Browse Source

gnu: Use 'modify-phases' syntax.

* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
gn-latest-20200428
Kei Kebreau 4 years ago
committed by Kei Kebreau
parent
commit
dc1d3cdef7
No known key found for this signature in database GPG Key ID: E6A5EE3C19467A0D
81 changed files with 2114 additions and 2140 deletions
  1. +120
    -124
      gnu/packages/admin.scm
  2. +15
    -16
      gnu/packages/algebra.scm
  3. +12
    -13
      gnu/packages/apr.scm
  4. +91
    -104
      gnu/packages/audio.scm
  5. +17
    -17
      gnu/packages/backup.scm
  6. +128
    -130
      gnu/packages/bioinformatics.scm
  7. +17
    -16
      gnu/packages/bittorrent.scm
  8. +1
    -1
      gnu/packages/cdrom.scm
  9. +8
    -8
      gnu/packages/compression.scm
  10. +15
    -16
      gnu/packages/conky.scm
  11. +50
    -52
      gnu/packages/databases.scm
  12. +36
    -34
      gnu/packages/debug.scm
  13. +12
    -11
      gnu/packages/display-managers.scm
  14. +1
    -1
      gnu/packages/dns.scm
  15. +38
    -36
      gnu/packages/emacs.scm
  16. +21
    -22
      gnu/packages/engineering.scm
  17. +24
    -24
      gnu/packages/firmware.scm
  18. +10
    -11
      gnu/packages/flashing-tools.scm
  19. +21
    -21
      gnu/packages/fltk.scm
  20. +15
    -16
      gnu/packages/freedesktop.scm
  21. +10
    -9
      gnu/packages/gd.scm
  22. +1
    -4
      gnu/packages/gkrellm.scm
  23. +1
    -1
      gnu/packages/gl.scm
  24. +17
    -16
      gnu/packages/glib.scm
  25. +71
    -74
      gnu/packages/gnome.scm
  26. +9
    -8
      gnu/packages/gprolog.scm
  27. +10
    -9
      gnu/packages/gps.scm
  28. +6
    -7
      gnu/packages/graphics.scm
  29. +41
    -39
      gnu/packages/gtk.scm
  30. +41
    -40
      gnu/packages/guile-wm.scm
  31. +18
    -18
      gnu/packages/guile.scm
  32. +31
    -30
      gnu/packages/hugs.scm
  33. +29
    -31
      gnu/packages/hurd.scm
  34. +6
    -7
      gnu/packages/image-viewers.scm
  35. +9
    -9
      gnu/packages/libcanberra.scm
  36. +136
    -132
      gnu/packages/linux.scm
  37. +29
    -32
      gnu/packages/lisp.scm
  38. +59
    -60
      gnu/packages/lout.scm
  39. +1
    -1
      gnu/packages/lua.scm
  40. +42
    -46
      gnu/packages/machine-learning.scm
  41. +45
    -45
      gnu/packages/mail.scm
  42. +2
    -2
      gnu/packages/man.scm
  43. +50
    -50
      gnu/packages/maths.scm
  44. +13
    -14
      gnu/packages/messaging.scm
  45. +45
    -43
      gnu/packages/mp3.scm
  46. +51
    -51
      gnu/packages/music.scm
  47. +39
    -40
      gnu/packages/noweb.scm
  48. +61
    -59
      gnu/packages/patchutils.scm
  49. +31
    -30
      gnu/packages/pdf.scm
  50. +14
    -15
      gnu/packages/perl.scm
  51. +8
    -7
      gnu/packages/photo.scm
  52. +9
    -8
      gnu/packages/popt.scm
  53. +33
    -32
      gnu/packages/pretty-print.scm
  54. +17
    -16
      gnu/packages/pumpio.scm
  55. +21
    -24
      gnu/packages/python.scm
  56. +20
    -20
      gnu/packages/rdf.scm
  57. +10
    -10
      gnu/packages/regex.scm
  58. +10
    -9
      gnu/packages/rrdtool.scm
  59. +20
    -20
      gnu/packages/ruby.scm
  60. +25
    -25
      gnu/packages/sawfish.scm
  61. +67
    -67
      gnu/packages/scheme.scm
  62. +23
    -23
      gnu/packages/sdl.scm
  63. +8
    -7
      gnu/packages/serveez.scm
  64. +15
    -14
      gnu/packages/skribilo.scm
  65. +9
    -8
      gnu/packages/smalltalk.scm
  66. +2
    -2
      gnu/packages/suckless.scm
  67. +8
    -7
      gnu/packages/tcl.scm
  68. +6
    -6
      gnu/packages/telephony.scm
  69. +12
    -13
      gnu/packages/textutils.scm
  70. +10
    -10
      gnu/packages/time.scm
  71. +7
    -7
      gnu/packages/tor.scm
  72. +12
    -12
      gnu/packages/uucp.scm
  73. +4
    -5
      gnu/packages/video.scm
  74. +5
    -5
      gnu/packages/web-browsers.scm
  75. +7
    -8
      gnu/packages/web.scm
  76. +106
    -108
      gnu/packages/wicd.scm
  77. +1
    -1
      gnu/packages/wm.scm
  78. +3
    -2
      gnu/packages/xdisorg.scm
  79. +11
    -11
      gnu/packages/xfce.scm
  80. +36
    -38
      gnu/packages/xfig.scm
  81. +19
    -20
      gnu/packages/xorg.scm

+ 120
- 124
gnu/packages/admin.scm View File

@ -361,32 +361,31 @@ login, passwd, su, groupadd, and useradd.")
"05yxrp44ky2kg6qknk1ih0kvwkgbn9fbz77r3vci7agslh5wjm8g"))))
(build-system gnu-build-system)
(arguments
`(#:phases (alist-replace 'configure
(lambda* (#:key inputs outputs
#:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man8 (string-append
out "/share/man/man8"))
(sbin (string-append out "/sbin"))
(shadow (assoc-ref inputs "shadow"))
(login (string-append shadow
"/bin/login")))
(substitute* "Makefile"
(("^SBINDIR.*")
(string-append "SBINDIR = " out
"/sbin\n"))
(("^MANDIR.*")
(string-append "MANDIR = " out
"/share/man/man8\n")))
;; Pick the right 'login' by default.
(substitute* "mingetty.c"
(("\"/bin/login\"")
(string-append "\"" login "\"")))
(mkdir-p sbin)
(mkdir-p man8)))
%standard-phases)
`(#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man8 (string-append out "/share/man/man8"))
(sbin (string-append out "/sbin"))
(shadow (assoc-ref inputs "shadow"))
(login (string-append shadow "/bin/login")))
(substitute* "Makefile"
(("^SBINDIR.*")
(string-append "SBINDIR = " out
"/sbin\n"))
(("^MANDIR.*")
(string-append "MANDIR = " out
"/share/man/man8\n")))
;; Pick the right 'login' by default.
(substitute* "mingetty.c"
(("\"/bin/login\"")
(string-append "\"" login "\"")))
(mkdir-p sbin)
(mkdir-p man8))
#t)))
#:tests? #f)) ; no tests
(inputs `(("shadow" ,shadow)))
@ -725,25 +724,25 @@ by bandwidth they use.")
("perl-x11-protocol" ,perl-x11-protocol)))
(arguments
`(#:phases
(alist-cons-after
'install 'set-load-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Put the perl-tk and perl-x11-protocol modules in the perl inc
;; path for PROG
(let* ((out (assoc-ref outputs "out"))
(prog (string-append out "/bin/cssh"))
(perl-ver ,(package-version perl))
(x11-inc (string-append
(assoc-ref inputs "perl-x11-protocol")
"/lib/perl5/site_perl/" perl-ver))
(tk-inc (string-append
(assoc-ref inputs "perl-tk")
"/lib/perl5/site_perl/" perl-ver
"/x86_64-linux")))
(wrap-program
prog
`("PERL5LIB" ":" prefix (,x11-inc ,tk-inc)))))
%standard-phases)))
(modify-phases %standard-phases
(add-after 'install 'set-load-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Put the perl-tk and perl-x11-protocol modules in the perl inc
;; path for PROG
(let* ((out (assoc-ref outputs "out"))
(prog (string-append out "/bin/cssh"))
(perl-ver ,(package-version perl))
(x11-inc (string-append
(assoc-ref inputs "perl-x11-protocol")
"/lib/perl5/site_perl/" perl-ver))
(tk-inc (string-append
(assoc-ref inputs "perl-tk")
"/lib/perl5/site_perl/" perl-ver
"/x86_64-linux")))
(wrap-program
prog
`("PERL5LIB" ":" prefix (,x11-inc ,tk-inc))))
#t)))))
;; The clusterssh.sourceforge.net address requires login to view
(home-page "https://sourceforge.net/projects/clusterssh/")
(synopsis "Secure concurrent multi-server terminal control")
@ -908,13 +907,14 @@ commands and their arguments.")
"0l0l5gz3d5j9bqjsbjlfcv4w4jwndllp9fmyai4x9kg6qhs6v4xl"))))
(build-system gnu-build-system)
(arguments
'(#:phases (alist-replace
'configure
(lambda* (#:key outputs #:allow-other-keys)
(chdir "wpa_supplicant")
(copy-file "defconfig" ".config")
(let ((port (open-file ".config" "al")))
(display "
'(#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(chdir "wpa_supplicant")
(copy-file "defconfig" ".config")
(let ((port (open-file ".config" "al")))
(display "
CONFIG_DEBUG_SYSLOG=y
# Choose GnuTLS (the default is OpenSSL.)
@ -924,26 +924,23 @@ commands and their arguments.")
CFLAGS += $(shell pkg-config libnl-3.0 --cflags)
CONFIG_LIBNL32=y
CONFIG_READLINE=y\n" port)
(close-port port)))
(alist-cons-after
'install 'install-man-pages
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man (string-append out "/share/man"))
(man5 (string-append man "/man5"))
(man8 (string-append man "/man8")))
(define (copy-man-page target)
(lambda (file)
(install-file file target)))
(mkdir-p man5) (mkdir man8)
(for-each (copy-man-page man5)
(find-files "doc/docbook" "\\.5"))
(for-each (copy-man-page man8)
(find-files "doc/docbook" "\\.8"))
#t))
%standard-phases))
(close-port port))))
(add-after 'install 'install-man-pages
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man (string-append out "/share/man"))
(man5 (string-append man "/man5"))
(man8 (string-append man "/man8")))
(define (copy-man-page target)
(lambda (file)
(install-file file target)))
(mkdir-p man5) (mkdir man8)
(for-each (copy-man-page man5)
(find-files "doc/docbook" "\\.5"))
(for-each (copy-man-page man8)
(find-files "doc/docbook" "\\.8"))
#t))))
#:make-flags (list "CC=gcc"
(string-append "BINDIR=" (assoc-ref %outputs "out")
@ -980,25 +977,24 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
(arguments
(substitute-keyword-arguments (package-arguments wpa-supplicant-minimal)
((#:phases phases)
`(alist-cons-after
'configure 'configure-for-dbus
(lambda _
(let ((port (open-file ".config" "al")))
(display "
`(modify-phases ,phases
(add-after 'configure 'configure-for-dbus
(lambda _
(let ((port (open-file ".config" "al")))
(display "
CONFIG_CTRL_IFACE_DBUS=y
CONFIG_CTRL_IFACE_DBUS_NEW=y
CONFIG_CTRL_IFACE_DBUS_INTRO=y\n" port)
(close-port port))
#t)
(alist-cons-after
'install-man-pages 'install-dbus-conf
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(dir (string-append out "/etc/dbus-1/system.d")))
(mkdir-p dir)
(copy-file "dbus/dbus-wpa_supplicant.conf"
(string-append dir "/wpa_supplicant.conf"))))
,phases)))))))
(close-port port))
#t))
(add-after 'install-man-pages 'install-dbus-conf
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(dir (string-append out "/etc/dbus-1/system.d")))
(mkdir-p dir)
(copy-file "dbus/dbus-wpa_supplicant.conf"
(string-append dir "/wpa_supplicant.conf")))
#t))))))))
(define-public wakelan
(package
@ -1014,22 +1010,22 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
"0vydqpf44146ir6k87gmqaq6xy66xhc1gkr3nsd7jj3nhy7ypx9x"))))
(build-system gnu-build-system)
(arguments
'(#:phases (alist-replace
'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir-p (string-append out "/bin"))
(mkdir-p (string-append out "/share/man/man1"))
;; It's an old configure script that doesn't understand
;; the extra options we pass.
(setenv "CONFIG_SHELL" (which "bash"))
(zero?
(system* "./configure"
(string-append "--prefix=" out)
(string-append "--mandir=" out
"/share/man")))))
%standard-phases)
'(#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir-p (string-append out "/bin"))
(mkdir-p (string-append out "/share/man/man1"))
;; It's an old configure script that doesn't understand
;; the extra options we pass.
(setenv "CONFIG_SHELL" (which "bash"))
(zero?
(system* "./configure"
(string-append "--prefix=" out)
(string-append "--mandir=" out
"/share/man")))))))
#:tests? #f))
(home-page "http://kernel.org") ; really, no home page
(synopsis "Send a wake-on-LAN packet")
@ -1088,7 +1084,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
"HOST=_LINUX"
"OPT_CFLAGS=-Wall -fno-strict-aliasing")
#:tests? #f ; no 'check' target.
#:phases (alist-delete 'configure %standard-phases)))
#:phases (modify-phases %standard-phases (delete 'configure))))
(home-page "http://acpica.org/")
(synopsis "Tools for the development and debug of ACPI tables")
(description
@ -1198,7 +1194,7 @@ recover lost partitions and/or make non-booting disks bootable again.")
(base32 "04kviw799qxly08zb8n5mgxfd96gyis6x69q2qiw86jnh87c4mv9"))))
(build-system gnu-build-system)
(arguments
'(#:phases (alist-delete 'configure %standard-phases)
'(#:phases (modify-phases %standard-phases (delete 'configure))
#:tests? #f ; no check target
#:make-flags (let ((out (assoc-ref %outputs "out")))
(list (string-append "prefix=" out)))))
@ -1227,23 +1223,23 @@ environment variable is set and output is to tty.")
"#!$SHELL")))))
(build-system gnu-build-system)
(arguments
'(#:phases (alist-cons-before
'build 'patch-/bin/sh
(lambda* (#:key inputs #:allow-other-keys)
;; Use the right shell when executing the watcher and
;; user-provided shell commands.
(let ((bash (assoc-ref inputs "bash")))
(substitute* '("src/direvent.c" "src/progman.c")
(("\"/bin/sh\"")
(string-append "\"" bash "/bin/sh\"")))
;; Adjust the 'shell.at' test accordingly.
(substitute* "tests/testsuite"
(("SHELL=/bin/sh")
(string-append "SHELL=" bash "/bin/sh")))
#t))
%standard-phases)))
'(#:phases
(modify-phases %standard-phases
(add-before 'build 'patch-/bin/sh
(lambda* (#:key inputs #:allow-other-keys)
;; Use the right shell when executing the watcher and
;; user-provided shell commands.
(let ((bash (assoc-ref inputs "bash")))
(substitute* '("src/direvent.c" "src/progman.c")
(("\"/bin/sh\"")
(string-append "\"" bash "/bin/sh\"")))
;; Adjust the 'shell.at' test accordingly.
(substitute* "tests/testsuite"
(("SHELL=/bin/sh")
(string-append "SHELL=" bash "/bin/sh")))
#t))))))
(home-page "https://www.gnu.org/software/direvent/")
(synopsis "Daemon to monitor directories for events such as file removal")
(description
@ -1700,7 +1696,7 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
(list (string-append "DESTDIR=" out)
"prefix=/"))
;; no configure script
#:phases (alist-delete 'configure %standard-phases)))
#:phases (modify-phases %standard-phases (delete 'configure))))
(inputs `(("python-2" ,python-2)))
(synopsis "Versatile resource statistics tool")
(description "Dstat is a versatile replacement for @command{vmstat},


+ 15
- 16
gnu/packages/algebra.scm View File

@ -334,22 +334,21 @@ fast arithmetic.")
("mpfr" ,mpfr)))
(arguments
`(#:phases
(alist-replace
'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(flint (assoc-ref inputs "flint"))
(gmp (assoc-ref inputs "gmp"))
(mpfr (assoc-ref inputs "mpfr")))
;; do not pass "--enable-fast-install", which makes the
;; homebrew configure process fail
(zero? (system*
"./configure"
(string-append "--prefix=" out)
(string-append "--with-flint=" flint)
(string-append "--with-gmp=" gmp)
(string-append "--with-mpfr=" mpfr)))))
%standard-phases)))
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(flint (assoc-ref inputs "flint"))
(gmp (assoc-ref inputs "gmp"))
(mpfr (assoc-ref inputs "mpfr")))
;; do not pass "--enable-fast-install", which makes the
;; homebrew configure process fail
(zero? (system*
"./configure"
(string-append "--prefix=" out)
(string-append "--with-flint=" flint)
(string-append "--with-gmp=" gmp)
(string-append "--with-mpfr=" mpfr)))))))))
(synopsis "Arbitrary precision floating-point ball arithmetic")
(description
"Arb is a C library for arbitrary-precision floating-point ball


+ 12
- 13
gnu/packages/apr.scm View File

@ -80,19 +80,18 @@ around or take advantage of platform-specific deficiencies or features.")
`(("expat" ,expat)))
(arguments
'(#:phases
(alist-replace
'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(apr (assoc-ref inputs "apr"))
(expat (assoc-ref inputs "expat")))
(setenv "CONFIG_SHELL" (which "bash"))
(zero?
(system* "./configure"
(string-append "--prefix=" out)
(string-append "--with-apr=" apr)
(string-append "--with-expat=" expat)))))
%standard-phases)
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(apr (assoc-ref inputs "apr"))
(expat (assoc-ref inputs "expat")))
(setenv "CONFIG_SHELL" (which "bash"))
(zero?
(system* "./configure"
(string-append "--prefix=" out)
(string-append "--with-apr=" apr)
(string-append "--with-expat=" expat)))))))
;; There are race conditions during 'make check'. Typically, the
;; 'testall' executable is not built yet by the time 'make check' tries


+ 91
- 104
gnu/packages/audio.scm View File

@ -617,23 +617,21 @@ language and software synthesizer.")
`(#:tests? #f ; no "check" target
#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(alist-cons-after
'unpack 'patch-makefile-and-enter-directory
(lambda _
(substitute* "libs/Makefile"
(("/sbin/ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
(chdir "libs")
#t)
(alist-cons-after
'install
'install-symlink
(lambda _
(symlink "libclalsadrv.so"
(string-append (assoc-ref %outputs "out")
"/lib/libclalsadrv.so.2")))
;; no configure script
(alist-delete 'configure %standard-phases)))))
(modify-phases %standard-phases
(add-after 'unpack 'patch-makefile-and-enter-directory
(lambda _
(substitute* "libs/Makefile"
(("/sbin/ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
(chdir "libs")
#t))
(add-after 'install 'install-symlink
(lambda _
(symlink "libclalsadrv.so"
(string-append (assoc-ref %outputs "out")
"/lib/libclalsadrv.so.2")))
;; no configure script
(modify-phases %standard-phases (delete 'configure))))))
(inputs
`(("alsa-lib" ,alsa-lib)
("fftw" ,fftw)))
@ -972,11 +970,9 @@ follower.")
(build-system gnu-build-system)
(arguments
`(#:phases
(alist-cons-after
'unpack
'remove-broken-symlinks
(lambda _ (delete-file-recursively "m4") #t)
%standard-phases)))
(modify-phases %standard-phases
(add-after 'unpack 'remove-broken-symlinks
(lambda _ (delete-file-recursively "m4") #t)))))
(inputs
`(("libsndfile" ,libsndfile)
("alsa-lib" ,alsa-lib)
@ -1015,12 +1011,11 @@ also play midifiles using a Soundfont.")
("unzip" ,unzip)))
(arguments
'(#:phases
(alist-cons-after
'unpack 'bootstrap
(lambda _
(substitute* "bootstrap" (("\r\n") "\n"))
(zero? (system* "sh" "bootstrap")))
%standard-phases)))
(modify-phases %standard-phases
(add-after 'unpack 'bootstrap
(lambda _
(substitute* "bootstrap" (("\r\n") "\n"))
(zero? (system* "sh" "bootstrap")))))))
(home-page "http://www.audiocoding.com/faad2.html")
(synopsis "MPEG-4 and MPEG-2 AAC decoder")
(description
@ -1674,7 +1669,7 @@ software.")
"TYPE=mdaPiano"
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:tests? #f ; no check target
#:phases (alist-delete 'configure %standard-phases)))
#:phases (modify-phases %standard-phases (delete 'configure))))
(inputs
`(("lv2" ,lv2)
("lvtk" ,lvtk)))
@ -1697,7 +1692,7 @@ software.")
"TYPE=mdaEPiano"
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:tests? #f ; no check target
#:phases (alist-delete 'configure %standard-phases)))
#:phases (modify-phases %standard-phases (delete 'configure))))
(home-page "http://elephly.net/lv2/mdaepiano.html")
(synopsis "LV2 port of the mda EPiano plugin")
(description "An LV2 port of the mda EPiano VSTi.")))
@ -2090,19 +2085,19 @@ Suil currently supports every combination of Gtk 2, Qt 4, and X11.")
(string-append "--with-default-path="
(assoc-ref %outputs "out") "/etc/timidity"))
#:phases
(alist-cons-after
'install 'install-config
(lambda _
(let ((out (string-append (assoc-ref %outputs "out")
"/etc/timidity")))
(mkdir-p out)
(call-with-output-file
(string-append out "/timidity.cfg")
(lambda (port)
(format port (string-append "source "
(assoc-ref %build-inputs "freepats")
"/share/freepats/freepats.cfg"))))))
%standard-phases)))
(modify-phases %standard-phases
(add-after 'install 'install-config
(lambda _
(let ((out (string-append (assoc-ref %outputs "out")
"/etc/timidity")))
(mkdir-p out)
(call-with-output-file
(string-append out "/timidity.cfg")
(lambda (port)
(format port (string-append "source "
(assoc-ref %build-inputs "freepats")
"/share/freepats/freepats.cfg")))))
#t)))))
(inputs
`(("alsa-lib" ,alsa-lib)
("ao" ,ao)
@ -2141,16 +2136,15 @@ disks as various audio file formats.")
(arguments
`(#:tests? #f ; no check target
#:phases
(alist-cons-after
'install 'remove-libvamp-hostsdk.la
(lambda* (#:key outputs #:allow-other-keys)
;; https://bugs.launchpad.net/ubuntu/+source/vamp-plugin-sdk/+bug/1253656
(for-each delete-file
(let ((out (assoc-ref outputs "out")))
(list (string-append out "/lib/libvamp-sdk.la")
(string-append out "/lib/libvamp-hostsdk.la"))))
#t)
%standard-phases)))
(modify-phases %standard-phases
(add-after 'install 'remove-libvamp-hostsdk.la
(lambda* (#:key outputs #:allow-other-keys)
;; https://bugs.launchpad.net/ubuntu/+source/vamp-plugin-sdk/+bug/1253656
(for-each delete-file
(let ((out (assoc-ref outputs "out")))
(list (string-append out "/lib/libvamp-sdk.la")
(string-append out "/lib/libvamp-hostsdk.la"))))
#t)s))))
(inputs
`(("libsndfile" ,libsndfile)))
(native-inputs
@ -2312,11 +2306,10 @@ Tracker 3 S3M and Impulse Tracker IT files.")
("file" ,file)))
(arguments
'(#:phases
(alist-cons-after
'unpack 'bootstrap
(lambda _
(zero? (system* "sh" "bootstrap")))
%standard-phases)))
(modify-phases %standard-phases
(add-after 'unpack 'bootstrap
(lambda _
(zero? (system* "sh" "bootstrap")))))))
(home-page "http://www.surina.net/soundtouch/")
(synopsis
"Audio processing library for changing tempo, pitch and playback rate")
@ -2450,11 +2443,10 @@ portions of LAME.")
'(#:phases
;; Autoreconf is necessary because the audacity-compat patch modifies
;; .in files.
(alist-cons-after
'unpack 'autoreconf
(lambda _
(zero? (system* "autoreconf" "-vif")))
%standard-phases)
(modify-phases %standard-phases
(add-after 'unpack 'autoreconf
(lambda _
(zero? (system* "autoreconf" "-vif")))))
#:tests? #f)) ;no 'check' target
(home-page "http://www.portaudio.com/")
(synopsis "Audio I/O library")
@ -2518,14 +2510,13 @@ synthesizer written in C++.")
("pulseaudio" ,pulseaudio)))
(arguments
'(#:phases
(alist-replace
'configure
(lambda* (#:key outputs #:allow-other-keys)
(setenv "CC" "gcc")
(zero?
(system* "./configure"
(string-append "--prefix=" (assoc-ref outputs "out")))))
%standard-phases)
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(setenv "CC" "gcc")
(zero?
(system* "./configure"
(string-append "--prefix=" (assoc-ref outputs "out")))))))
;; No 'check' target.
#:tests? #f))
(home-page "http://themaister.net/rsound.html")
@ -2592,22 +2583,20 @@ result.")
`(#:tests? #f ; no "check" target
#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(alist-cons-after
'unpack 'patch-makefile-and-enter-directory
(lambda _
(substitute* "libs/Makefile"
(("ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
(chdir "libs") #t)
(alist-cons-after
'install
'install-symlink
(lambda _
(symlink "libzita-convolver.so"
(string-append (assoc-ref %outputs "out")
"/lib/libzita-convolver.so.3")))
;; no configure script
(alist-delete 'configure %standard-phases)))))
(modify-phases %standard-phases
(add-after 'unpack 'patch-makefile-and-enter-directory
(lambda _
(substitute* "libs/Makefile"
(("ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
(chdir "libs") #t)
(add-after 'install 'install-symlink
(lambda _
(symlink "libzita-convolver.so"
(string-append (assoc-ref %outputs "out")
"/lib/libzita-convolver.so.3"))))
;; no configure script
(delete 'configure)))))
(inputs `(("fftwf" ,fftwf)))
(home-page "http://kokkinizita.linuxaudio.org")
(synopsis "Fast, partitioned convolution engine library")
@ -2682,23 +2671,21 @@ provide high-quality sample rate conversion.")
`(#:tests? #f ; no "check" target
#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(alist-cons-after
'unpack 'patch-makefile-and-enter-directory
(lambda _
(substitute* "libs/Makefile"
(("ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
(chdir "libs")
#t)
(alist-cons-after
'install
'install-symlink
(lambda _
(symlink "libzita-alsa-pcmi.so"
(string-append (assoc-ref %outputs "out")
"/lib/libzita-alsa-pcmi.so.0")))
;; no configure script
(alist-delete 'configure %standard-phases)))))
(modify-phases %standard-phases
(add-after 'unpack 'patch-makefile-and-enter-directory
(lambda _
(substitute* "libs/Makefile"
(("ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
(chdir "libs")
#t))
(add-after 'install 'install-symlink
(lambda _
(symlink "libzita-alsa-pcmi.so"
(string-append (assoc-ref %outputs "out")
"/lib/libzita-alsa-pcmi.so.0"))))
;; no configure script
(delete 'configure))))
(inputs
`(("alsa-lib" ,alsa-lib)
("fftw" ,fftw)))


+ 17
- 17
gnu/packages/backup.scm View File

@ -293,20 +293,20 @@ random access nor for in-place modification.")
("nettle" ,nettle)))
(arguments
`(#:parallel-build? #f ;race conditions
#:phases (alist-cons-before
'build 'remove-Werror
;; rdup uses a deprecated function from libarchive
(lambda _
(substitute* "GNUmakefile"
(("^(CFLAGS=.*)-Werror" _ front) front)))
(alist-cons-before
'check 'pre-check
(lambda _
(setenv "HOME" (getcwd))
(substitute* "testsuite/rdup/rdup.rdup-up-t-with-file.exp"
(("/bin/cat") (which "cat"))))
%standard-phases))))
#:phases
(modify-phases %standard-phases
(add-before 'build 'remove-Werror
;; rdup uses a deprecated function from libarchive
(lambda _
(substitute* "GNUmakefile"
(("^(CFLAGS=.*)-Werror" _ front) front))
#t))
(add-before 'check 'pre-check
(lambda _
(setenv "HOME" (getcwd))
(substitute* "testsuite/rdup/rdup.rdup-up-t-with-file.exp"
(("/bin/cat") (which "cat")))
#t)))))
(home-page "http://archive.miek.nl/projects/rdup/index.html")
(synopsis "Provide a list of files to backup")
(description
@ -336,9 +336,9 @@ list and implement the backup strategy.")
"CC=gcc")
#:tests? #f ;test input not distributed
#:phases
(alist-delete
'configure ;no configure phase
%standard-phases)))
;; no configure phase
(modify-phases %standard-phases
(delete 'configure))))
(home-page "http://viric.name/cgi-bin/btar/doc/trunk/doc/home.wiki")
(synopsis "Tar-compatible archiver")
(description


+ 128
- 130
gnu/packages/bioinformatics.scm View File

@ -369,32 +369,33 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
'(#:tests? #f
#:make-flags (list (string-append "BINDIR=" %output "/bin"))
#:phases
(alist-cons-after
'unpack 'unpack-tarballs
(lambda _
;; FIXME: Bedops includes tarballs of minimally patched upstream
;; libraries jansson, zlib, and bzip2. We cannot just use stock
;; libraries because at least one of the libraries (zlib) is
;; patched to add a C++ function definition (deflateInit2cpp).
;; Until the Bedops developers offer a way to link against system
;; libraries we have to build the in-tree copies of these three
;; libraries.
;; See upstream discussion:
;; https://github.com/bedops/bedops/issues/124
;; Unpack the tarballs to benefit from shebang patching.
(with-directory-excursion "third-party"
(and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
(zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
(zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
;; Disable unpacking of tarballs in Makefile.
(substitute* "system.mk/Makefile.linux"
(("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
(("\\./configure") "CONFIG_SHELL=bash ./configure"))
(substitute* "third-party/zlib-1.2.7/Makefile.in"
(("^SHELL=.*$") "SHELL=bash\n")))
(alist-delete 'configure %standard-phases))))
(modify-phases %standard-phases
(add-after 'unpack 'unpack-tarballs
(lambda _
;; FIXME: Bedops includes tarballs of minimally patched upstream
;; libraries jansson, zlib, and bzip2. We cannot just use stock
;; libraries because at least one of the libraries (zlib) is
;; patched to add a C++ function definition (deflateInit2cpp).
;; Until the Bedops developers offer a way to link against system
;; libraries we have to build the in-tree copies of these three
;; libraries.
;; See upstream discussion:
;; https://github.com/bedops/bedops/issues/124
;; Unpack the tarballs to benefit from shebang patching.
(with-directory-excursion "third-party"
(and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
(zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
(zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
;; Disable unpacking of tarballs in Makefile.
(substitute* "system.mk/Makefile.linux"
(("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
(("\\./configure") "CONFIG_SHELL=bash ./configure"))
(substitute* "third-party/zlib-1.2.7/Makefile.in"
(("^SHELL=.*$") "SHELL=bash\n"))
#t))
(delete 'configure))))
(home-page "https://github.com/bedops/bedops")
(synopsis "Tools for high-performance genomic feature operations")
(description
@ -1325,20 +1326,21 @@ splice junctions between exons.")
(arguments
'(#:tests? #f ;no "check" target
#:phases
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append
(assoc-ref outputs "out") "/bin"))
(doc (string-append
(assoc-ref outputs "out") "/share/doc/bwa"))
(man (string-append
(assoc-ref outputs "out") "/share/man/man1")))
(install-file "bwa" bin)
(install-file "README.md" doc)
(install-file "bwa.1" man)))
;; no "configure" script
(alist-delete 'configure %standard-phases))))
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append
(assoc-ref outputs "out") "/bin"))
(doc (string-append
(assoc-ref outputs "out") "/share/doc/bwa"))
(man (string-append
(assoc-ref outputs "out") "/share/man/man1")))
(install-file "bwa" bin)
(install-file "README.md" doc)
(install-file "bwa.1" man))
#t))
;; no "configure" script
(delete 'configure))))
(inputs `(("zlib" ,zlib)))
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
@ -1815,10 +1817,9 @@ time.")
(arguments
`(#:python ,python-2
#:phases
(alist-cons-after
'unpack 'set-env
(lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
%standard-phases)))
(modify-phases %standard-phases
(add-after 'unpack 'set-env
(lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
(inputs
`(("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
@ -2365,19 +2366,18 @@ dynamic programming or a variety of heuristics.")
(arguments
`(#:tests? #f ;no "check" target
#:phases
(alist-cons-after
'unpack 'use-shared-boost-libs-and-set-bamtools-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
(("set\\(Boost_USE_STATIC_LIBS ON\\)")
"set(Boost_USE_STATIC_LIBS OFF)")
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
(substitute* "src/CMakeLists.txt"
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
(string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
#t)
%standard-phases)))
(modify-phases %standard-phases
(add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
(("set\\(Boost_USE_STATIC_LIBS ON\\)")
"set(Boost_USE_STATIC_LIBS OFF)")
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
(substitute* "src/CMakeLists.txt"
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
(string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
#t)))))
(inputs
`(("boost" ,boost)
("bamtools" ,bamtools)
@ -2544,15 +2544,15 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(assoc-ref %outputs "out")
"/bin/"))
#:phases
(alist-replace
'check
(lambda* (#:key outputs #:allow-other-keys)
(setenv "PATH" (string-append
(assoc-ref outputs "out") "/bin:"
(getenv "PATH")))
(chdir "../flexbar_v2.5_src/test")
(zero? (system* "bash" "flexbar_validate.sh")))
(alist-delete 'install %standard-phases))))
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key outputs #:allow-other-keys)
(setenv "PATH" (string-append
(assoc-ref outputs "out") "/bin:"
(getenv "PATH")))
(chdir "../flexbar_v2.5_src/test")
(zero? (system* "bash" "flexbar_validate.sh"))))
(delete 'install))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)))
@ -2788,21 +2788,21 @@ association studies (GWAS).")
(arguments
`(#:python ,python-2
#:phases
(alist-cons-after
'unpack 'generate-from-cython-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Delete these C files to force fresh generation from pyx sources.
(delete-file "grit/sparsify_support_fns.c")
(delete-file "grit/call_peaks_support_fns.c")
(substitute* "setup.py"
(("Cython.Setup") "Cython.Build")
;; Add numpy include path to fix compilation
(("pyx\", \\]")
(string-append "pyx\", ], include_dirs = ['"
(assoc-ref inputs "python-numpy")
"/lib/python2.7/site-packages/numpy/core/include/"
"']"))) #t)
%standard-phases)))
(modify-phases %standard-phases
(add-after 'unpack 'generate-from-cython-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Delete these C files to force fresh generation from pyx sources.
(delete-file "grit/sparsify_support_fns.c")
(delete-file "grit/call_peaks_support_fns.c")
(substitute* "setup.py"
(("Cython.Setup") "Cython.Build")
;; Add numpy include path to fix compilation
(("pyx\", \\]")
(string-append "pyx\", ], include_dirs = ['"
(assoc-ref inputs "python-numpy")
"/lib/python2.7/site-packages/numpy/core/include/"
"']")))
#t)))))
(inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
@ -2845,28 +2845,29 @@ estimates transcript expression.")
'()
'("POPCNT_CAPABILITY=0")))
#:phases
(alist-cons-after
'unpack 'patch-sources
(lambda _
;; XXX Cannot use snippet because zip files are not supported
(substitute* "Makefile"
(("^CC = .*$") "CC = gcc")
(("^CPP = .*$") "CPP = g++")
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
(substitute* '("hisat-build" "hisat-inspect")
(("/usr/bin/env") (which "env"))))
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(for-each (lambda (file)
(install-file file bin))
(find-files
"."
"hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
(alist-delete 'configure %standard-phases)))))
(modify-phases %standard-phases
(add-after 'unpack 'patch-sources
(lambda _
;; XXX Cannot use snippet because zip files are not supported
(substitute* "Makefile"
(("^CC = .*$") "CC = gcc")
(("^CPP = .*$") "CPP = g++")
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
(substitute* '("hisat-build" "hisat-inspect")
(("/usr/bin/env") (which "env")))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(for-each (lambda (file)
(install-file file bin))
(find-files
"."
"hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))
#t))
(delete 'configure))))
(native-inputs
`(("unzip" ,unzip)))
(inputs
@ -4680,23 +4681,21 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:phases
(alist-replace
'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; Allow 'konfigure.perl' to find 'package.prl'.
(setenv "PERL5LIB"
(string-append ".:" (getenv "PERL5LIB")))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system* "./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" out)))))
(alist-cons-after
'unpack 'enter-dir
(lambda _ (chdir "ngs-sdk") #t)
%standard-phases))))
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; Allow 'konfigure.perl' to find 'package.prl'.
(setenv "PERL5LIB"
(string-append ".:" (getenv "PERL5LIB")))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system* "./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" out))))))
(add-after 'unpack 'enter-dir
(lambda _ (chdir "ngs-sdk") #t)))))
(native-inputs `(("perl" ,perl)))
;; According to the test
;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
@ -5460,17 +5459,16 @@ sequences.")
"-f" "Makefile.Linux"
"CC=gcc ${CCFLAGS}")
#:phases
(alist-cons-after
'unpack 'enter-dir
(lambda _ (chdir "src") #t)
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(mkdir-p bin)
(copy-recursively "../bin" bin)))
(modify-phases %standard-phases
(add-after 'unpack 'enter-dir
(lambda _ (chdir "src") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(mkdir-p bin)
(copy-recursively "../bin" bin))))
;; no "configure" script
(alist-delete 'configure %standard-phases)))))
(delete 'configure))))
(inputs `(("zlib" ,zlib)))
(home-page "http://bioinf.wehi.edu.au/subread-package/")
(synopsis "Tool kit for processing next-gen sequencing data")


+ 17
- 16
gnu/packages/bittorrent.scm View File

@ -74,23 +74,24 @@
"gui")) ; graphical user interface
(arguments
'(#:glib-or-gtk-wrap-excluded-outputs '("out")
#:phases (alist-cons-after
'install 'move-gui
(lambda* (#:key outputs #:allow-other-keys)
;; Move the GUI to its own output, so that "out" doesn't
;; depend on GTK+.
(let ((out (assoc-ref outputs "out"))
(gui (assoc-ref outputs "gui")))
(mkdir-p (string-append gui "/bin"))
(rename-file (string-append out "/bin/transmission-gtk")
(string-append gui
"/bin/transmission-gtk"))
#:phases
(modify-phases %standard-phases
(add-after 'install 'move-gui
(lambda* (#:key outputs #:allow-other-keys)
;; Move the GUI to its own output, so that "out" doesn't
;; depend on GTK+.
(let ((out (assoc-ref outputs "out"))
(gui (assoc-ref outputs "gui")))
(mkdir-p (string-append gui "/bin"))
(rename-file (string-append out "/bin/transmission-gtk")
(string-append gui
"/bin/transmission-gtk"))
;; Move the '.desktop' file as well.
(mkdir (string-append gui "/share"))
(rename-file (string-append out "/share/applications")
(string-append gui "/share/applications"))))
%standard-phases)))
;; Move the '.desktop' file as well.
(mkdir (string-append gui "/share"))
(rename-file (string-append out "/share/applications")
(string-append gui "/share/applications")))
#t)))))
(inputs
`(("inotify-tools" ,inotify-tools)
("libevent" ,libevent)


+ 1
- 1
gnu/packages/cdrom.scm View File

@ -454,7 +454,7 @@ the data.")
(build-system gnu-build-system)
(arguments
'(#:tests? #f
#:phases (alist-delete 'configure %standard-phases)
#:phases (modify-phases %standard-phases (delete 'configure))
#:make-flags (list "CC=gcc"
(string-append "PREFIX="
(assoc-ref %outputs "out")))))


+ 8
- 8
gnu/packages/compression.scm View File

@ -521,14 +521,14 @@ decompressors when faced with corrupted input.")
`(("which" ,which)))
(arguments
`(#:phases
(alist-cons-after
'patch-source-shebangs 'unpatch-source-shebang
;; revert the patch-shebang phase on a script which is
;; in fact test data
(lambda _
(substitute* "tests/shar-1.ok"
(((which "sh")) "/bin/sh")))
%standard-phases)))
(modify-phases %standard-phases
(add-after 'patch-source-shebangs 'unpatch-source-shebang
;; revert the patch-shebang phase on a script which is
;; in fact test data
(lambda _
(substitute* "tests/shar-1.ok"
(((which "sh")) "/bin/sh"))
#t)))))
(home-page "https://www.gnu.org/software/sharutils/")
(synopsis "Archives in shell scripts, uuencode/uudecode")
(description


+ 15
- 16
gnu/packages/conky.scm View File

@ -50,22 +50,21 @@
;; TODO: add 'ncurses.pc' to the ncurses package.
"-DBUILD_NCURSES=false")
#:phases
(alist-cons-after
'unpack 'add-freetype-to-search-path
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "cmake/ConkyPlatformChecks.cmake"
(("set\\(INCLUDE_SEARCH_PATH")
(string-append
"set(INCLUDE_SEARCH_PATH "
(assoc-ref inputs "freetype") "/include/freetype2 ")))
#t)
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
(install-file "src/conky" bin)))
%standard-phases))))
(modify-phases %standard-phases
(add-after 'unpack 'add-freetype-to-search-path
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "cmake/ConkyPlatformChecks.cmake"
(("set\\(INCLUDE_SEARCH_PATH")
(string-append
"set(INCLUDE_SEARCH_PATH "
(assoc-ref inputs "freetype") "/include/freetype2 ")))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
(install-file "src/conky" bin))
#t)))))
(inputs
`(("freetype" ,freetype)
("ncurses" ,ncurses)


+ 50
- 52
gnu/packages/databases.scm View File

@ -167,34 +167,33 @@ and provides interfaces to the traditional file format.")
'(#:tests? #f ; no check target available
#:disallowed-references ("doc")
#:phases
(alist-replace
'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(doc (assoc-ref outputs "doc")))
;; '--docdir' is not honored, so we need to patch.
(substitute* "dist/Makefile.in"
(("docdir[[:blank:]]*=.*")
(string-append "docdir = " doc "/share/doc/bdb")))
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(doc (assoc-ref outputs "doc")))
;; '--docdir' is not honored, so we need to patch.
(substitute* "dist/Makefile.in"
(("docdir[[:blank:]]*=.*")
(string-append "docdir = " doc "/share/doc/bdb")))
(zero?
(system* "./dist/configure"
(string-append "--prefix=" out)
(string-append "CONFIG_SHELL=" (which "bash"))
(string-append "SHELL=" (which "bash"))
(zero?
(system* "./dist/configure"
(string-append "--prefix=" out)
(string-append "CONFIG_SHELL=" (which "bash"))
(string-append "SHELL=" (which "bash"))
;; Remove 7 MiB of .a files.
"--disable-static"
;; Remove 7 MiB of .a files.
"--disable-static"
;; The compatibility mode is needed by some packages,
;; notably iproute2.
"--enable-compat185"
;; The compatibility mode is needed by some packages,
;; notably iproute2.
"--enable-compat185"
;; The following flag is needed so that the inclusion
;; of db_cxx.h into C++ files works; it leads to
;; HAVE_CXX_STDHEADERS being defined in db_cxx.h.
"--enable-cxx"))))
%standard-phases)))
;; The following flag is needed so that the inclusion
;; of db_cxx.h into C++ files works; it leads to
;; HAVE_CXX_STDHEADERS being defined in db_cxx.h.
"--enable-cxx"))))))))
(synopsis "Berkeley database")
(description
"Berkeley DB is an embeddable database allowing developers the choice of
@ -222,39 +221,38 @@ SQL, Key/Value, XML/XQuery or Java Object storage for their data model.")
`(#:tests? #f ; no check target available
#:disallowed-references ("doc")
#:phases
(alist-replace
'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(doc (assoc-ref outputs "doc")))
;; '--docdir' is not honored, so we need to patch.
(substitute* "dist/Makefile.in"
(("docdir[[:blank:]]*=.*")
(string-append "docdir = " doc "/share/doc/bdb")))
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(doc (assoc-ref outputs "doc")))
;; '--docdir' is not honored, so we need to patch.
(substitute* "dist/Makefile.in"
(("docdir[[:blank:]]*=.*")
(string-append "docdir = " doc "/share/doc/bdb")))
(zero?
(system* "./dist/configure"
(string-append "--prefix=" out)
(string-append "CONFIG_SHELL=" (which "bash"))
(string-append "SHELL=" (which "bash"))
(zero?
(system* "./dist/configure"
(string-append "--prefix=" out)
(string-append "CONFIG_SHELL=" (which "bash"))
(string-append "SHELL=" (which "bash"))
;; Bdb doesn't recognize aarch64 as an architecture.
,@(if (string=? "aarch64-linux" (%current-system))
'("--build=aarch64-unknown-linux-gnu")
'())
;; Bdb doesn't recognize aarch64 as an architecture.
,@(if (string=? "aarch64-linux" (%current-system))
'("--build=aarch64-unknown-linux-gnu")
'())
;; Remove 7 MiB of .a files.
"--disable-static"
;; Remove 7 MiB of .a files.
"--disable-static"
;; The compatibility mode is needed by some packages,
;; notably iproute2.
"--enable-compat185"
;; The compatibility mode is needed by some packages,
;; notably iproute2.
"--enable-compat185"
;; The following flag is needed so that the inclusion
;; of db_cxx.h into C++ files works; it leads to
;; HAVE_CXX_STDHEADERS being defined in db_cxx.h.
"--enable-cxx"))))
%standard-phases)))))
;; The following flag is needed so that the inclusion
;; of db_cxx.h into C++ files works; it leads to
;; HAVE_CXX_STDHEADERS being defined in db_cxx.h.
"--enable-cxx"))))))))))
(define-public leveldb
(package


+ 36
- 34
gnu/packages/debug.scm View File

@ -58,23 +58,24 @@
`(("perl" ,perl)))
(arguments
`(#:phases
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
;; Makefile contains no install target
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(doc (string-append out "/share/doc/delta-" ,version)))
(begin
(mkdir-p bin)
(mkdir-p doc)
(for-each (lambda (h)
(install-file h doc))
`("License.txt" ,@(find-files "www" ".*\\.html")))
(for-each (lambda (b)
(install-file b bin))
`("delta" "multidelta" "topformflat")))))
(alist-delete 'configure %standard-phases))))
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
;; Makefile contains no install target
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(doc (string-append out "/share/doc/delta-" ,version)))
(begin
(mkdir-p bin)
(mkdir-p doc)
(for-each (lambda (h)
(install-file h doc))
`("License.txt" ,@(find-files "www" ".*\\.html")))
(for-each (lambda (b)
(install-file b bin))
`("delta" "multidelta" "topformflat"))))
#t))
(delete 'configure))))
(home-page "http://delta.tigris.org/")
(synopsis "Heuristical file minimizer")
(description
@ -114,23 +115,24 @@ program to exhibit a bug.")
("sys-cpu" ,perl-sys-cpu)
("term-readkey" ,perl-term-readkey)))
(arguments
`(#:phases (alist-cons-after
'install 'set-load-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Tell creduce where to find the perl modules it needs.
(let* ((out (assoc-ref outputs "out"))
(prog (string-append out "/bin/creduce")))
(wrap-program
prog
`("PERL5LIB" ":" prefix
,(map (lambda (p)
(string-append (assoc-ref inputs p)
"/lib/perl5/site_perl/"
,(package-version perl)))
'("term-readkey" "exporter-lite"
"file-which" "getopt-tabular"
"regex-common" "sys-cpu"))))))
%standard-phases)))
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'set-load-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Tell creduce where to find the perl modules it needs.
(let* ((out (assoc-ref outputs "out"))
(prog (string-append out "/bin/creduce")))
(wrap-program
prog
`("PERL5LIB" ":" prefix
,(map (lambda (p)
(string-append (assoc-ref inputs p)
"/lib/perl5/site_perl/"
,(package-version perl)))
'("term-readkey" "exporter-lite"
"file-which" "getopt-tabular"
"regex-common" "sys-cpu")))))
#t)))))
(home-page "http://embed.cs.utah.edu/creduce")
(synopsis "Reducer for interesting code")
(description


+ 12
- 11
gnu/packages/display-managers.scm View File

@ -337,17 +337,18 @@ GTK+, lets you select a desktop session and log in to it.")
(native-inputs
`(("pkg-config" ,pkg-config)))
(arguments
'(#:phases (alist-cons-before
'configure 'set-new-etc-location
(lambda _
(substitute* "CMakeLists.txt"
(("/etc")
(string-append (assoc-ref %outputs "out") "/etc"))
(("install.*systemd.*")
;; The build system's logic here is: if "Linux", then
;; "systemd". Strip that.
"")))
%standard-phases)
'(#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-new-etc-location
(lambda _
(substitute* "CMakeLists.txt"
(("/etc")
(string-append (assoc-ref %outputs "out") "/etc"))
(("install.*systemd.*")
;; The build system's logic here is: if "Linux", then
;; "systemd". Strip that.
""))
#t)))
#:configure-flags '("-DUSE_PAM=yes"
"-DUSE_CONSOLEKIT=no")
#:tests? #f))


+ 1
- 1
gnu/packages/dns.scm