Update build system files.

BIMSBbioinfo · Jul 5, 2018 · d751101 · d751101
1 parent 298c316
commit d751101
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diff --git a/pipelines/rnaseq/aclocal.m4 b/pipelines/rnaseq/aclocal.m4
@@ -1,6 +1,6 @@
-# generated automatically by aclocal 1.15.1 -*- Autoconf -*-
+# generated automatically by aclocal 1.16.1 -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -20,7 +20,7 @@ You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically 'autoreconf'.])])
 
-# Copyright (C) 2002-2017 Free Software Foundation, Inc.
+# Copyright (C) 2002-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
 # generated from the m4 files accompanying Automake X.Y.
 # (This private macro should not be called outside this file.)
 AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.15'
+[am__api_version='1.16'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.15.1], [],
+m4_if([$1], [1.16.1], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -51,14 +51,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15.1])dnl
+[AM_AUTOMAKE_VERSION([1.16.1])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -110,7 +110,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd`
 
 # Do all the work for Automake.                             -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -197,8 +197,8 @@ AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
 AC_REQUIRE([AC_PROG_MKDIR_P])dnl
 # For better backward compatibility.  To be removed once Automake 1.9.x
 # dies out for good.  For more background, see:
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <https://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
 AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
 # We need awk for the "check" target (and possibly the TAP driver).  The
 # system "awk" is bad on some platforms.
@@ -265,7 +265,7 @@ END
 Aborting the configuration process, to ensure you take notice of the issue.
 
 You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
+that behaves properly: <https://www.gnu.org/software/coreutils/>.
 
 If you want to complete the configuration process using your problematic
 'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
@@ -307,7 +307,7 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -328,7 +328,7 @@ if test x"${install_sh+set}" != xset; then
 fi
 AC_SUBST([install_sh])])
 
-# Copyright (C) 2003-2017 Free Software Foundation, Inc.
+# Copyright (C) 2003-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -349,7 +349,7 @@ AC_SUBST([am__leading_dot])])
 
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
-# Copyright (C) 1997-2017 Free Software Foundation, Inc.
+# Copyright (C) 1997-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -388,7 +388,7 @@ fi
 
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -417,7 +417,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -450,10 +450,12 @@ AC_DEFUN([AM_PATH_PYTHON],
  [
   dnl Find a Python interpreter.  Python versions prior to 2.0 are not
   dnl supported. (2.0 was released on October 16, 2000).
-  dnl FIXME: Remove the need to hard-code Python versions here.
   m4_define_default([_AM_PYTHON_INTERPRETER_LIST],
-[python python2 python3 python3.5 python3.4 python3.3 python3.2 python3.1 python3.0 python2.7 dnl
- python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0])
+[python python2 python3 dnl
+ python3.9 python3.8 python3.7 python3.6 python3.5 python3.4 python3.3 dnl
+ python3.2 python3.1 python3.0 dnl
+ python2.7 python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 dnl
+ python2.0])
 
   AC_ARG_VAR([PYTHON], [the Python interpreter])
 
@@ -653,7 +655,7 @@ for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[[i]]
 sys.exit(sys.hexversion < minverhex)"
   AS_IF([AM_RUN_LOG([$1 -c "$prog"])], [$3], [$4])])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -672,7 +674,7 @@ AC_DEFUN([AM_RUN_LOG],
 
 # Check to make sure that the build environment is sane.    -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -753,7 +755,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
 ])
 
-# Copyright (C) 2009-2017 Free Software Foundation, Inc.
+# Copyright (C) 2009-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -813,7 +815,7 @@ AC_SUBST([AM_BACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -841,7 +843,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006-2017 Free Software Foundation, Inc.
+# Copyright (C) 2006-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -860,7 +862,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004-2017 Free Software Foundation, Inc.
+# Copyright (C) 2004-2018 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

diff --git a/pipelines/rnaseq/build-aux/install-sh b/pipelines/rnaseq/build-aux/install-sh
@@ -1,7 +1,7 @@
 #!/bin/sh
 # install - install a program, script, or datafile
 
-scriptversion=2016-01-11.22; # UTC
+scriptversion=2018-03-11.20; # UTC
 
 # This originates from X11R5 (mit/util/scripts/install.sh), which was
 # later released in X11R6 (xc/config/util/install.sh) with the
@@ -271,15 +271,18 @@ do
     fi
     dst=$dst_arg
 
-    # If destination is a directory, append the input filename; won't work
-    # if double slashes aren't ignored.
+    # If destination is a directory, append the input filename.
     if test -d "$dst"; then
       if test "$is_target_a_directory" = never; then
         echo "$0: $dst_arg: Is a directory" >&2
         exit 1
       fi
       dstdir=$dst
-      dst=$dstdir/`basename "$src"`
+      dstbase=`basename "$src"`
+      case $dst in
+	*/) dst=$dst$dstbase;;
+	*)  dst=$dst/$dstbase;;
+      esac
       dstdir_status=0
     else
       dstdir=`dirname "$dst"`
@@ -288,6 +291,11 @@ do
     fi
   fi
 
+  case $dstdir in
+    */) dstdirslash=$dstdir;;
+    *)  dstdirslash=$dstdir/;;
+  esac
+
   obsolete_mkdir_used=false
 
   if test $dstdir_status != 0; then
@@ -324,34 +332,43 @@ do
             # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
             ;;
           *)
+            # Note that $RANDOM variable is not portable (e.g. dash);  Use it
+            # here however when possible just to lower collision chance.
             tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
-            trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
 
+            trap 'ret=$?; rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+            # Because "mkdir -p" follows existing symlinks and we likely work
+            # directly in world-writeable /tmp, make sure that the '$tmpdir'
+            # directory is successfully created first before we actually test
+            # 'mkdir -p' feature.
             if (umask $mkdir_umask &&
-                exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+                $mkdirprog $mkdir_mode "$tmpdir" &&
+                exec $mkdirprog $mkdir_mode -p -- "$tmpdir/a/b") >/dev/null 2>&1
             then
               if test -z "$dir_arg" || {
                    # Check for POSIX incompatibilities with -m.
                    # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
                    # other-writable bit of parent directory when it shouldn't.
                    # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
-                   ls_ld_tmpdir=`ls -ld "$tmpdir"`
+                   test_tmpdir="$tmpdir/a"
+                   ls_ld_tmpdir=`ls -ld "$test_tmpdir"`
                    case $ls_ld_tmpdir in
                      d????-?r-*) different_mode=700;;
                      d????-?--*) different_mode=755;;
                      *) false;;
                    esac &&
-                   $mkdirprog -m$different_mode -p -- "$tmpdir" && {
-                     ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+                   $mkdirprog -m$different_mode -p -- "$test_tmpdir" && {
+                     ls_ld_tmpdir_1=`ls -ld "$test_tmpdir"`
                      test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
                    }
                  }
               then posix_mkdir=:
               fi
-              rmdir "$tmpdir/d" "$tmpdir"
+              rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir"
             else
               # Remove any dirs left behind by ancient mkdir implementations.
-              rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+              rmdir ./$mkdir_mode ./-p ./-- "$tmpdir" 2>/dev/null
             fi
             trap '' 0;;
         esac;;
@@ -427,8 +444,8 @@ do
   else
 
     # Make a couple of temp file names in the proper directory.
-    dsttmp=$dstdir/_inst.$$_
-    rmtmp=$dstdir/_rm.$$_
+    dsttmp=${dstdirslash}_inst.$$_
+    rmtmp=${dstdirslash}_rm.$$_
 
     # Trap to clean up those temp files at exit.
     trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
@@ -493,7 +510,7 @@ do
 done
 
 # Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
+# eval: (add-hook 'before-save-hook 'time-stamp)
 # time-stamp-start: "scriptversion="
 # time-stamp-format: "%:y-%02m-%02d.%02H"
 # time-stamp-time-zone: "UTC0"

diff --git a/pipelines/rnaseq/build-aux/missing b/pipelines/rnaseq/build-aux/missing
@@ -1,9 +1,9 @@
 #!/bin/sh
 # Common wrapper for a few potentially missing GNU programs.
 
-scriptversion=2016-01-11.22; # UTC
+scriptversion=2018-03-07.03; # UTC
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2018 Free Software Foundation, Inc.
 # Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
 
 # This program is free software; you can redistribute it and/or modify
@@ -17,7 +17,7 @@ scriptversion=2016-01-11.22; # UTC
 # GNU General Public License for more details.
 
 # You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
@@ -101,9 +101,9 @@ else
   exit $st
 fi
 
-perl_URL=http://www.perl.org/
-flex_URL=http://flex.sourceforge.net/
-gnu_software_URL=http://www.gnu.org/software
+perl_URL=https://www.perl.org/
+flex_URL=https://github.com/westes/flex
+gnu_software_URL=https://www.gnu.org/software
 
 program_details ()
 {
@@ -207,7 +207,7 @@ give_advice "$1" | sed -e '1s/^/WARNING: /' \
 exit $st
 
 # Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
+# eval: (add-hook 'before-save-hook 'time-stamp)
 # time-stamp-start: "scriptversion="
 # time-stamp-format: "%:y-%02m-%02d.%02H"
 # time-stamp-time-zone: "UTC0"

diff --git a/pipelines/rnaseq/build-aux/test-driver b/pipelines/rnaseq/build-aux/test-driver
@@ -1,9 +1,9 @@
 #!/bin/sh
 # test-driver - basic testsuite driver script.
 
-scriptversion=2016-01-11.22; # UTC
+scriptversion=2018-03-07.03; # UTC
 
-# Copyright (C) 2011-2017 Free Software Foundation, Inc.
+# Copyright (C) 2011-2018 Free Software Foundation, Inc.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -16,7 +16,7 @@ scriptversion=2016-01-11.22; # UTC
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
@@ -140,7 +140,7 @@ echo ":copy-in-global-log: $gcopy" >> $trs_file
 # Local Variables:
 # mode: shell-script
 # sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
+# eval: (add-hook 'before-save-hook 'time-stamp)
 # time-stamp-start: "scriptversion="
 # time-stamp-format: "%:y-%02m-%02d.%02H"
 # time-stamp-time-zone: "UTC0"