.3 From acf6f7e0c35b3f6e8942c02d07bd2f8612410f01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:15:23 +0200 Subject: gnu: r-impute: Update to 1.48.0. * gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a74f588e76..eba1c0b0c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6736,13 +6736,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0v9ibgv8kp8il52miz7b7z65mv6irqxylx6lfzkxgvxd970dgrz0")))) + "1164zvnikbjd0ybdn9xwn520rlmdjd824vmhnl83zgv3v9lzp9bm")))) (inputs `(("gfortran" ,gfortran))) (build-system r-build-system) -- cgit v1.3 From e92dd6f5e0c62994ded216260d9877fd19f1ad25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:15:51 +0200 Subject: gnu: r-seqpattern: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0. [propagated-inputs]: Add r-kernsmooth. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eba1c0b0c0..78eb8016bd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6756,13 +6756,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1dj9hfnbdj11yjxwd8jmxrdkj7n6gmaaj6244g2psgarhjcp4wfb")))) + "0lsa5pz36xapi3yiv78k3z286a5md5sm5g21pgfyg8zmhmkxr7y8")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -6770,6 +6770,7 @@ microarray data, using nearest neighbor averaging.") `(("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) ("r-plotrix" ,r-plotrix))) (home-page "http://bioconductor.org/packages/seqPattern") (synopsis "Visualising oligonucleotide patterns and motif occurrences") -- cgit v1.3 From 51c3c4900fabf4762440a7840bd74b1d7a9c1eb7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:16:27 +0200 Subject: gnu: r-genomation: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0. [propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors. [inputs]: Add zlib. --- gnu/packages/bioinformatics.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78eb8016bd..f238988f1e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6783,13 +6783,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "017hxh3yhizlsswd2vw8504arkckrcgq5zraiw67lldq9wzs5qzg")))) + "1m4mz7wihj8yqivwkzw68div8ybk4rjsai3ffki7xp7sh21ax03y")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -6805,11 +6805,17 @@ reference point and sorted by a user defined feature.") ("r-matrixstats" ,r-matrixstats) ("r-plotrix" ,r-plotrix) ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) ("r-readr" ,r-readr) ("r-reshape2" ,r-reshape2) + ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) + ("r-runit" ,r-runit) + ("r-s4vectors" ,r-s4vectors) ("r-seqpattern" ,r-seqpattern))) + (inputs + `(("zlib" ,zlib))) (home-page "http://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description -- cgit v1.3 From 21d6c7a3e15ee7baed14ed7580be850ab3825a58 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:17:20 +0200 Subject: gnu: r-seqlogo: Update to 1.40.0. * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f238988f1e..231eeb5347 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6964,14 +6964,14 @@ annotations for the genome of the model mouse Mus musculus.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "01jddx62nhi3r7czbh9hxy0wwpazbc9ax1fgagfxl6p4kx9xz9rb")))) + "18bajdl75h3039559d81rgllqqvnq8ygsfxfx081xphxs0v6xggy")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "http://bioconductor.org/packages/seqLogo") -- cgit v1.3 From 809251e164a703241f9ca7e972515b6cf560d7df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:17:42 +0200 Subject: gnu: r-motifrg: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 231eeb5347..d7c5751d1c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7175,14 +7175,14 @@ Biostrings objects.") (define-public r-motifrg (package (name "r-motifrg") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "1ds22paqc0923y6z1fy0arw0wxvvmglfvfgarhywv1qywhq68mbq")))) + "1pa97aj6c5f3gx4bgriw110764dj3m9h104ddi8rv2bpy41yd98d")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From da22da862b2ce6d4ff365e47bd55550c4a300dca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:18:03 +0200 Subject: gnu: r-zlibbioc: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d7c5751d1c..5aac5b5ab3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7227,13 +7227,13 @@ two-dimensional genome scans.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0m8l7zpx1l3qsk73k3ibkxxzzff938x3qhnwki1ymf3cnsg8cb36")))) + "0hbk90q5hl0fycfvy5nxxa4hxgglag9lzp7i0fg849bqygg5nbyq")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit v1.3 From 53ca52f0136b297ef4f415eaa9181bb026e51934 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:18:29 +0200 Subject: gnu: r-rhtslib: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0. [native-inputs]: Add autoconf. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5aac5b5ab3..af145a8582 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7246,20 +7246,22 @@ libraries for systems that do not have these available via other means.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.4.3") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1wgpn9x8abjj7fc087pdavqc3fz0pl5xdh231mgjila18irwlhb3")))) + "1vk3ng61dhi3pbia1lp3gl3mlr3i1vb2lkq83qb53i9dzz128wh9")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("autoconf" ,autoconf))) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description -- cgit v1.3 From e357bec836d6d2ea9567dabb11db5d070806fa8c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:19:06 +0200 Subject: gnu: r-bamsignals: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af145a8582..fdc248bf2a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7273,14 +7273,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.4.3") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "1xqiqvg52p6fcvhr4146djbz79r3j1kmh75mq7rndwglmiybpwmy")))) + "1k42gvk5mgq4la1fp0in3an2zfdz69h6522jsqhmk0f6i75kg4mb")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.3 From 59198f8fffe43e0afb4cbf86559675fc4239dbb0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 09:24:47 +0200 Subject: gnu: r-genomationdata: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fdc248bf2a..b71cde8aba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6832,7 +6832,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -6842,7 +6842,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") "genomationData_" version ".tar.gz")) (sha256 (base32 - "1zl7gg144fs7zfycsmq5492sm1bqy7l527xbc2zj04schd9wsan2")))) + "16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y")))) (build-system r-build-system) ;; As this package provides little more than large data files, it doesn't ;; make sense to build substitutes. -- cgit v1.3 From 19262a718e97d6ebc782c8dc7e53d04cfb5f794d Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 26 Oct 2016 10:18:35 +0200 Subject: gnu: opensmtpd: Fix 'license' field. * gnu/packages/mail.scm (opensmtpd)[license]: Use LICENSE:OPENSSL, not OPENSSL. (opensmtpd-extras)[license]: Likewise. --- gnu/packages/mail.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index eee7d1831f..62a3678604 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1618,7 +1618,7 @@ some additional standard extensions. It allows ordinary machines to exchange e-mails with other systems speaking the SMTP protocol.") (home-page "https://www.opensmtpd.org") (license (list bsd-2 bsd-3 bsd-4 (non-copyleft "file://COPYING") - public-domain isc openssl)))) + public-domain isc license:openssl)))) (define-public opensmtpd-extras (package @@ -1681,8 +1681,8 @@ e-mails with other systems speaking the SMTP protocol.") (assoc-ref %build-inputs "python-2")) (string-append "--with-lua=" (assoc-ref %build-inputs "lua"))))) - (license (list bsd-2 bsd-3 bsd-4 non-copyleft - public-domain isc openssl)) + (license (list bsd-2 bsd-3 bsd-4 + public-domain isc license:openssl)) (synopsis "Extra tables, filters, and various other addons for OpenSMTPD") (description "This package provides extra tables, filters, and various other addons -- cgit v1.3 From 1df790d50d7980d83937bfa93d9b270bcc2b1be8 Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 4 Oct 2016 08:34:28 +0000 Subject: gnu: Add psyclpc. * gnu/packages/psyc.scm (psyclpc): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/psyc.scm | 82 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/psyc.scm b/gnu/packages/psyc.scm index 57042946d5..a55f78e4c0 100644 --- a/gnu/packages/psyc.scm +++ b/gnu/packages/psyc.scm @@ -18,15 +18,24 @@ (define-module (gnu packages psyc) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix build-system perl) #:use-module (guix build-system gnu) #:use-module (gnu packages) #:use-module (gnu packages admin) + #:use-module (gnu packages autotools) + #:use-module (gnu packages bison) + #:use-module (gnu packages compression) + #:use-module (gnu packages gettext) #:use-module (gnu packages linux) + #:use-module (gnu packages man) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) + #:use-module (gnu packages pcre) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages tls) #:use-module (gnu packages web)) (define-public perl-net-psyc @@ -143,3 +152,76 @@ core aspects of PSYC, useful for all kinds of clients and servers including psyced.") (synopsis "PSYC library in C") (license license:agpl3+))) + +;; This commit removes the historic bundled pcre, not released as a tarball so far. +(define-public psyclpc + (let* ((commit "8bd51f2a4847860ba8b82dc79348ab37d516011e") + (revision "1")) + (package + (name "psyclpc") + (version (string-append "20160821-" revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "git://git.psyced.org/git/psyclpc") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "10w4kx9ygcv1lcmd7j4knvjiy8dac1y3hjfv3lhp67jpv6w3iagz")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests/checks. + #:configure-flags + ;; If you have questions about this part, look at + ;; "src/settings/psyced" and the ebuild. + (list + "--enable-use-tls=yes" + "--enable-use-mccp" ; Mud Client Compression Protocol, leave this enabled. + (string-append "--prefix=" + (assoc-ref %outputs "out")) + ;; src/Makefile: Set MUD_LIB to the directory which contains + ;; the mud data. defaults to MUD_LIB = @libdir@ + (string-append "--libdir=" + (assoc-ref %outputs "out") + "/opt/psyced/world") + (string-append "--bindir=" + (assoc-ref %outputs "out") + "/opt/psyced/bin") + ;; src/Makefile: Set ERQ_DIR to directory which contains the + ;; stuff which ERQ can execute (hopefully) savely. Was formerly + ;; defined in config.h. defaults to ERQ_DIR= @libexecdir@ + (string-append "--libexecdir=" + (assoc-ref %outputs "out") + "/opt/psyced/run")) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir-to-src + ;; We need to pass this as env variables + ;; and manually change the directory. + (lambda _ + (chdir "src") + (setenv "CONFIG_SHELL" (which "sh")) + (setenv "SHELL" (which "sh")) + #t))) + #:make-flags (list "install-all"))) + (inputs + `(("zlib" ,zlib) + ("openssl" ,openssl) + ("pcre" ,pcre))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("bison" ,bison) + ("gnu-gettext" ,gnu-gettext) + ("help2man" ,help2man) + ("autoconf" ,autoconf) + ("automake" ,automake))) + (home-page "http://lpc.psyc.eu/") + (synopsis "psycLPC is a multi-user network server programming language") + (description + "LPC is a bytecode language, invented to specifically implement +multi user virtual environments on the internet. This technology is used for +MUDs and also the psyced implementation of the Protocol for SYnchronous +Conferencing (PSYC). psycLPC is a fork of LDMud with some new features and +many bug fixes.") + (license license:gpl2)))) -- cgit v1.3 From 7bc7ffc24339d83e9003bb9bea6fad568bcf0204 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 Oct 2016 22:34:04 +0300 Subject: gnu: Add x265. * gnu/packages/video.scm (x265): New variable. --- gnu/packages/video.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index bd82eb8397..68f78847b3 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -250,6 +250,37 @@ H.264 (MPEG-4 AVC) video streams.") "file://extras/cl.h" "See extras/cl.h in the distribution."))))) +(define-public x265 + (package + (name "x265") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://download.videolan.org/videolan/x265/" + "x265_" version ".tar.gz")) + (sha256 + (base32 + "0hx6sr9l7586gs4qds2sj0i1m5brxkaqq3cwmibhfb559fpvkz48")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "source/compat/getopt")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; tests are skipped if cpu-optimized code isn't built + #:phases + (modify-phases %standard-phases + (add-before 'configure 'prepare-build + (lambda _ + (delete-file-recursively "build") + (chdir "source") + #t))))) + (home-page "http://x265.org/") + (synopsis "Library for encoding h.265/HEVC video streams") + (description "x265 is a H.265 / HEVC video encoder application library, +designed to encode video or images into an H.265 / HEVC encoded bitstream.") + (license license:gpl2+))) + (define-public libass (package (name "libass") -- cgit v1.3 From d505801a061f6ff89ab9bb20947c283059408f88 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 Oct 2016 22:49:33 +0300 Subject: gnu: ffmpeg: Add x265 support. * gnu/packages/video.scm (ffmpeg)[inputs]: Add x265. [arguments]: Add '--enable-libx265' flag. --- gnu/packages/video.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 68f78847b3..7f346dcc50 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -466,6 +466,7 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).") ("soxr" ,soxr) ("speex" ,speex) ("twolame" ,twolame) + ("x265" ,x265) ("xvid" ,xvid) ("zlib" ,zlib))) (native-inputs @@ -549,6 +550,7 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).") "--enable-libvpx" "--enable-libxvid" "--enable-libx264" + "--enable-libx265" "--enable-openal" "--enable-opengl" "--enable-x11grab" -- cgit v1.3 From e3cb00d2105a559c315255a98b71bf07a32a409e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 Oct 2016 22:53:41 +0300 Subject: gnu: gst-plugins-bad: Add x265 support. * gnu/packages/gstreamer.scm (gst-plugins-bad)[inputs]: Add x265. --- gnu/packages/gstreamer.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index b1785e95c9..4aea514411 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -292,7 +292,7 @@ developers consider to have good quality code and correct functionality.") ;; vo-amrwbenc, vo-aacenc, bs2b, chromaprint, directfb, daala, libdts, ;; faac, flite, libgsm, libde265, libmms, libmimic, mjpegtools, ;; mpeg2enc, libofa, opencv, openh264, openni2, libtimemmgr, wildmidi, - ;; openspc, gme, sbc, schroedinger, zbar, librtmp, spandsp, x265 + ;; openspc, gme, sbc, schroedinger, zbar, librtmp, spandsp `(("bluez" ,bluez) ("curl" ,curl) ("faad2" ,faad2) @@ -328,6 +328,7 @@ developers consider to have good quality code and correct functionality.") ;("qtdeclarative" ,qtdeclarative) ;("qtx11extras" ,qtx11extras) ("soundtouch" ,soundtouch) + ("x265" ,x265) ("wayland" ,wayland))) (home-page "http://gstreamer.freedesktop.org/") (synopsis "Plugins for the GStreamer multimedia library") -- cgit v1.3 From 8f5f6c922fe6fe06c732bfa18df2f8100c59c2fb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 Oct 2016 22:54:48 +0300 Subject: gnu: vlc: Add x265 support. * gnu/packages/video.scm (vlc)[inputs]: Add x265. --- gnu/packages/video.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 7f346dcc50..acf50f3e99 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -680,6 +680,7 @@ audio/video codec library.") ("sdl" ,sdl) ("sdl-image" ,sdl-image) ("speex" ,speex) + ("x265" ,x265) ("xcb-util-keysyms" ,xcb-util-keysyms))) (arguments `(#:configure-flags -- cgit v1.3 From d2a9b531fbb60c75ff5d3267e108383350c4da72 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Oct 2016 20:10:35 +0100 Subject: gnu: notmuch: Update to 0.23.1. * gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/mail.scm (notmuch): Update to 0.23.1. Remove patch. --- gnu/local.mk | 1 - gnu/packages/mail.scm | 8 +--- .../notmuch-emacs-25-compatibility-fix.patch | 46 ---------------------- 3 files changed, 2 insertions(+), 53 deletions(-) delete mode 100644 gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index ff2d9767ab..87fb76de01 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -728,7 +728,6 @@ dist_patch_DATA = \ %D%/packages/patches/ninja-tests.patch \ %D%/packages/patches/ninja-zero-mtime.patch \ %D%/packages/patches/node-9077.patch \ - %D%/packages/patches/notmuch-emacs-25-compatibility-fix.patch \ %D%/packages/patches/nss-pkgconfig.patch \ %D%/packages/patches/nvi-assume-preserve-path.patch \ %D%/packages/patches/nvi-dbpagesize-binpower.patch \ diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 62a3678604..e73364f86a 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -501,18 +501,14 @@ invoking @command{notifymuch} from the post-new hook.") (define-public notmuch (package (name "notmuch") - (version "0.23") + (version "0.23.1") (source (origin (method url-fetch) (uri (string-append "https://notmuchmail.org/releases/notmuch-" version ".tar.gz")) (sha256 (base32 - "1f51l34rdhjf8lvafrwybkxdsdwx8k9397m7qxd8rdg2irjmpry5")) - (patches - ;; Remove this for the next release. See this thread for context: - ;; https://notmuchmail.org/pipermail/notmuch/2016/023227.html - (search-patches "notmuch-emacs-25-compatibility-fix.patch")))) + "106ijsnilqf8760z4cq99rqzjsvyaw86d0lgnzz7v95gm4d2l0g8")))) (build-system gnu-build-system) (arguments '(#:make-flags (list "V=1") ; Verbose test output. diff --git a/gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch b/gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch deleted file mode 100644 index 9ddfd4fe10..0000000000 --- a/gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch +++ /dev/null @@ -1,46 +0,0 @@ -This fixes a test failure with emacs-25. Picked from -https://git.notmuchmail.org/git?p=notmuch;a=commit;h=f575a346df09c82691bb9e7c462836d982fe31f7 - -From f575a346df09c82691bb9e7c462836d982fe31f7 Mon Sep 17 00:00:00 2001 -From: David Bremner -Date: Sun, 9 Oct 2016 19:30:44 -0300 -Subject: [PATCH] emacs/show: force notmuch-show-buttonise-links to act on - lines - -This seems to fix a problem with emacs 25 creating partial buttons by -calling n-s-b-l with a region that does not include the whole button. -I'm not 100% sure it's legit to act outside the region passed by -jit-lock, but goto-address-fontify-region (where I borrowed the code -from) already does this, so this patch to not make things worse. ---- - emacs/notmuch-show.el | 12 +++++++----- - 1 file changed, 7 insertions(+), 5 deletions(-) - -diff --git a/emacs/notmuch-show.el b/emacs/notmuch-show.el -index 641398d..e7d16f8 100644 ---- a/emacs/notmuch-show.el -+++ b/emacs/notmuch-show.el -@@ -1174,13 +1174,15 @@ This also turns id:\"\"-parts and mid: links into - buttons for a corresponding notmuch search." - (goto-address-fontify-region start end) - (save-excursion -- (let (links) -- (goto-char start) -- (while (re-search-forward notmuch-id-regexp end t) -+ (let (links -+ (beg-line (progn (goto-char start) (line-beginning-position))) -+ (end-line (progn (goto-char end) (line-end-position)))) -+ (goto-char beg-line) -+ (while (re-search-forward notmuch-id-regexp end-line t) - (push (list (match-beginning 0) (match-end 0) - (match-string-no-properties 0)) links)) -- (goto-char start) -- (while (re-search-forward notmuch-mid-regexp end t) -+ (goto-char beg-line) -+ (while (re-search-forward notmuch-mid-regexp end-line t) - (let* ((mid-cid (match-string-no-properties 1)) - (mid (save-match-data - (string-match "^[^/]*" mid-cid) --- -2.10.1 - -- cgit v1.3 From 7a6213cbd7427bdac28e7fef47c6a0c224175940 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Oct 2016 02:49:53 +0100 Subject: gnu: offlineimap: Install documentation. * gnu/packages/mail.scm (offlineimap)[native-inputs]: Add asciidoc and libxslt. [arguments]: Add phases 'build-documentation' and 'install-documentation' to build and install manpages. Also remove unneeded key 'inputs' from 'wrap-binary' phase. --- gnu/packages/mail.scm | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index e73364f86a..e1b490e51d 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2016 Clément Lassieur ;;; Copyright © 2016 Arun Isaac ;;; Copyright © 2016 John Darrington +;;; Copyright © 2016 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -47,6 +48,7 @@ #:use-module (gnu packages databases) #:use-module (gnu packages dejagnu) #:use-module (gnu packages dns) + #:use-module (gnu packages documentation) #:use-module (gnu packages emacs) #:use-module (gnu packages enchant) #:use-module (gnu packages ghostscript) @@ -319,6 +321,9 @@ and corrections. It is based on a Bayesian filter.") (base32 "0smxh5ag3cbn92kp49jq950j5m2pivs9kr04prpd1lw62hy7gnhr")))) (build-system python-build-system) + (native-inputs + `(("asciidoc" ,asciidoc) + ("libxslt" ,libxslt))) ; for xsltproc (inputs `(("python2-pysqlite" ,python2-pysqlite) ("python2-six" ,python2-six))) (arguments @@ -328,8 +333,21 @@ and corrections. It is based on a Bayesian filter.") #:tests? #f #:phases (modify-phases %standard-phases - (add-after 'install 'wrap-binary - (lambda* (#:key inputs outputs #:allow-other-keys) + (add-after 'build 'build-documentation + (lambda _ + (substitute* "docs/Makefile" + ;; Prevent xmllint and xsltproc from downloading a DTD file. + (("a2x -v") "a2x --no-xmllint --xsltproc-opts=--nonet -v")) + (zero? (system* "make" "-C" "docs" "man")))) + (add-after 'install 'install-documentation + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (man (string-append out "/share/man"))) + (install-file "docs/offlineimap.1" (string-append man "/man1")) + (install-file "docs/offlineimapui.7" (string-append man "/man7")) + #t))) + (add-after 'install-documentation 'wrap-binary + (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin/offlineimap"))) (wrap-program bin -- cgit v1.3 From f9c339603d751783e40ce99c9f09639f168ba731 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Oct 2016 07:33:24 +0100 Subject: gnu: yubico.scm: Rename to security-token.scm. * gnu/packages/yubico.scm: Delete file. * gnu/packages/security-token.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly. --- gnu/local.mk | 2 +- gnu/packages/security-token.scm | 77 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/yubico.scm | 77 ----------------------------------------- 3 files changed, 78 insertions(+), 78 deletions(-) create mode 100644 gnu/packages/security-token.scm delete mode 100644 gnu/packages/yubico.scm (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 87fb76de01..cf1b542b8a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -326,6 +326,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/sdcc.scm \ %D%/packages/sdl.scm \ %D%/packages/search.scm \ + %D%/packages/security-token.scm \ %D%/packages/serialization.scm \ %D%/packages/serveez.scm \ %D%/packages/shells.scm \ @@ -385,7 +386,6 @@ GNU_SYSTEM_MODULES = \ %D%/packages/xdisorg.scm \ %D%/packages/xorg.scm \ %D%/packages/xfce.scm \ - %D%/packages/yubico.scm \ %D%/packages/zile.scm \ %D%/packages/zip.scm \ \ diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm new file mode 100644 index 0000000000..48a9346573 --- /dev/null +++ b/gnu/packages/security-token.scm @@ -0,0 +1,77 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2014 Ludovic Courtès +;;; Copyright © 2016 Efraim Flashner +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages security-token) + #:use-module (gnu packages) + #:use-module (guix licenses) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system gnu) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages man) + #:use-module (gnu packages curl)) + +(define-public libyubikey + (package + (name "libyubikey") + (version "1.13") + (source (origin + (method url-fetch) + (uri (string-append + "https://developers.yubico.com/yubico-c/Releases/" + name "-" version ".tar.gz")) + (sha256 + (base32 + "009l3k2zyn06dbrlja2d4p2vfnzjhlcqxi88v02mlrnb17mx1v84")))) + (build-system gnu-build-system) + (synopsis "Development kit for the YubiKey authentication device") + (description + "This package contains a C library and command-line tools that make up +the low-level development kit for the Yubico YubiKey authentication device.") + (home-page "https://developers.yubico.com/yubico-c/") + (license bsd-2))) + +(define-public ykclient + (package + (name "ykclient") + (version "2.15") + (source (origin + (method url-fetch) + (uri (string-append + "https://developers.yubico.com/yubico-c-client/Releases/" + name "-" version ".tar.gz")) + (sha256 + (base32 + "05jhx9waj3pl120ddnwap1v3bjrnbfhvf3lxs2xmhpcmwzpwsqgl")))) + (build-system gnu-build-system) + + ;; There's just one test, and it requires network access to access + ;; yubico.com, so skip it. + (arguments '(#:tests? #f)) + + (native-inputs `(("pkg-config" ,pkg-config) + ("help2man" ,help2man))) + (inputs `(("curl" ,curl))) + (synopsis "C library to validate one-time-password YubiKeys") + (description + "YubiKey C Client Library (libykclient) is a C library used to validate a +one-time-password (OTP) YubiKey against Yubico’s servers. See the Yubico +website for more information about Yubico and the YubiKey.") + (home-page "https://developers.yubico.com/yubico-c-client/") + (license bsd-2))) diff --git a/gnu/packages/yubico.scm b/gnu/packages/yubico.scm deleted file mode 100644 index 469d93d0dc..0000000000 --- a/gnu/packages/yubico.scm +++ /dev/null @@ -1,77 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014 Ludovic Courtès -;;; Copyright © 2016 Efraim Flashner -;;; -;;; This file is part of GNU Guix. -;;; -;;; GNU Guix is free software; you can redistribute it and/or modify it -;;; under the terms of the GNU General Public License as published by -;;; the Free Software Foundation; either version 3 of the License, or (at -;;; your option) any later version. -;;; -;;; GNU Guix is distributed in the hope that it will be useful, but -;;; WITHOUT ANY WARRANTY; without even the implied warranty of -;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -;;; GNU General Public License for more details. -;;; -;;; You should have received a copy of the GNU General Public License -;;; along with GNU Guix. If not, see . - -(define-module (gnu packages yubico) - #:use-module (gnu packages) - #:use-module (guix licenses) - #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix build-system gnu) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages man) - #:use-module (gnu packages curl)) - -(define-public libyubikey - (package - (name "libyubikey") - (version "1.13") - (source (origin - (method url-fetch) - (uri (string-append - "https://developers.yubico.com/yubico-c/Releases/" - name "-" version ".tar.gz")) - (sha256 - (base32 - "009l3k2zyn06dbrlja2d4p2vfnzjhlcqxi88v02mlrnb17mx1v84")))) - (build-system gnu-build-system) - (synopsis "Development kit for the YubiKey authentication device") - (description - "This package contains a C library and command-line tools that make up -the low-level development kit for the Yubico YubiKey authentication device.") - (home-page "https://developers.yubico.com/yubico-c/") - (license bsd-2))) - -(define-public ykclient - (package - (name "ykclient") - (version "2.15") - (source (origin - (method url-fetch) - (uri (string-append - "https://developers.yubico.com/yubico-c-client/Releases/" - name "-" version ".tar.gz")) - (sha256 - (base32 - "05jhx9waj3pl120ddnwap1v3bjrnbfhvf3lxs2xmhpcmwzpwsqgl")))) - (build-system gnu-build-system) - - ;; There's just one test, and it requires network access to access - ;; yubico.com, so skip it. - (arguments '(#:tests? #f)) - - (native-inputs `(("pkg-config" ,pkg-config) - ("help2man" ,help2man))) - (inputs `(("curl" ,curl))) - (synopsis "C library to validate one-time-password YubiKeys") - (description - "YubiKey C Client Library (libykclient) is a C library used to validate a -one-time-password (OTP) YubiKey against Yubico’s servers. See the Yubico -website for more information about Yubico and the YubiKey.") - (home-page "https://developers.yubico.com/yubico-c-client/") - (license bsd-2))) -- cgit v1.3 From 07b1fb86753cad7eced6eaca7fc972562d321c3a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Oct 2016 11:00:58 +0100 Subject: gnu: security-token: Use 'license:' prefix. * gnu/packages/security-token.scm (libyubikey)[license]: Add prefix. (ykclient)[license]: Add prefix. --- gnu/packages/security-token.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index 48a9346573..36ccaa5203 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -19,7 +19,7 @@ (define-module (gnu packages security-token) #:use-module (gnu packages) - #:use-module (guix licenses) + #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) @@ -45,7 +45,7 @@ "This package contains a C library and command-line tools that make up the low-level development kit for the Yubico YubiKey authentication device.") (home-page "https://developers.yubico.com/yubico-c/") - (license bsd-2))) + (license license:bsd-2))) (define-public ykclient (package @@ -74,4 +74,4 @@ the low-level development kit for the Yubico YubiKey authentication device.") one-time-password (OTP) YubiKey against Yubico’s servers. See the Yubico website for more information about Yubico and the YubiKey.") (home-page "https://developers.yubico.com/yubico-c-client/") - (license bsd-2))) + (license license:bsd-2))) -- cgit v1.3 From b2a2232c33e34aab6de02eb72c56494e006abc9d Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 13 Sep 2016 01:38:17 +0000 Subject: gnu: python-certifi: Update to 2016.8.31. * gnu/packages/python.scm (python-certifi): Update to 2016.8.31. Signed-off-by: Efraim Flashner --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 24073687d0..cff9897dd4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2276,13 +2276,13 @@ files.") (define-public python-certifi (package (name "python-certifi") - (version "2015.11.20.1") + (version "2016.8.31") (source (origin (method url-fetch) (uri (pypi-uri "certifi" version)) (sha256 (base32 - "05lgwf9rz1kn465azy2bpb3zmpnsn9gkypbhnjlclchv98ssgc1h")))) + "06c9dcyv8ss050gkv5xjivbxhm6qm0s9vzy4r33wqabgv118lw7p")))) (build-system python-build-system) (inputs `(("python-setuptools" ,python-setuptools))) -- cgit v1.3 From 39df253e2bb260e67d8ce81431a9aa3478689774 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Oct 2016 06:39:34 +0100 Subject: gnu: mupdf: Modify CVE-2016-8674 patch to apply to 1.9a. The fix from upstream did not apply cleanly due to many context changes. This was adapted by cloning mupdf 1.9a from git and fixing conflicts after applying our patches and cherry-picking upstream commit 1e03c06. This is a follow-up to 47a04fca999b91309d196afc9ebf4d8ac6f2083f. * gnu/packages/patches/mupdf-CVE-2016-8674.patch: Adapt to 1.9a. --- gnu/packages/patches/mupdf-CVE-2016-8674.patch | 83 +++++++++++++------------- 1 file changed, 41 insertions(+), 42 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/patches/mupdf-CVE-2016-8674.patch b/gnu/packages/patches/mupdf-CVE-2016-8674.patch index 62e4a0237a..2a35619761 100644 --- a/gnu/packages/patches/mupdf-CVE-2016-8674.patch +++ b/gnu/packages/patches/mupdf-CVE-2016-8674.patch @@ -3,17 +3,17 @@ Fix CVE-2016-8674 (use-after-free in pdf_to_num()). https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8674 https://security-tracker.debian.org/tracker/CVE-2016-8674 -Patch copied from upstream source repository: +Patch adapted from upstream source repository: http://git.ghostscript.com/?p=mupdf.git;h=1e03c06456d997435019fb3526fa2d4be7dbc6ec diff --git a/include/mupdf/pdf/document.h b/include/mupdf/pdf/document.h -index aabf05f..0078c4a 100644 +index f8ef0cd..e8345b7 100644 --- a/include/mupdf/pdf/document.h +++ b/include/mupdf/pdf/document.h -@@ -269,6 +269,10 @@ struct pdf_document_s - fz_hash_table *images; - fz_hash_table *fonts; - } resources; +@@ -258,6 +258,10 @@ struct pdf_document_s + fz_font **type3_fonts; + + pdf_resource_tables *resources; + + int orphans_max; + int orphans_count; @@ -22,10 +22,10 @@ index aabf05f..0078c4a 100644 /* diff --git a/include/mupdf/pdf/object.h b/include/mupdf/pdf/object.h -index 5bc3dca..bf57455 100644 +index 346a2f1..02d4119 100644 --- a/include/mupdf/pdf/object.h +++ b/include/mupdf/pdf/object.h -@@ -110,6 +110,7 @@ pdf_obj *pdf_dict_gets(fz_context *ctx, pdf_obj *dict, const char *key); +@@ -109,6 +109,7 @@ pdf_obj *pdf_dict_gets(fz_context *ctx, pdf_obj *dict, const char *key); pdf_obj *pdf_dict_getsa(fz_context *ctx, pdf_obj *dict, const char *key, const char *abbrev); void pdf_dict_put(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val); void pdf_dict_put_drop(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val); @@ -34,10 +34,10 @@ index 5bc3dca..bf57455 100644 void pdf_dict_puts_drop(fz_context *ctx, pdf_obj *dict, const char *key, pdf_obj *val); void pdf_dict_putp(fz_context *ctx, pdf_obj *dict, const char *path, pdf_obj *val); diff --git a/source/pdf/pdf-object.c b/source/pdf/pdf-object.c -index b4e33f3..1c19ba4 100644 +index f2e4551..a0d0d8e 100644 --- a/source/pdf/pdf-object.c +++ b/source/pdf/pdf-object.c -@@ -1265,11 +1265,14 @@ pdf_dict_geta(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *abbrev) +@@ -1240,9 +1240,13 @@ pdf_dict_geta(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *abbrev) return pdf_dict_get(ctx, obj, abbrev); } @@ -46,27 +46,26 @@ index b4e33f3..1c19ba4 100644 +static void +pdf_dict_get_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val, pdf_obj **old_val) { - int i; - ++ + if (old_val) + *old_val = NULL; + RESOLVE(obj); - if (!OBJ_IS_DICT(obj)) - fz_throw(ctx, FZ_ERROR_GENERIC, "not a dict (%s)", pdf_objkindstr(obj)); -@@ -1295,7 +1298,10 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) - { - pdf_obj *d = DICT(obj)->items[i].v; - DICT(obj)->items[i].v = pdf_keep_obj(ctx, val); -- pdf_drop_obj(ctx, d); -+ if (old_val) -+ *old_val = d; -+ else -+ pdf_drop_obj(ctx, d); + if (obj >= PDF_OBJ__LIMIT) + { +@@ -1282,7 +1286,10 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) + { + pdf_obj *d = DICT(obj)->items[i].v; + DICT(obj)->items[i].v = pdf_keep_obj(ctx, val); +- pdf_drop_obj(ctx, d); ++ if (old_val) ++ *old_val = d; ++ else ++ pdf_drop_obj(ctx, d); + } } - } - else -@@ -1316,10 +1322,27 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) + else +@@ -1305,10 +1312,27 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val) } void @@ -96,10 +95,10 @@ index b4e33f3..1c19ba4 100644 pdf_drop_obj(ctx, val); fz_catch(ctx) diff --git a/source/pdf/pdf-repair.c b/source/pdf/pdf-repair.c -index 690bf15..167f609 100644 +index fdd4648..212c8b7 100644 --- a/source/pdf/pdf-repair.c +++ b/source/pdf/pdf-repair.c -@@ -260,6 +260,27 @@ pdf_repair_obj_stm(fz_context *ctx, pdf_document *doc, int stm_num) +@@ -259,6 +259,27 @@ pdf_repair_obj_stm(fz_context *ctx, pdf_document *doc, int num, int gen) } } @@ -127,12 +126,12 @@ index 690bf15..167f609 100644 void pdf_repair_xref(fz_context *ctx, pdf_document *doc) { -@@ -528,12 +549,13 @@ pdf_repair_xref(fz_context *ctx, pdf_document *doc) +@@ -520,12 +541,13 @@ pdf_repair_xref(fz_context *ctx, pdf_document *doc) /* correct stream length for unencrypted documents */ if (!encrypt && list[i].stm_len >= 0) { + pdf_obj *old_obj = NULL; - dict = pdf_load_object(ctx, doc, list[i].num); + dict = pdf_load_object(ctx, doc, list[i].num, list[i].gen); length = pdf_new_int(ctx, doc, list[i].stm_len); - pdf_dict_put(ctx, dict, PDF_NAME_Length, length); @@ -145,22 +144,22 @@ index 690bf15..167f609 100644 } } diff --git a/source/pdf/pdf-xref.c b/source/pdf/pdf-xref.c -index 7d21775..0cf20d4 100644 +index 3de1cd2..6682741 100644 --- a/source/pdf/pdf-xref.c +++ b/source/pdf/pdf-xref.c -@@ -1620,6 +1620,12 @@ pdf_drop_document_imp(fz_context *ctx, pdf_document *doc) +@@ -1626,6 +1626,12 @@ pdf_close_document(fz_context *ctx, pdf_document *doc) - pdf_drop_resource_tables(ctx, doc); + pdf_drop_resource_tables(ctx, doc); -+ for (i = 0; i < doc->orphans_count; i++) -+ { -+ pdf_drop_obj(ctx, doc->orphans[i]); -+ } -+ fz_free(ctx, doc->orphans); ++ for (i = 0; i < doc->orphans_count; i++) ++ { ++ pdf_drop_obj(ctx, doc->orphans[i]); ++ } ++ fz_free(ctx, doc->orphans); + - fz_free(ctx, doc); - } - fz_always(ctx) + fz_free(ctx, doc); + } + -- -2.9.1 +2.10.1 -- cgit v1.3 From c70271ec4821969e5f5f46de8ee242152bec0366 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:32:29 +0200 Subject: gnu: bioperl-minimal: Update to 1.7.0. * gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0. --- gnu/packages/bioinformatics.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b71cde8aba..025d2317d7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -602,15 +602,19 @@ e.g. microbiome samples, genomes, metagenomes.") (map (compose package-transitive-target-inputs cadr) inputs)))))) (package (name "bioperl-minimal") - (version "1.6.924") + (version "1.7.0") (source (origin (method url-fetch) - (uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-" - version ".tar.gz")) + (uri (string-append "https://github.com/bioperl/bioperl-live/" + "archive/release-" + (string-map (lambda (c) + (if (char=? c #\.) + #\- c)) version) + ".tar.gz")) (sha256 (base32 - "1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1")))) + "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) (build-system perl-build-system) (arguments `(#:phases -- cgit v1.3 From 8e1369f19a9acdc37dd203bae48f8c3e5df58830 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:34:09 +0200 Subject: gnu: r-rmarkdown: Update to 1.1. * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.1. [propagated-inputs]: Add r-evaluate, r-tibble. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2a42153df6..1c9859c45f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2133,14 +2133,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "0c7gs9c8xdjfxviw0syh13pf3vys2b2ssixmnyqbji64xdscn7pz")))) + "1czvkaz1ji3jyj6qrvbswisqs9d05ljqc4vjkfdrf6hygix7azd0")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (arguments @@ -2159,6 +2159,8 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") #t))))) (propagated-inputs `(("r-catools" ,r-catools) + ("r-evaluate" ,r-evaluate) + ("r-tibble" ,r-tibble) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-base64enc" ,r-base64enc) -- cgit v1.3 From 7397cd9e3f05cc5e7ecbfb1d230d146e2a7d01b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:41:28 +0200 Subject: gnu: armadillo: Update to 7.500.0. * gnu/packages/maths.scm (armadillo): Update to 7.500.0. --- gnu/packages/maths.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1b43bdabc7..479dc794de 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1987,14 +1987,14 @@ full text searching.") (define-public armadillo (package (name "armadillo") - (version "6.700.7") + (version "7.500.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/arma/armadillo-" - version ".tar.gz")) + version ".tar.xz")) (sha256 (base32 - "0xbidcxrvbq33xf7iysg2nic2ai9a043psl33kiv6ifkk7p8hcra")))) + "1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ;no test target (inputs -- cgit v1.3 From 062737a178ac42059f2e571cc0affb4b08e032ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:42:05 +0200 Subject: gnu: r-rcpparmadillo: Update to 0.7.500.0.0. * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to 7.500.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.500.0.0. --- gnu/packages/maths.scm | 4 ++-- gnu/packages/statistics.scm | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 479dc794de..0fa97327da 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2015,14 +2015,14 @@ associated functions (eg. contiguous and non-contiguous submatrix views).") (define-public armadillo-for-rcpparmadillo (package (inherit armadillo) - (version "7.400.2") + (version "7.500.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/arma/armadillo-" version ".tar.xz")) (sha256 (base32 - "0xmpnqhm9mwr1lssjyarj0cl8b4svbqv6z1xa1dxlwd2ly1srkg4")))))) + "1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks")))))) (define-public muparser ;; When switching download sites, muparser re-issued a 2.2.5 release with a diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1c9859c45f..4b7923063f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2049,13 +2049,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.7.400.2.0") + (version "0.7.500.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0g2658iy43higy1cay00ljibgnwh0zv5gcwvbhckjs48y8z1a2pb")) + "06qb6877c5qd8lvnc4b27z8fwb5r5pyylkj0g6kj1rn868zkh5ps")) (modules '((guix build utils))) ;; Remove bundled armadillo sources (snippet -- cgit v1.3 From a46cc723ff1c5cc5cf3ec1a8a8e9daebb2acaed0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:43:54 +0200 Subject: gnu: r-seqinr: Update to 3.3-3. * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 025d2317d7..fa35531868 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6086,14 +6086,14 @@ S4Vectors package itself.") (define-public r-seqinr (package (name "r-seqinr") - (version "3.3-1") + (version "3.3-3") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "1al83y6m7739dz2j895yihksm0s5l45ialid4yw911ylbg3w6cm1")))) + "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) -- cgit v1.3 From 2ffcd6607b793d85d0923b86110afdbc0d840da0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:47:29 +0200 Subject: gnu: r-curl: Update to 2.2. * gnu/packages/web.scm (r-curl): Update to 2.2. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index cabf1e6b49..c343e0cc8b 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3310,13 +3310,13 @@ applications.") (define-public r-curl (package (name "r-curl") - (version "1.2") + (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "04fwasg400v8dvkcn1fcha1jzdz8lbyxi0679q7flsyrp57b3jrf")))) + "0hyvyjzf5ja7kfhzmlfgp86hg1lxrriiwbnr6pxabwwslswj3cmj")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.3 From e1c2b7e2e1339a9324149239bb6e434d98431457 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:47:53 +0200 Subject: gnu: r-jsonlite: Update to 1.1. * gnu/packages/web.scm (r-jsonlite): Update to 1.1. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index c343e0cc8b..30d0677c1b 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3204,13 +3204,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "0bcnzzycvwwkm0lv0ka9xf55z5c1795b7c2vhmf53z73cxixsmnp")))) + "0mrfzh0mxxrhqdmxai434wvyd7skkw28vxr7pyls19yrg941g6r3")))) (build-system r-build-system) (home-page "http://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") -- cgit v1.3 From 9e087a1fdea1b12c1ac7538e766c148f648ffd38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:48:16 +0200 Subject: gnu: r-colorspace: Update to 1.2-7. * gnu/packages/statistics.scm (r-colorspace): Update to 1.2-7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4b7923063f..a1c1af1209 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -198,13 +198,13 @@ available, greatly increasing its breadth and scope.") (define-public r-colorspace (package (name "r-colorspace") - (version "1.2-6") + (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 - (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds")))) + (base32 "0flw97iwwpkxy6si9cn982jhl61wb1rxi3r0nz2xxf0c3fzw18d5")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") -- cgit v1.3 From 03f72a1e1fab46fd5a94d8c0880985005d5334ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:48:55 +0200 Subject: gnu: r-matrix: Update to 1.2-7.1. * gnu/packages/statistics.scm (r-matrix): Update to 1.2-7.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a1c1af1209..65c5d91d75 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -408,14 +408,14 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see (define-public r-matrix (package (name "r-matrix") - (version "1.2-7") + (version "1.2-7.1") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "18x3mdq5cdhbk1lw5cj7vbr41lk8w9p4i5kzh8wslgq6p3d9ac3c")))) + "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From c2a9e991348eb61f76e19b07d9058bcf1341f5a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:49:30 +0200 Subject: gnu: r-stringi: Update to 1.1.2. * gnu/packages/statistics.scm (r-stringi): Update to 1.1.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 65c5d91d75..bbeeb36a7f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -556,14 +556,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "0rg14hga1g2havd3imhk04iyh1dnisnmxf7yhiiwhs7y72hphc94")))) + "13i1p6j8mx31hsw2s4c2phm2llrrdakzixkm6i0axsxprri722z5")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.3 From 2d9da70bbe601326e02ade8939364a9a0c4d6bb7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:50:05 +0200 Subject: gnu: r-reshape2: Update to 1.4.2. * gnu/packages/statistics.scm (r-reshape2): Update to 1.4.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index bbeeb36a7f..2870d8dabd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -606,13 +606,13 @@ the input of another.") (define-public r-reshape2 (package (name "r-reshape2") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "reshape2" version)) (sha256 - (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v")))) + (base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) -- cgit v1.3 From e0a9093139df5a9d5f81d881cdee336931d568d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:50:38 +0200 Subject: gnu: r-evaluate: Update to 0.10. * gnu/packages/statistics.scm (r-evaluate): Update to 0.10. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2870d8dabd..28f701115f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -809,13 +809,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "1bn6bympg9prr8d16g1g530bddii8i04hf4i2bkw0yf4dsfqq4g8")))) + "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) -- cgit v1.3 From bff4dc632480f5a00756882b2e9ae10e42baa4ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:51:06 +0200 Subject: gnu: r-r6: Update to 2.2.0. * gnu/packages/statistics.scm (r-r6): Update to 2.2.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 28f701115f..b382791e38 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1129,13 +1129,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.1.3") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "19qrkgxvssyi51fm80h93sabzz0n2vgqgv1w8xjqbsap0nx379vy")))) + "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") -- cgit v1.3 From e7622804aaed46bd41b5f61547fae4a11ea56788 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:51:38 +0200 Subject: gnu: r-acepack: Update to 1.4.0. * gnu/packages/statistics.scm (r-acepack): Update to 1.4.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b382791e38..3b99051bba 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1207,14 +1207,14 @@ database.") (define-public r-acepack (package (name "r-acepack") - (version "1.3-3.3") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "acepack" version)) (sha256 (base32 - "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y")))) + "0brivhr0imf2qq1flc9qxibybg1zi5m8pxz8cjn5a8gb42bcv96n")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) -- cgit v1.3 From 130410d941bf7511f8daecf064b6cde88c460a3e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:52:10 +0200 Subject: gnu: r-cluster: Update to 2.0.5. * gnu/packages/statistics.scm (r-cluster): Update to 2.0.5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3b99051bba..694390aaf6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1228,14 +1228,14 @@ transformations.") (define-public r-cluster (package (name "r-cluster") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "cluster" version)) (sha256 (base32 - "1r669aaaia05i8sv8hxiig1ddah7hm8qw869wgig5i0zzk22bnfl")))) + "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) -- cgit v1.3 From 72263db73d9fd4798aab1a84d9468467c5705b6b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:52:47 +0200 Subject: gnu: r-foreign: Update to 0.8-67. * gnu/packages/statistics.scm (r-foreign): Update to 0.8-67. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 694390aaf6..d9d7de7f7c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1250,14 +1250,14 @@ Groups in Data\".") (define-public r-foreign (package (name "r-foreign") - (version "0.8-66") + (version "0.8-67") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "19278jm85728zb20800w6hq9q8jy8ywdn81mgmlnxkmrr9giwh6p")))) + "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software in R") -- cgit v1.3 From 41bc22a7debfbb34486439e82bf80ecbd98e62f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:53:23 +0200 Subject: gnu: r-backports: Update to 1.0.4. * gnu/packages/statistics.scm (r-backports): Update to 1.0.4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d9d7de7f7c..241bf5961b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1613,14 +1613,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "0s04mbb7imqc00jl37i081y4yf7qdimk687dyrkvb20nixvjvjyh")))) + "0fssh5rnnvpp8wm0ml9gk765idwrgj07xyxpkhpidl9zwydxzif2")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") -- cgit v1.3 From cf738e961e134f86a4c80431659a09c7885b6a74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:54:04 +0200 Subject: gnu: r-snow: Update to 0.4-2. * gnu/packages/statistics.scm (r-snow): Update to 0.4-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 241bf5961b..7c5a9eceb4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2413,13 +2413,13 @@ multiple breakpoints are allowed.") (define-public r-snow (package (name "r-snow") - (version "0.4-1") + (version "0.4-2") (source (origin (method url-fetch) (uri (cran-uri "snow" version)) (sha256 (base32 - "19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w")))) + "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/snow") (synopsis "Support for simple parallel computing in R") -- cgit v1.3 From 4f2ebc16ce7e5ec9b104c147a0468193d766fd97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:54:31 +0200 Subject: gnu: r-codetools: Update to 0.2-15. * gnu/packages/statistics.scm (r-codetools): Update to 0.2-15. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7c5a9eceb4..75fa482a5c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2477,14 +2477,14 @@ data.") (define-public r-codetools (package (name "r-codetools") - (version "0.2-14") + (version "0.2-15") (source (origin (method url-fetch) (uri (cran-uri "codetools" version)) (sha256 (base32 - "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397")))) + "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/codetools") (synopsis "Code analysis tools for R") -- cgit v1.3 From 89242ea47fa48464091de62d65d7ffcdcd2b1875 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:55:10 +0200 Subject: gnu: r-irlba: Update to 2.1.2. * gnu/packages/statistics.scm (r-irlba): Update to 2.1.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 75fa482a5c..b86a6ebec4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2621,14 +2621,14 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "0yb8b8g6f3cb0f56r702fn2px8nf5rx8cyy2scq36xai9w7f25jj")))) + "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/irlba") (synopsis "Methods for eigendecomposition of large matrices") -- cgit v1.3 From fd54f65e72f8ebdca9e9df523e389dab19e8ab55 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:55:43 +0200 Subject: gnu: r-r-utils: Update to 2.4.0. * gnu/packages/statistics.scm (r-r-utils): Update to 2.4.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b86a6ebec4..2489adde11 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2897,13 +2897,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.3.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "0f4z7ka1wb7bgxc5wyqihqxsnqwgyyzbglwvfwmx0gn8i0wzi647")))) + "0cn0wlmgwclmqak05825wrk9q894xa4qjqa7rn0i9p4ss7k6vifj")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs -- cgit v1.3 From a8e893b0b88d7c6907e8a23ab5d5afb665b552d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 15:56:14 +0200 Subject: gnu: r-matrixstats: Update to 0.51.0. * gnu/packages/statistics.scm (r-matrixstats): Update to 0.51.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2489adde11..1b8d074de1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2995,13 +2995,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.50.2") + (version "0.51.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0zj27xxx9cyrq16rn4g3l0krqg68p8f2qp18w1w4i767j87amlbj")))) + "0bsalx605kgb9nl7mfnq1qinkyd9s97p8plymsyfja1gmcnjrcpj")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (native-inputs -- cgit v1.3 From aba646397501e6daf0018c0c11b215ee93b9548e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Oct 2016 18:14:17 +0200 Subject: gnu: r: Update to 3.3.1. * gnu/packages/statistics.scm (r): Update to 3.3.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1b8d074de1..29eaadf394 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -101,7 +101,7 @@ be output in text, PostScript, PDF or HTML.") (define-public r (package (name "r") - (version "3.3.0") + (version "3.3.1") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -109,7 +109,7 @@ be output in text, PostScript, PDF or HTML.") version ".tar.gz")) (sha256 (base32 - "1r0i0cqs3p0vrpiwq0zg5kbrmja9rmaijyzf9f23v6d5n5ab2mlj")))) + "1qm9znh8akfy9fkzzi6f1vz2w1dd0chsr6qn7kw80lqzhgjrmi9x")))) (build-system gnu-build-system) (arguments `(#:make-flags -- cgit v1.3 From 8caeb11772cc1df06cb6bf227c3280ae6858bd59 Mon Sep 17 00:00:00 2001 From: Christopher Allan Webber Date: Mon, 8 Feb 2016 16:01:49 -0800 Subject: gnu: Add autossh. * gnu/packages/ssh.scm (autossh): New variable. --- gnu/packages/ssh.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index af5aae1029..5fdeeb74a4 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2015, 2016 Efraim Flashner ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2016 Nicolas Goaziou +;;; Copyright © 2016 Christopher Allan Webber ;;; ;;; This file is part of GNU Guix. ;;; @@ -506,3 +507,28 @@ manipulating key files.") authentication with SSH's so-called @dfn{interactive keyboard password authentication}.") (license license:gpl2+))) + +(define-public autossh + (package + (name "autossh") + (version "1.4e") + (source + (origin + (method url-fetch) + (uri (string-append + "http://www.harding.motd.ca/autossh/autossh-" + version ".tgz")) + (sha256 + (base32 "0mlicw28vq2jxa0jf0dys5ja75v0fxpjavlq9dpif6bnknji13ly")))) + (build-system gnu-build-system) + (arguments `(#:tests? #f)) ; There is no "make check" or anything similar + (inputs `(("openssh" ,openssh))) + (synopsis "Automatically restart SSH sessions and tunnels") + (description "autossh is a program to start a copy of @command{ssh} and +monitor it, restarting it as necessary should it die or stop passing traffic.") + (home-page "http://www.harding.motd.ca/autossh/") + (license + ;; Why point to a source file? Well, all the individual files have a + ;; copy of this license in their headers, but there's no separate file + ;; with that information. + (license:non-copyleft "file://autossh.c")))) -- cgit v1.3 From 5d73e3000030006b00e7e6644f3ced5d6176376e Mon Sep 17 00:00:00 2001 From: ng0 Date: Sat, 15 Oct 2016 21:01:00 +0000 Subject: gnu: Add lci. * gnu/packages/lolcode.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Signed-off-by: Efraim Flashner --- gnu/local.mk | 1 + gnu/packages/lolcode.scm | 58 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 gnu/packages/lolcode.scm (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index cf1b542b8a..f306180694 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -228,6 +228,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/llvm.scm \ %D%/packages/lout.scm \ %D%/packages/logging.scm \ + %D%/packages/lolcode.scm \ %D%/packages/lsof.scm \ %D%/packages/lua.scm \ %D%/packages/lxde.scm \ diff --git a/gnu/packages/lolcode.scm b/gnu/packages/lolcode.scm new file mode 100644 index 0000000000..4c7d18217d --- /dev/null +++ b/gnu/packages/lolcode.scm @@ -0,0 +1,58 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 ng0 +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages lolcode) + #:use-module (gnu packages) + #:use-module (gnu packages python) + #:use-module (gnu packages readline) + #:use-module (guix build-system cmake) + #:use-module (guix download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages)) + +(define-public lci + (package + (name "lci") + (version "0.11.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/justinmeza/lci/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "1li7ikcrs7wqah7gqkirg0k61n6pm12w7pydin966x1sdn9na46b")) + (file-name (string-append name "-" version ".tar.gz")))) + (build-system cmake-build-system) + (inputs + `(("readline" ,readline))) + (native-inputs + `(("python-2" ,python-2))) ; for the tests + (synopsis "LOLCODE interpreter written in C") + (description + "@code{lci} is a LOLCODE interpreter written in C and is designed to be +correct, portable, fast, and precisely documented. +@enumerate +@item correct: Every effort has been made to test lci's conformance to the +LOLCODE language specification. Unit tests come packaged with the lci source code. +@item portable: lci follows the widely ported ANSI C specification allowing it +to compile on a broad range of systems. +@item fast: Much effort has gone into producing simple and efficient code +whenever possible to the extent that the above points are not compromized. +@end enumerate") + (home-page "http://lolcode.org/") + (license license:gpl3+))) -- cgit v1.3