From d10092b849153dc27cfed0a9601fde6c7bdec918 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sun, 30 Jul 2017 21:02:35 -0400
Subject: gnu: Put autoconf-related phases immediately after the 'unpack phase.

* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
---
 gnu/packages/bioinformatics.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f1b686c71..5e8eef4e1c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3450,7 +3450,7 @@ sequences).")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))
              #t))
-         (add-before 'configure 'autoconf
+         (add-after 'fix-includes 'autoconf
            (lambda _ (zero? (system* "autoconf")))))))
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -4486,7 +4486,7 @@ distribution, coverage uniformity, strand specificity, etc.")
                        "Data2DB"
                        "PCL2Bin")))
            (modify-phases %standard-phases
-             (add-before 'configure 'bootstrap
+             (add-after 'unpack 'bootstrap
                (lambda _
                  (zero? (system* "bash" "gen_auto"))))
              (add-after 'build 'build-additional-tools
@@ -6164,8 +6164,8 @@ track.  The database is exposed as a @code{TxDb} object.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autogen
-                     (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+         (add-after 'unpack 'autogen
+           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      `(("zlib" ,zlib)
        ("bzip2" ,bzip2)
@@ -8381,14 +8381,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
 AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
 AM_CONDITIONAL(AMPNG, true)"))
              #t))
-         (add-after 'unpack 'disable-update-check
+         (add-after 'fix-checks 'disable-update-check
            (lambda _
              ;; At build time there is no connection to the Internet, so
              ;; looking for updates will not work.
              (substitute* "Makefile.am"
                (("\\$\\(bindir\\)/embossupdate") ""))
              #t))
-         (add-before 'configure 'autogen
+         (add-after 'disable-update-check 'autogen
            (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      `(("perl" ,perl)
@@ -9453,7 +9453,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
        (substitute-keyword-arguments (package-arguments htslib)
          ((#:phases phases)
           `(modify-phases  ,phases
-             (add-before 'configure 'bootstrap
+             (add-after 'unpack 'bootstrap
                (lambda _
                  (zero? (system* "autoreconf" "-vif"))))))))
       (native-inputs
-- 
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