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| author | Marius Bakke <mbakke@fastmail.com> | 2018-08-25 16:38:51 +0200 |
|---|---|---|
| committer | Marius Bakke <mbakke@fastmail.com> | 2018-08-25 16:38:51 +0200 |
| commit | 173d291466175fd8c2ba117272685ef9722a5b7f (patch) | |
| tree | 5658fb5ea06aba970e8ae26fe88f8ba4fd0c8255 /gnu/packages | |
| parent | 233df51ebc162bf95dfadf914914cbfbc6984651 (diff) | |
| parent | 94e9d750a22e30459732d2ae14d71c5f3acabd91 (diff) | |
| download | guix-patches-173d291466175fd8c2ba117272685ef9722a5b7f.tar guix-patches-173d291466175fd8c2ba117272685ef9722a5b7f.tar.gz | |
Merge branch 'master' into staging
Diffstat (limited to 'gnu/packages')
33 files changed, 726 insertions, 450 deletions
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 82533da4bb..f7f831918b 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2004,17 +2004,17 @@ and ALSA.") (define-public qjackctl (package (name "qjackctl") - (version "0.5.1") + (version "0.5.3") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/qjackctl/qjackctl/" version "/qjackctl-" version ".tar.gz")) (sha256 (base32 - "0jw1s4qh4qjxnysddjv3j2lchwlslj9p4iisv9i89d3m7pf1svs4")))) + "0x08af8m5l8qy9av3dlldsg58ny9nc69h1s4i6hqkvj24jwy6fw1")))) (build-system gnu-build-system) (arguments - '(#:tests? #f)) ; no check target + '(#:tests? #f)) ; no check target (inputs `(("jack" ,jack-1) ("alsa-lib" ,alsa-lib) @@ -2582,15 +2582,18 @@ Tracker 3 S3M and Impulse Tracker IT files.") (define-public soundtouch (package (name "soundtouch") - (version "1.8.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (string-append "http://www.surina.net/soundtouch/soundtouch-" version ".tar.gz")) + (patches (search-patches "soundtouch-CVE-2018-14044-14045.patch" + "soundtouch-CVE-2018-1000223.patch")) (sha256 - (base32 "0sqn3wk4qz20vf0vz853l6dl1gnj1yhqxfwxqsc5lp529kbn2h9x")))) + (base32 + "09cxr02mfyj2bg731bj0i9hh565x8l9p91aclxs8wpqv8b8zf96j")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 754dfa1a40..b36bb74f6f 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -67,7 +67,7 @@ (define-public duplicity (package (name "duplicity") - (version "0.7.17") + (version "0.7.18") (source (origin (method url-fetch) @@ -77,10 +77,10 @@ version ".tar.gz")) (sha256 (base32 - "0jmh3h09680xyf33hzxxxl74bwz66zqhzvjlj7j89r9rz3qwa91p")))) + "1qlika4l1k1nx8zr657ihcy0yzr1c1cdnjlbs325l5krvc3zbc5b")))) (build-system python-build-system) (native-inputs - `(("util-linux" ,util-linux) ;setsid command, for the tests + `(("util-linux" ,util-linux) ; setsid command, for the tests ("par2cmdline" ,par2cmdline) ("python-pexpect" ,python2-pexpect) ("python-fasteners" ,python2-fasteners) @@ -91,23 +91,23 @@ (inputs `(("librsync" ,librsync) ("lftp" ,lftp) - ("gnupg" ,gnupg) ;gpg executable needed - ("util-linux" ,util-linux) ;for setsid + ("gnupg" ,gnupg) ; gpg executable needed + ("util-linux" ,util-linux) ; for setsid ("tzdata" ,tzdata))) (arguments - `(#:python ,python-2 ;setup assumes Python 2 + `(#:python ,python-2 ; setup assumes Python 2 #:test-target "test" #:phases (modify-phases %standard-phases (add-before 'build 'patch-source (lambda* (#:key inputs #:allow-other-keys) - ;; embed gpg store name + ;; Embed gpg store name. (substitute* "duplicity/gpginterface.py" (("self.call = 'gpg'") (string-append "self.call = '" (assoc-ref inputs "gnupg") "/bin/gpg'"))) ;; This matches up with an unreleased upstream fix, it should be - ;; removed when the package is updated + ;; removed when the package is updated. ;; https://bazaar.launchpad.net/~duplicity-team/duplicity/0.8-series/revision/1308 (substitute* "duplicity/gpg.py" (("--no-secmem-warning'\\)") @@ -120,8 +120,8 @@ #t)) (add-before 'check 'check-setup (lambda* (#:key inputs #:allow-other-keys) - (setenv "HOME" (getcwd)) ;gpg needs to write to $HOME - (setenv "TZDIR" ;some timestamp checks need TZDIR + (setenv "HOME" (getcwd)) ; gpg needs to write to $HOME + (setenv "TZDIR" ; some timestamp checks need TZDIR (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")) #t))))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dce8ab62f1..cb3c4bc1fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13406,3 +13406,55 @@ conversions, region filtering, FASTA sequence extraction and more.") ;; gffread is under Expat, but gclib is under Artistic 2.0 (license (list license:expat license:artistic2.0))))) + +(define-public find-circ + ;; The last release was in 2015. The license was clarified in 2017, so we + ;; take the latest commit. + (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d") + (revision "1")) + (package + (name "find-circ") + (version (git-version "1.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marvin-jens/find_circ.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + ;; There is no actual build system. + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (path (getenv "PYTHONPATH"))) + (for-each (lambda (script) + (install-file script bin) + (wrap-program (string-append bin "/" script) + `("PYTHONPATH" ":" prefix (,path)))) + '("cmp_bed.py" + "find_circ.py" + "maxlength.py" + "merge_bed.py" + "unmapped2anchors.py"))) + #t))))) + (inputs + `(("python2" ,python-2) + ("python2-pysam" ,python2-pysam) + ("python2-numpy" ,python2-numpy))) + (home-page "https://github.com/marvin-jens/find_circ") + (synopsis "circRNA detection from RNA-seq reads") + (description "This package provides tools to detect head-to-tail +spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) +in RNA-seq data.") + (license license:gpl3)))) diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index d00f96de64..cf70a29775 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -110,6 +110,22 @@ across a broad spectrum of applications.") (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt" "Some components have other similar licences.")))) +(define-public boost-for-mysql + ;; Older version for MySQL 5.7.23. + (package + (inherit boost) + (version "1.59.0") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/boost/boost/" version "/boost_" + (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version) + ".tar.bz2")) + (sha256 + (base32 + "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj")))) + (properties '((hidden? . #t))))) + (define-public boost-sync (let ((commit "c72891d9b90e2ceb466ec859f640cd012b2d8709") (version "1.55") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b541f1c327..eb6bf9c38b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> +;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -482,13 +483,13 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.17") + (version "0.12.18") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "08xg8h3w25sdb3xr18g9pa0x8cirkdgljqapxmw56ss1j9fc89s2")))) + (base32 "006kpg2ph109rh1l13lqk26pp4as4fvl5661vrcczjygacgd1v7w")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -4847,3 +4848,99 @@ differential equations} (ODE). It includes routines that: approach). @end enumerate\n") (license license:gpl2+))) + +(define-public r-abcanalysis + (package + (name "r-abcanalysis") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABCanalysis" version)) + (sha256 + (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) + (properties `((upstream-name . "ABCanalysis"))) + (build-system r-build-system) + (propagated-inputs `(("r-plotrix" ,r-plotrix))) + (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") + (synopsis "Computed ABC Analysis") + (description + "Multivariate data sets often differ in several factors or derived statistical +parameters, which have to be selected for a valid interpretation. Basing this +selection on traditional statistical limits leads occasionally to the perception +of losing information from a data set. This package provides tools to calculate +these limits on the basis of the mathematical properties of the distribution of +the analyzed items.") + (license license:gpl3))) + +(define-public r-slam + (package + (name "r-slam") + (version "0.1-43") + (source + (origin + (method url-fetch) + (uri (cran-uri "slam" version)) + (sha256 + (base32 "0hy4qzngcgafxxr6ld7n9a9wy979ji998gpcc32vidwyab66dj5h")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/slam/") + (synopsis "Sparse lightweight arrays and matrices") + (description + "This package contains data structures and algorithms for sparse arrays and matrices, +based on index arrays and simple triplet representations, respectively.") + (license license:gpl2))) + +(define-public r-manipulatewidget + (package + (name "r-manipulatewidget") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "manipulateWidget" version)) + (sha256 + (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x")))) + (properties + `((upstream-name . "manipulateWidget"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-codetools" ,r-codetools) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-knitr" ,r-knitr) + ("r-miniui" ,r-miniui) + ("r-shiny" ,r-shiny) + ("r-webshot" ,r-webshot))) + (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") + (synopsis "Add even more interactivity to interactive charts") + (description + "This package lets you create in just a few lines of R code a nice user interface to +modify the data or the graphical parameters of one or multiple interactive +charts. It is useful to quickly explore visually some data or for package +developers to generate user interfaces easy to maintain.") + (license license:gpl2+))) + +(define-public r-a3 + (package + (name "r-a3") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "A3" version)) + (sha256 + (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) + (properties `((upstream-name . "A3"))) + (build-system r-build-system) + (propagated-inputs + `(("r-pbapply" ,r-pbapply) + ("r-xtable" ,r-xtable))) + (home-page "https://cran.r-project.org/web/packages/A3/") + (synopsis "Error metrics for predictive models") + (description + "This package supplies tools for tabulating and analyzing the results of predictive +models. The methods employed are applicable to virtually any predictive model +and make comparisons between different methodologies straightforward.") + (license license:gpl2+))) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index a6e447894c..dc8e52036c 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -549,20 +549,6 @@ RDBMS systems (which are deep in functionality).") ;; Some parts are licensed under the Apache License license:asl2.0)))) -(define boost-for-mysql - (package - (inherit boost) - (version "1.59.0") - (source (origin - (method url-fetch) - (uri (string-append - "mirror://sourceforge/boost/boost/" version "/boost_" - (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version) - ".tar.bz2")) - (sha256 - (base32 - "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj")))))) - ;; XXX When updating, check whether boost-for-mysql is still needed. ;; It might suffice to patch ‘cmake/boost.cmake’ as done in the past. (define-public mysql @@ -1474,16 +1460,15 @@ columns, primary keys, unique constraints and relationships.") (define-public perl-dbd-mysql (package (name "perl-dbd-mysql") - (version "4.043") + (version "4.046") (source (origin (method url-fetch) - (uri (string-append "mirror://cpan/authors/id/M/MI/MICHIELB/" + (uri (string-append "mirror://cpan/authors/id/C/CA/CAPTTOFU/" "DBD-mysql-" version ".tar.gz")) (sha256 (base32 - "16bg7l28n65ngi1abjxvwk906a80i2vd5vzjn812dx8phdg8d7v2")) - (patches (search-patches "perl-dbd-mysql-CVE-2017-10788.patch")))) + "1xziv9w87cl3fbl1mqkdrx28mdqly3gs6gs1ynbmpl2rr4p6arb1")))) (build-system perl-build-system) ;; Tests require running MySQL server (arguments `(#:tests? #f)) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index b66b8d72bf..f11ce71f5a 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1008,7 +1008,7 @@ language, ADMS transforms Verilog-AMS code into other target languages.") (define-public capstone (package (name "capstone") - (version "3.0.5-rc2") + (version "3.0.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/aquynh/capstone/archive/" @@ -1016,22 +1016,20 @@ language, ADMS transforms Verilog-AMS code into other target languages.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1cqms9r2p43aiwp5spd84zaccp16ih03r7sjhrv16nddahj0jz2q")))) + "1wbd1g3r32ni6zd9vwrq3kn7fdp9y8qwn9zllrrbk8n5wyaxcgci")))) (build-system gnu-build-system) (arguments `(#:tests? #f - #:make-flags (list (string-append "PREFIX=" %output) + #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) "CC=gcc") #:phases (modify-phases %standard-phases - (delete 'configure) - ;; cstool's Makefile overrides LDFLAGS, so we cannot pass it as a make flag. + (delete 'configure) ; no configure script + ;; cstool's Makefile ‘+=’s LDFLAGS, so we cannot pass it as a make flag. (add-before 'build 'fix-cstool-ldflags (lambda* (#:key outputs #:allow-other-keys) - (substitute* "cstool/Makefile" - (("LDFLAGS =") - (string-append "LDFLAGS = -Wl,-rpath=" (assoc-ref outputs "out") - "/lib"))) + (setenv "LDFLAGS" (string-append "-Wl,-rpath=" + (assoc-ref outputs "out") "/lib")) #t))))) (home-page "http://www.capstone-engine.org") (synopsis "Lightweight multi-platform, multi-architecture disassembly framework") diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index dd91d77c6c..4d02b4bc62 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -621,7 +621,7 @@ languages, plus Greek and Cyrillic.") (define-public font-gnu-unifont (package (name "font-gnu-unifont") - (version "11.0.01") + (version "11.0.02") (source (origin (method url-fetch) (uri (string-append @@ -629,7 +629,7 @@ languages, plus Greek and Cyrillic.") version ".tar.gz")) (sha256 (base32 - "1nkapra0ic4fp3lmnvfc6jly62yskhcdkwrnq29hvh3xs51ncc52")))) + "1di8i44c163b9l5f08jcrjfijnqz0j7p7hpfvf8dcms6cm6s4wvy")))) (build-system gnu-build-system) (outputs '("out" ; TrueType version "pcf" ; PCF (bitmap) version @@ -662,8 +662,9 @@ languages, plus Greek and Cyrillic.") "install") ;; Move Texinfo file to the right place. (mkdir (string-append bin "/share/info")) - (rename-file (string-append bin "/share/unifont/unifont.info.gz") - (string-append bin "/share/info/unifont.info.gz")) + (invoke "gzip" "-9n" "doc/unifont.info") + (install-file "doc/unifont.info.gz" + (string-append bin "/share/info")) #t)))))) (inputs `(("perl" ,perl))) ; for utilities diff --git a/gnu/packages/gdb.scm b/gnu/packages/gdb.scm index 36ccb79d67..f0c4c8b804 100644 --- a/gnu/packages/gdb.scm +++ b/gnu/packages/gdb.scm @@ -37,14 +37,14 @@ (define-public gdb (package (name "gdb") - (version "8.1") + (version "8.1.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gdb/gdb-" version ".tar.xz")) (sha256 (base32 - "0d2bpqk58fqlx21rbnk8mbcjlggzc9kb5sjirrfrrrjq70ka0qdg")))) + "0g6hv9xk12aa58w77fydaldqr9a6b0a6bnwsq87jfc6lkcbc7p4p")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; FIXME "make check" fails on single-processor systems. diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 70e7ddbe58..d5fb12650f 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages curl) #:use-module (gnu packages crypto) #:use-module (gnu packages emacs) + #:use-module (gnu packages guile) #:use-module (gnu packages openldap) #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) @@ -56,6 +57,7 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages security-token) #:use-module (gnu packages swig) + #:use-module (gnu packages texinfo) #:use-module (gnu packages tls) #:use-module (gnu packages tor) #:use-module (gnu packages web) @@ -451,6 +453,38 @@ QGpgME was originally developed as part of libkleo and incorporated into gpgpme starting with version 1.7.") (license license:gpl2+))) ;; Note: this differs from gpgme +(define-public guile-gcrypt + (package + (name "guile-gcrypt") + (version "0.1.0") + (home-page "https://notabug.org/cwebber/guile-gcrypt") + (source (origin + (method git-fetch) + (uri (git-reference + (url (string-append home-page ".git")) + (commit (string-append "v" version)))) + (sha256 + (base32 + "1lhgh3105yi0ggrjsjibv4wp1ipz8s17pa820hk2wln3rc04wpvf")) + (file-name (string-append name "-" version "-checkout")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("texinfo" ,texinfo))) + (inputs + `(("guile" ,guile-2.2) + ("libgcrypt" ,libgcrypt))) + (synopsis "Cryptography library for Guile using Libgcrypt") + (description + "Guile-Gcrypt provides a Guile 2.x interface to a subset of the +GNU Libgcrypt crytographic library. It provides modules for cryptographic +hash functions, message authentication codes (MAC), public-key cryptography, +strong randomness, and more. It is implemented using the foreign function +interface (FFI) of Guile.") + (license license:gpl3+))) + (define-public python-gpg (package (name "python-gpg") diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 30d2e2612c..f2a252b8d3 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -850,27 +850,18 @@ The library is shipped with documentation in Info format and usage examples.") (define-public guile-lib (package (name "guile-lib") - (version "0.2.6") + (version "0.2.6.1") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/guile-lib/guile-lib-" version ".tar.gz")) (sha256 (base32 - "0n1lf5bsr5s9gqi07sdfkl1hpin6dzvkcj1xa63jd1w8aglwv8r1")) - (modules '((guix build utils))) - (snippet - '(begin - ;; 'pre-inst-env' sets an incorrect load path, missing the - ;; "/src" bit. Add it. - (substitute* "pre-inst-env.in" - (("abs_top_(builddir|srcdir)=([[:graph:]]+)" _ dir value) - (string-append "abs_top_" dir "=" value "/src"))) - #t)))) + "0aizxdif5dpch9cvs8zz5g8ds5s4xhfnwza2il5ji7fv2h7ks7bd")))) (build-system gnu-build-system) (arguments '(#:make-flags - '("GUILE_AUTO_COMPILE=0") ;to prevent guild errors + '("GUILE_AUTO_COMPILE=0") ; to prevent guild errors #:phases (modify-phases %standard-phases (add-before 'configure 'patch-module-dir @@ -1243,7 +1234,6 @@ above command-line parameters.") ("automake" ,automake) ("pkg-config" ,pkg-config) ("guile" ,guile-2.2))) - (home-page "https://savannah.nongnu.org/projects/guile-redis/") (synopsis "Redis client library for Guile") (description "Guile-redis provides a Scheme interface to the Redis key-value cache and store.") diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index 1d673c606a..c3ef85f3f0 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017 rsiddharth <s@ricketyspace.net> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Tonton <tonton@riseup.net> +;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -342,7 +343,7 @@ development.") (define-public ghc-quickcheck-instances (package (name "ghc-quickcheck-instances") - (version "0.3.16.1") + (version "0.3.18") (source (origin (method url-fetch) @@ -352,8 +353,10 @@ development.") version ".tar.gz")) (sha256 (base32 - "01v5bs7r9yvhkvb4yc9bqnacy8r6cy2gr9lnmwx40n5apgi0gcbz")))) + "1bh1pzz5fdcqvzdcirqxna6fnjms02min5md716299g5niz46w55")))) (build-system haskell-build-system) + (arguments + `(#:configure-flags (list "--allow-newer=base-compat"))) (inputs `(("ghc-quickcheck" ,ghc-quickcheck) ("ghc-base-compat" ,ghc-base-compat) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 7347c87534..759ca6044e 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Tonton <tonton@riseup.net> ;;; Copyright © 2018 Timothy Sample <samplet@ngyro.com> +;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -40,6 +41,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) + #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-check) #:use-module (gnu packages haskell-crypto) #:use-module (gnu packages haskell-web) @@ -1938,7 +1940,7 @@ literals.") (define-public ghc-zlib (package (name "ghc-zlib") - (version "0.6.1.1") + (version "0.6.2") (outputs '("out" "doc")) (source (origin @@ -1949,7 +1951,7 @@ literals.") ".tar.gz")) (sha256 (base32 - "0dd79dxf56d8f6ad9if3j87s9gg7yd17ckypjxwplrbkahlb9xf5")))) + "1vbzf0awb6zb456xf48za1kl22018646cfzq4frvxgb9ay97vk0d")))) (build-system haskell-build-system) ;; Tests require older versions of testy. (arguments `(#:tests? #f)) @@ -3380,7 +3382,7 @@ variety of traversals.") (define-public ghc-fgl (package (name "ghc-fgl") - (version "5.5.3.0") + (version "5.6.0.0") (outputs '("out" "doc")) (source (origin @@ -3391,10 +3393,11 @@ variety of traversals.") ".tar.gz")) (sha256 (base32 - "0fbyb6jxy9whgrv6dgnkzz70cmy98arx3q2gnkhgl4a3d7idh36p")))) + "1i6cp4b3w7sjk7y1dq3fh6bci2sm5h3lnbbaw9ln19nwncg2wwll")))) (build-system haskell-build-system) (arguments - `(#:configure-flags (list "--allow-newer=QuickCheck"))) + `(#:configure-flags (list "--allow-newer=QuickCheck" + "--allow-newer=hspec"))) (inputs `(("ghc-mtl" ,ghc-mtl) ("ghc-hspec" ,ghc-hspec) @@ -4092,7 +4095,7 @@ system.") (define-public ghc-base-compat (package (name "ghc-base-compat") - (version "0.9.3") + (version "0.10.4") (source (origin (method url-fetch) @@ -4102,7 +4105,7 @@ system.") ".tar.gz")) (sha256 (base32 - "0452l6zf6fjhy4kxqwv6i6hhg6yfx4wcg450k3axpyj30l7jnq3x")))) + "0ksp990gxs731mq19rzbxrbs43nazfljjc8krlx5bjqblw3kfs8d")))) (build-system haskell-build-system) (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck) @@ -6846,7 +6849,7 @@ this problem.") (define-public ghc-sandi (package (name "ghc-sandi") - (version "0.4.0") ; darcs-2.12.4 needs == 0.4.* + (version "0.4.2") (source (origin (method url-fetch) @@ -6855,7 +6858,7 @@ this problem.") version ".tar.gz")) (sha256 (base32 - "1smf3bq44qni4zbgxpw7cy7b9g95fbrr73j8njjf6139naj9bj20")))) + "0dvkpk91n9kz2ha04rvp231ra9sgd1ilyc1qkzf9l03iir7zrh9b")))) (build-system haskell-build-system) (inputs `(("ghc-stringsearch" ,ghc-stringsearch) @@ -7045,7 +7048,7 @@ supported. A module of colour names (\"Data.Colour.Names\") is provided.") (define-public ghc-wl-pprint-text (package (name "ghc-wl-pprint-text") - (version "1.1.0.4") + (version "1.2.0.0") (source (origin (method url-fetch) @@ -7054,10 +7057,11 @@ supported. A module of colour names (\"Data.Colour.Names\") is provided.") version ".tar.gz")) (sha256 (base32 - "1xgizzimfw17mpmw2afvmnvyag976j8ggn7k5r564rkw9f0m6bgz")))) + "0g3w92rad6x5appfb22rbzcas2ix2h0hy91sdxhq8a4a5cnlrpa0")))) (build-system haskell-build-system) (inputs - `(("ghc-text" ,ghc-text))) + `(("ghc-base-compat" ,ghc-base-compat) + ("ghc-text" ,ghc-text))) (home-page "https://hackage.haskell.org/package/wl-pprint-text") (synopsis "Wadler/Leijen Pretty Printer for Text values") (description @@ -7079,7 +7083,8 @@ supported. A module of colour names (\"Data.Colour.Names\") is provided.") "0ln1szgfy8fa78l3issq4fx3aqnnd54w3cb4wssrfi48vd5rkfjm")))) (build-system haskell-build-system) (arguments - `(#:configure-flags (list "--allow-newer=QuickCheck"))) + `(#:configure-flags (list "--allow-newer=QuickCheck" + "--allow-newer=hspec"))) (inputs `(("ghc-fgl" ,ghc-fgl) ("ghc-quickcheck" ,ghc-quickcheck) @@ -7096,14 +7101,14 @@ for generating graph-like data structures.") (define-public ghc-graphviz (package (name "ghc-graphviz") - (version "2999.18.1.2") + (version "2999.20.0.2") (source (origin (method url-fetch) (uri (string-append "https://hackage.haskell.org/package/" "graphviz/graphviz-" version ".tar.gz")) (sha256 (base32 - "1z453is01v0rnxlv6xx4iyaqv5vrp3bpz829mpv1a341sck2135h")))) + "0kj7ap0gnliviq2p8lscw1m06capnsa90vpvcys24nqy5nw2wrp7")))) (build-system haskell-build-system) (arguments `(#:configure-flags (list "--allow-newer=QuickCheck"))) @@ -7117,6 +7122,10 @@ for generating graph-like data structures.") ("ghc-temporary" ,ghc-temporary) ("ghc-text" ,ghc-text) ("ghc-wl-pprint-text" ,ghc-wl-pprint-text))) + (native-inputs + `(("ghc-hspec" ,ghc-hspec) + ("graphviz" ,graphviz) + ("hspec-discover" ,hspec-discover))) (home-page "https://hackage.haskell.org/package/graphviz") (synopsis "Bindings to Graphviz for graph visualisation") (description @@ -7261,7 +7270,7 @@ which can't be decoded in the current locale encoding.") (define-public ghc-shelly (package (name "ghc-shelly") - (version "1.7.0.1") + (version "1.8.1") (source (origin (method url-fetch) @@ -7270,7 +7279,7 @@ which can't be decoded in the current locale encoding.") version ".tar.gz")) (sha256 (base32 - "0a4ngy8jqcscqhimgiyz7f9kqm23is7x7gyjxr0j6iq1dy57ahq3")))) + "023fbvbqs5gdwm30j5517gbdcc7fvz0md70dgwgpypkskj3i926y")))) (build-system haskell-build-system) (inputs `(("ghc-mtl" ,ghc-mtl) @@ -7286,7 +7295,8 @@ which can't be decoded in the current locale encoding.") ("ghc-async" ,ghc-async) ("ghc-transformers-base" ,ghc-transformers-base) ("ghc-hunit" ,ghc-hunit) - ("ghc-hspec" ,ghc-hspec))) + ("ghc-hspec" ,ghc-hspec) + ("ghc-hspec-contrib" ,ghc-hspec-contrib))) (home-page "https://github.com/yesodweb/Shelly.hs") (synopsis "Shell-like (systems) programming in Haskell") (description diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 968beb52ee..9b9cf01560 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -404,8 +404,8 @@ It has been modified to remove all non-free binary blobs.") ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.18.3") -(define %linux-libre-hash "0z7nnkmk5d2npilviqxa0m6nn30f5arhviysby78kkb3j2isx9jx") +(define %linux-libre-version "4.18.4") +(define %linux-libre-hash "1q3bndhwxwcrlyi0qcgxjsp5fl92wkfgk4y41qwrrywfv9xj3sl7") (define %linux-libre-4.18-patches (list %boot-logo-patch @@ -435,8 +435,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-4.18-patches #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.65") -(define %linux-libre-4.14-hash "0sdv2c0ix2mdc5h10d56bwi77hpb4gibmrsl1ydyb95hgg37k6h0") +(define %linux-libre-4.14-version "4.14.66") +(define %linux-libre-4.14-hash "1sf18m6xjyg535yviz3yjbislf57s180y67z7mzbcl5pq9352bg9") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version @@ -445,14 +445,14 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.122" - "1yjld5q0xpsv4pd285hjp50kr2i41p3yiy1afp8nf88322i2947w" + (make-linux-libre "4.9.123" + "1rljdp3vzhmdc6qha6b9dq0d1a3xz06rn51pb4ad3a2y61mph9sv" %intel-compatible-systems #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.150" - "0dbz6bzxnr8dgp91lnf3jp42cw6dld4yq7ngigpq7s6ymr59j3ah" + (make-linux-libre "4.4.151" + "0irzdq4p8a6dxyx5basgrc7af7w48hmyjwbk5hff8wn8jy71p9zm" %intel-compatible-systems #:configuration-file kernel-config)) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 29d59c5de4..2554ec9efd 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -185,7 +185,7 @@ player daemon.") (define-public ncmpc (package (name "ncmpc") - (version "0.27") + (version "0.29") (source (origin (method url-fetch) (uri @@ -194,12 +194,16 @@ player daemon.") "/ncmpc-" version ".tar.xz")) (sha256 (base32 - "1n8m7syhpgx24hfipixv66h2izn229jkxsmh2q5dzkv9r0znm8pr")))) - (build-system gnu-build-system) + "04jzv1hfdvgbn391523jb2h3yhq9a40pjrg41sl3wf3jf6vajs7g")))) + (build-system meson-build-system) + (arguments + `(#:configure-flags + (list "-Dcurses=ncurses"))) (inputs `(("glib" ,glib) ("libmpdclient" ,libmpdclient) ("ncurses" ,ncurses))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs `(("gettext" ,gettext-minimal) ; for xgettext + ("pkg-config" ,pkg-config))) (synopsis "Curses Music Player Daemon client") (description "ncmpc is a fully featured MPD client, which runs in a terminal using ncurses.") diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 599a1d8943..af2dcf8eaf 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -384,7 +384,7 @@ many input formats and provides a customisable Vi-style user interface.") ;; Denemo's documentation says to use this command to run its ;; testsuite. (lambda _ - (zero? (system* "make" "-C" "tests" "check")))) + (invoke "make" "-C" "tests" "check"))) (add-before 'build 'set-lilypond ;; This phase sets the default path for lilypond to its current ;; location in the store. @@ -411,7 +411,7 @@ many input formats and provides a customisable Vi-style user interface.") "Clarinet in Bb.denemo")) #t))))) (native-inputs - `(("glib:bin" ,glib "bin") ; for gtester + `(("glib:bin" ,glib "bin") ; for gtester ("pkg-config" ,pkg-config))) (inputs `(("alsa-lib" ,alsa-lib) @@ -1289,7 +1289,7 @@ users to select LV2 plugins and run them with jalv.") (define-public synthv1 (package (name "synthv1") - (version "0.9.0") + (version "0.9.2") (source (origin (method url-fetch) (uri @@ -1297,10 +1297,10 @@ users to select LV2 plugins and run them with jalv.") "/synthv1-" version ".tar.gz")) (sha256 (base32 - "1skynjg6ip0qfbqqkybfjh6xcwxagq89ghl08f7sp7j0sz5qdcwp")))) + "1r60l286n8y4a4rrlnbc3h7xk4s2pvqykvskls89prxg0lkpz7kl")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests. + `(#:tests? #f ; there are no tests #:configure-flags '("CXXFLAGS=-std=gnu++11"))) (inputs @@ -1313,7 +1313,7 @@ users to select LV2 plugins and run them with jalv.") ("qttools" ,qttools))) (native-inputs `(("pkg-config" ,pkg-config))) - (home-page "http://synthv1.sourceforge.net") + (home-page "https://synthv1.sourceforge.io") (synopsis "Polyphonic subtractive synthesizer") (description "Synthv1 is an old-school subtractive polyphonic synthesizer with four @@ -1323,7 +1323,7 @@ oscillators and stereo effects.") (define-public drumkv1 (package (name "drumkv1") - (version "0.9.0") + (version "0.9.2") (source (origin (method url-fetch) (uri @@ -1331,10 +1331,10 @@ oscillators and stereo effects.") "/drumkv1-" version ".tar.gz")) (sha256 (base32 - "1vm8lrk3lykdic6fyfpl12jx1xg6rcaid242s8sij30p1ix4zdab")))) + "1z9l43z91d01b9rzam2cj9qmmg6s5y65fjvb83ms4iaa1p0mnwrn")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests. + `(#:tests? #f ; there are no tests #:configure-flags '("CXXFLAGS=-std=gnu++11"))) (inputs @@ -1348,7 +1348,7 @@ oscillators and stereo effects.") (native-inputs `(("pkg-config" ,pkg-config) ("qttools" ,qttools))) - (home-page "http://drumkv1.sourceforge.net") + (home-page "https://drumkv1.sourceforge.io") (synopsis "Drum-kit sampler synthesizer with stereo effects") (description "Drumkv1 is an old-school drum-kit sampler synthesizer with stereo @@ -1358,7 +1358,7 @@ effects.") (define-public samplv1 (package (name "samplv1") - (version "0.9.0") + (version "0.9.2") (source (origin (method url-fetch) (uri @@ -1366,10 +1366,10 @@ effects.") "/samplv1-" version ".tar.gz")) (sha256 (base32 - "0g67vm9ilmq5nlvk0f3abia9pbinr4ck5v4mll6igni1rxz2n7wk")))) + "0rfcp4v971qfhw1hb43hw12wlxmg2q13l0m1h93pyfi5l4mfjkds")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests. + `(#:tests? #f ; there are no tests #:configure-flags '("CXXFLAGS=-std=gnu++11"))) (inputs @@ -1383,7 +1383,7 @@ effects.") (native-inputs `(("pkg-config" ,pkg-config) ("qttools" ,qttools))) - (home-page "http://samplv1.sourceforge.net") + (home-page "https://samplv1.sourceforge.io") (synopsis "Polyphonic sampler synthesizer with stereo effects") (description "Samplv1 is an old-school polyphonic sampler synthesizer with stereo @@ -1393,7 +1393,7 @@ effects.") (define-public padthv1 (package (name "padthv1") - (version "0.9.0") + (version "0.9.2") (source (origin (method url-fetch) (uri @@ -1401,10 +1401,10 @@ effects.") "/padthv1-" version ".tar.gz")) (sha256 (base32 - "0c519qk2g0dk8gqf9ywqfp7dnr4b25lsnxxbf2l1spnnvf8nysvh")))) + "1alfl0l5qdll0w5lwhrwzj5dina1big1zmjg5imi9h06dzhz51xl")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests. + `(#:tests? #f ; there are no tests #:configure-flags '("CXXFLAGS=-std=gnu++11"))) (inputs @@ -1418,7 +1418,7 @@ effects.") (native-inputs `(("pkg-config" ,pkg-config) ("qttools" ,qttools))) - (home-page "http://padthv1.sourceforge.net") + (home-page "https://padthv1.sourceforge.io") (synopsis "Polyphonic additive synthesizer") (description "Padthv1 is an old-school polyphonic additive synthesizer with stereo @@ -1624,7 +1624,7 @@ is subjective.") (define-public tuxguitar (package (name "tuxguitar") - (version "1.5") + (version "1.5.2") (source (origin (method url-fetch) (uri (string-append @@ -1632,19 +1632,12 @@ is subjective.") version "/tuxguitar-" version "-src.tar.gz")) (sha256 (base32 - "1yd5wv17sh6i8pkndxayfd6r2k1ccgnc4w3nda3lpniv8cpjzz3k")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Delete pre-built classes - (delete-file-recursively "TuxGuitar-android-gdrive/bin") - (delete-file-recursively "TuxGuitar-android-gdrive-gdaa/bin") - #t)))) + "10arfpgm2pw7mn922klklzn05lw5ifqx070shdrar81afmkfbbd9")))) (build-system ant-build-system) (arguments `(#:build-target "build" #:jdk ,icedtea-8 - #:tests? #f ; no tests + #:tests? #f ; no tests #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-dir @@ -1663,7 +1656,7 @@ is subjective.") ((assoc-ref %standard-phases 'build) #:build-target "build") (begin - ;; Generate default build.xml + ;; Generate default build.xml. ((@@ (guix build ant-build-system) default-build.xml) (string-append (string-downcase dir) ".jar") (string-append (assoc-ref outputs "out") @@ -1686,15 +1679,15 @@ is subjective.") (lib (string-append share "/java")) (swt (assoc-ref inputs "java-swt"))) (mkdir-p bin) - ;; install all jars + ;; Install all jars. (for-each (lambda (file) (install-file file lib)) (find-files ".." "\\.jar$")) - ;; install all resources + ;; Install all resources. (copy-recursively "share" share) - ;; create wrapper + ;; Create wrapper. (call-with-output-file (string-append bin "/tuxguitar") (lambda (port) (let ((classpath (string-join (append (find-files lib "\\.jar$") @@ -2055,14 +2048,14 @@ improves on support for JACK features, such as JACK MIDI.") (define-public libgig (package (name "libgig") - (version "4.0.0") + (version "4.1.0") (source (origin (method url-fetch) (uri (string-append "http://download.linuxsampler.org/packages/" "libgig-" version ".tar.bz2")) (sha256 (base32 - "1wr8mwjmqpnyz6bx9757lspiii1zzn8zfbqsvn2ipzpgqkxv6kaz")))) + "02xx6bqxzgkvrawwnzrnxx1ypk244q4kpwfd58266f9ji8kq18h6")))) (build-system gnu-build-system) (inputs `(("libuuid" ,util-linux) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 16da879c3f..95cdd5c513 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2191,6 +2191,11 @@ and check if the WLAN key or the master key was transmitted unencrypted.") (base32 "19rqzj167q73ag20zxpvswhkk0bj56r5maf83v5016sw7vrcz5sc")))) (build-system gnu-build-system) + (arguments + ;; XXX: The dynamic socks library doesn't work with 'libc.so' (GNU ld + ;; script). When preloading is enabled, 'sockd' failed with: + ;; … Failed to open library "libc.so": …: invalid ELF header + '(#:configure-flags '("--disable-preload"))) (home-page "https://www.inet.no/dante/") (synopsis "SOCKS server and client") (description "Dante is a SOCKS client and server implementation. It can diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index a7fe44243a..ec1fae6470 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -48,7 +48,7 @@ (define-public parallel (package (name "parallel") - (version "20180722") + (version "20180822") (source (origin (method url-fetch) @@ -56,7 +56,7 @@ version ".tar.bz2")) (sha256 (base32 - "06635p9w4kl0mvqlbgglsndl1zm06f65ckzrjl9p8n4cswf443fg")))) + "0jjs7fpvdjjb5v0j39a6k7hq9h5ap3db1j7vg1r2dq4swk23h9bm")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index b9653693c6..a63fd9bb36 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -100,7 +100,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.3.3") + (version "2.3.4") (source (origin (method url-fetch) @@ -109,27 +109,17 @@ human.") version "-src.tar.xz")) (sha256 (base32 - "1m8alsp39vk21zgcvy5zswk0dc1xmajbwnccg7n0lndsi7pqbzyg")))) + "02kq0a7a7hpw824n03apma00yq1c6dds224g15mrnnqqjn4af90c")))) (build-system cmake-build-system) (arguments '(#:configure-flags '("-DWITH_XC_NETWORKING=YES" "-DWITH_XC_BROWSER=YES" - "-DWITH_XC_SSHAGENT=YES") - #:phases - (modify-phases %standard-phases - ;; should be fixed in 2.3.3+, see: - ;; https://github.com/keepassxreboot/keepassxc/pull/1964 - (add-after 'unpack 'patch-sources - (lambda _ - (substitute* "src/gui/entry/EditEntryWidget.cpp" - (("#include <QColorDialog>") "#include <QColorDialog> -#include <QButtonGroup>")) - #t))))) + "-DWITH_XC_SSHAGENT=YES"))) (inputs `(("argon2" ,argon2) - ("curl" ,curl) ; XC_NETWORKING + ("curl" ,curl) ; XC_NETWORKING ("libgcrypt" ,libgcrypt) - ("libsodium" ,libsodium) ; XC_BROWSER + ("libsodium" ,libsodium) ; XC_BROWSER ("libxi" ,libxi) ("libxtst" ,libxtst) ("qtbase" ,qtbase) @@ -144,7 +134,7 @@ manage your passwords in a secure way. You can put all your passwords in one database, which is locked with one master key or a key-file which can be stored on an external storage device. The databases are encrypted using the algorithms AES or Twofish.") - ;; Non functional parts use various licences. + ;; Non-functional parts use various licences. (license license:gpl3))) (define-public keepassx diff --git a/gnu/packages/patches/byobu-writable-status.patch b/gnu/packages/patches/byobu-writable-status.patch index 2858280273..31dc1f2fd3 100644 --- a/gnu/packages/patches/byobu-writable-status.patch +++ b/gnu/packages/patches/byobu-writable-status.patch @@ -1,13 +1,13 @@ Skeleton status files are installed read-only. When copying to the config dir upon initialization, make sure they end up writable. ---- byobu-5.98/usr/bin/byobu-janitor.in -+++ byobu-5.98/usr/bin/byobu-janitor.in +--- byobu-5.127/usr/bin/byobu-janitor.in ++++ byobu-5.127/usr/bin/byobu-janitor.in @@ -82,6 +82,7 @@ if [ ! -r "$BYOBU_CONFIG_DIR/$f" ]; then # Copy from skeleton, if possible cp -f "$BYOBU_PREFIX/share/$PKG/status/$f" "$BYOBU_CONFIG_DIR/$f" + chmod +w "$BYOBU_CONFIG_DIR/$f" - # Enable ec2_cost, if we're in ec2 and seeding a new setup - if metadata_available; then - $BYOBU_SED_INLINE -e "s/#ec2_cost/ec2_cost/g" "$($BYOBU_READLINK -f $BYOBU_CONFIG_DIR/$f)" + fi + done + diff --git a/gnu/packages/patches/openssh-CVE-2018-15473.patch b/gnu/packages/patches/openssh-CVE-2018-15473.patch deleted file mode 100644 index 26b2dc59c3..0000000000 --- a/gnu/packages/patches/openssh-CVE-2018-15473.patch +++ /dev/null @@ -1,165 +0,0 @@ -Fix CVE-2018-15473, a method by which remote clients can enumerate -usernames on the server: - -http://seclists.org/oss-sec/2018/q3/124 -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-15473 - -Patch adapted from upstream source repository: - -https://anongit.mindrot.org/openssh.git/commit/?id=74287f5df9966a0648b4a68417451dd18f079ab8 - -From 74287f5df9966a0648b4a68417451dd18f079ab8 Mon Sep 17 00:00:00 2001 -From: "djm@openbsd.org" <djm@openbsd.org> -Date: Tue, 31 Jul 2018 03:10:27 +0000 -Subject: [PATCH] upstream: delay bailout for invalid authentic - -=?UTF-8?q?ating=20user=20until=20after=20the=20packet=20containing=20the?= -=?UTF-8?q?=20request=20has=20been=20fully=20parsed.=20Reported=20by=20Dar?= -=?UTF-8?q?iusz=20Tytko=20and=20Micha=C5=82=20Sajdak;=20ok=20deraadt?= -MIME-Version: 1.0 -Content-Type: text/plain; charset=UTF-8 -Content-Transfer-Encoding: 8bit - -OpenBSD-Commit-ID: b4891882fbe413f230fe8ac8a37349b03bd0b70d ---- - auth2-gss.c | 11 +++++++---- - auth2-hostbased.c | 11 ++++++----- - auth2-pubkey.c | 25 +++++++++++++++---------- - 3 files changed, 28 insertions(+), 19 deletions(-) - -# Adapted from upstream to apply to OpenSSH 7.7p1. -diff --git a/auth2-gss.c b/auth2-gss.c -index 589283b7..1d7cfb39 100644 ---- a/auth2-gss.c -+++ b/auth2-gss.c -@@ -69,9 +69,6 @@ userauth_gssapi(struct ssh *ssh) - u_int len; - u_char *doid = NULL; - -- if (!authctxt->valid || authctxt->user == NULL) -- return (0); -- - mechs = packet_get_int(); - if (mechs == 0) { - debug("Mechanism negotiation is not supported"); -diff --git a/auth2-gss.c b/auth2-gss.c -index 47308c5c..9351e042 100644 ---- a/auth2-gss.c -+++ b/auth2-gss.c -@@ -106,6 +103,12 @@ userauth_gssapi(struct ssh *ssh) - return (0); - } - -+ if (!authctxt->valid || authctxt->user == NULL) { -+ debug2("%s: disabled because of invalid user", __func__); -+ free(doid); -+ return (0); -+ } -+ - if (GSS_ERROR(PRIVSEP(ssh_gssapi_server_ctx(&ctxt, &goid)))) { - if (ctxt != NULL) - ssh_gssapi_delete_ctx(&ctxt); -diff --git a/auth2-hostbased.c b/auth2-hostbased.c -index 60159a56..35939329 100644 ---- a/auth2-hostbased.c -+++ b/auth2-hostbased.c -@@ -67,10 +67,6 @@ userauth_hostbased(struct ssh *ssh) - size_t alen, blen, slen; - int r, pktype, authenticated = 0; - -- if (!authctxt->valid) { -- debug2("%s: disabled because of invalid user", __func__); -- return 0; -- } - /* XXX use sshkey_froms() */ - if ((r = sshpkt_get_cstring(ssh, &pkalg, &alen)) != 0 || - (r = sshpkt_get_string(ssh, &pkblob, &blen)) != 0 || -@@ -117,6 +113,11 @@ userauth_hostbased(struct ssh *ssh) - goto done; - } - -+ if (!authctxt->valid || authctxt->user == NULL) { -+ debug2("%s: disabled because of invalid user", __func__); -+ goto done; -+ } -+ - if ((b = sshbuf_new()) == NULL) - fatal("%s: sshbuf_new failed", __func__); - /* reconstruct packet */ -diff --git a/auth2-pubkey.c b/auth2-pubkey.c -index c4d0f790..e1c15040 100644 ---- a/auth2-pubkey.c -+++ b/auth2-pubkey.c -@@ -89,19 +89,15 @@ userauth_pubkey(struct ssh *ssh) - { - Authctxt *authctxt = ssh->authctxt; - struct passwd *pw = authctxt->pw; -- struct sshbuf *b; -+ struct sshbuf *b = NULL; - struct sshkey *key = NULL; -- char *pkalg, *userstyle = NULL, *key_s = NULL, *ca_s = NULL; -- u_char *pkblob, *sig, have_sig; -+ char *pkalg = NULL, *userstyle = NULL, *key_s = NULL, *ca_s = NULL; -+ u_char *pkblob = NULL, *sig = NULL, have_sig; - size_t blen, slen; - int r, pktype; - int authenticated = 0; - struct sshauthopt *authopts = NULL; - -- if (!authctxt->valid) { -- debug2("%s: disabled because of invalid user", __func__); -- return 0; -- } - if ((r = sshpkt_get_u8(ssh, &have_sig)) != 0 || - (r = sshpkt_get_cstring(ssh, &pkalg, NULL)) != 0 || - (r = sshpkt_get_string(ssh, &pkblob, &blen)) != 0) -@@ -167,6 +163,11 @@ userauth_pubkey(struct ssh *ssh) - fatal("%s: sshbuf_put_string session id: %s", - __func__, ssh_err(r)); - } -+ if (!authctxt->valid || authctxt->user == NULL) { -+ debug2("%s: disabled because of invalid user", -+ __func__); -+ goto done; -+ } - /* reconstruct packet */ - xasprintf(&userstyle, "%s%s%s", authctxt->user, - authctxt->style ? ":" : "", -@@ -183,7 +184,6 @@ userauth_pubkey(struct ssh *ssh) - #ifdef DEBUG_PK - sshbuf_dump(b, stderr); - #endif -- - /* test for correct signature */ - authenticated = 0; - if (PRIVSEP(user_key_allowed(ssh, pw, key, 1, &authopts)) && -@@ -194,7 +194,6 @@ userauth_pubkey(struct ssh *ssh) - authenticated = 1; - } - sshbuf_free(b); -- free(sig); - auth2_record_key(authctxt, authenticated, key); - } else { - debug("%s: test pkalg %s pkblob %s%s%s", -@@ -205,6 +204,11 @@ userauth_pubkey(struct ssh *ssh) - if ((r = sshpkt_get_end(ssh)) != 0) - fatal("%s: %s", __func__, ssh_err(r)); - -+ if (!authctxt->valid || authctxt->user == NULL) { -+ debug2("%s: disabled because of invalid user", -+ __func__); -+ goto done; -+ } - /* XXX fake reply and always send PK_OK ? */ - /* - * XXX this allows testing whether a user is allowed -@@ -238,6 +242,7 @@ done: - free(pkblob); - free(key_s); - free(ca_s); -+ free(sig); - return authenticated; - } - --- -2.18.0 diff --git a/gnu/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch b/gnu/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch deleted file mode 100644 index 74613cb632..0000000000 --- a/gnu/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch +++ /dev/null @@ -1,62 +0,0 @@ -Fix CVE-2017-10788: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-10788 - -Patch written to match corrected documentation specifications: - -Old: http://web.archive.org/web/20161220021610/https://dev.mysql.com/doc/refman/5.7/en/mysql-stmt-close.html -New: https://dev.mysql.com/doc/refman/5.7/en/mysql-stmt-close.html - -The patch itself is from https://github.com/perl5-dbi/DBD-mysql/issues/120#issuecomment-312420660. - -From 9ce10cfae7138c37c3a0cb2ba2a1d682482943d0 Mon Sep 17 00:00:00 2001 -From: Pali <pali@cpan.org> -Date: Sun, 25 Jun 2017 10:07:39 +0200 -Subject: [PATCH] Fix use-after-free after calling mysql_stmt_close() - -Ignore return value from mysql_stmt_close() and also its error message -because it points to freed memory after mysql_stmt_close() was called. ---- - dbdimp.c | 8 ++------ - mysql.xs | 7 ++----- - 2 files changed, 4 insertions(+), 11 deletions(-) - -diff --git a/dbdimp.c b/dbdimp.c -index c60a5f6..a6410e5 100644 ---- a/dbdimp.c -+++ b/dbdimp.c -@@ -4894,12 +4894,8 @@ void dbd_st_destroy(SV *sth, imp_sth_t *imp_sth) { - - if (imp_sth->stmt) - { -- if (mysql_stmt_close(imp_sth->stmt)) -- { -- do_error(DBIc_PARENT_H(imp_sth), mysql_stmt_errno(imp_sth->stmt), -- mysql_stmt_error(imp_sth->stmt), -- mysql_stmt_sqlstate(imp_sth->stmt)); -- } -+ mysql_stmt_close(imp_sth->stmt); -+ imp_sth->stmt= NULL; - } - #endif - -diff --git a/mysql.xs b/mysql.xs -index 55376e1..affde59 100644 ---- a/mysql.xs -+++ b/mysql.xs -@@ -434,11 +434,8 @@ do(dbh, statement, attr=Nullsv, ...) - if (bind) - Safefree(bind); - -- if(mysql_stmt_close(stmt)) -- { -- fprintf(stderr, "\n failed while closing the statement"); -- fprintf(stderr, "\n %s", mysql_stmt_error(stmt)); -- } -+ mysql_stmt_close(stmt); -+ stmt= NULL; - - if (retval == -2) /* -2 means error */ - { --- -1.7.9.5 diff --git a/gnu/packages/patches/soundtouch-CVE-2018-1000223.patch b/gnu/packages/patches/soundtouch-CVE-2018-1000223.patch new file mode 100644 index 0000000000..961a183565 --- /dev/null +++ b/gnu/packages/patches/soundtouch-CVE-2018-1000223.patch @@ -0,0 +1,143 @@ +Fix CVE-2018-1000223: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1000223 +https://gitlab.com/soundtouch/soundtouch/issues/6 + +Patches copied from upstream source repository: + +https://gitlab.com/soundtouch/soundtouch/commit/9e02d9b04fda6c1f44336ff00bb5af1e2ffc039e +https://gitlab.com/soundtouch/soundtouch/commit/e0240689056e4182fffdc2a16aa6e3425a15e275 +https://gitlab.com/soundtouch/soundtouch/commit/46531e5b92dd80dd9a7947463d6224fc7cb21967 + +From 9e02d9b04fda6c1f44336ff00bb5af1e2ffc039e Mon Sep 17 00:00:00 2001 +From: oparviainen <oparviai@iki.fi> +Date: Sun, 12 Aug 2018 20:24:37 +0300 +Subject: [PATCH] Added minimum size check for WAV header block lengh values + +--- + source/SoundStretch/WavFile.cpp | 10 +++++++++- + 1 file changed, 9 insertions(+), 1 deletion(-) + +diff --git a/source/SoundStretch/WavFile.cpp b/source/SoundStretch/WavFile.cpp +index 7e7ade2..68818c9 100644 +--- a/source/SoundStretch/WavFile.cpp ++++ b/source/SoundStretch/WavFile.cpp +@@ -530,7 +530,11 @@ int WavInFile::readHeaderBlock() + // read length of the format field
+ if (fread(&nLen, sizeof(int), 1, fptr) != 1) return -1;
+ // swap byte order if necessary
+- _swap32(nLen); // int format_len;
++ _swap32(nLen);
++
++ // verify that header length isn't smaller than expected
++ if (nLen < sizeof(header.format) - 8) return -1;
++
+ header.format.format_len = nLen;
+
+ // calculate how much length differs from expected
+@@ -572,6 +576,10 @@ int WavInFile::readHeaderBlock() + if (fread(&nLen, sizeof(int), 1, fptr) != 1) return -1;
+ // swap byte order if necessary
+ _swap32(nLen); // int fact_len;
++
++ // verify that fact length isn't smaller than expected
++ if (nLen < sizeof(header.fact) - 8) return -1;
++
+ header.fact.fact_len = nLen;
+
+ // calculate how much length differs from expected
+-- +2.18.0 + +From e0240689056e4182fffdc2a16aa6e3425a15e275 Mon Sep 17 00:00:00 2001 +From: oparviainen <oparviai@iki.fi> +Date: Mon, 13 Aug 2018 19:16:16 +0300 +Subject: [PATCH] Fixed WavFile header/fact not-too-small check + +--- + source/SoundStretch/WavFile.cpp | 22 +++++++++++----------- + 1 file changed, 11 insertions(+), 11 deletions(-) + +diff --git a/source/SoundStretch/WavFile.cpp b/source/SoundStretch/WavFile.cpp +index 4af7a4c..3421bca 100644 +--- a/source/SoundStretch/WavFile.cpp ++++ b/source/SoundStretch/WavFile.cpp +@@ -518,13 +518,13 @@ int WavInFile::readHeaderBlock() + // swap byte order if necessary
+ _swap32(nLen);
+
+- // verify that header length isn't smaller than expected
+- if (nLen < sizeof(header.format) - 8) return -1;
++ // calculate how much length differs from expected
++ nDump = nLen - ((int)sizeof(header.format) - 8);
+
+- header.format.format_len = nLen;
++ // verify that header length isn't smaller than expected structure
++ if (nDump < 0) return -1;
+
+- // calculate how much length differs from expected
+- nDump = nLen - ((int)sizeof(header.format) - 8);
++ header.format.format_len = nLen;
+
+ // if format_len is larger than expected, read only as much data as we've space for
+ if (nDump > 0)
+@@ -561,16 +561,16 @@ int WavInFile::readHeaderBlock() + // read length of the fact field
+ if (fread(&nLen, sizeof(int), 1, fptr) != 1) return -1;
+ // swap byte order if necessary
+- _swap32(nLen); // int fact_len;
+-
+- // verify that fact length isn't smaller than expected
+- if (nLen < sizeof(header.fact) - 8) return -1;
+-
+- header.fact.fact_len = nLen;
++ _swap32(nLen);
+
+ // calculate how much length differs from expected
+ nDump = nLen - ((int)sizeof(header.fact) - 8);
+
++ // verify that fact length isn't smaller than expected structure
++ if (nDump < 0) return -1;
++
++ header.fact.fact_len = nLen;
++
+ // if format_len is larger than expected, read only as much data as we've space for
+ if (nDump > 0)
+ {
+-- +2.18.0 + +From 46531e5b92dd80dd9a7947463d6224fc7cb21967 Mon Sep 17 00:00:00 2001 +From: olli <oparviai@iki.fi> +Date: Mon, 13 Aug 2018 19:42:58 +0300 +Subject: [PATCH] Improved WavFile header/fact not-too-small check + +--- + source/SoundStretch/WavFile.cpp | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/source/SoundStretch/WavFile.cpp b/source/SoundStretch/WavFile.cpp +index 3421bca..9d90b8a 100644 +--- a/source/SoundStretch/WavFile.cpp ++++ b/source/SoundStretch/WavFile.cpp +@@ -522,7 +522,7 @@ int WavInFile::readHeaderBlock() + nDump = nLen - ((int)sizeof(header.format) - 8);
+
+ // verify that header length isn't smaller than expected structure
+- if (nDump < 0) return -1;
++ if ((nLen < 0) || (nDump < 0)) return -1;
+
+ header.format.format_len = nLen;
+
+@@ -567,7 +567,7 @@ int WavInFile::readHeaderBlock() + nDump = nLen - ((int)sizeof(header.fact) - 8);
+
+ // verify that fact length isn't smaller than expected structure
+- if (nDump < 0) return -1;
++ if ((nLen < 0) || (nDump < 0)) return -1;
+
+ header.fact.fact_len = nLen;
+
+-- +2.18.0 + diff --git a/gnu/packages/patches/soundtouch-CVE-2018-14044-14045.patch b/gnu/packages/patches/soundtouch-CVE-2018-14044-14045.patch new file mode 100644 index 0000000000..cc0282fc7b --- /dev/null +++ b/gnu/packages/patches/soundtouch-CVE-2018-14044-14045.patch @@ -0,0 +1,138 @@ +Fix CVE-2018-14044 and CVE-2018-14045: + +https://gitlab.com/soundtouch/soundtouch/issues/7 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-14044 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-14045 + +Patch copied from upstream source repository: + +https://gitlab.com/soundtouch/soundtouch/commit/107f2c5d201a4dfea1b7f15c5957ff2ac9e5f260 + +From 107f2c5d201a4dfea1b7f15c5957ff2ac9e5f260 Mon Sep 17 00:00:00 2001 +From: oparviainen <oparviai@iki.fi> +Date: Sun, 12 Aug 2018 20:00:56 +0300 +Subject: [PATCH] Replaced illegal-number-of-channel assertions with run-time + exception + +--- + include/FIFOSamplePipe.h | 12 ++++++++++++ + include/STTypes.h | 3 +++ + source/SoundTouch/FIFOSampleBuffer.cpp | 3 ++- + source/SoundTouch/RateTransposer.cpp | 5 ++--- + source/SoundTouch/SoundTouch.cpp | 8 ++------ + source/SoundTouch/TDStretch.cpp | 5 ++--- + 6 files changed, 23 insertions(+), 13 deletions(-) + +diff --git a/include/FIFOSamplePipe.h b/include/FIFOSamplePipe.h +index 4ec9275..b08f836 100644 +--- a/include/FIFOSamplePipe.h ++++ b/include/FIFOSamplePipe.h +@@ -51,6 +51,18 @@ namespace soundtouch + /// Abstract base class for FIFO (first-in-first-out) sample processing classes.
+ class FIFOSamplePipe
+ {
++protected:
++
++ bool verifyNumberOfChannels(int nChannels) const
++ {
++ if ((nChannels > 0) && (nChannels <= SOUNDTOUCH_MAX_CHANNELS))
++ {
++ return true;
++ }
++ ST_THROW_RT_ERROR("Error: Illegal number of channels");
++ return false;
++ }
++
+ public:
+ // virtual default destructor
+ virtual ~FIFOSamplePipe() {}
+diff --git a/include/STTypes.h b/include/STTypes.h +index 03e7e07..862505e 100644 +--- a/include/STTypes.h ++++ b/include/STTypes.h +@@ -56,6 +56,9 @@ typedef unsigned long ulong; +
+ namespace soundtouch
+ {
++ /// Max allowed number of channels
++ #define SOUNDTOUCH_MAX_CHANNELS 16
++
+ /// Activate these undef's to overrule the possible sampletype
+ /// setting inherited from some other header file:
+ //#undef SOUNDTOUCH_INTEGER_SAMPLES
+diff --git a/source/SoundTouch/FIFOSampleBuffer.cpp b/source/SoundTouch/FIFOSampleBuffer.cpp +index f0d5e42..706e869 100644 +--- a/source/SoundTouch/FIFOSampleBuffer.cpp ++++ b/source/SoundTouch/FIFOSampleBuffer.cpp +@@ -73,7 +73,8 @@ void FIFOSampleBuffer::setChannels(int numChannels) + {
+ uint usedBytes;
+
+- assert(numChannels > 0);
++ if (!verifyNumberOfChannels(numChannels)) return;
++
+ usedBytes = channels * samplesInBuffer;
+ channels = (uint)numChannels;
+ samplesInBuffer = usedBytes / channels;
+diff --git a/source/SoundTouch/RateTransposer.cpp b/source/SoundTouch/RateTransposer.cpp +index 8b66be3..d115a4c 100644 +--- a/source/SoundTouch/RateTransposer.cpp ++++ b/source/SoundTouch/RateTransposer.cpp +@@ -179,11 +179,10 @@ void RateTransposer::processSamples(const SAMPLETYPE *src, uint nSamples) + // Sets the number of channels, 1 = mono, 2 = stereo
+ void RateTransposer::setChannels(int nChannels)
+ {
+- assert(nChannels > 0);
++ if (!verifyNumberOfChannels(nChannels) ||
++ (pTransposer->numChannels == nChannels)) return;
+
+- if (pTransposer->numChannels == nChannels) return;
+ pTransposer->setChannels(nChannels);
+-
+ inputBuffer.setChannels(nChannels);
+ midBuffer.setChannels(nChannels);
+ outputBuffer.setChannels(nChannels);
+diff --git a/source/SoundTouch/SoundTouch.cpp b/source/SoundTouch/SoundTouch.cpp +index 7b6756b..06bdd56 100644 +--- a/source/SoundTouch/SoundTouch.cpp ++++ b/source/SoundTouch/SoundTouch.cpp +@@ -139,18 +139,14 @@ uint SoundTouch::getVersionId() + // Sets the number of channels, 1 = mono, 2 = stereo
+ void SoundTouch::setChannels(uint numChannels)
+ {
+- /*if (numChannels != 1 && numChannels != 2)
+- {
+- //ST_THROW_RT_ERROR("Illegal number of channels");
+- return;
+- }*/
++ if (!verifyNumberOfChannels(numChannels)) return;
++
+ channels = numChannels;
+ pRateTransposer->setChannels((int)numChannels);
+ pTDStretch->setChannels((int)numChannels);
+ }
+
+
+-
+ // Sets new rate control value. Normal rate = 1.0, smaller values
+ // represent slower rate, larger faster rates.
+ void SoundTouch::setRate(double newRate)
+diff --git a/source/SoundTouch/TDStretch.cpp b/source/SoundTouch/TDStretch.cpp +index 149cdb9..be2dc88 100644 +--- a/source/SoundTouch/TDStretch.cpp ++++ b/source/SoundTouch/TDStretch.cpp +@@ -588,9 +588,8 @@ void TDStretch::setTempo(double newTempo) + // Sets the number of channels, 1 = mono, 2 = stereo
+ void TDStretch::setChannels(int numChannels)
+ {
+- assert(numChannels > 0);
+- if (channels == numChannels) return;
+-// assert(numChannels == 1 || numChannels == 2);
++ if (!verifyNumberOfChannels(numChannels) ||
++ (channels == numChannels)) return;
+
+ channels = numChannels;
+ inputBuffer.setChannels(channels);
+-- +2.18.0 + diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 39d8931c13..3c46102da1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8667,33 +8667,32 @@ CloudFront content delivery network.") (define-public python-pkgconfig (package (name "python-pkgconfig") - (version "1.1.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (pypi-uri "pkgconfig" version)) (sha256 (base32 - "1pw0kmvc57sjmaxi6c54fqsnihqj6hvhc9y1vaz36axafzqam7bh")))) + "107x2wmchlch8saixb488cgjz9n6inl38wi7nxkb942rbaapxiqb")))) (build-system python-build-system) (native-inputs `(("python-nose" ,python-nose))) (inputs `(("pkg-config" ,pkg-config))) (arguments - `(;; Tests fail with "ValueError: _type_ 'v' not supported" on Python 3, - ;; and on Python 2 they need the dl module deprecated since Python 2.6. - #:tests? #f - ;; Hard-code the path to pkg-config. - #:phases + `(#:phases (modify-phases %standard-phases - (add-before - 'build 'patch - (lambda _ - (substitute* "pkgconfig/pkgconfig.py" - (("cmd = 'pkg-config") - (string-append "cmd = '" (which "pkg-config")))) - #t))))) + (add-before 'build 'patch + ;; Hard-code the path to pkg-config. + (lambda _ + (substitute* "pkgconfig/pkgconfig.py" + (("cmd = 'pkg-config") + (string-append "cmd = '" (which "pkg-config")))) + #t)) + (replace 'check + (lambda _ + (invoke "nosetests" "test.py")))))) (home-page "https://github.com/matze/pkgconfig") (synopsis "Python interface for pkg-config") (description "This module provides a Python interface to pkg-config. It diff --git a/gnu/packages/screen.scm b/gnu/packages/screen.scm index 940afcc2d5..38df2594f2 100644 --- a/gnu/packages/screen.scm +++ b/gnu/packages/screen.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com> ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com> -;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -102,7 +102,7 @@ controlling terminal and attach to it later.") (define-public byobu (package (name "byobu") - (version "5.98") + (version "5.127") (source (origin (method url-fetch) @@ -111,11 +111,11 @@ controlling terminal and attach to it later.") version ".orig.tar.gz")) (sha256 (base32 - "1s8nh4wbds1nh52i0d1hy1b308jjf4siwpq92lna1zh9ll4x71j5")) + "0fznlj454vgxgzfw3avmvvjpawggs66da5l8k6v0lnzzd75wgbsb")) (patches (search-patches "byobu-writable-status.patch")))) (build-system gnu-build-system) (inputs - `(("python" ,python-wrapper) ;for config and session GUIs + `(("python" ,python-wrapper) ; for config and session GUIs ("python-newt" ,newt "python"))) (arguments `(#:phases @@ -123,7 +123,7 @@ controlling terminal and attach to it later.") (add-before 'configure 'provide-locale (lambda* (#:key inputs #:allow-other-keys) - (let ((libc (assoc-ref inputs "libc"))) ;implicit input + (let ((libc (assoc-ref inputs "libc"))) ; implicit input (substitute* "usr/bin/byobu.in" (("locale") (string-append libc "/bin/locale"))) #t))) @@ -141,7 +141,7 @@ controlling terminal and attach to it later.") (wrap-program select `("BYOBU_PYTHON" = (,python))) #t)))))) - (home-page "http://byobu.co/index.html") + (home-page "https://byobu.org/") (synopsis "Text-based window manager and terminal multiplexer") (description "Byobu is a Japanese term for decorative, multi-panel screens that serve diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index d4e0437a5b..4b748b6644 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -274,7 +274,7 @@ authentication, encryption and digital signatures. OpenSC implements the PKCS (define-public yubico-piv-tool (package (name "yubico-piv-tool") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append @@ -282,7 +282,7 @@ authentication, encryption and digital signatures. OpenSC implements the PKCS name "-" version ".tar.gz")) (sha256 (base32 - "1p0df35qfm2xch64hc1x6k4gpgfl4hiqph5ai30bq8w7yxa3lvfc")))) + "10xgdc51xvszkxmsvqnbjs8ixxz7rfnfahh3wn8glllynmszbhwi")))) (build-system gnu-build-system) (inputs `(("gengetopt" ,gengetopt) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index 0d9bd5a119..a58ebff481 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -148,15 +148,14 @@ a server that supports the SSH-2 protocol.") (define-public openssh (package (name "openssh") - (version "7.7p1") + (version "7.8p1") (source (origin (method url-fetch) (uri (string-append "mirror://openbsd/OpenSSH/portable/" name "-" version ".tar.gz")) - (patches (search-patches "openssh-CVE-2018-15473.patch")) (sha256 (base32 - "13vbbrvj3mmfhj83qyrg5c0ipr6bzw5s65dy4k8gr7p9hkkfffyp")))) + "1jj4f586r9lhakp2w0zv7j616d6x62m15q8l4nxq7haja6qlnj0s")))) (build-system gnu-build-system) (native-inputs `(("groff" ,groff))) (inputs `(("openssl" ,openssl) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9f76ff3677..5c01a4ae06 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -725,13 +725,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.15") + (version "0.6.16") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "1ia4ak956gnn0f5aqhwgam6g9z6f1y57zz8jv45jc8h79yxp8bl8")))) + (base32 "1lhs59pdjhpb63jyy98pi1shk9shw044k6vl0mvw0f40v08326ar")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -1619,13 +1619,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.7.5") + (version "0.7.6") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0l6smzdgb8w505gyl8gnwlg988a6cmafh3rssiv00rsrd8qqzg9g")))) + "0c43h13s5mr0fklikbbm89gs6z5n66rkjzdv6w3w6kl5af5wr2fl")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -2364,13 +2364,13 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.13.5") + (version "1.13.6") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "1x3wsk7dh3yakii61kbfvafx9yz66h40ixiwfkf03dnp2n24hngs")))) + "1d9n49djydywfyp9w3njgxs5lag4ac7719wmxy1lkgcmn3l9sx5r")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -2562,13 +2562,13 @@ vectors.") (define-public r-catools (package (name "r-catools") - (version "1.17.1") + (version "1.17.1.1") (source (origin (method url-fetch) (uri (cran-uri "caTools" version)) (sha256 (base32 - "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank")))) + "01hccp05gz25vhz9nnxv1c91lrxlr7drcw9xf124gggifxf2qgnm")))) (properties `((upstream-name . "caTools"))) (build-system r-build-system) (propagated-inputs @@ -3323,14 +3323,14 @@ bigmemory and synchronicity packages.") (define-public r-synchronicity (package (name "r-synchronicity") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "synchronicity" version)) (sha256 (base32 - "1km5hx82gy71m5nc6pkcksv0dn32fylhg2axpdsnarrxva14mgdg")))) + "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -4851,14 +4851,14 @@ multivariate analysis.") (define-public r-trimcluster (package (name "r-trimcluster") - (version "0.1-2") + (version "0.1-2.1") (source (origin (method url-fetch) (uri (cran-uri "trimcluster" version)) (sha256 (base32 - "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2")))) + "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/trimcluster") (synopsis "Cluster analysis with trimming") @@ -5172,14 +5172,14 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-0") + (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 (base32 - "1ks2jaav8lbxhzw56vpbnysjk3pvpmqh6avd574k0bha1226k81h")))) + "0rdk7hgahs38j6yv861i31wpmsmyvksxcv8jarvvcjl60whizhb2")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index b7c8736339..5e0b497ace 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org> ;;; Copyright © 2018 Christopher Baines <mail@cbaines.net> ;;; Copyright © 2018 Timothy Sample <samplet@ngyro.com> +;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1779,7 +1780,7 @@ be served with a HTTP file server of your choice.") (define-public darcs (package (name "darcs") - (version "2.12.5") + (version "2.14.1") (source (origin (method url-fetch) @@ -1787,7 +1788,7 @@ be served with a HTTP file server of your choice.") "darcs-" version ".tar.gz")) (sha256 (base32 - "0lrm0sal5pl453mkqn8b9fc9l7lwinc140iqihya9g17bk408nrm")) + "0dfd6bp2wy0aabxx7l93gi3dmq21j970cds424xdy1mgmjcvrpb1")) (modules '((guix build utils))) ;; Remove time-dependent code for reproducibility. (snippet @@ -1795,18 +1796,19 @@ be served with a HTTP file server of your choice.") (substitute* "darcs/darcs.hs" (("__DATE__") "\"1970-01-01\"") (("__TIME__") "\"00:00:00\"")) - (substitute* "src/impossible.h" - (("__DATE__") "\"\"") - (("__TIME__") "\"\"")) #t)))) (build-system haskell-build-system) (arguments `(#:configure-flags '("-fpkgconfig" "-fcurl" "-flibiconv" "-fthreaded" "-fnetwork-uri" "-fhttp" "--flag=executable" - "--flag=library" - "--allow-newer=shelly") - ;; FIXME: darcs is not compatible with the latest QuickCheck - #:tests? #f)) + "--flag=library") + #:phases + (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'patch-sh + (lambda _ + (substitute* "tests/issue538.sh" + (("/bin/sh") (which "sh"))) + #t))))) (inputs `(("ghc-cmdargs" ,ghc-cmdargs) ("ghc-split" ,ghc-split) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 3d9b1695b6..aea75654be 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -27,6 +27,7 @@ ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> +;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -6780,3 +6781,26 @@ compressed JSON header blocks. provided by Guix. The list of packages is searchable and provides instructions on how to use Guix in a shared HPC environment.") (license l:agpl3+)))) + +(define-public r-miniui + (package + (name "r-miniui") + (version "0.1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "miniUI" version)) + (sha256 + (base32 + "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) + (properties `((upstream-name . "miniUI"))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-shiny" ,r-shiny))) + (home-page "https://cran.r-project.org/web/packages/miniUI/") + (synopsis "Shiny UI widgets for small screens") + (description + "This package provides UI widget and layout functions for writing Shiny apps that +work well on small screens.") + (license l:gpl3))) diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 0f3d227732..9c1257b2a1 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -24,6 +25,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system trivial) @@ -226,38 +228,38 @@ integrate Windows applications into your desktop.") (version "3.14") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/wine-staging/wine-staging/archive/v" - version ".zip")) - (file-name (string-append name "-" version ".zip")) - (sha256 - (base32 - "1w3n90ab3xyhdzxw1mnkp2cw76lpm5l75hy9xkw3kz2fwzq6lwz7")))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/wine-staging/wine-staging") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0h6gck0p92hin0m13q1hnlfnqs4vy474w66ppinvqms2zn3vibgi")))) (build-system trivial-build-system) (native-inputs `(("bash" ,bash) - ("coreutils" ,coreutils) - ("unzip" ,unzip))) + ("coreutils" ,coreutils))) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) - (let* ((out (assoc-ref %outputs "out")) - (wine-staging (string-append out "/share/wine-staging")) + (let* ((build-directory ,(string-append name "-" version)) (source (assoc-ref %build-inputs "source")) - (sh (string-append (assoc-ref %build-inputs "bash") "/bin/bash")) - (env (string-append (assoc-ref %build-inputs "coreutils") "/bin/env")) - (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))) - (copy-file source (string-append ,name "-" ,version ".zip")) - (invoke unzip (string-append ,name "-" ,version ".zip")) - (substitute* (string-append "wine-staging-" ,version - "/patches/patchinstall.sh") (("/bin/sh") sh)) - (substitute* (string-append "wine-staging-" ,version - "/patches/gitapply.sh") (("/usr/bin/env") env)) - (mkdir-p wine-staging) - (copy-recursively (string-append "wine-staging-" ,version) - wine-staging) + (bash (assoc-ref %build-inputs "bash")) + (coreutils (assoc-ref %build-inputs "coreutils")) + (out (assoc-ref %outputs "out")) + (wine-staging (string-append out "/share/wine-staging"))) + (copy-recursively source build-directory) + (with-directory-excursion build-directory + (substitute* "patches/patchinstall.sh" + (("/bin/sh") + (string-append bash "/bin/sh"))) + (substitute* "patches/gitapply.sh" + (("/usr/bin/env") + (string-append coreutils "/bin/env")))) + (copy-recursively build-directory wine-staging) #t)))) (home-page "https://github.com/wine-staging") (synopsis "Patchset for Wine") diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 0a78b8ee70..3875765d25 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5239,6 +5239,7 @@ draggable titlebars and borders.") (package (name "libx11") (version "1.6.5") + (replacement libx11-1.6.6) (source (origin (method url-fetch) @@ -5268,6 +5269,20 @@ draggable titlebars and borders.") (description "Xorg Core X11 protocol client library.") (license license:x11))) +;; Replacement package to fix multiple security bugs: +;; <http://seclists.org/oss-sec/2018/q3/146>. +(define-public libx11-1.6.6 + (package + (inherit libx11) + (version "1.6.6") + (source (origin + (method url-fetch) + (uri (string-append "mirror://xorg/individual/lib/libX11-" + version ".tar.bz2")) + (sha256 + (base32 + "0ks1mxlda7nxfmffihi15ljsn50q8dknl33i2xag8xzc80fiizk5")))))) + ;; packages of height 5 in the propagated-inputs tree (define-public libxcursor |