;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;;
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<div class='path'>path: <a href='/guix/commit/?id=d85c0f98424444eee10c721a03b400498cc89a6a'>root</a>/<a href='/guix/commit/tests?id=d85c0f98424444eee10c721a03b400498cc89a6a'>tests</a>/<a href='/guix/commit/tests/lzlib.scm?id=d85c0f98424444eee10c721a03b400498cc89a6a'>lzlib.scm</a></div><div class='content'><div class='cgit-panel'><b>diff options</b><form method='get'><input type='hidden' name='id' value='d85c0f98424444eee10c721a03b400498cc89a6a'/><table><tr><td colspan='2'/></tr><tr><td class='label'>context:</td><td class='ctrl'><select name='context' onchange='this.form.submit();'><option value='1'>1</option><option value='2'>2</option><option value='3' selected='selected'>3</option><option value='4'>4</option><option value='5'>5</option><option value='6'>6</option><option value='7'>7</option><option value='8'>8</option><option value='9'>9</option><option value='10'>10</option><option value='15'>15</option><option value='20'>20</option><option value='25'>25</option><option value='30'>30</option><option value='35'>35</option><option value='40'>40</option></select></td></tr><tr><td class='label'>space:</td><td class='ctrl'><select name='ignorews' onchange='this.form.submit();'><option value='0' selected='selected'>include</option><option value='1'>ignore</option></select></td></tr><tr><td class='label'>mode:</td><td class='ctrl'><select name='dt' onchange='this.form.submit();'><option value='0' selected='selected'>unified</option><option value='1'>ssdiff</option><option value='2'>stat only</option></select></td></tr><tr><td/><td class='ctrl'><noscript><input type='submit' value='reload'/></noscript></td></tr></table></form></div><table summary='commit info' class='commit-info'>
<tr><th>author</th><td>Ricardo Wurmus &lt;rekado@elephly.net&gt;</td><td class='right'>2019-08-30 22:42:29 +0200</td></tr>
<tr><th>committer</th><td>Ricardo Wurmus &lt;rekado@elephly.net&gt;</td><td class='right'>2019-08-30 22:42:50 +0200</td></tr>
<tr><th>commit</th><td colspan='2' class='oid'><a href='/guix/commit/tests/lzlib.scm?id=d85c0f98424444eee10c721a03b400498cc89a6a'>d85c0f98424444eee10c721a03b400498cc89a6a</a> (<a href='/guix/patch/tests/lzlib.scm?id=d85c0f98424444eee10c721a03b400498cc89a6a'>patch</a>)</td></tr>
<tr><th>tree</th><td colspan='2' class='oid'><a href='/guix/tree/?id=d85c0f98424444eee10c721a03b400498cc89a6a'>ca7af7e9f091feee764e607366b191ecd97bc18f</a> /<a href='/guix/tree/tests/lzlib.scm?id=d85c0f98424444eee10c721a03b400498cc89a6a'>tests/lzlib.scm</a></td></tr>
<tr><th>parent</th><td colspan='2' class='oid'><a href='/guix/commit/tests/lzlib.scm?id=06947252d3de55aff765334b88cde5990efa6abf'>06947252d3de55aff765334b88cde5990efa6abf</a> (<a href='/guix/diff/tests/lzlib.scm?id=d85c0f98424444eee10c721a03b400498cc89a6a&amp;id2=06947252d3de55aff765334b88cde5990efa6abf'>diff</a>)</td></tr><tr><th>download</th><td colspan='2' class='oid'><a href='/guix/snapshot/guix-d85c0f98424444eee10c721a03b400498cc89a6a.tar.gz'>guix-d85c0f98424444eee10c721a03b400498cc89a6a.tar.gz</a><br/><a href='/guix/snapshot/guix-d85c0f98424444eee10c721a03b400498cc89a6a.zip'>guix-d85c0f98424444eee10c721a03b400498cc89a6a.zip</a><br/></td></tr></table>
<div class='commit-subject'>gnu: Add r-genie3.</div><div class='commit-msg'>* gnu/packages/bioconductor.scm (r-genie3): New variable.
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 "include"))                   ;headers used by extensions
     (inputs `(("readline" ,readline)
               ("ncurses" ,ncurses)))             ;TODO: add texinfo
     (arguments
      `(;; When cross-compiling, `configure' incorrectly guesses that job
        ;; control is missing.
        #:configure-flags ,(if (%current-target-system)
                               `(cons* "bash_cv_job_control_missing=no"
                                       ,configure-flags)
                               configure-flags)

        ;; Bash is reportedly not parallel-safe.  See, for instance,
        ;; <http://patches.openembedded.org/patch/32745/> and
        ;; <http://git.buildroot.net/buildroot/commit/?h=79e2d802a>.
        #:parallel-build? #f
        #:parallel-tests? #f

        ;; XXX: The tests have a lot of hard-coded paths, so disable them
        ;; for now.
        #:tests? #f

        #:modules ((srfi srfi-26)
                   (guix build utils)
                   (guix build gnu-build-system))

        #:phases
        (modify-phases %standard-phases
          (add-after 'install 'install-sh-symlink
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Add a `sh' -> `bash' link.
              (let ((out (assoc-ref outputs "out")))
                (with-directory-excursion (string-append out "/bin")
                  (symlink "bash" "sh")
                  #t))))

          (add-after 'install 'move-development-files
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Move 'Makefile.inc' and 'bash.pc' to "include" to avoid
              ;; circular references among the outputs.
              (let ((out     (assoc-ref outputs "out"))
                    (include (assoc-ref outputs "include"))
                    (lib     (cut string-append <> "/lib/bash")))
                (mkdir-p (lib include))
                (rename-file (string-append (lib out)
                                            "/Makefile.inc")
                             (string-append (lib include)
                                            "/Makefile.inc"))
                (rename-file (string-append out "/lib/pkgconfig")
                             (string-append include
                                            "/lib/pkgconfig"))

                ;; Don't capture the absolute file name of 'install' to avoid
                ;; retaining a dependency on Coreutils.
                (substitute* (string-append (lib include)
                                            "/Makefile.inc")
                  (("^INSTALL =.*")
                   "INSTALL = install -c\n"))
                #t))))))

     (native-search-paths
      (list (search-path-specification            ;new in 4.4
             (variable "BASH_LOADABLES_PATH")
             (files '("lib/bash")))))

     (synopsis "The GNU Bourne-Again SHell")
     (description
      "Bash is the shell, or command-line interpreter, of the GNU system.  It
is compatible with the Bourne Shell, but it also integrates useful features
from the Korn Shell and the C Shell and new improvements of its own.  It
allows command-line editing, unlimited command history, shell functions and
aliases, and job control while still allowing most sh scripts to be run
without modification.")
     (license gpl3+)
     (home-page "https://www.gnu.org/software/bash/"))))

(define-public bash-minimal
  ;; A stripped-down Bash for non-interactive use.
  (package (inherit bash)
    (name "bash-minimal")
    (inputs '())                                ; no readline, no curses

    ;; No "include" output because there's no support for loadable modules.
    (outputs (delete "include" (package-outputs bash)))

    (arguments
     (substitute-keyword-arguments (package-arguments bash)
       ((#:modules _ '())
        '((guix build gnu-build-system)
          (guix build utils)
          (srfi srfi-1)
          (srfi srfi-26)))
       ((#:configure-flags flags '())
        `(list "--without-bash-malloc"
               "--disable-readline"
               "--disable-history"
               "--disable-help-builtin"
               "--disable-progcomp"
               "--disable-net-redirections"
               "--disable-nls"

               ;; Pretend 'dlopen' is missing so we don't build loadable
               ;; modules and related code.
               "ac_cv_func_dlopen=no"

               ,@(if (%current-target-system)
                     '("bash_cv_job_control_missing=no"
                       "bash_cv_getcwd_malloc=yes")
                     '())))
       ((#:phases phases)
        `(modify-phases ,phases
           ;; No loadable modules.
           (delete 'move-development-files)))))))

(define-public static-bash
  ;; Statically-linked Bash that contains nothing but the 'bash' binary and
  ;; 'sh' symlink, without any reference.
  (let ((bash (static-package bash-minimal)))
    (package
      (inherit bash)
      (name "bash-static")
      (arguments
       (substitute-keyword-arguments
           `(#:allowed-references ("out") ,@(package-arguments bash))
         ((#:phases phases)
          `(modify-phases ,phases
             (add-after 'strip 'remove-everything-but-the-binary
               (lambda* (#:key outputs #:allow-other-keys)
                 (let* ((out (assoc-ref outputs "out"))
                        (bin (string-append out "/bin")))
                   (remove-store-references (string-append bin "/bash"))
                   (delete-file (string-append bin "/bashbug"))
                   (delete-file-recursively (string-append out "/share"))
                   #t))))))))))

(define-public bash-completion
  (package
    (name "bash-completion")
    (version "2.8")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/scop/" name "/releases/download/"
                    version "/" name "-" version ".tar.xz"))
              (sha256
               (base32
                "0kgmflrr1ga9wfk770vmakna3nj46ylb5ky9ipd0v2k9ymq5a7y0"))
              (patches
               (search-patches "bash-completion-directories.patch"))))
    (build-system gnu-build-system)
    (native-inputs `(("util-linux" ,util-linux)))
    (arguments
     `(#:phases (modify-phases %standard-phases
                  (add-after
                   'install 'remove-redundant-completions
                   (lambda* (#:key
                             inputs native-inputs
                             outputs #:allow-other-keys)
                     ;; Util-linux comes with a bunch of completion files for
                     ;; its own commands which are more sophisticated and
                     ;; up-to-date than those of bash-completion.  Remove those
                     ;; from bash-completion.
                     (let* ((out         (assoc-ref outputs "out"))
                            (util-linux  (assoc-ref (or native-inputs inputs)
                                                    "util-linux"))
                            (completions (string-append out
                                                        "/share/bash-completion"
                                                        "/completions"))
                            (already     (find-files
                                          (string-append
                                           util-linux
                                           "/etc/bash_completion.d"))))
                       (with-directory-excursion completions
                         (for-each (lambda (file)
                                     (when (file-exists? file)
                                       (delete-file file)))
                                   (map basename already)))
                       #t))))))
    (synopsis "Bash completions for common commands")
    (description
     "This package provides extensions that allow Bash to provide adapted
completion for many common commands.")
    (home-page "https://github.com/scop/bash-completion")
    (license gpl2+)))

(define-public bash-tap
  (package
    (name "bash-tap")
    (version "1.0.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/illusori/bash-tap")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "13zz9h6bhhnk3hiwhlpafrnf2isws249h3fz785dcgymk02arz9c"))))
    ;; There is no compilation process to use this package, however, the bash
    ;; scripts installed by this package start with "#!/bin/bash".  To fix
    ;; these lines, we use the patch-shebangs of the GNU build system.  The
    ;; project does not use a Makefile.
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; There is no test suite.
       #:phases
       (modify-phases %standard-phases
         ;; Because there are no configure scripts or Makefile, we can
         ;; remove these phases.
         (delete 'configure)
         (delete 'build)
         ;; The installation involves manually copying the files to a location.
         ;; To make them easily accessible by setting PATH, we add the scripts
         ;; to the "bin" folder.
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (install-file "bash-tap" bin)
               (install-file "bash-tap-bootstrap" bin)
               (install-file "bash-tap-mock" bin)))))))
    (home-page "https://www.illusori.co.uk/projects/bash-tap/")
    (synopsis "Bash port of a Test::More/Test::Builder-style TAP-compliant
test library")
    (description "Bash TAP is a TAP-compliant Test::More-style testing library
for Bash shell scripts and functions.  Along with the Test::More-style testing
helpers it provides helper functions for mocking commands and in-process output
capturing.")
    (license expat)))

(define-public bats
  (package
    (name "bats")
    (version "1.2.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/bats-core/bats-core")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0f59zh4d4pa1a7ybs5zl6h0csbqqv11lbnq0jl1dgwm1s6p49bsq"))))
    (inputs
     `(("bash" ,bash)
       ("coreutils" ,coreutils)
       ("guile" ,guile-3.0) ;for wrap-script
       ("grep" ,grep)))
    (arguments
     `(#:modules ((guix build utils))
       #:builder
       (begin
         (use-modules (guix build utils))
         (copy-recursively (assoc-ref %build-inputs "source") ".")
         (setenv "PATH"
                 (string-append (assoc-ref %build-inputs "bash") "/bin"
                                ":" (assoc-ref %build-inputs "coreutils") "/bin"
                                ":" (assoc-ref %build-inputs "grep") "/bin"
                                ":" (assoc-ref %build-inputs "guile") "/bin"
                                ":" (getenv "PATH")))
         (for-each (lambda (file) (patch-shebang file)) (find-files "."))
         (substitute* "bin/bats"
           (("export BATS_ROOT" line)
            (string-append "BATS_ROOT=\"${BATS_ROOT:-" %output "/libexec/bats-core}\"\n"
                           line)))
         ;; Install phase
         (invoke "./install.sh" %output)
         (wrap-script (string-append %output "/bin/bats")
                      (list "PATH" 'prefix (string-split (getenv "PATH")
                                                         #\:))))))
    (build-system trivial-build-system)
    (home-page "https://github.com/bats-core/bats-core/")
    (synopsis "Bash Automated Testing System")
    (description
     "Bats is a @acronym{TAP, Test Anything Protocol}-compliant testing
framework for Bash.  It provides a simple way to verify that the UNIX programs
you write behave as expected.  Bats is most useful when testing software written
in Bash, but you can use it to test any UNIX program.")
    (license expat)))