mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-11-07 15:36:20 -05:00
Merge branch 'master' into core-updates
This commit is contained in:
Marius Bakke
commit
64461ba20a
20 changed files with 781 additions and 379 deletions
|
|
@ -51,6 +51,7 @@ Copyright @copyright{} 2018 Mike Gerwitz@*
|
|||
Copyright @copyright{} 2018 Pierre-Antoine Rouby@*
|
||||
Copyright @copyright{} 2018 Gábor Boskovits@*
|
||||
Copyright @copyright{} 2018 Florian Pelz@*
|
||||
Copyright @copyright{} 2018 Laura Lazzati@*
|
||||
|
||||
Permission is granted to copy, distribute and/or modify this document
|
||||
under the terms of the GNU Free Documentation License, Version 1.3 or
|
||||
|
|
@ -354,6 +355,7 @@ configuration in a transactional, reproducible, and stateless fashion
|
|||
(@pxref{System Configuration}).
|
||||
|
||||
@cindex functional package management
|
||||
@cindex isolation
|
||||
Under the hood, Guix implements the @dfn{functional package management}
|
||||
discipline pioneered by Nix (@pxref{Acknowledgments}).
|
||||
In Guix, the package build and installation process is seen
|
||||
|
|
@ -387,6 +389,7 @@ garbage collection of packages (@pxref{Features}).
|
|||
@chapter Installation
|
||||
|
||||
@cindex installing Guix
|
||||
@cindex official website
|
||||
GNU Guix is available for download from its website at
|
||||
@url{http://www.gnu.org/software/guix/}. This section describes the
|
||||
software requirements of Guix, as well as how to install it and get
|
||||
|
|
@ -398,6 +401,8 @@ instead, you want to install the complete GNU operating system,
|
|||
@pxref{System Installation}.
|
||||
|
||||
@cindex foreign distro
|
||||
@cindex directories related to foreign distro
|
||||
|
||||
When installed on a running GNU/Linux system---thereafter called a
|
||||
@dfn{foreign distro}---GNU@tie{}Guix complements the available tools
|
||||
without interference. Its data lives exclusively in two directories,
|
||||
|
|
@ -420,6 +425,7 @@ Once installed, Guix can be updated by running @command{guix pull}
|
|||
@section Binary Installation
|
||||
|
||||
@cindex installing Guix from binaries
|
||||
@cindex installer script
|
||||
This section describes how to install Guix on an arbitrary system from a
|
||||
self-contained tarball providing binaries for Guix and for all its
|
||||
dependencies. This is often quicker than installing from source, which
|
||||
|
|
|
|||
|
|
@ -813,6 +813,7 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/higan-remove-march-native-flag.patch \
|
||||
%D%/packages/patches/hubbub-sort-entities.patch \
|
||||
%D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch \
|
||||
%D%/packages/patches/hplip-remove-imageprocessor.patch \
|
||||
%D%/packages/patches/hydra-disable-darcs-test.patch \
|
||||
%D%/packages/patches/icecat-avoid-bundled-libraries.patch \
|
||||
%D%/packages/patches/icecat-CVE-2018-12383.patch \
|
||||
|
|
@ -1230,7 +1231,6 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch \
|
||||
%D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch \
|
||||
%D%/packages/patches/wpa-supplicant-krack-followups.patch \
|
||||
%D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch \
|
||||
%D%/packages/patches/x265-detect512-all-arches.patch \
|
||||
%D%/packages/patches/xboing-CVE-2004-0149.patch \
|
||||
%D%/packages/patches/xf86-video-ark-remove-mibstore.patch \
|
||||
|
|
|
|||
|
|
@ -753,15 +753,15 @@ (define-public python2-biom-format
|
|||
(package
|
||||
(inherit base)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
;; Do not require the unmaintained pyqi library.
|
||||
(add-after 'unpack 'remove-pyqi
|
||||
(lambda _
|
||||
(substitute* "setup.py"
|
||||
(("install_requires.append\\(\"pyqi\"\\)") "pass"))
|
||||
#t)))
|
||||
,@(package-arguments base))))))
|
||||
(substitute-keyword-arguments (package-arguments base)
|
||||
((#:phases phases)
|
||||
`(modify-phases ,phases
|
||||
;; Do not require the unmaintained pyqi library.
|
||||
(add-after 'unpack 'remove-pyqi
|
||||
(lambda _
|
||||
(substitute* "setup.py"
|
||||
(("install_requires.append\\(\"pyqi\"\\)") "pass"))
|
||||
#t)))))))))
|
||||
|
||||
(define-public bioperl-minimal
|
||||
(let* ((inputs `(("perl-module-build" ,perl-module-build)
|
||||
|
|
@ -2716,8 +2716,10 @@ (define-public fraggenescan
|
|||
(string-append " strcpy(train_dir, \"" share "/train/\");"))))
|
||||
#t))
|
||||
(replace 'build
|
||||
(lambda _ (and (zero? (system* "make" "clean"))
|
||||
(zero? (system* "make" "fgs")))))
|
||||
(lambda _
|
||||
(invoke "make" "clean")
|
||||
(invoke "make" "fgs")
|
||||
#t))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (string-append (assoc-ref outputs "out")))
|
||||
|
|
@ -2734,21 +2736,24 @@ (define-public fraggenescan
|
|||
(let* ((out (string-append (assoc-ref outputs "out")))
|
||||
(bin (string-append out "/bin/"))
|
||||
(frag (string-append bin "run_FragGeneScan.pl")))
|
||||
(and (zero? (system* frag ; Test complete genome.
|
||||
"-genome=./example/NC_000913.fna"
|
||||
"-out=./test2"
|
||||
"-complete=1"
|
||||
"-train=complete"))
|
||||
(file-exists? "test2.faa")
|
||||
(file-exists? "test2.ffn")
|
||||
(file-exists? "test2.gff")
|
||||
(file-exists? "test2.out")
|
||||
(zero? (system* ; Test incomplete sequences.
|
||||
frag
|
||||
"-genome=./example/NC_000913-fgs.ffn"
|
||||
"-out=out"
|
||||
"-complete=0"
|
||||
"-train=454_30")))))))))
|
||||
;; Test complete genome.
|
||||
(invoke frag
|
||||
"-genome=./example/NC_000913.fna"
|
||||
"-out=./test2"
|
||||
"-complete=1"
|
||||
"-train=complete")
|
||||
(unless (and (file-exists? "test2.faa")
|
||||
(file-exists? "test2.ffn")
|
||||
(file-exists? "test2.gff")
|
||||
(file-exists? "test2.out"))
|
||||
(error "Expected files do not exist."))
|
||||
;; Test incomplete sequences.
|
||||
(invoke frag
|
||||
"-genome=./example/NC_000913-fgs.ffn"
|
||||
"-out=out"
|
||||
"-complete=0"
|
||||
"-train=454_30")
|
||||
#t))))))
|
||||
(inputs
|
||||
`(("perl" ,perl)
|
||||
("python" ,python-2))) ;not compatible with python 3.
|
||||
|
|
@ -3471,26 +3476,28 @@ (define-public java-picard-1.113
|
|||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(mkdir-p "lib/jni")
|
||||
(mkdir-p "jdk-src")
|
||||
(and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
|
||||
"-xf" (assoc-ref inputs "jdk-src")))
|
||||
(zero? (system* "javah" "-jni"
|
||||
"-classpath" "classes"
|
||||
"-d" "lib/"
|
||||
"net.sf.samtools.util.zip.IntelDeflater"))
|
||||
(with-directory-excursion "src/c/inteldeflater"
|
||||
(zero? (system* "gcc" "-I../../../lib" "-I."
|
||||
(string-append "-I" (assoc-ref inputs "jdk")
|
||||
"/include/linux")
|
||||
"-I../../../jdk-src/src/share/native/common/"
|
||||
"-I../../../jdk-src/src/solaris/native/common/"
|
||||
"-c" "-O3" "-fPIC" "IntelDeflater.c"))
|
||||
(zero? (system* "gcc" "-shared"
|
||||
"-o" "../../../lib/jni/libIntelDeflater.so"
|
||||
"IntelDeflater.o" "-lz" "-lstdc++"))))))
|
||||
(invoke "tar" "--strip-components=1" "-C" "jdk-src"
|
||||
"-xf" (assoc-ref inputs "jdk-src"))
|
||||
(invoke "javah" "-jni"
|
||||
"-classpath" "classes"
|
||||
"-d" "lib/"
|
||||
"net.sf.samtools.util.zip.IntelDeflater")
|
||||
(with-directory-excursion "src/c/inteldeflater"
|
||||
(invoke "gcc" "-I../../../lib" "-I."
|
||||
(string-append "-I" (assoc-ref inputs "jdk")
|
||||
"/include/linux")
|
||||
"-I../../../jdk-src/src/share/native/common/"
|
||||
"-I../../../jdk-src/src/solaris/native/common/"
|
||||
"-c" "-O3" "-fPIC" "IntelDeflater.c")
|
||||
(invoke "gcc" "-shared"
|
||||
"-o" "../../../lib/jni/libIntelDeflater.so"
|
||||
"IntelDeflater.o" "-lz" "-lstdc++"))
|
||||
#t))
|
||||
;; We can only build everything else after building the JNI library.
|
||||
(add-after 'build-jni 'build-rest
|
||||
(lambda* (#:key make-flags #:allow-other-keys)
|
||||
(zero? (apply system* `("ant" "all" ,@make-flags)))))
|
||||
(apply invoke `("ant" "all" ,@make-flags))
|
||||
#t))
|
||||
(add-before 'build 'set-JAVA6_HOME
|
||||
(lambda _
|
||||
(setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
|
||||
|
|
@ -3977,16 +3984,16 @@ (define-public mafft
|
|||
(define-public mash
|
||||
(package
|
||||
(name "mash")
|
||||
(version "2.0")
|
||||
(version "2.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/marbl/mash/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/marbl/mash.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
|
||||
"049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
|
|
@ -4011,9 +4018,7 @@ (define-public mash
|
|||
"src/mash/CommandScreen.cpp")
|
||||
(("^#include \"kseq\\.h\"")
|
||||
"#include \"htslib/kseq.h\""))
|
||||
#t))
|
||||
(add-after 'fix-includes 'autoconf
|
||||
(lambda _ (zero? (system* "autoconf")))))))
|
||||
#t)))))
|
||||
(native-inputs
|
||||
`(("autoconf" ,autoconf)
|
||||
;; Capnproto and htslib are statically embedded in the final
|
||||
|
|
@ -4040,13 +4045,14 @@ (define-public metabat
|
|||
(version "2.12.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://bitbucket.org/berkeleylab/metabat.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
|
||||
"0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
|
||||
(patches (search-patches "metabat-fix-compilation.patch"))))
|
||||
(build-system scons-build-system)
|
||||
(arguments
|
||||
|
|
@ -4109,16 +4115,16 @@ (define-public metabat
|
|||
(define-public minced
|
||||
(package
|
||||
(name "minced")
|
||||
(version "0.2.0")
|
||||
(version "0.3.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/ctSkennerton/minced/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ctSkennerton/minced.git")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
|
||||
"1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:test-target "test"
|
||||
|
|
@ -4230,12 +4236,13 @@ (define-public muscle
|
|||
(delete 'configure)
|
||||
(replace 'check
|
||||
;; There are no tests, so just test if it runs.
|
||||
(lambda _ (zero? (system* "./muscle" "-version"))))
|
||||
(lambda _ (invoke "./muscle" "-version") #t))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(bin (string-append out "/bin")))
|
||||
(install-file "muscle" bin)))))))
|
||||
(install-file "muscle" bin)
|
||||
#t))))))
|
||||
(home-page "http://www.drive5.com/muscle")
|
||||
(synopsis "Multiple sequence alignment program")
|
||||
(description
|
||||
|
|
@ -4260,11 +4267,6 @@ (define-public newick-utils
|
|||
(base32
|
||||
"1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'autoconf
|
||||
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
|
||||
(inputs
|
||||
;; XXX: TODO: Enable Lua and Guile bindings.
|
||||
;; https://github.com/tjunier/newick_utils/issues/13
|
||||
|
|
@ -4309,19 +4311,20 @@ (define-public orfm
|
|||
(license license:lgpl3+)))
|
||||
|
||||
(define-public pplacer
|
||||
(let ((commit "g807f6f3"))
|
||||
(let ((commit "807f6f3"))
|
||||
(package
|
||||
(name "pplacer")
|
||||
;; The commit should be updated with each version change.
|
||||
(version "1.1.alpha19")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/matsen/pplacer/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/matsen/pplacer.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
|
||||
(base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
|
||||
(build-system ocaml-build-system)
|
||||
(arguments
|
||||
`(#:ocaml ,ocaml-4.01
|
||||
|
|
@ -4338,11 +4341,12 @@ (define-public pplacer
|
|||
(local-dir "cddlib_guix"))
|
||||
(mkdir local-dir)
|
||||
(with-directory-excursion local-dir
|
||||
(system* "tar" "xvf" cddlib-src))
|
||||
(invoke "tar" "xvf" cddlib-src))
|
||||
(let ((cddlib-src-folder
|
||||
(string-append local-dir "/"
|
||||
(list-ref (scandir local-dir) 2)
|
||||
"/lib-src")))
|
||||
(for-each make-file-writable (find-files "cdd_src" ".*"))
|
||||
(for-each
|
||||
(lambda (file)
|
||||
(copy-file file
|
||||
|
|
@ -4406,8 +4410,7 @@ (define pplacer-scripts
|
|||
(add-after 'unpack 'enter-scripts-dir
|
||||
(lambda _ (chdir "scripts")))
|
||||
(replace 'check
|
||||
(lambda _
|
||||
(zero? (system* "python" "-m" "unittest" "discover" "-v"))))
|
||||
(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
|
||||
(add-after 'install 'wrap-executables
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
|
|
@ -4667,13 +4670,14 @@ (define-public pyicoteo
|
|||
(version "2.0.7")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
|
||||
"pyicoteo/get/v" version ".tar.bz2"))
|
||||
(file-name (string-append name "-" version ".tar.bz2"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
|
||||
"0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(#:python ,python-2 ; does not work with Python 3
|
||||
|
|
@ -4757,10 +4761,11 @@ (define-public roary
|
|||
(getenv "PATH")))
|
||||
(setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
|
||||
(getenv "PERL5LIB")))
|
||||
(zero? (length (filter (lambda (file)
|
||||
(display file)(display "\n")
|
||||
(not (zero? (system* "perl" file))))
|
||||
(find-files "t" ".*\\.t$"))))))
|
||||
(for-each (lambda (file)
|
||||
(display file)(display "\n")
|
||||
(invoke "perl" file))
|
||||
(find-files "t" ".*\\.t$"))
|
||||
#t))
|
||||
(replace 'install
|
||||
;; There is no 'install' target in the Makefile.
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
|
|
@ -4849,18 +4854,17 @@ (define-public roary
|
|||
(define-public raxml
|
||||
(package
|
||||
(name "raxml")
|
||||
(version "8.2.10")
|
||||
(version "8.2.12")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
(string-append
|
||||
"https://github.com/stamatak/standard-RAxML/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/stamatak/standard-RAxML.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
|
||||
"1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests.
|
||||
|
|
@ -5053,21 +5057,24 @@ (define-public seek
|
|||
(modify-phases %standard-phases
|
||||
(replace 'bootstrap
|
||||
(lambda _
|
||||
(invoke "bash" "gen_auto")))
|
||||
(substitute* "gen_tools_am"
|
||||
(("/usr/bin/env.*") (which "perl")))
|
||||
(invoke "bash" "gen_auto")
|
||||
#t))
|
||||
(add-after 'build 'build-additional-tools
|
||||
(lambda* (#:key make-flags #:allow-other-keys)
|
||||
(every (lambda (dir)
|
||||
(with-directory-excursion (string-append "tools/" dir)
|
||||
(zero? (apply system* "make" make-flags))))
|
||||
dirs)))
|
||||
(for-each (lambda (dir)
|
||||
(with-directory-excursion (string-append "tools/" dir)
|
||||
(apply invoke "make" make-flags)))
|
||||
dirs)
|
||||
#t))
|
||||
(add-after 'install 'install-additional-tools
|
||||
(lambda* (#:key make-flags #:allow-other-keys)
|
||||
(fold (lambda (dir result)
|
||||
(with-directory-excursion (string-append "tools/" dir)
|
||||
(and result
|
||||
(zero? (apply system*
|
||||
`("make" ,@make-flags "install"))))))
|
||||
#t dirs)))))))
|
||||
(for-each (lambda (dir)
|
||||
(with-directory-excursion (string-append "tools/" dir)
|
||||
(apply invoke `("make" ,@make-flags "install"))))
|
||||
dirs)
|
||||
#t))))))
|
||||
(inputs
|
||||
`(("gsl" ,gsl)
|
||||
("boost" ,boost)
|
||||
|
|
@ -5233,17 +5240,16 @@ (define-public mosaik
|
|||
(define-public ngs-sdk
|
||||
(package
|
||||
(name "ngs-sdk")
|
||||
(version "1.3.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
(string-append "https://github.com/ncbi/ngs/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
|
||||
(version "2.9.3")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ncbi/ngs.git")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:parallel-build? #f ; not supported
|
||||
|
|
@ -5259,9 +5265,10 @@ (define-public ngs-sdk
|
|||
|
||||
;; The 'configure' script doesn't recognize things like
|
||||
;; '--enable-fast-install'.
|
||||
(zero? (system* "./configure"
|
||||
(string-append "--build-prefix=" (getcwd) "/build")
|
||||
(string-append "--prefix=" out))))))
|
||||
(invoke "./configure"
|
||||
(string-append "--build-prefix=" (getcwd) "/build")
|
||||
(string-append "--prefix=" out))
|
||||
#t)))
|
||||
(add-after 'unpack 'enter-dir
|
||||
(lambda _ (chdir "ngs-sdk") #t)))))
|
||||
(native-inputs `(("perl" ,perl)))
|
||||
|
|
@ -5299,23 +5306,24 @@ (define-public java-ngs
|
|||
(define-public ncbi-vdb
|
||||
(package
|
||||
(name "ncbi-vdb")
|
||||
(version "2.8.2")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
(string-append "https://github.com/ncbi/ncbi-vdb/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
|
||||
(version "2.9.3")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ncbi/ncbi-vdb.git")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:parallel-build? #f ; not supported
|
||||
#:tests? #f ; no "check" target
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'make-files-writable
|
||||
(lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
|
||||
(add-before 'configure 'set-perl-search-path
|
||||
(lambda _
|
||||
;; Work around "dotless @INC" build failure.
|
||||
|
|
@ -5349,8 +5357,7 @@ (define-public ncbi-vdb
|
|||
|
||||
;; The 'configure' script doesn't recognize things like
|
||||
;; '--enable-fast-install'.
|
||||
(zero? (system*
|
||||
"./configure"
|
||||
(invoke "./configure"
|
||||
(string-append "--build-prefix=" (getcwd) "/build")
|
||||
(string-append "--prefix=" (assoc-ref outputs "out"))
|
||||
(string-append "--debug")
|
||||
|
|
@ -5359,7 +5366,8 @@ (define-public ncbi-vdb
|
|||
(string-append "--with-ngs-sdk-prefix="
|
||||
(assoc-ref inputs "ngs-sdk"))
|
||||
(string-append "--with-hdf5-prefix="
|
||||
(assoc-ref inputs "hdf5")))))))
|
||||
(assoc-ref inputs "hdf5")))
|
||||
#t)))
|
||||
(add-after 'install 'install-interfaces
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
;; Install interface libraries. On i686 the interface libraries
|
||||
|
|
@ -5464,12 +5472,13 @@ (define-public plink-ng
|
|||
(version "1.90b4")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/chrchang/plink-ng.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
|
||||
(base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f ;no "check" target
|
||||
|
|
@ -5551,14 +5560,14 @@ (define-public smithlab-cpp
|
|||
(define-public preseq
|
||||
(package
|
||||
(name "preseq")
|
||||
(version "2.0")
|
||||
(version "2.0.3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/smithlabcode/"
|
||||
"preseq/archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(uri (string-append "https://github.com/smithlabcode/preseq/"
|
||||
"releases/download/v" version
|
||||
"/preseq_v" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
|
||||
(base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet '(begin
|
||||
;; Remove bundled samtools.
|
||||
|
|
@ -5648,17 +5657,17 @@ (define-public python2-screed
|
|||
(define-public sra-tools
|
||||
(package
|
||||
(name "sra-tools")
|
||||
(version "2.8.2-1")
|
||||
(version "2.9.3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
(string-append "https://github.com/ncbi/sra-tools/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ncbi/sra-tools.git")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
|
||||
"0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:parallel-build? #f ; not supported
|
||||
|
|
@ -5708,8 +5717,7 @@ (define-public sra-tools
|
|||
|
||||
;; The 'configure' script doesn't recognize things like
|
||||
;; '--enable-fast-install'.
|
||||
(zero? (system*
|
||||
"./configure"
|
||||
(invoke "./configure"
|
||||
(string-append "--build-prefix=" (getcwd) "/build")
|
||||
(string-append "--prefix=" (assoc-ref outputs "out"))
|
||||
(string-append "--debug")
|
||||
|
|
@ -5727,18 +5735,7 @@ (define-public sra-tools
|
|||
(string-append "--with-ngs-sdk-prefix="
|
||||
(assoc-ref inputs "ngs-sdk"))
|
||||
(string-append "--with-hdf5-prefix="
|
||||
(assoc-ref inputs "hdf5"))))))
|
||||
;; This version of sra-tools fails to build with glibc because of a
|
||||
;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
|
||||
;; contains a definition of "canonicalize", so we rename it.
|
||||
;;
|
||||
;; See upstream bug report:
|
||||
;; https://github.com/ncbi/sra-tools/issues/67
|
||||
(add-after 'unpack 'patch-away-glibc-conflict
|
||||
(lambda _
|
||||
(substitute* "tools/bam-loader/bam.c"
|
||||
(("canonicalize\\(" line)
|
||||
(string-append "sra_tools_" line)))
|
||||
(assoc-ref inputs "hdf5")))
|
||||
#t)))))
|
||||
(native-inputs `(("perl" ,perl)))
|
||||
(inputs
|
||||
|
|
@ -5865,24 +5862,16 @@ (define-public seqmagick
|
|||
(define-public seqtk
|
||||
(package
|
||||
(name "seqtk")
|
||||
(version "1.2")
|
||||
(version "1.3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/lh3/seqtk/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/lh3/seqtk.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
;; Remove extraneous header files, as is done in the seqtk
|
||||
;; master branch.
|
||||
(for-each (lambda (file) (delete-file file))
|
||||
(list "ksort.h" "kstring.h" "kvec.h"))
|
||||
#t))))
|
||||
"1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
|
|
@ -5890,11 +5879,12 @@ (define-public seqtk
|
|||
(delete 'configure)
|
||||
(replace 'check
|
||||
;; There are no tests, so we just run a sanity check.
|
||||
(lambda _ (zero? (system* "./seqtk" "seq"))))
|
||||
(lambda _ (invoke "./seqtk" "seq") #t))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
|
||||
(install-file "seqtk" bin)))))))
|
||||
(install-file "seqtk" bin)
|
||||
#t))))))
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
(home-page "https://github.com/lh3/seqtk")
|
||||
|
|
@ -5910,20 +5900,20 @@ (define-public snap-aligner
|
|||
(name "snap-aligner")
|
||||
(version "1.0beta.18")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/amplab/snap/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/amplab/snap.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
|
||||
"01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
(replace 'check (lambda _ (zero? (system* "./unit_tests"))))
|
||||
(replace 'check (lambda _ (invoke "./unit_tests") #t))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
|
|
@ -5952,14 +5942,14 @@ (define-public sortmerna
|
|||
(version "2.1b")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/biocore/sortmerna/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/biocore/sortmerna.git")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
|
||||
"0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf"))))
|
||||
(build-system gnu-build-system)
|
||||
(outputs '("out" ;for binaries
|
||||
"db")) ;for sequence databases
|
||||
|
|
@ -6205,8 +6195,7 @@ (define-public taxtastic
|
|||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace 'check
|
||||
(lambda _
|
||||
(zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
|
||||
(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
|
||||
(propagated-inputs
|
||||
`(("python-sqlalchemy" ,python2-sqlalchemy)
|
||||
("python-decorator" ,python2-decorator)
|
||||
|
|
@ -6839,17 +6828,17 @@ (define-public r-sparql
|
|||
(define-public vsearch
|
||||
(package
|
||||
(name "vsearch")
|
||||
(version "2.8.0")
|
||||
(version "2.9.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/torognes/vsearch/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/torognes/vsearch.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
|
||||
"0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
|
||||
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
|
||||
(snippet
|
||||
'(begin
|
||||
|
|
@ -6860,11 +6849,6 @@ (define-public vsearch
|
|||
(delete-file "src/city.cc")
|
||||
#t))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'autogen
|
||||
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
|
||||
(inputs
|
||||
`(("zlib" ,zlib)
|
||||
("bzip2" ,bzip2)
|
||||
|
|
@ -8874,13 +8858,14 @@ (define-public r-seqgl
|
|||
(version "1.1.4")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/ManuSetty/SeqGL/"
|
||||
"archive/" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ManuSetty/SeqGL.git")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
|
||||
"1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-biostrings" ,r-biostrings)
|
||||
|
|
@ -9042,7 +9027,7 @@ (define-public emboss
|
|||
(("\\$\\(bindir\\)/embossupdate") ""))
|
||||
#t))
|
||||
(add-after 'disable-update-check 'autogen
|
||||
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
|
||||
(lambda _ (invoke "autoreconf" "-vif") #t)))))
|
||||
(inputs
|
||||
`(("perl" ,perl)
|
||||
("libpng" ,libpng)
|
||||
|
|
@ -9215,12 +9200,14 @@ (define-public filevercmp
|
|||
(name "filevercmp")
|
||||
(version (string-append "0-1." (string-take commit 7)))
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/ekg/filevercmp/archive/"
|
||||
commit ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/filevercmp.git")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name commit))
|
||||
(sha256
|
||||
(base32
|
||||
"1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests to run.
|
||||
|
|
@ -9230,7 +9217,8 @@ (define-public filevercmp
|
|||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
(install-file "filevercmp" bin)))))))
|
||||
(install-file "filevercmp" bin)
|
||||
#t))))))
|
||||
(home-page "https://github.com/ekg/filevercmp")
|
||||
(synopsis "This program compares version strings")
|
||||
(description "This program compares version strings. It intends to be a
|
||||
|
|
@ -11259,16 +11247,16 @@ (define-public sambamba
|
|||
(define-public ritornello
|
||||
(package
|
||||
(name "ritornello")
|
||||
(version "1.0.0")
|
||||
(version "2.0.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/KlugerLab/"
|
||||
"Ritornello/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/KlugerLab/Ritornello.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
|
||||
"1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; there are no tests
|
||||
|
|
@ -11277,7 +11265,7 @@ (define-public ritornello
|
|||
(add-after 'unpack 'patch-samtools-references
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* '("src/SamStream.h"
|
||||
"src/BufferedGenomeReader.h")
|
||||
"src/FLD.cpp")
|
||||
(("<sam.h>") "<samtools/sam.h>"))
|
||||
#t))
|
||||
(delete 'configure)
|
||||
|
|
@ -11503,15 +11491,16 @@ (define-public imp
|
|||
(define-public tadbit
|
||||
(package
|
||||
(name "tadbit")
|
||||
(version "0.2")
|
||||
(version "0.2.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/3DGenomes/TADbit/"
|
||||
"archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/3DGenomes/TADbit.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
|
||||
"07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(;; Tests are included and must be run after installation, but
|
||||
|
|
@ -11566,13 +11555,14 @@ (define-public kentutils
|
|||
(version "302.0.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
|
||||
"archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ENCODE-DCC/kentUtils.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
|
||||
"0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
|
||||
(modules '((guix build utils)
|
||||
(srfi srfi-26)
|
||||
(ice-9 ftw)))
|
||||
|
|
@ -11623,6 +11613,8 @@ (define-public kentutils
|
|||
#:tests? #f
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'fix-permissions
|
||||
(lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
|
||||
(add-after 'unpack 'fix-paths
|
||||
(lambda _
|
||||
(substitute* "Makefile"
|
||||
|
|
@ -11918,14 +11910,14 @@ (define-public libgff
|
|||
(name "libgff")
|
||||
(version "1.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/Kingsford-Group/"
|
||||
"libgff/archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/Kingsford-Group/libgff.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
|
||||
"0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments `(#:tests? #f)) ; no tests included
|
||||
(home-page "https://github.com/Kingsford-Group/libgff")
|
||||
|
|
@ -11970,14 +11962,14 @@ (define-public sailfish
|
|||
(name "sailfish")
|
||||
(version "0.10.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
(string-append "https://github.com/kingsfordgroup/"
|
||||
"sailfish/archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/kingsfordgroup/sailfish.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
|
||||
"1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
|
|
@ -12025,10 +12017,10 @@ (define-public sailfish
|
|||
(include "external/install/include/rapmap/")
|
||||
(rapmap (assoc-ref inputs "rapmap")))
|
||||
(mkdir-p "/tmp/rapmap")
|
||||
(system* "tar" "xf"
|
||||
(assoc-ref inputs "rapmap")
|
||||
"-C" "/tmp/rapmap"
|
||||
"--strip-components=1")
|
||||
(invoke "tar" "xf"
|
||||
(assoc-ref inputs "rapmap")
|
||||
"-C" "/tmp/rapmap"
|
||||
"--strip-components=1")
|
||||
(mkdir-p src)
|
||||
(mkdir-p include)
|
||||
(for-each (lambda (file)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
|
||||
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
|
||||
;;;
|
||||
|
|
@ -160,8 +160,7 @@ (define-public pcc
|
|||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace 'check
|
||||
(lambda _
|
||||
(zero? (system* "make" "-C" "cc/cpp" "test")))))))
|
||||
(lambda _ (invoke "make" "-C" "cc/cpp" "test") #t)))))
|
||||
(native-inputs
|
||||
`(("bison" ,bison)
|
||||
("flex" ,flex)))
|
||||
|
|
|
|||
|
|
@ -391,9 +391,13 @@ (define-public hplip
|
|||
(base32
|
||||
"0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290"))
|
||||
(modules '((guix build utils)))
|
||||
(patches (search-patches "hplip-remove-imageprocessor.patch"))
|
||||
(snippet
|
||||
;; Fix type mismatch.
|
||||
'(begin
|
||||
;; Delete non-free blobs
|
||||
(for-each delete-file (find-files "." "\\.so$"))
|
||||
(delete-file "prnt/hpcups/ImageProcessor.h")
|
||||
;; Fix type mismatch.
|
||||
(substitute* "prnt/hpcups/genPCLm.cpp"
|
||||
(("boolean") "bool"))
|
||||
#t))))
|
||||
|
|
|
|||
|
|
@ -848,14 +848,14 @@ (define-public postgresql-9.6
|
|||
(package
|
||||
(inherit postgresql)
|
||||
(name "postgresql")
|
||||
(version "9.6.9")
|
||||
(version "9.6.11")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
|
||||
version "/postgresql-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"0biy8j69dbvdmrag55pdszpc0702agzqhhcwdx21xp02mzim4ydr"))))))
|
||||
"0c55akrkzqd6p6a8hr0338wk246hl76r9j16p4zn3s51d7f0l99q"))))))
|
||||
|
||||
(define-public python-pymysql
|
||||
(package
|
||||
|
|
|
|||
|
|
@ -12463,3 +12463,78 @@ (define-public emacs-helm-slime
|
|||
@item helm-slime-repl-history: Select an input from the SLIME REPL history and insert it.
|
||||
@end itemize\n")
|
||||
(license license:gpl3+))))
|
||||
|
||||
(define-public emacs-clang-format
|
||||
(let ((commit "5556c31528af2661bed3011bd63ffc0ed44e18a0"))
|
||||
(package
|
||||
(name "emacs-clang-format")
|
||||
(version (git-version "0.0.0" "1" commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/emacsorphanage/clang-format")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ynvnp3vrcpngmwakb23xv4xn7jbkg43s196q7pg9nkl13x4n2nq"))))
|
||||
(build-system emacs-build-system)
|
||||
(inputs
|
||||
`(("clang" ,clang)))
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'configure
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((clang (assoc-ref inputs "clang")))
|
||||
;; Repo is read-only.
|
||||
(chmod "clang-format.el" #o644)
|
||||
(emacs-substitute-variables "clang-format.el"
|
||||
("clang-format-executable"
|
||||
(string-append clang "/bin/clang-format"))))
|
||||
#t)))))
|
||||
(home-page "https://github.com/emacsorphanage/clang-format")
|
||||
(synopsis "Format code using clang-format")
|
||||
(description "This package allows to filter code through clang-format to
|
||||
fix its formatting. @command{clang-format} is a tool that formats C/C++/Obj-C
|
||||
code according to a set of style options, see
|
||||
@url{http://clang.llvm.org/docs/ClangFormatStyleOptions.html}.")
|
||||
(license license:gpl3+))))
|
||||
|
||||
(define-public emacs-gtk-look
|
||||
(package
|
||||
(name "emacs-gtk-look")
|
||||
(version "29")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri "https://download.tuxfamily.org/user42/gtk-look.el")
|
||||
(sha256
|
||||
(base32
|
||||
"14p2nwrd51cr1v06fxbjjn6jdrkf9d6vcxhmscm0kl677s25ypsp"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'configure
|
||||
(lambda _
|
||||
;; File is read-only.
|
||||
(chmod "gtk-look.el" #o644)
|
||||
(emacs-substitute-variables "gtk-look.el"
|
||||
("gtk-lookup-devhelp-indices"
|
||||
'(list (expand-file-name "~/.guix-profile/share/gtk-doc/html/*/*.devhelp*"))))
|
||||
#t)))))
|
||||
(home-page "http://user42.tuxfamily.org/gtk-look/index.html")
|
||||
(synopsis "Find and display HTML documentation for GTK, GNOME and Glib")
|
||||
(description "@command{gtk-look} finds and displays HTML documentation for
|
||||
GTK, GNOME and Glib functions and variables in Emacs, similar to what
|
||||
info-lookup-symbol does for info files (C-h S). The documentation is expected
|
||||
to be devhelp indexes with HTML files. The location of the indexes can be
|
||||
customized. In addition to C code development @command{gtk-look} is good for
|
||||
|
||||
@itemize
|
||||
@item @command{perl-gtk2}, recognising class funcs like
|
||||
@command{Gtk2::Label->new} and bare method names like @command{set_text}.
|
||||
@item @command{guile-gnome}, recognising methods like @command{set-text} and
|
||||
classes like @command{<gtk-window>}.
|
||||
@end itemize\n")
|
||||
(license license:gpl3+)))
|
||||
|
|
|
|||
|
|
@ -1632,6 +1632,33 @@ (define-public graphene
|
|||
input.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public spread-sheet-widget
|
||||
(package
|
||||
(name "spread-sheet-widget")
|
||||
(version "0.3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://alpha.gnu.org/gnu/ssw/"
|
||||
name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "1h93yyh2by6yrmkwqg38nd5knids05k5nqzcihc1hdwgzg3c4b8y"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
`(("glib" ,glib "bin") ; for glib-genmarshal, etc.
|
||||
("pkg-config" ,pkg-config)))
|
||||
;; In 'Requires' of spread-sheet-widget.pc.
|
||||
(propagated-inputs
|
||||
`(("glib" ,glib)
|
||||
("gtk+" ,gtk+)))
|
||||
(home-page "https://www.gnu.org/software/ssw/")
|
||||
(synopsis "Gtk+ widget for dealing with 2-D tabular data")
|
||||
(description
|
||||
"GNU Spread Sheet Widget is a library for Gtk+ which provides a widget for
|
||||
viewing and manipulating 2 dimensional tabular data in a manner similar to many
|
||||
popular spread sheet programs.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public yad
|
||||
(package
|
||||
(name "yad")
|
||||
|
|
|
|||
|
|
@ -2246,8 +2246,8 @@ (define-public guile-debbugs
|
|||
|
||||
;; There has not been any release yet.
|
||||
(define-public guile-newt
|
||||
(let ((commit "596ad760bee1be419d71271732f0f30eaee55143")
|
||||
(revision "0"))
|
||||
(let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")
|
||||
(revision "1"))
|
||||
(package
|
||||
(name "guile-newt")
|
||||
(version (string-append "0-" revision "." (string-take commit 9)))
|
||||
|
|
@ -2259,7 +2259,7 @@ (define-public guile-newt
|
|||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"18qqbi0bc7vp2vlrhib3p3wwgn7wrlv5728dn0avirhw4fxxivnf"))))
|
||||
"0ww7jbdsmjlsxm60ym6cb5s5kc4ljz8bn4y2lvcqnap0aihqfk10"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:make-flags
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@
|
|||
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
|
||||
;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
|
||||
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
|
||||
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -48,6 +49,7 @@ (define-module (gnu packages kodi)
|
|||
#:use-module (gnu packages gl)
|
||||
#:use-module (gnu packages glib)
|
||||
#:use-module (gnu packages gperf)
|
||||
#:use-module (gnu packages groff)
|
||||
#:use-module (gnu packages gnunet)
|
||||
#:use-module (gnu packages gnupg)
|
||||
#:use-module (gnu packages image)
|
||||
|
|
@ -62,6 +64,7 @@ (define-module (gnu packages kodi)
|
|||
#:use-module (gnu packages python)
|
||||
#:use-module (gnu packages samba)
|
||||
#:use-module (gnu packages sdl)
|
||||
#:use-module (gnu packages serialization)
|
||||
#:use-module (gnu packages ssh)
|
||||
#:use-module (gnu packages swig)
|
||||
#:use-module (gnu packages textutils)
|
||||
|
|
@ -75,11 +78,12 @@ (define-module (gnu packages kodi)
|
|||
#:use-module (gnu packages assembly))
|
||||
|
||||
(define-public crossguid
|
||||
(let ((commit "8f399e8bd4252be9952f3dfa8199924cc8487ca4"))
|
||||
(let ((commit "fef89a4174a7bf8cd99fa9154864ce9e8e3bf989")
|
||||
(revision "2"))
|
||||
(package
|
||||
(name "crossguid")
|
||||
(version (string-append "0.0-1." (string-take commit 7)))
|
||||
;; There's no official release. Just a Git repository.
|
||||
(version (string-append "0.0-" revision "." (string-take commit 7)))
|
||||
;; This is the commit that Kodi wants.
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
|
|
@ -88,13 +92,12 @@ (define-public crossguid
|
|||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1i29y207qqddvaxbn39pk2fbh3gx8zvdprfp35wasj9rw2wjk3s9"))))
|
||||
"1blrkc7zcqrqcr5msvhyhm98s2jvm9hr0isqs4288q2r4mdnrfq0"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; no configure script
|
||||
;; There's no build system here, so we have to do it ourselves.
|
||||
(replace 'build
|
||||
(lambda _
|
||||
(invoke "g++" "-c" "guid.cpp" "-o" "guid.o"
|
||||
|
|
@ -129,7 +132,7 @@ (define-public crossguid
|
|||
;; of the standard build process. To make things easier, we bootstrap
|
||||
;; and patch shebangs here, so we don't have to worry about it later.
|
||||
(define libdvdnav/kodi
|
||||
(let ((commit "6.0.0-Leia-Alpha-1"))
|
||||
(let ((commit "6.0.0-Leia-Alpha-3"))
|
||||
(package
|
||||
(name "libdvdnav-bootstrapped")
|
||||
(version commit)
|
||||
|
|
@ -141,7 +144,7 @@ (define libdvdnav/kodi
|
|||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1xiyfgf8v8aknlxlzsvk6pbzkhclz0hbh3s1b0w6ivkng2k310j9"))))
|
||||
"0qwlf4lgahxqxk1r2pzl866mi03pbp7l1fc0rk522sc0ak2s9jhb"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f
|
||||
|
|
@ -164,7 +167,7 @@ (define libdvdnav/kodi
|
|||
(license license:gpl2+))))
|
||||
|
||||
(define libdvdread/kodi
|
||||
(let ((commit "6.0.0-Leia-Alpha-1"))
|
||||
(let ((commit "6.0.0-Leia-Alpha-3"))
|
||||
(package
|
||||
(name "libdvdread-bootstrapped")
|
||||
(version commit)
|
||||
|
|
@ -176,7 +179,7 @@ (define libdvdread/kodi
|
|||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1c3g18n2vwhgcfz3dka1pmw58bnv2ram7xjvizfiykb3sgi9zfwp"))))
|
||||
"1xxn01mhkdnp10cqdr357wx77vyzfb5glqpqyg8m0skyi75aii59"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f
|
||||
|
|
@ -199,7 +202,7 @@ (define libdvdread/kodi
|
|||
(license (list license:gpl2+ license:lgpl2.1+)))))
|
||||
|
||||
(define libdvdcss/kodi
|
||||
(let ((commit "1.4.1-Leia-Alpha-1"))
|
||||
(let ((commit "1.4.2-Leia-Beta-5"))
|
||||
(package
|
||||
(name "libdvdcss-bootstrapped")
|
||||
(version commit)
|
||||
|
|
@ -211,7 +214,7 @@ (define libdvdcss/kodi
|
|||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"0adafwsawxssj3nilkql447v0l4a2584rdpmy5rfjmznh91lykgh"))))
|
||||
"0j41ydzx0imaix069s3z07xqw9q95k7llh06fc27dcn6f7b8ydyl"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f
|
||||
|
|
@ -233,28 +236,53 @@ (define libdvdcss/kodi
|
|||
(description (package-description libdvdcss))
|
||||
(license license:gpl2+))))
|
||||
|
||||
(define-public fstrcmp
|
||||
(package
|
||||
(name "fstrcmp")
|
||||
(version "0.7.D001")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://fstrcmp.sourceforge.net/fstrcmp-"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0xilghiy3mz78bjmfldi39qyy7jvw5b6wafsx370lw401y2qw0g4"))))
|
||||
(build-system gnu-build-system)
|
||||
(home-page "http://fstrcmp.sourceforge.net/")
|
||||
(arguments
|
||||
'(#:configure-flags '("SH=sh")))
|
||||
(native-inputs
|
||||
`(("ghostscript" ,ghostscript) ; ps2pdf
|
||||
("groff" ,groff)
|
||||
("libtool" ,libtool)
|
||||
("which" ,which)))
|
||||
(synopsis "fuzzy comparison of strings")
|
||||
(description
|
||||
"The fstrcmp project provides a library that is used to make fuzzy
|
||||
comparisons of strings and byte arrays, including multi-byte character strings.
|
||||
This can be useful in error messages, enabling the suggestion of likely valid
|
||||
alternatives. In compilers, this can reduce the cascade of secondary errors.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public kodi
|
||||
;; We package the git version because the current released
|
||||
;; version was cut while the cmake transition was in turmoil.
|
||||
(let ((commit "ec16dbca4dcf2923f53f819695a6d47c52e68d74")
|
||||
(revision "8"))
|
||||
(package
|
||||
(name "kodi")
|
||||
(version (git-version "18.0_alpha" revision commit))
|
||||
(version "18.0b5")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/xbmc/xbmc.git")
|
||||
(commit commit)))
|
||||
(commit (string-append version "-Leia"))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1rxg752cl59124cfpfwmyjldn6qpq5jginxddpzvgagfadf10i4d"))
|
||||
"042qzvhys3sajby6ywgmrsymhji37qk0iqgppznrvm53vrizwsam"))
|
||||
(snippet
|
||||
'(begin
|
||||
(use-modules (guix build utils))
|
||||
(for-each delete-file-recursively
|
||||
'("project/BuildDependencies/bin/"
|
||||
'("project/BuildDependencies/"
|
||||
;; TODO: Purge these jars.
|
||||
;;"tools/codegenerator/groovy"
|
||||
;; And these sources:
|
||||
|
|
@ -370,10 +398,12 @@ (define-public kodi
|
|||
("eudev" ,eudev)
|
||||
("ffmpeg" ,ffmpeg)
|
||||
("flac" ,flac)
|
||||
("flatbuffers" ,flatbuffers)
|
||||
("fmt" ,fmt)
|
||||
("fontconfig" ,fontconfig)
|
||||
("freetype" ,freetype)
|
||||
("fribidi" ,fribidi)
|
||||
("fstrcmp" ,fstrcmp)
|
||||
("giflib" ,giflib)
|
||||
("glew" ,glew)
|
||||
("gnutls" ,gnutls)
|
||||
|
|
@ -427,7 +457,7 @@ (define-public kodi
|
|||
license:expat ;cpluff, dbwrappers
|
||||
license:public-domain ;cpluff/examples
|
||||
license:bsd-3 ;misc, gtest
|
||||
license:bsd-2))))) ;xbmc/freebsd
|
||||
license:bsd-2)))) ;xbmc/freebsd
|
||||
|
||||
(define-public kodi-cli
|
||||
(let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for
|
||||
|
|
|
|||
|
|
@ -2763,18 +2763,16 @@ (define-public maxima
|
|||
(define-public wxmaxima
|
||||
(package
|
||||
(name "wxmaxima")
|
||||
(version "18.02.0")
|
||||
(version "18.10.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/andrejv/" name "/archive"
|
||||
"/Version-" version ".tar.gz"))
|
||||
(uri (string-append "https://github.com/wxMaxima-developers/" name
|
||||
"/archive/Version-" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
|
||||
(patches
|
||||
(search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
|
||||
"0c2blq65r0am509p3rjqpwqk6vl5r2yg1p9nh2jczf80vhi3ldas"))))
|
||||
(build-system cmake-build-system)
|
||||
(native-inputs
|
||||
`(("gettext" ,gettext-minimal)))
|
||||
|
|
|
|||
|
|
@ -309,29 +309,27 @@ (define-public cmus
|
|||
(name "cmus")
|
||||
(version "2.7.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/" name "/" name "/archive/v"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/cmus/cmus.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0raixgjavkm7hxppzsc5zqbfbh2bhjcmbiplhnsxsmyj8flafyc1"))))
|
||||
"0xd96py21bl869qlv1353zw7xsgq6v5s8szr0ldr63zj5fgc2ps5"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; cmus does not include tests
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace
|
||||
'configure
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((out (assoc-ref outputs "out")))
|
||||
|
||||
;; It's an idiosyncratic configure script that doesn't
|
||||
;; understand --prefix=..; it wants prefix=.. instead.
|
||||
(zero?
|
||||
(system* "./configure"
|
||||
(string-append "prefix=" out)))))))))
|
||||
(replace 'configure
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((out (assoc-ref outputs "out")))
|
||||
;; It's an idiosyncratic configure script that doesn't
|
||||
;; understand --prefix=..; it wants prefix=.. instead.
|
||||
(invoke "./configure"
|
||||
(string-append "prefix=" out))
|
||||
#t))))))
|
||||
;; TODO: cmus optionally supports the following formats, which haven't yet
|
||||
;; been added to Guix:
|
||||
;;
|
||||
|
|
@ -1144,14 +1142,14 @@ (define-public powertabeditor
|
|||
(name "powertabeditor")
|
||||
(version "2.0.0-alpha10")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/powertab/powertabeditor/archive/"
|
||||
version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/powertab/powertabeditor.git")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1fr14ql0yhlqvh6y08yaanszm2nvca5i50rqym396kfvga3ky18x"))
|
||||
"1z4fhdp71ck9synr12rg1p6365xnypd8ih40c5icj4si36khvksk"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
|
|
@ -1185,14 +1183,14 @@ (define-public powertabeditor
|
|||
(modify-phases %standard-phases
|
||||
(replace 'check
|
||||
(lambda _
|
||||
(zero? (system* "bin/pte_tests"
|
||||
;; FIXME: these tests fail
|
||||
"exclude:Actions/EditStaff"
|
||||
"exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
|
||||
"exclude:Score/ViewFilter/FilterRule"
|
||||
"exclude:Score/ViewFilter/ViewFilter"
|
||||
"exclude:Formats/PowerTabOldImport/Directions"
|
||||
))))
|
||||
(invoke "bin/pte_tests"
|
||||
;; FIXME: these tests fail
|
||||
"exclude:Actions/EditStaff"
|
||||
"exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
|
||||
"exclude:Score/ViewFilter/FilterRule"
|
||||
"exclude:Score/ViewFilter/ViewFilter"
|
||||
"exclude:Formats/PowerTabOldImport/Directions")
|
||||
#t))
|
||||
;; FIXME: This bug has been fixed upstream, but no release has been
|
||||
;; made yet. See https://github.com/powertab/powertabeditor/issues/257
|
||||
(add-after 'unpack 'fix-boost-bug
|
||||
|
|
@ -1751,9 +1749,7 @@ (define-public pd
|
|||
(lambda _
|
||||
(substitute* "tcl/pd-gui.tcl"
|
||||
(("exec wish ") (string-append "exec " (which "wish8.6") " ")))
|
||||
#t))
|
||||
(add-after 'unpack 'autoconf
|
||||
(lambda _ (zero? (system* "bash" "./autogen.sh")))))))
|
||||
#t)))))
|
||||
(native-inputs
|
||||
`(("autoconf" ,autoconf)
|
||||
("automake" ,automake)
|
||||
|
|
@ -4071,14 +4067,15 @@ (define-public libmusicbrainz
|
|||
(base32
|
||||
"0ikb9igyyk28jm34raxfzkw2qyn4nzzwsymdyprp7cmvi6g2ajb7"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments `(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace 'check
|
||||
(lambda _
|
||||
(and
|
||||
;; requires network connections
|
||||
;; (zero? (system* "tests/mbtest"))
|
||||
(zero? (system* "tests/ctest"))))))))
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace 'check
|
||||
(lambda _
|
||||
;; requires network connections
|
||||
;; (invoke "tests/mbtest")
|
||||
(invoke "tests/ctest")
|
||||
#t)))))
|
||||
(inputs `(("neon" ,neon)
|
||||
("libxml2" ,libxml2)))
|
||||
(native-inputs `(("pkg-config" ,pkg-config)))
|
||||
|
|
|
|||
232
gnu/packages/patches/hplip-remove-imageprocessor.patch
Normal file
232
gnu/packages/patches/hplip-remove-imageprocessor.patch
Normal file
|
|
@ -0,0 +1,232 @@
|
|||
This patch is based heavily on the Debian patch.
|
||||
|
||||
https://salsa.debian.org/printing-team/hplip/raw/debian/3.18.10+dfsg0-1/debian/patches/0025-Remove-all-ImageProcessor-functionality-which-is-clo.patch
|
||||
|
||||
---
|
||||
Makefile.am | 22 +++-------------------
|
||||
Makefile.in | 33 +++++----------------------------
|
||||
prnt/hpcups/HPCupsFilter.cpp | 21 ---------------------
|
||||
3 files changed, 8 insertions(+), 68 deletions(-)
|
||||
|
||||
diff --git a/Makefile.am b/Makefile.am
|
||||
index ef6480f..ecada5c 100644
|
||||
--- a/Makefile.am
|
||||
+++ b/Makefile.am
|
||||
@@ -166,7 +166,7 @@ if !HPLIP_CLASS_DRIVER
|
||||
dist_hplip_SCRIPTS = hpssd.py __init__.py hpdio.py
|
||||
endif #HPLIP_CLASS_DRIVER
|
||||
|
||||
-dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
|
||||
+dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
|
||||
dist_noinst_SCRIPTS += dat2drv.py install.py hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
|
||||
|
||||
if !HPLIP_CLASS_DRIVER
|
||||
@@ -590,11 +590,10 @@ hpcups_SOURCES = prnt/hpcups/HPCupsFilter.cpp prnt/hpcups/HPCupsFilter.h prnt/hp
|
||||
prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
|
||||
prnt/hpcups/genPCLm.h \
|
||||
common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
|
||||
- prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
|
||||
- prnt/hpcups/ImageProcessor.h
|
||||
+ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
|
||||
|
||||
hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
|
||||
-hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
|
||||
+hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
|
||||
#else
|
||||
#hpcupsdir = $(cupsfilterdir)
|
||||
#hpcups_PROGRAMS = hpcups
|
||||
@@ -679,21 +678,10 @@ printpluginsdir=$(cupsfilterdir)
|
||||
|
||||
|
||||
dist_filter_DATA = hpcups hpps dat2drv
|
||||
-dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
|
||||
endif #HPLIP_CLASS_DRIVER
|
||||
|
||||
install-data-hook:
|
||||
if HPLIP_BUILD
|
||||
- if [ \( "$(UNAME)" = "x86_64" -a -d "$(libdir)/" \) ]; then \
|
||||
- cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
|
||||
- chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
|
||||
- ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
|
||||
- fi; \
|
||||
- if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
|
||||
- cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
|
||||
- chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
|
||||
- ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
|
||||
- fi
|
||||
if !HPLIP_CLASS_DRIVER
|
||||
# If scanner build, add hpaio entry to sane dll.conf.
|
||||
if [ "$(scan_build)" = "yes" ]; then \
|
||||
@@ -874,10 +862,6 @@ if HPLIP_CLASS_DRIVER
|
||||
rm -rf $(distdir)/setup.py
|
||||
rm -rf $(distdir)/systray.py
|
||||
rm -rf $(distdir)/timedate.py
|
||||
- rm -rf $(distdir)/prnt/plugins/lj-arm32.so
|
||||
- rm -rf $(distdir)/prnt/plugins/lj-arm64.so
|
||||
- rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
|
||||
- rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
|
||||
rm -rf $(distdir)/hpijs-drv
|
||||
rm -rf $(distdir)/prnt/hpcups/
|
||||
rm -rf $(distdir)/prnt/ps/
|
||||
diff --git a/Makefile.in b/Makefile.in
|
||||
index 910a268..cd44203 100644
|
||||
--- a/Makefile.in
|
||||
+++ b/Makefile.in
|
||||
@@ -103,7 +103,7 @@ DIST_COMMON = $(am__configure_deps) \
|
||||
|
||||
# ip library
|
||||
@HPLIP_BUILD_TRUE@am__append_12 = libhpip.la
|
||||
-@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
|
||||
+@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
|
||||
@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_14 = dat2drv.py install.py hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
|
||||
@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@am__append_15 = scan/sane/hpaio.desc \
|
||||
@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@ installer/text_install.py \
|
||||
@@ -500,8 +500,7 @@ am__hpcups_SOURCES_DIST = prnt/hpcups/HPCupsFilter.cpp \
|
||||
prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
|
||||
prnt/hpcups/genPCLm.h common/utils.c common/utils.h \
|
||||
prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
|
||||
- prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
|
||||
- prnt/hpcups/ImageProcessor.h
|
||||
+ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
|
||||
@HPCUPS_INSTALL_TRUE@am_hpcups_OBJECTS = \
|
||||
@HPCUPS_INSTALL_TRUE@ hpcups-HPCupsFilter.$(OBJEXT) \
|
||||
@HPCUPS_INSTALL_TRUE@ hpcups-dbuscomm.$(OBJEXT) \
|
||||
@@ -723,8 +722,7 @@ am__dist_locatedriver_DATA_DIST = locatedriver
|
||||
am__dist_models_DATA_DIST = data/models/models.dat
|
||||
am__dist_noinst_DATA_DIST = prnt/drv/hpijs.drv.in.template \
|
||||
prnt/drv/hpcups.drv.in.template \
|
||||
- prnt/hpcups/libImageProcessor-x86_64.so \
|
||||
- prnt/hpcups/libImageProcessor-x86_32.so scan/sane/hpaio.desc \
|
||||
+ scan/sane/hpaio.desc \
|
||||
installer/text_install.py data/localization/hplip_de.ts \
|
||||
data/localization/hplip_es.ts data/localization/hplip_fr.ts \
|
||||
data/localization/hplip_it.ts data/localization/hplip_pt.ts \
|
||||
@@ -1932,11 +1930,6 @@ am__dist_ppd_DATA_DIST = prnt/ps/hp-designjet_z6810ps_42in-ps.ppd.gz \
|
||||
ppd/classppd/ps/hp-postscript-inkjet.ppd.gz \
|
||||
ppd/classppd/ps/hp-postscript-laserjet-pro.ppd.gz \
|
||||
ppd/classppd/ps/hp-postscript-laserjet.ppd.gz
|
||||
-am__dist_printplugins_DATA_DIST = prnt/plugins/hbpl1-arm32.so \
|
||||
- prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so \
|
||||
- prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so \
|
||||
- prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so \
|
||||
- prnt/plugins/lj-x86_64.so
|
||||
am__dist_prnt_DATA_DIST = prnt/cups.py prnt/__init__.py prnt/ldl.py \
|
||||
prnt/pcl.py prnt/colorcal.py
|
||||
am__dist_rules_DATA_DIST = data/rules/56-hpmud.rules \
|
||||
@@ -4665,11 +4658,10 @@ libapdk_la_CFLAGS = $(libapdk_la_CXXFLAGS) -Iprnt/hpijs
|
||||
@HPCUPS_INSTALL_TRUE@ prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
|
||||
@HPCUPS_INSTALL_TRUE@ prnt/hpcups/genPCLm.h \
|
||||
@HPCUPS_INSTALL_TRUE@ common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
|
||||
-@HPCUPS_INSTALL_TRUE@ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
|
||||
-@HPCUPS_INSTALL_TRUE@ prnt/hpcups/ImageProcessor.h
|
||||
+@HPCUPS_INSTALL_TRUE@ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
|
||||
|
||||
@HPCUPS_INSTALL_TRUE@hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
|
||||
-@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
|
||||
+@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
|
||||
#else
|
||||
#hpcupsdir = $(cupsfilterdir)
|
||||
#hpcups_PROGRAMS = hpcups
|
||||
@@ -4717,7 +4709,6 @@ ppddir = $(hpppddir)
|
||||
@HPLIP_CLASS_DRIVER_TRUE@filterdir = $(cupsfilterdir)
|
||||
@HPLIP_CLASS_DRIVER_TRUE@printpluginsdir = $(cupsfilterdir)
|
||||
@HPLIP_CLASS_DRIVER_TRUE@dist_filter_DATA = hpcups hpps dat2drv
|
||||
-@HPLIP_CLASS_DRIVER_TRUE@dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
|
||||
all: all-am
|
||||
|
||||
.SUFFIXES:
|
||||
@@ -9380,16 +9371,6 @@ uninstall-am: uninstall-apparmor_abstractionDATA \
|
||||
|
||||
|
||||
install-data-hook:
|
||||
-@HPLIP_BUILD_TRUE@ if [ \( "$(UNAME)" = "x86_64" -a -d "$(libdir)/" \) ]; then \
|
||||
-@HPLIP_BUILD_TRUE@ cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
|
||||
-@HPLIP_BUILD_TRUE@ chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
|
||||
-@HPLIP_BUILD_TRUE@ ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
|
||||
-@HPLIP_BUILD_TRUE@ fi; \
|
||||
-@HPLIP_BUILD_TRUE@ if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
|
||||
-@HPLIP_BUILD_TRUE@ cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
|
||||
-@HPLIP_BUILD_TRUE@ chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
|
||||
-@HPLIP_BUILD_TRUE@ ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
|
||||
-@HPLIP_BUILD_TRUE@ fi
|
||||
# If scanner build, add hpaio entry to sane dll.conf.
|
||||
@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@ if [ "$(scan_build)" = "yes" ]; then \
|
||||
@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@ $(mkinstalldirs) $(DESTDIR)/etc/sane.d; \
|
||||
@@ -9556,10 +9537,6 @@ dist-hook:
|
||||
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/setup.py
|
||||
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/systray.py
|
||||
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/timedate.py
|
||||
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-arm32.so
|
||||
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-arm64.so
|
||||
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
|
||||
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
|
||||
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/hpijs-drv
|
||||
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/hpcups/
|
||||
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/ps/
|
||||
diff --git a/prnt/hpcups/HPCupsFilter.cpp b/prnt/hpcups/HPCupsFilter.cpp
|
||||
index 5b282d8..0bacfaf 100644
|
||||
--- a/prnt/hpcups/HPCupsFilter.cpp
|
||||
+++ b/prnt/hpcups/HPCupsFilter.cpp
|
||||
@@ -31,7 +31,6 @@
|
||||
\*****************************************************************************/
|
||||
|
||||
#include "HPCupsFilter.h"
|
||||
-#include "ImageProcessor.h"
|
||||
|
||||
#include <signal.h>
|
||||
#include <sys/wait.h>
|
||||
@@ -637,16 +636,10 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
|
||||
|
||||
|
||||
sprintf(hpPreProcessedRasterFile, "%s/hp_%s_cups_SwapedPagesXXXXXX",CUPS_TMP_DIR, m_JA.user_name);
|
||||
- image_processor_t* imageProcessor = imageProcessorCreate();
|
||||
|
||||
while (cupsRasterReadHeader2(cups_raster, &cups_header))
|
||||
{
|
||||
|
||||
- IMAGE_PROCESSOR_ERROR result = imageProcessorStartPage(imageProcessor, &cups_header);
|
||||
- if (result != IPE_SUCCESS){
|
||||
- dbglog("DEBUG: imageProcessorStartPage failed result = %d\n", result);
|
||||
- }
|
||||
-
|
||||
current_page_number++;
|
||||
|
||||
if (current_page_number == 1) {
|
||||
@@ -745,12 +738,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
|
||||
color_raster = rgbRaster;
|
||||
black_raster = kRaster;
|
||||
|
||||
- result = imageProcessorProcessLine(imageProcessor, m_pPrinterBuffer, cups_header.cupsBytesPerLine);
|
||||
- if (result != IPE_SUCCESS){
|
||||
- dbglog("DEBUG: imageProcessorProcessLine failed result = %d\n", result);
|
||||
- }
|
||||
-
|
||||
-
|
||||
if ((y == 0) && !is_ljmono) {
|
||||
//For ljmono, make sure that first line is not a blankRaster line.Otherwise printer
|
||||
//may not skip blank lines before actual data
|
||||
@@ -780,12 +767,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
|
||||
}
|
||||
} // for() loop end
|
||||
|
||||
- result = imageProcessorEndPage(imageProcessor);
|
||||
- if (result != IPE_SUCCESS){
|
||||
- dbglog("DEBUG: imageProcessorEndPage failed result = %d\n", result);
|
||||
- }
|
||||
-
|
||||
-
|
||||
m_Job.NewPage();
|
||||
if (err != NO_ERROR) {
|
||||
break;
|
||||
@@ -800,8 +781,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
|
||||
rgbRaster = NULL;
|
||||
}
|
||||
|
||||
- imageProcessorDestroy(imageProcessor);
|
||||
-
|
||||
unlink(hpPreProcessedRasterFile);
|
||||
return ret_status;
|
||||
}
|
||||
--
|
||||
2.19.1
|
||||
|
||||
|
|
@ -6,7 +6,7 @@ index e56a8a2..4adcc48 100644
|
|||
if TARGET_PPC
|
||||
AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
|
||||
else
|
||||
-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g
|
||||
-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
|
||||
+AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -lcityhash
|
||||
endif
|
||||
|
||||
|
|
@ -39,7 +39,7 @@ index e56a8a2..4adcc48 100644
|
|||
-
|
||||
if TARGET_WIN
|
||||
|
||||
-libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g -D_MSC_VER
|
||||
-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare -D_MSC_VER
|
||||
-__top_builddir__bin_vsearch_LDFLAGS = -static
|
||||
-__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a
|
||||
+__top_builddir__bin_vsearch_LDFLAGS = -static -lcityhash
|
||||
|
|
@ -47,7 +47,7 @@ index e56a8a2..4adcc48 100644
|
|||
|
||||
else
|
||||
|
||||
-libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g
|
||||
-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare
|
||||
-
|
||||
if TARGET_PPC
|
||||
-__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu.a
|
||||
|
|
|
|||
|
|
@ -1,26 +0,0 @@
|
|||
This fixes the wxplot2d plotting issue found at
|
||||
https://github.com/andrejv/wxmaxima/issues/973.
|
||||
|
||||
From 5a0693c97ceaa4935b908f1e478126896952f399 Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Gunter=20K=C3=B6nigsmann?= <gunter@peterpall.de>
|
||||
Date: Mon, 19 Feb 2018 05:37:35 +0100
|
||||
Subject: [PATCH] Seems I accidentally made wxMaxima to default to parameters
|
||||
for old gnuplots. Resolves #973
|
||||
|
||||
---
|
||||
data/wxmathml.lisp.in | 2 +-
|
||||
1 file changed, 1 insertion(+), 1 deletion(-)
|
||||
|
||||
diff --git a/data/wxmathml.lisp.in b/data/wxmathml.lisp.in
|
||||
index a32e3fc3..4e19acaf 100644
|
||||
--- a/data/wxmathml.lisp.in
|
||||
+++ b/data/wxmathml.lisp.in
|
||||
@@ -43,7 +43,7 @@
|
||||
(defvar $wxsubscripts t
|
||||
"Recognize TeX-style subscripts")
|
||||
(defvar $wxplot_pngcairo nil "Use gnuplot's pngcairo terminal for new plots?")
|
||||
-(defmvar $wxplot_old_gnuplot t)
|
||||
+(defmvar $wxplot_old_gnuplot nil)
|
||||
|
||||
(defun $wxstatusbar (status)
|
||||
(format t "<statusbar>~a</statusbar>~%" status))
|
||||
|
|
@ -10530,6 +10530,31 @@ (define-public python-validictory
|
|||
(define-public python2-validictory
|
||||
(package-with-python2 python-validictory))
|
||||
|
||||
(define-public python-pyelftools
|
||||
(package
|
||||
(name "python-pyelftools")
|
||||
(version "0.25")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "pyelftools" version))
|
||||
(sha256
|
||||
(base32
|
||||
"090vdksbz341f7ljvr0zswblw4lspa8qaiikzyjkf318arpxmil9"))))
|
||||
(build-system python-build-system)
|
||||
;; Test suite requires python-setuptools
|
||||
(native-inputs
|
||||
`(("python-setuptools" ,python-setuptools)))
|
||||
(home-page
|
||||
"https://github.com/eliben/pyelftools")
|
||||
(synopsis
|
||||
"Analyze binary and library file information")
|
||||
(description "This Python library provides interfaces for parsing and
|
||||
analyzing two binary and library file formats; the Executable and Linking
|
||||
Format (ELF), and debugging information in the Debugging With Attributed
|
||||
Record Format (DWARF).")
|
||||
(license license:public-domain)))
|
||||
|
||||
(define-public python-pyev
|
||||
(package
|
||||
(name "python-pyev")
|
||||
|
|
@ -14532,14 +14557,14 @@ (define-public python-dask
|
|||
(define-public python-ilinkedlist
|
||||
(package
|
||||
(name "python-ilinkedlist")
|
||||
(version "0.2.0")
|
||||
(version "0.3.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "ilinkedlist" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0klb846q5vs62d8f89my7wan1sji4yjj6pjhjch9dha3p8vlncd2"))))
|
||||
"04wpv7km8jggrngc4bjg3nm615czd3bjdvpsy2icg6c1c8162zyg"))))
|
||||
(build-system python-build-system)
|
||||
(native-inputs `(("python-pytest" ,python-pytest)))
|
||||
(inputs `(("python" ,python)))
|
||||
|
|
|
|||
|
|
@ -39,6 +39,7 @@ (define-module (gnu packages statistics)
|
|||
#:use-module (guix build-system trivial)
|
||||
#:use-module (gnu packages)
|
||||
#:use-module (gnu packages algebra)
|
||||
#:use-module (gnu packages autotools)
|
||||
#:use-module (gnu packages bash)
|
||||
#:use-module (gnu packages check)
|
||||
#:use-module (gnu packages compression)
|
||||
|
|
@ -75,7 +76,7 @@ (define-module (gnu packages statistics)
|
|||
(define-public pspp
|
||||
(package
|
||||
(name "pspp")
|
||||
(version "1.0.1")
|
||||
(version "1.2.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -83,7 +84,7 @@ (define-public pspp
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
|
||||
"07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("cairo" ,cairo)
|
||||
|
|
@ -94,11 +95,15 @@ (define-public pspp
|
|||
("readline" ,readline)
|
||||
("gtk" ,gtk+)
|
||||
("gtksourceview" ,gtksourceview)
|
||||
("spread-sheet-widget" ,spread-sheet-widget)
|
||||
("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(("glib" ,glib "bin") ;for glib-genmarshal
|
||||
`(("autoconf" ,autoconf) ;for tests
|
||||
("glib" ,glib "bin") ;for glib-genmarshal
|
||||
("perl" ,perl)
|
||||
("pkg-config" ,pkg-config)))
|
||||
("pkg-config" ,pkg-config)
|
||||
("python" ,python-2) ;for tests
|
||||
("texinfo" ,texinfo)))
|
||||
(home-page "https://www.gnu.org/software/pspp/")
|
||||
(synopsis "Statistical analysis")
|
||||
(description
|
||||
|
|
@ -116,7 +121,7 @@ (define-public pspp
|
|||
(define r-with-tests
|
||||
(package
|
||||
(name "r-with-tests")
|
||||
(version "3.5.0")
|
||||
(version "3.5.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://cran/src/base/R-"
|
||||
|
|
@ -124,7 +129,7 @@ (define r-with-tests
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
|
||||
"1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:disallowed-references (,tzdata-for-tests)
|
||||
|
|
|
|||
|
|
@ -19,6 +19,7 @@
|
|||
;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
|
||||
;;; Copyright © 2017 Petter <petter@mykolab.ch>
|
||||
;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
|
||||
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -39,6 +40,7 @@ (define-module (gnu packages xml)
|
|||
#:use-module (gnu packages)
|
||||
#:use-module (gnu packages autotools)
|
||||
#:use-module (gnu packages compression)
|
||||
#:use-module (gnu packages curl)
|
||||
#:use-module (gnu packages gnupg)
|
||||
#:use-module (gnu packages java)
|
||||
#:use-module (gnu packages gnuzilla)
|
||||
|
|
@ -2111,3 +2113,39 @@ (define-public ghc-hxt
|
|||
"The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
|
||||
introduces a more general approach for processing XML with Haskell.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public xmlrpc-c
|
||||
(package
|
||||
(name "xmlrpc-c")
|
||||
(version "1.43.08")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://sourceforge/xmlrpc-c/Xmlrpc-c%20Super%20Stable/"
|
||||
version "/xmlrpc-c-" version ".tgz"))
|
||||
(sha256
|
||||
(base32
|
||||
"18zwbj6i2hpcn5riiyp8i6rml0sfv60dd7phw1x8g4r4lj2bbxf9"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("curl" ,curl)))
|
||||
(native-inputs
|
||||
`(;; For tools, if ever needed.
|
||||
("perl" ,perl)))
|
||||
(arguments
|
||||
`(#:make-flags ; Add $libdir to the RUNPATH of all the executables.
|
||||
(list (string-append "LDFLAGS_PERSONAL=-Wl,-rpath=" %output "/lib"))
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'fix-/bin/sh-in-tests
|
||||
(lambda _
|
||||
(substitute* "GNUmakefile"
|
||||
(("#! /bin/sh") (which "sh")))
|
||||
#t)))))
|
||||
(home-page "http://xmlrpc-c.sourceforge.net/")
|
||||
(synopsis "Lightweight RPC library based on XML and HTTP")
|
||||
(description
|
||||
"XML-RPC is a quick-and-easy way to make procedure calls over the Internet.
|
||||
It converts the procedure call into an XML document, sends it to a remote
|
||||
server using HTTP, and gets back the response as XML. This library provides a
|
||||
modular implementation of XML-RPC for C and C++.")
|
||||
(license (list license:psfl license:expat))))
|
||||
|
|
|
|||
|
|
@ -672,7 +672,7 @@ (define-syntax-rule (ini-file config file clause ...)
|
|||
("KillUserProcesses" (yesno elogind-kill-user-processes?))
|
||||
("KillOnlyUsers" (user-name-list elogind-kill-only-users))
|
||||
("KillExcludeUsers" (user-name-list elogind-kill-exclude-users))
|
||||
("InhibitDelayMaxSecs" (non-negative-integer elogind-inhibit-delay-max-seconds))
|
||||
("InhibitDelayMaxSec" (non-negative-integer elogind-inhibit-delay-max-seconds))
|
||||
("HandlePowerKey" (handle-action elogind-handle-power-key))
|
||||
("HandleSuspendKey" (handle-action elogind-handle-suspend-key))
|
||||
("HandleHibernateKey" (handle-action elogind-handle-hibernate-key))
|
||||
|
|
@ -682,16 +682,16 @@ (define-syntax-rule (ini-file config file clause ...)
|
|||
("SuspendKeyIgnoreInhibited" (yesno elogind-suspend-key-ignore-inhibited?))
|
||||
("HibernateKeyIgnoreInhibited" (yesno elogind-hibernate-key-ignore-inhibited?))
|
||||
("LidSwitchIgnoreInhibited" (yesno elogind-lid-switch-ignore-inhibited?))
|
||||
("HoldoffTimeoutSecs" (non-negative-integer elogind-holdoff-timeout-seconds))
|
||||
("HoldoffTimeoutSec" (non-negative-integer elogind-holdoff-timeout-seconds))
|
||||
("IdleAction" (handle-action elogind-idle-action))
|
||||
("IdleActionSeconds" (non-negative-integer elogind-idle-action-seconds))
|
||||
("IdleActionSec" (non-negative-integer elogind-idle-action-seconds))
|
||||
("RuntimeDirectorySize"
|
||||
(identity
|
||||
(lambda (config)
|
||||
(match (elogind-runtime-directory-size-percent config)
|
||||
(#f (non-negative-integer (elogind-runtime-directory-size config)))
|
||||
(percent (string-append (non-negative-integer percent) "%"))))))
|
||||
("RemoveIpc" (yesno elogind-remove-ipc?))
|
||||
("RemoveIPC" (yesno elogind-remove-ipc?))
|
||||
"[Sleep]"
|
||||
("SuspendState" (sleep-list elogind-suspend-state))
|
||||
("SuspendMode" (sleep-list elogind-suspend-mode))
|
||||
|
|
|
|||
|
|
@ -177,7 +177,7 @@ (define update-profile
|
|||
(update-profile profile manifest
|
||||
#:dry-run? dry-run?)
|
||||
(munless dry-run?
|
||||
(display-profile-news profile)))))
|
||||
(return (display-profile-news profile))))))
|
||||
|
||||
(define (honor-lets-encrypt-certificates! store)
|
||||
"Tell Guile-Git to use the Let's Encrypt certificates."
|
||||
|
|
|
|||
Loading…
Reference in a new issue