Browse code

update to latest GSTRUCT

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@123972 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/11/2016 21:54:30
Showing 1 changed files
... ...
@@ -3,7 +3,7 @@
3 3
 
4 4
 scriptversion=2012-10-14.11; # UTC
5 5
 
6
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
6
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
7 7
 # Written by Tom Tromey <tromey@cygnus.com>.
8 8
 #
9 9
 # This program is free software; you can redistribute it and/or modify
Browse code

resurrect improvements that we reverted before the April release, expect breakage for a while

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110039 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/10/2015 18:51:00
Showing 1 changed files
... ...
@@ -1,9 +1,9 @@
1 1
 #! /bin/sh
2
-# Wrapper for compilers which do not understand `-c -o'.
2
+# Wrapper for compilers which do not understand '-c -o'.
3 3
 
4
-scriptversion=2005-05-14.22
4
+scriptversion=2012-10-14.11; # UTC
5 5
 
6
-# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
6
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
7 7
 # Written by Tom Tromey <tromey@cygnus.com>.
8 8
 #
9 9
 # This program is free software; you can redistribute it and/or modify
... ...
@@ -17,8 +17,7 @@ scriptversion=2005-05-14.22
17 17
 # GNU General Public License for more details.
18 18
 #
19 19
 # You should have received a copy of the GNU General Public License
20
-# along with this program; if not, write to the Free Software
21
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
20
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
22 21
 
23 22
 # As a special exception to the GNU General Public License, if you
24 23
 # distribute this file as part of a program that contains a
... ...
@@ -29,21 +28,224 @@ scriptversion=2005-05-14.22
29 28
 # bugs to <bug-automake@gnu.org> or send patches to
30 29
 # <automake-patches@gnu.org>.
31 30
 
31
+nl='
32
+'
33
+
34
+# We need space, tab and new line, in precisely that order.  Quoting is
35
+# there to prevent tools from complaining about whitespace usage.
36
+IFS=" ""	$nl"
37
+
38
+file_conv=
39
+
40
+# func_file_conv build_file lazy
41
+# Convert a $build file to $host form and store it in $file
42
+# Currently only supports Windows hosts. If the determined conversion
43
+# type is listed in (the comma separated) LAZY, no conversion will
44
+# take place.
45
+func_file_conv ()
46
+{
47
+  file=$1
48
+  case $file in
49
+    / | /[!/]*) # absolute file, and not a UNC file
50
+      if test -z "$file_conv"; then
51
+	# lazily determine how to convert abs files
52
+	case `uname -s` in
53
+	  MINGW*)
54
+	    file_conv=mingw
55
+	    ;;
56
+	  CYGWIN*)
57
+	    file_conv=cygwin
58
+	    ;;
59
+	  *)
60
+	    file_conv=wine
61
+	    ;;
62
+	esac
63
+      fi
64
+      case $file_conv/,$2, in
65
+	*,$file_conv,*)
66
+	  ;;
67
+	mingw/*)
68
+	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
69
+	  ;;
70
+	cygwin/*)
71
+	  file=`cygpath -m "$file" || echo "$file"`
72
+	  ;;
73
+	wine/*)
74
+	  file=`winepath -w "$file" || echo "$file"`
75
+	  ;;
76
+      esac
77
+      ;;
78
+  esac
79
+}
80
+
81
+# func_cl_dashL linkdir
82
+# Make cl look for libraries in LINKDIR
83
+func_cl_dashL ()
84
+{
85
+  func_file_conv "$1"
86
+  if test -z "$lib_path"; then
87
+    lib_path=$file
88
+  else
89
+    lib_path="$lib_path;$file"
90
+  fi
91
+  linker_opts="$linker_opts -LIBPATH:$file"
92
+}
93
+
94
+# func_cl_dashl library
95
+# Do a library search-path lookup for cl
96
+func_cl_dashl ()
97
+{
98
+  lib=$1
99
+  found=no
100
+  save_IFS=$IFS
101
+  IFS=';'
102
+  for dir in $lib_path $LIB
103
+  do
104
+    IFS=$save_IFS
105
+    if $shared && test -f "$dir/$lib.dll.lib"; then
106
+      found=yes
107
+      lib=$dir/$lib.dll.lib
108
+      break
109
+    fi
110
+    if test -f "$dir/$lib.lib"; then
111
+      found=yes
112
+      lib=$dir/$lib.lib
113
+      break
114
+    fi
115
+    if test -f "$dir/lib$lib.a"; then
116
+      found=yes
117
+      lib=$dir/lib$lib.a
118
+      break
119
+    fi
120
+  done
121
+  IFS=$save_IFS
122
+
123
+  if test "$found" != yes; then
124
+    lib=$lib.lib
125
+  fi
126
+}
127
+
128
+# func_cl_wrapper cl arg...
129
+# Adjust compile command to suit cl
130
+func_cl_wrapper ()
131
+{
132
+  # Assume a capable shell
133
+  lib_path=
134
+  shared=:
135
+  linker_opts=
136
+  for arg
137
+  do
138
+    if test -n "$eat"; then
139
+      eat=
140
+    else
141
+      case $1 in
142
+	-o)
143
+	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
144
+	  eat=1
145
+	  case $2 in
146
+	    *.o | *.[oO][bB][jJ])
147
+	      func_file_conv "$2"
148
+	      set x "$@" -Fo"$file"
149
+	      shift
150
+	      ;;
151
+	    *)
152
+	      func_file_conv "$2"
153
+	      set x "$@" -Fe"$file"
154
+	      shift
155
+	      ;;
156
+	  esac
157
+	  ;;
158
+	-I)
159
+	  eat=1
160
+	  func_file_conv "$2" mingw
161
+	  set x "$@" -I"$file"
162
+	  shift
163
+	  ;;
164
+	-I*)
165
+	  func_file_conv "${1#-I}" mingw
166
+	  set x "$@" -I"$file"
167
+	  shift
168
+	  ;;
169
+	-l)
170
+	  eat=1
171
+	  func_cl_dashl "$2"
172
+	  set x "$@" "$lib"
173
+	  shift
174
+	  ;;
175
+	-l*)
176
+	  func_cl_dashl "${1#-l}"
177
+	  set x "$@" "$lib"
178
+	  shift
179
+	  ;;
180
+	-L)
181
+	  eat=1
182
+	  func_cl_dashL "$2"
183
+	  ;;
184
+	-L*)
185
+	  func_cl_dashL "${1#-L}"
186
+	  ;;
187
+	-static)
188
+	  shared=false
189
+	  ;;
190
+	-Wl,*)
191
+	  arg=${1#-Wl,}
192
+	  save_ifs="$IFS"; IFS=','
193
+	  for flag in $arg; do
194
+	    IFS="$save_ifs"
195
+	    linker_opts="$linker_opts $flag"
196
+	  done
197
+	  IFS="$save_ifs"
198
+	  ;;
199
+	-Xlinker)
200
+	  eat=1
201
+	  linker_opts="$linker_opts $2"
202
+	  ;;
203
+	-*)
204
+	  set x "$@" "$1"
205
+	  shift
206
+	  ;;
207
+	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
208
+	  func_file_conv "$1"
209
+	  set x "$@" -Tp"$file"
210
+	  shift
211
+	  ;;
212
+	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
213
+	  func_file_conv "$1" mingw
214
+	  set x "$@" "$file"
215
+	  shift
216
+	  ;;
217
+	*)
218
+	  set x "$@" "$1"
219
+	  shift
220
+	  ;;
221
+      esac
222
+    fi
223
+    shift
224
+  done
225
+  if test -n "$linker_opts"; then
226
+    linker_opts="-link$linker_opts"
227
+  fi
228
+  exec "$@" $linker_opts
229
+  exit 1
230
+}
231
+
232
+eat=
233
+
32 234
 case $1 in
33 235
   '')
34
-     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
236
+     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
35 237
      exit 1;
36 238
      ;;
37 239
   -h | --h*)
38 240
     cat <<\EOF
39 241
 Usage: compile [--help] [--version] PROGRAM [ARGS]
40 242
 
41
-Wrapper for compilers which do not understand `-c -o'.
42
-Remove `-o dest.o' from ARGS, run PROGRAM with the remaining
243
+Wrapper for compilers which do not understand '-c -o'.
244
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
43 245
 arguments, and rename the output as expected.
44 246
 
45 247
 If you are trying to build a whole package this is not the
46
-right script to run: please start by reading the file `INSTALL'.
248
+right script to run: please start by reading the file 'INSTALL'.
47 249
 
48 250
 Report bugs to <bug-automake@gnu.org>.
49 251
 EOF
... ...
@@ -53,11 +255,13 @@ EOF
53 255
     echo "compile $scriptversion"
54 256
     exit $?
55 257
     ;;
258
+  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
259
+    func_cl_wrapper "$@"      # Doesn't return...
260
+    ;;
56 261
 esac
57 262
 
58 263
 ofile=
59 264
 cfile=
60
-eat=
61 265
 
62 266
 for arg
63 267
 do
... ...
@@ -66,8 +270,8 @@ do
66 270
   else
67 271
     case $1 in
68 272
       -o)
69
-	# configure might choose to run compile as `compile cc -o foo foo.c'.
70
-	# So we strip `-o arg' only if arg is an object.
273
+	# configure might choose to run compile as 'compile cc -o foo foo.c'.
274
+	# So we strip '-o arg' only if arg is an object.
71 275
 	eat=1
72 276
 	case $2 in
73 277
 	  *.o | *.obj)
... ...
@@ -94,22 +298,22 @@ do
94 298
 done
95 299
 
96 300
 if test -z "$ofile" || test -z "$cfile"; then
97
-  # If no `-o' option was seen then we might have been invoked from a
301
+  # If no '-o' option was seen then we might have been invoked from a
98 302
   # pattern rule where we don't need one.  That is ok -- this is a
99 303
   # normal compilation that the losing compiler can handle.  If no
100
-  # `.c' file was seen then we are probably linking.  That is also
304
+  # '.c' file was seen then we are probably linking.  That is also
101 305
   # ok.
102 306
   exec "$@"
103 307
 fi
104 308
 
105 309
 # Name of file we expect compiler to create.
106
-cofile=`echo "$cfile" | sed -e 's|^.*/||' -e 's/\.c$/.o/'`
310
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
107 311
 
108 312
 # Create the lock directory.
109
-# Note: use `[/.-]' here to ensure that we don't use the same name
313
+# Note: use '[/\\:.-]' here to ensure that we don't use the same name
110 314
 # that we are using for the .o file.  Also, base the name on the expected
111 315
 # object file name, since that is what matters with a parallel build.
112
-lockdir=`echo "$cofile" | sed -e 's|[/.-]|_|g'`.d
316
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
113 317
 while true; do
114 318
   if mkdir "$lockdir" >/dev/null 2>&1; then
115 319
     break
... ...
@@ -124,9 +328,9 @@ trap "rmdir '$lockdir'; exit 1" 1 2 15
124 328
 ret=$?
125 329
 
126 330
 if test -f "$cofile"; then
127
-  mv "$cofile" "$ofile"
331
+  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
128 332
 elif test -f "${cofile}bj"; then
129
-  mv "${cofile}bj" "$ofile"
333
+  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
130 334
 fi
131 335
 
132 336
 rmdir "$lockdir"
... ...
@@ -138,5 +342,6 @@ exit $ret
138 342
 # eval: (add-hook 'write-file-hooks 'time-stamp)
139 343
 # time-stamp-start: "scriptversion="
140 344
 # time-stamp-format: "%:y-%02m-%02d.%02H"
141
-# time-stamp-end: "$"
345
+# time-stamp-time-zone: "UTC"
346
+# time-stamp-end: "; # UTC"
142 347
 # End:
Browse code

Reverted to r101133, along with NAMESPACE fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102487 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:40:44
Showing 1 changed files
... ...
@@ -1,9 +1,9 @@
1 1
 #! /bin/sh
2
-# Wrapper for compilers which do not understand '-c -o'.
2
+# Wrapper for compilers which do not understand `-c -o'.
3 3
 
4
-scriptversion=2012-10-14.11; # UTC
4
+scriptversion=2005-05-14.22
5 5
 
6
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
6
+# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
7 7
 # Written by Tom Tromey <tromey@cygnus.com>.
8 8
 #
9 9
 # This program is free software; you can redistribute it and/or modify
... ...
@@ -17,7 +17,8 @@ scriptversion=2012-10-14.11; # UTC
17 17
 # GNU General Public License for more details.
18 18
 #
19 19
 # You should have received a copy of the GNU General Public License
20
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
20
+# along with this program; if not, write to the Free Software
21
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
21 22
 
22 23
 # As a special exception to the GNU General Public License, if you
23 24
 # distribute this file as part of a program that contains a
... ...
@@ -28,224 +29,21 @@ scriptversion=2012-10-14.11; # UTC
28 29
 # bugs to <bug-automake@gnu.org> or send patches to
29 30
 # <automake-patches@gnu.org>.
30 31
 
31
-nl='
32
-'
33
-
34
-# We need space, tab and new line, in precisely that order.  Quoting is
35
-# there to prevent tools from complaining about whitespace usage.
36
-IFS=" ""	$nl"
37
-
38
-file_conv=
39
-
40
-# func_file_conv build_file lazy
41
-# Convert a $build file to $host form and store it in $file
42
-# Currently only supports Windows hosts. If the determined conversion
43
-# type is listed in (the comma separated) LAZY, no conversion will
44
-# take place.
45
-func_file_conv ()
46
-{
47
-  file=$1
48
-  case $file in
49
-    / | /[!/]*) # absolute file, and not a UNC file
50
-      if test -z "$file_conv"; then
51
-	# lazily determine how to convert abs files
52
-	case `uname -s` in
53
-	  MINGW*)
54
-	    file_conv=mingw
55
-	    ;;
56
-	  CYGWIN*)
57
-	    file_conv=cygwin
58
-	    ;;
59
-	  *)
60
-	    file_conv=wine
61
-	    ;;
62
-	esac
63
-      fi
64
-      case $file_conv/,$2, in
65
-	*,$file_conv,*)
66
-	  ;;
67
-	mingw/*)
68
-	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
69
-	  ;;
70
-	cygwin/*)
71
-	  file=`cygpath -m "$file" || echo "$file"`
72
-	  ;;
73
-	wine/*)
74
-	  file=`winepath -w "$file" || echo "$file"`
75
-	  ;;
76
-      esac
77
-      ;;
78
-  esac
79
-}
80
-
81
-# func_cl_dashL linkdir
82
-# Make cl look for libraries in LINKDIR
83
-func_cl_dashL ()
84
-{
85
-  func_file_conv "$1"
86
-  if test -z "$lib_path"; then
87
-    lib_path=$file
88
-  else
89
-    lib_path="$lib_path;$file"
90
-  fi
91
-  linker_opts="$linker_opts -LIBPATH:$file"
92
-}
93
-
94
-# func_cl_dashl library
95
-# Do a library search-path lookup for cl
96
-func_cl_dashl ()
97
-{
98
-  lib=$1
99
-  found=no
100
-  save_IFS=$IFS
101
-  IFS=';'
102
-  for dir in $lib_path $LIB
103
-  do
104
-    IFS=$save_IFS
105
-    if $shared && test -f "$dir/$lib.dll.lib"; then
106
-      found=yes
107
-      lib=$dir/$lib.dll.lib
108
-      break
109
-    fi
110
-    if test -f "$dir/$lib.lib"; then
111
-      found=yes
112
-      lib=$dir/$lib.lib
113
-      break
114
-    fi
115
-    if test -f "$dir/lib$lib.a"; then
116
-      found=yes
117
-      lib=$dir/lib$lib.a
118
-      break
119
-    fi
120
-  done
121
-  IFS=$save_IFS
122
-
123
-  if test "$found" != yes; then
124
-    lib=$lib.lib
125
-  fi
126
-}
127
-
128
-# func_cl_wrapper cl arg...
129
-# Adjust compile command to suit cl
130
-func_cl_wrapper ()
131
-{
132
-  # Assume a capable shell
133
-  lib_path=
134
-  shared=:
135
-  linker_opts=
136
-  for arg
137
-  do
138
-    if test -n "$eat"; then
139
-      eat=
140
-    else
141
-      case $1 in
142
-	-o)
143
-	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
144
-	  eat=1
145
-	  case $2 in
146
-	    *.o | *.[oO][bB][jJ])
147
-	      func_file_conv "$2"
148
-	      set x "$@" -Fo"$file"
149
-	      shift
150
-	      ;;
151
-	    *)
152
-	      func_file_conv "$2"
153
-	      set x "$@" -Fe"$file"
154
-	      shift
155
-	      ;;
156
-	  esac
157
-	  ;;
158
-	-I)
159
-	  eat=1
160
-	  func_file_conv "$2" mingw
161
-	  set x "$@" -I"$file"
162
-	  shift
163
-	  ;;
164
-	-I*)
165
-	  func_file_conv "${1#-I}" mingw
166
-	  set x "$@" -I"$file"
167
-	  shift
168
-	  ;;
169
-	-l)
170
-	  eat=1
171
-	  func_cl_dashl "$2"
172
-	  set x "$@" "$lib"
173
-	  shift
174
-	  ;;
175
-	-l*)
176
-	  func_cl_dashl "${1#-l}"
177
-	  set x "$@" "$lib"
178
-	  shift
179
-	  ;;
180
-	-L)
181
-	  eat=1
182
-	  func_cl_dashL "$2"
183
-	  ;;
184
-	-L*)
185
-	  func_cl_dashL "${1#-L}"
186
-	  ;;
187
-	-static)
188
-	  shared=false
189
-	  ;;
190
-	-Wl,*)
191
-	  arg=${1#-Wl,}
192
-	  save_ifs="$IFS"; IFS=','
193
-	  for flag in $arg; do
194
-	    IFS="$save_ifs"
195
-	    linker_opts="$linker_opts $flag"
196
-	  done
197
-	  IFS="$save_ifs"
198
-	  ;;
199
-	-Xlinker)
200
-	  eat=1
201
-	  linker_opts="$linker_opts $2"
202
-	  ;;
203
-	-*)
204
-	  set x "$@" "$1"
205
-	  shift
206
-	  ;;
207
-	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
208
-	  func_file_conv "$1"
209
-	  set x "$@" -Tp"$file"
210
-	  shift
211
-	  ;;
212
-	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
213
-	  func_file_conv "$1" mingw
214
-	  set x "$@" "$file"
215
-	  shift
216
-	  ;;
217
-	*)
218
-	  set x "$@" "$1"
219
-	  shift
220
-	  ;;
221
-      esac
222
-    fi
223
-    shift
224
-  done
225
-  if test -n "$linker_opts"; then
226
-    linker_opts="-link$linker_opts"
227
-  fi
228
-  exec "$@" $linker_opts
229
-  exit 1
230
-}
231
-
232
-eat=
233
-
234 32
 case $1 in
235 33
   '')
236
-     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
34
+     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
237 35
      exit 1;
238 36
      ;;
239 37
   -h | --h*)
240 38
     cat <<\EOF
241 39
 Usage: compile [--help] [--version] PROGRAM [ARGS]
242 40
 
243
-Wrapper for compilers which do not understand '-c -o'.
244
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
41
+Wrapper for compilers which do not understand `-c -o'.
42
+Remove `-o dest.o' from ARGS, run PROGRAM with the remaining
245 43
 arguments, and rename the output as expected.
246 44
 
247 45
 If you are trying to build a whole package this is not the
248
-right script to run: please start by reading the file 'INSTALL'.
46
+right script to run: please start by reading the file `INSTALL'.
249 47
 
250 48
 Report bugs to <bug-automake@gnu.org>.
251 49
 EOF
... ...
@@ -255,13 +53,11 @@ EOF
255 53
     echo "compile $scriptversion"
256 54
     exit $?
257 55
     ;;
258
-  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
259
-    func_cl_wrapper "$@"      # Doesn't return...
260
-    ;;
261 56
 esac
262 57
 
263 58
 ofile=
264 59
 cfile=
60
+eat=
265 61
 
266 62
 for arg
267 63
 do
... ...
@@ -270,8 +66,8 @@ do
270 66
   else
271 67
     case $1 in
272 68
       -o)
273
-	# configure might choose to run compile as 'compile cc -o foo foo.c'.
274
-	# So we strip '-o arg' only if arg is an object.
69
+	# configure might choose to run compile as `compile cc -o foo foo.c'.
70
+	# So we strip `-o arg' only if arg is an object.
275 71
 	eat=1
276 72
 	case $2 in
277 73
 	  *.o | *.obj)
... ...
@@ -298,22 +94,22 @@ do
298 94
 done
299 95
 
300 96
 if test -z "$ofile" || test -z "$cfile"; then
301
-  # If no '-o' option was seen then we might have been invoked from a
97
+  # If no `-o' option was seen then we might have been invoked from a
302 98
   # pattern rule where we don't need one.  That is ok -- this is a
303 99
   # normal compilation that the losing compiler can handle.  If no
304
-  # '.c' file was seen then we are probably linking.  That is also
100
+  # `.c' file was seen then we are probably linking.  That is also
305 101
   # ok.
306 102
   exec "$@"
307 103
 fi
308 104
 
309 105
 # Name of file we expect compiler to create.
310
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
106
+cofile=`echo "$cfile" | sed -e 's|^.*/||' -e 's/\.c$/.o/'`
311 107
 
312 108
 # Create the lock directory.
313
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
109
+# Note: use `[/.-]' here to ensure that we don't use the same name
314 110
 # that we are using for the .o file.  Also, base the name on the expected
315 111
 # object file name, since that is what matters with a parallel build.
316
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
112
+lockdir=`echo "$cofile" | sed -e 's|[/.-]|_|g'`.d
317 113
 while true; do
318 114
   if mkdir "$lockdir" >/dev/null 2>&1; then
319 115
     break
... ...
@@ -328,9 +124,9 @@ trap "rmdir '$lockdir'; exit 1" 1 2 15
328 124
 ret=$?
329 125
 
330 126
 if test -f "$cofile"; then
331
-  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
127
+  mv "$cofile" "$ofile"
332 128
 elif test -f "${cofile}bj"; then
333
-  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
129
+  mv "${cofile}bj" "$ofile"
334 130
 fi
335 131
 
336 132
 rmdir "$lockdir"
... ...
@@ -342,6 +138,5 @@ exit $ret
342 138
 # eval: (add-hook 'write-file-hooks 'time-stamp)
343 139
 # time-stamp-start: "scriptversion="
344 140
 # time-stamp-format: "%:y-%02m-%02d.%02H"
345
-# time-stamp-time-zone: "UTC"
346
-# time-stamp-end: "; # UTC"
141
+# time-stamp-end: "$"
347 142
 # End:
Browse code

Recent work towards supporting the new features... will revert back to a stable version immediately...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102485 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:32:10
Showing 1 changed files
... ...
@@ -3,7 +3,7 @@
3 3
 
4 4
 scriptversion=2012-10-14.11; # UTC
5 5
 
6
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
6
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
7 7
 # Written by Tom Tromey <tromey@cygnus.com>.
8 8
 #
9 9
 # This program is free software; you can redistribute it and/or modify
Browse code

update gstruct/bamtally

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@101176 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 25/03/2015 20:25:05
Showing 1 changed files
... ...
@@ -1,9 +1,9 @@
1 1
 #! /bin/sh
2
-# Wrapper for compilers which do not understand `-c -o'.
2
+# Wrapper for compilers which do not understand '-c -o'.
3 3
 
4
-scriptversion=2005-05-14.22
4
+scriptversion=2012-10-14.11; # UTC
5 5
 
6
-# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
6
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
7 7
 # Written by Tom Tromey <tromey@cygnus.com>.
8 8
 #
9 9
 # This program is free software; you can redistribute it and/or modify
... ...
@@ -17,8 +17,7 @@ scriptversion=2005-05-14.22
17 17
 # GNU General Public License for more details.
18 18
 #
19 19
 # You should have received a copy of the GNU General Public License
20
-# along with this program; if not, write to the Free Software
21
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
20
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
22 21
 
23 22
 # As a special exception to the GNU General Public License, if you
24 23
 # distribute this file as part of a program that contains a
... ...
@@ -29,21 +28,224 @@ scriptversion=2005-05-14.22
29 28
 # bugs to <bug-automake@gnu.org> or send patches to
30 29
 # <automake-patches@gnu.org>.
31 30
 
31
+nl='
32
+'
33
+
34
+# We need space, tab and new line, in precisely that order.  Quoting is
35
+# there to prevent tools from complaining about whitespace usage.
36
+IFS=" ""	$nl"
37
+
38
+file_conv=
39
+
40
+# func_file_conv build_file lazy
41
+# Convert a $build file to $host form and store it in $file
42
+# Currently only supports Windows hosts. If the determined conversion
43
+# type is listed in (the comma separated) LAZY, no conversion will
44
+# take place.
45
+func_file_conv ()
46
+{
47
+  file=$1
48
+  case $file in
49
+    / | /[!/]*) # absolute file, and not a UNC file
50
+      if test -z "$file_conv"; then
51
+	# lazily determine how to convert abs files
52
+	case `uname -s` in
53
+	  MINGW*)
54
+	    file_conv=mingw
55
+	    ;;
56
+	  CYGWIN*)
57
+	    file_conv=cygwin
58
+	    ;;
59
+	  *)
60
+	    file_conv=wine
61
+	    ;;
62
+	esac
63
+      fi
64
+      case $file_conv/,$2, in
65
+	*,$file_conv,*)
66
+	  ;;
67
+	mingw/*)
68
+	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
69
+	  ;;
70
+	cygwin/*)
71
+	  file=`cygpath -m "$file" || echo "$file"`
72
+	  ;;
73
+	wine/*)
74
+	  file=`winepath -w "$file" || echo "$file"`
75
+	  ;;
76
+      esac
77
+      ;;
78
+  esac
79
+}
80
+
81
+# func_cl_dashL linkdir
82
+# Make cl look for libraries in LINKDIR
83
+func_cl_dashL ()
84
+{
85
+  func_file_conv "$1"
86
+  if test -z "$lib_path"; then
87
+    lib_path=$file
88
+  else
89
+    lib_path="$lib_path;$file"
90
+  fi
91
+  linker_opts="$linker_opts -LIBPATH:$file"
92
+}
93
+
94
+# func_cl_dashl library
95
+# Do a library search-path lookup for cl
96
+func_cl_dashl ()
97
+{
98
+  lib=$1
99
+  found=no
100
+  save_IFS=$IFS
101
+  IFS=';'
102
+  for dir in $lib_path $LIB
103
+  do
104
+    IFS=$save_IFS
105
+    if $shared && test -f "$dir/$lib.dll.lib"; then
106
+      found=yes
107
+      lib=$dir/$lib.dll.lib
108
+      break
109
+    fi
110
+    if test -f "$dir/$lib.lib"; then
111
+      found=yes
112
+      lib=$dir/$lib.lib
113
+      break
114
+    fi
115
+    if test -f "$dir/lib$lib.a"; then
116
+      found=yes
117
+      lib=$dir/lib$lib.a
118
+      break
119
+    fi
120
+  done
121
+  IFS=$save_IFS
122
+
123
+  if test "$found" != yes; then
124
+    lib=$lib.lib
125
+  fi
126
+}
127
+
128
+# func_cl_wrapper cl arg...
129
+# Adjust compile command to suit cl
130
+func_cl_wrapper ()
131
+{
132
+  # Assume a capable shell
133
+  lib_path=
134
+  shared=:
135
+  linker_opts=
136
+  for arg
137
+  do
138
+    if test -n "$eat"; then
139
+      eat=
140
+    else
141
+      case $1 in
142
+	-o)
143
+	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
144
+	  eat=1
145
+	  case $2 in
146
+	    *.o | *.[oO][bB][jJ])
147
+	      func_file_conv "$2"
148
+	      set x "$@" -Fo"$file"
149
+	      shift
150
+	      ;;
151
+	    *)
152
+	      func_file_conv "$2"
153
+	      set x "$@" -Fe"$file"
154
+	      shift
155
+	      ;;
156
+	  esac
157
+	  ;;
158
+	-I)
159
+	  eat=1
160
+	  func_file_conv "$2" mingw
161
+	  set x "$@" -I"$file"
162
+	  shift
163
+	  ;;
164
+	-I*)
165
+	  func_file_conv "${1#-I}" mingw
166
+	  set x "$@" -I"$file"
167
+	  shift
168
+	  ;;
169
+	-l)
170
+	  eat=1
171
+	  func_cl_dashl "$2"
172
+	  set x "$@" "$lib"
173
+	  shift
174
+	  ;;
175
+	-l*)
176
+	  func_cl_dashl "${1#-l}"
177
+	  set x "$@" "$lib"
178
+	  shift
179
+	  ;;
180
+	-L)
181
+	  eat=1
182
+	  func_cl_dashL "$2"
183
+	  ;;
184
+	-L*)
185
+	  func_cl_dashL "${1#-L}"
186
+	  ;;
187
+	-static)
188
+	  shared=false
189
+	  ;;
190
+	-Wl,*)
191
+	  arg=${1#-Wl,}
192
+	  save_ifs="$IFS"; IFS=','
193
+	  for flag in $arg; do
194
+	    IFS="$save_ifs"
195
+	    linker_opts="$linker_opts $flag"
196
+	  done
197
+	  IFS="$save_ifs"
198
+	  ;;
199
+	-Xlinker)
200
+	  eat=1
201
+	  linker_opts="$linker_opts $2"
202
+	  ;;
203
+	-*)
204
+	  set x "$@" "$1"
205
+	  shift
206
+	  ;;
207
+	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
208
+	  func_file_conv "$1"
209
+	  set x "$@" -Tp"$file"
210
+	  shift
211
+	  ;;
212
+	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
213
+	  func_file_conv "$1" mingw
214
+	  set x "$@" "$file"
215
+	  shift
216
+	  ;;
217
+	*)
218
+	  set x "$@" "$1"
219
+	  shift
220
+	  ;;
221
+      esac
222
+    fi
223
+    shift
224
+  done
225
+  if test -n "$linker_opts"; then
226
+    linker_opts="-link$linker_opts"
227
+  fi
228
+  exec "$@" $linker_opts
229
+  exit 1
230
+}
231
+
232
+eat=
233
+
32 234
 case $1 in
33 235
   '')
34
-     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
236
+     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
35 237
      exit 1;
36 238
      ;;
37 239
   -h | --h*)
38 240
     cat <<\EOF
39 241
 Usage: compile [--help] [-