New upstream version 2.0.5

School of Engineering, University of California, Santa Cruz, CA

--------------------------------------------------------------

Current release: 2.0 (December 2017)

Current release: 2.0.4 (September 2019)

tRNAscan-SE was written in the PERL (version 5) script language.

Input consists of DNA or RNA sequences in FASTA format. tRNA

#! /bin/sh

# depcomp - compile a program generating dependencies as side-effects

scriptversion=2009-04-28.21; # UTC

# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 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

# the Free Software Foundation; either version 2, or (at your option)

# any later version.

# This program is distributed in the hope that it will be useful,

# but WITHOUT ANY WARRANTY; without even the implied warranty of

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

# 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/>.

# As a special exception to the GNU General Public License, if you

# distribute this file as part of a program that contains a

# configuration script generated by Autoconf, you may include it under

# the same distribution terms that you use for the rest of that program.

# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.

case $1 in

  '')

     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2

     exit 1;

     ;;

  -h | --h*)

    cat <<\EOF

Usage: depcomp [--help] [--version] PROGRAM [ARGS]

Run PROGRAMS ARGS to compile a file, generating dependencies

as side-effects.

Environment variables:

  depmode     Dependency tracking mode.

  source      Source file read by `PROGRAMS ARGS'.

  object      Object file output by `PROGRAMS ARGS'.

  DEPDIR      directory where to store dependencies.

  depfile     Dependency file to output.

  tmpdepfile  Temporary file to use when outputing dependencies.

  libtool     Whether libtool is used (yes/no).

Report bugs to <bug-automake@gnu.org>.

EOF

    exit $?

    ;;

  -v | --v*)

    echo "depcomp $scriptversion"

    exit $?

    ;;

esac

if test -z "$depmode" || test -z "$source" || test -z "$object"; then

  echo "depcomp: Variables source, object and depmode must be set" 1>&2

  exit 1

fi

# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.

depfile=${depfile-`echo "$object" |

  sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}

tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}

rm -f "$tmpdepfile"

# Some modes work just like other modes, but use different flags.  We

# parameterize here, but still list the modes in the big case below,

# to make depend.m4 easier to write.  Note that we *cannot* use a case

# here, because this file can only contain one case statement.

if test "$depmode" = hp; then

  # HP compiler uses -M and no extra arg.

  gccflag=-M

  depmode=gcc

fi

if test "$depmode" = dashXmstdout; then

   # This is just like dashmstdout with a different argument.

   dashmflag=-xM

   depmode=dashmstdout

fi

cygpath_u="cygpath -u -f -"

if test "$depmode" = msvcmsys; then

   # This is just like msvisualcpp but w/o cygpath translation.

   # Just convert the backslash-escaped backslashes to single forward

   # slashes to satisfy depend.m4

   cygpath_u="sed s,\\\\\\\\,/,g"

   depmode=msvisualcpp

fi

case "$depmode" in

gcc3)

## gcc 3 implements dependency tracking that does exactly what

## we want.  Yay!  Note: for some reason libtool 1.4 doesn't like

## it if -MD -MP comes after the -MF stuff.  Hmm.

## Unfortunately, FreeBSD c89 acceptance of flags depends upon

## the command line argument order; so add the flags where they

## appear in depend2.am.  Note that the slowdown incurred here

## affects only configure: in makefiles, %FASTDEP% shortcuts this.

  for arg

  do

    case $arg in

    -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;

    *)  set fnord "$@" "$arg" ;;

    esac

    shift # fnord

    shift # $arg

  done

  "$@"

  stat=$?

  if test $stat -eq 0; then :

  else

    rm -f "$tmpdepfile"

    exit $stat

  fi

  mv "$tmpdepfile" "$depfile"

  ;;

gcc)

## There are various ways to get dependency output from gcc.  Here's

## why we pick this rather obscure method:

## - Don't want to use -MD because we'd like the dependencies to end

##   up in a subdir.  Having to rename by hand is ugly.

##   (We might end up doing this anyway to support other compilers.)

## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like

##   -MM, not -M (despite what the docs say).

## - Using -M directly means running the compiler twice (even worse

##   than renaming).

  if test -z "$gccflag"; then

    gccflag=-MD,

  fi

  "$@" -Wp,"$gccflag$tmpdepfile"

  stat=$?

  if test $stat -eq 0; then :

  else

    rm -f "$tmpdepfile"

    exit $stat

  fi

  rm -f "$depfile"

  echo "$object : \\" > "$depfile"

  alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz

## The second -e expression handles DOS-style file names with drive letters.

  sed -e 's/^[^:]*: / /' \

      -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"

## This next piece of magic avoids the `deleted header file' problem.

## The problem is that when a header file which appears in a .P file

## is deleted, the dependency causes make to die (because there is

## typically no way to rebuild the header).  We avoid this by adding

## dummy dependencies for each header file.  Too bad gcc doesn't do

## this for us directly.

  tr ' ' '

' < "$tmpdepfile" |

## Some versions of gcc put a space before the `:'.  On the theory

## that the space means something, we add a space to the output as

## well.

## Some versions of the HPUX 10.20 sed can't process this invocation

## correctly.  Breaking it into two sed invocations is a workaround.

    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"

  rm -f "$tmpdepfile"

  ;;

hp)

  # This case exists only to let depend.m4 do its work.  It works by

  # looking at the text of this script.  This case will never be run,

  # since it is checked for above.

  exit 1

  ;;

sgi)

  if test "$libtool" = yes; then

    "$@" "-Wp,-MDupdate,$tmpdepfile"

  else

    "$@" -MDupdate "$tmpdepfile"

  fi

  stat=$?

  if test $stat -eq 0; then :

  else

    rm -f "$tmpdepfile"

    exit $stat

  fi

  rm -f "$depfile"

  if test -f "$tmpdepfile"; then  # yes, the sourcefile depend on other files

    echo "$object : \\" > "$depfile"

    # Clip off the initial element (the dependent).  Don't try to be

    # clever and replace this with sed code, as IRIX sed won't handle

    # lines with more than a fixed number of characters (4096 in

    # IRIX 6.2 sed, 8192 in IRIX 6.5).  We also remove comment lines;

    # the IRIX cc adds comments like `#:fec' to the end of the

    # dependency line.

    tr ' ' '

' < "$tmpdepfile" \

    | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \

    tr '

' ' ' >> "$depfile"

    echo >> "$depfile"

    # The second pass generates a dummy entry for each header file.

    tr ' ' '

' < "$tmpdepfile" \

   | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \

   >> "$depfile"

  else

    # The sourcefile does not contain any dependencies, so just

    # store a dummy comment line, to avoid errors with the Makefile

    # "include basename.Plo" scheme.

    echo "#dummy" > "$depfile"

  fi

  rm -f "$tmpdepfile"

  ;;

aix)

  # The C for AIX Compiler uses -M and outputs the dependencies

  # in a .u file.  In older versions, this file always lives in the

  # current directory.  Also, the AIX compiler puts `$object:' at the

  # start of each line; $object doesn't have directory information.

  # Version 6 uses the directory in both cases.

  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`

  test "x$dir" = "x$object" && dir=

  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`

  if test "$libtool" = yes; then

    tmpdepfile1=$dir$base.u

    tmpdepfile2=$base.u

    tmpdepfile3=$dir.libs/$base.u

    "$@" -Wc,-M

  else

    tmpdepfile1=$dir$base.u

    tmpdepfile2=$dir$base.u

    tmpdepfile3=$dir$base.u

    "$@" -M

  fi

  stat=$?

  if test $stat -eq 0; then :

  else

    rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"

    exit $stat

  fi

  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"

  do

    test -f "$tmpdepfile" && break

  done

  if test -f "$tmpdepfile"; then

    # Each line is of the form `foo.o: dependent.h'.

    # Do two passes, one to just change these to

    # `$object: dependent.h' and one to simply `dependent.h:'.

    sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"

    # That's a tab and a space in the [].

    sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"

  else

    # The sourcefile does not contain any dependencies, so just

    # store a dummy comment line, to avoid errors with the Makefile

    # "include basename.Plo" scheme.

    echo "#dummy" > "$depfile"

  fi

  rm -f "$tmpdepfile"

  ;;

icc)

  # Intel's C compiler understands `-MD -MF file'.  However on

  #    icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c

  # ICC 7.0 will fill foo.d with something like

  #    foo.o: sub/foo.c

  #    foo.o: sub/foo.h

  # which is wrong.  We want:

  #    sub/foo.o: sub/foo.c

  #    sub/foo.o: sub/foo.h

  #    sub/foo.c:

  #    sub/foo.h:

  # ICC 7.1 will output

  #    foo.o: sub/foo.c sub/foo.h

  # and will wrap long lines using \ :

  #    foo.o: sub/foo.c ... \

  #     sub/foo.h ... \

  #     ...

  "$@" -MD -MF "$tmpdepfile"

  stat=$?

  if test $stat -eq 0; then :

  else

    rm -f "$tmpdepfile"

    exit $stat

  fi

  rm -f "$depfile"

  # Each line is of the form `foo.o: dependent.h',

  # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.

  # Do two passes, one to just change these to

  # `$object: dependent.h' and one to simply `dependent.h:'.

  sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"

  # Some versions of the HPUX 10.20 sed can't process this invocation

  # correctly.  Breaking it into two sed invocations is a workaround.

  sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |

    sed -e 's/$/ :/' >> "$depfile"

  rm -f "$tmpdepfile"

  ;;

hp2)

  # The "hp" stanza above does not work with aCC (C++) and HP's ia64

  # compilers, which have integrated preprocessors.  The correct option

  # to use with these is +Maked; it writes dependencies to a file named

  # 'foo.d', which lands next to the object file, wherever that

  # happens to be.

  # Much of this is similar to the tru64 case; see comments there.

  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`

  test "x$dir" = "x$object" && dir=

  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`

  if test "$libtool" = yes; then

    tmpdepfile1=$dir$base.d

    tmpdepfile2=$dir.libs/$base.d

    "$@" -Wc,+Maked

  else

    tmpdepfile1=$dir$base.d

    tmpdepfile2=$dir$base.d

    "$@" +Maked

  fi

  stat=$?

  if test $stat -eq 0; then :

  else

     rm -f "$tmpdepfile1" "$tmpdepfile2"

     exit $stat

  fi

  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"

  do

    test -f "$tmpdepfile" && break

  done

  if test -f "$tmpdepfile"; then

    sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"

    # Add `dependent.h:' lines.

    sed -ne '2,${

	       s/^ *//

	       s/ \\*$//

	       s/$/:/

	       p

	     }' "$tmpdepfile" >> "$depfile"

  else

    echo "#dummy" > "$depfile"

  fi

  rm -f "$tmpdepfile" "$tmpdepfile2"

  ;;

tru64)

   # The Tru64 compiler uses -MD to generate dependencies as a side

   # effect.  `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.

   # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put

   # dependencies in `foo.d' instead, so we check for that too.

   # Subdirectories are respected.

   dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`

   test "x$dir" = "x$object" && dir=

   base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`

   if test "$libtool" = yes; then

      # With Tru64 cc, shared objects can also be used to make a

      # static library.  This mechanism is used in libtool 1.4 series to

      # handle both shared and static libraries in a single compilation.

      # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.

      #

      # With libtool 1.5 this exception was removed, and libtool now

      # generates 2 separate objects for the 2 libraries.  These two

      # compilations output dependencies in $dir.libs/$base.o.d and

      # in $dir$base.o.d.  We have to check for both files, because

      # one of the two compilations can be disabled.  We should prefer

      # $dir$base.o.d over $dir.libs/$base.o.d because the latter is

      # automatically cleaned when .libs/ is deleted, while ignoring

      # the former would cause a distcleancheck panic.

      tmpdepfile1=$dir.libs/$base.lo.d   # libtool 1.4

      tmpdepfile2=$dir$base.o.d          # libtool 1.5

      tmpdepfile3=$dir.libs/$base.o.d    # libtool 1.5

      tmpdepfile4=$dir.libs/$base.d      # Compaq CCC V6.2-504

      "$@" -Wc,-MD

   else

      tmpdepfile1=$dir$base.o.d

      tmpdepfile2=$dir$base.d

      tmpdepfile3=$dir$base.d

      tmpdepfile4=$dir$base.d

      "$@" -MD

   fi

   stat=$?

   if test $stat -eq 0; then :

   else

      rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"

      exit $stat

   fi

   for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"

   do

     test -f "$tmpdepfile" && break

   done

   if test -f "$tmpdepfile"; then

      sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"

      # That's a tab and a space in the [].

      sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"

   else

      echo "#dummy" > "$depfile"

   fi

   rm -f "$tmpdepfile"

   ;;

#nosideeffect)

  # This comment above is used by automake to tell side-effect

  # dependency tracking mechanisms from slower ones.

dashmstdout)

  # Important note: in order to support this mode, a compiler *must*

  # always write the preprocessed file to stdout, regardless of -o.

  "$@" || exit $?

  # Remove the call to Libtool.

  if test "$libtool" = yes; then

    while test "X$1" != 'X--mode=compile'; do

      shift

    done

    shift

  fi

  # Remove `-o $object'.

  IFS=" "

  for arg

  do

    case $arg in

    -o)

      shift

      ;;

    $object)

      shift

      ;;

    *)

      set fnord "$@" "$arg"

      shift # fnord

      shift # $arg

      ;;

    esac

  done

  test -z "$dashmflag" && dashmflag=-M

  # Require at least two characters before searching for `:'

  # in the target name.  This is to cope with DOS-style filenames:

  # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.

  "$@" $dashmflag |

    sed 's:^[  ]*[^: ][^:][^:]*\:[    ]*:'"$object"'\: :' > "$tmpdepfile"

  rm -f "$depfile"

  cat < "$tmpdepfile" > "$depfile"

  tr ' ' '

' < "$tmpdepfile" | \

## Some versions of the HPUX 10.20 sed can't process this invocation

## correctly.  Breaking it into two sed invocations is a workaround.

    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"

  rm -f "$tmpdepfile"

  ;;

dashXmstdout)

  # This case only exists to satisfy depend.m4.  It is never actually

  # run, as this mode is specially recognized in the preamble.

  exit 1

  ;;

makedepend)

  "$@" || exit $?

  # Remove any Libtool call

  if test "$libtool" = yes; then

    while test "X$1" != 'X--mode=compile'; do

      shift

    done

    shift

  fi

  # X makedepend

  shift

  cleared=no eat=no

  for arg

  do

    case $cleared in

    no)

      set ""; shift

      cleared=yes ;;

    esac

    if test $eat = yes; then

      eat=no

      continue

    fi

    case "$arg" in

    -D*|-I*)

      set fnord "$@" "$arg"; shift ;;

    # Strip any option that makedepend may not understand.  Remove

    # the object too, otherwise makedepend will parse it as a source file.

    -arch)

      eat=yes ;;

    -*|$object)

      ;;

    *)

      set fnord "$@" "$arg"; shift ;;

    esac

  done

  obj_suffix=`echo "$object" | sed 's/^.*\././'`

  touch "$tmpdepfile"

  ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"

  rm -f "$depfile"

  cat < "$tmpdepfile" > "$depfile"

  sed '1,2d' "$tmpdepfile" | tr ' ' '

' | \

## Some versions of the HPUX 10.20 sed can't process this invocation

## correctly.  Breaking it into two sed invocations is a workaround.

    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"

  rm -f "$tmpdepfile" "$tmpdepfile".bak

  ;;

cpp)

  # Important note: in order to support this mode, a compiler *must*

  # always write the preprocessed file to stdout.

  "$@" || exit $?

  # Remove the call to Libtool.

  if test "$libtool" = yes; then

    while test "X$1" != 'X--mode=compile'; do

      shift

    done

    shift

  fi

  # Remove `-o $object'.

  IFS=" "

  for arg

  do

    case $arg in

    -o)

      shift

      ;;

    $object)

      shift

      ;;

    *)

      set fnord "$@" "$arg"

      shift # fnord

      shift # $arg

      ;;

    esac

  done

  "$@" -E |

    sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \

       -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |

    sed '$ s: \\$::' > "$tmpdepfile"

  rm -f "$depfile"

  echo "$object : \\" > "$depfile"

  cat < "$tmpdepfile" >> "$depfile"

  sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"

  rm -f "$tmpdepfile"

  ;;

msvisualcpp)

  # Important note: in order to support this mode, a compiler *must*

  # always write the preprocessed file to stdout.

  "$@" || exit $?

  # Remove the call to Libtool.

  if test "$libtool" = yes; then

    while test "X$1" != 'X--mode=compile'; do

      shift

    done

    shift

  fi

  IFS=" "

  for arg

  do

    case "$arg" in

    -o)

      shift

      ;;

    $object)

      shift

      ;;

    "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")

	set fnord "$@"

	shift

	shift

	;;

    *)

	set fnord "$@" "$arg"

	shift

	shift

	;;

    esac

  done

  "$@" -E 2>/dev/null |

  sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"

  rm -f "$depfile"

  echo "$object : \\" > "$depfile"

  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"

  echo "	" >> "$depfile"

  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"

  rm -f "$tmpdepfile"

  ;;

msvcmsys)

  # This case exists only to let depend.m4 do its work.  It works by

  # looking at the text of this script.  This case will never be run,

  # since it is checked for above.

  exit 1

  ;;

none)

  exec "$@"

  ;;

*)

  echo "Unknown depmode $depmode" 1>&2

  exit 1

  ;;

esac

exit 0

# Local Variables:

# mode: shell-script

# sh-indentation: 2

# eval: (add-hook 'write-file-hooks 'time-stamp)

# time-stamp-start: "scriptversion="

# time-stamp-format: "%:y-%02m-%02d.%02H"

# time-stamp-time-zone: "UTC"

# time-stamp-end: "; # UTC"

# End: