Attachment 'sage-4.1.1.patch'
Download 1 local/bin/sh 000755 001752 001752 00000000000 11226071440 017141 2/usr/local/bin/bash ustar 00peter peter 000000 000000 local/bin/make 000755 001752 001752 00000000000 11226071440 017613 2/usr/local/bin/gmake ustar 00peter peter 000000 000000 local/bin/gfortran 000755 001752 001752 00000000000 11236642376 021442 2/usr/local/bin/gfortran43 ustar 00peter peter 000000 000000 local/bin/gcc 000755 001752 001752 00000000000 11226071440 017251 2/usr/local/bin/gcc43 ustar 00peter peter 000000 000000 local/bin/g++ 000755 001752 001752 00000000000 11226071440 016711 2/usr/local/bin/g++43 ustar 00peter peter 000000 000000 spkg/base/sage-spkg 000755 001752 001752 00000024077 11237740730 015065 0 ustar 00peter peter 000000 000000 #!/usr/bin/env bash
2
3 # William Stein, 2005-12-20 -- removed "m" option from tar,
4 # which was seriously confusing the build process on some
5 # (too fast?) machines, especially for mpfr.
6
7 #######################################################
8 # Install a SAGE package. This script is
9 # typically invoked by giving the command
10 # sage -i <package name>
11 #
12 # A package may assume that the following environment
13 # variables are defined:
14 #
15 # SAGE_ROOT -- root directory of sage install
16 # SAGE_LOCAL -- $SAGE_ROOT/local
17 # SAGE_DATA -- $SAGE_ROOT/data
18 # LIBRARY_PATH, PYTHONPATH, LD_LIBRARY_PATH, DYLD_LIBRARY_PATH
19 # CC, CXX, CFLAGS, CXXFLAGS, LDFLAGS, MAKE
20 #
21 # Your package script should try to build using the giving CC, CXX,
22 # CFLAGS, MAKE, etc, via a file spkg-install in your script.
23 #
24 # This script does the following:
25 #
26 # 1. Set environment variables (by calling sage-env)
27 # 2. Decompress package into a build directory
28 # 3. Run the script in the package called spkg-install
29 # 4. Return error 1 if anything goes wrong.
30 #
31 #######################################################
32
33 mymkdir()
34 {
35 if [ ! -d $1 ]; then
36 mkdir $1
37 fi
38 }
39
40 # The following sets environment variables for building
41 # packages. (Using dot suggested by W. Cheung.)
42
43 . "$SAGE_ROOT/local/bin/sage-env"
44
45 cd "$SAGE_PACKAGES"
46
47 if [ $# -eq 0 ]; then
48 echo "Currently installed packages:"
49 /bin/ls -1 "$SAGE_PACKAGES/installed/"
50 exit 0
51 fi
52
53
54 cd "$SAGE_PACKAGES"
55 mymkdir "$BUILD"
56 mymkdir installed
57 cd "$BUILD"
58 mymkdir old
59
60 # the following two options are mutually exclusive -- i.e., you
61 # can give only one.
62
63 INFO=0
64 if [ $1 = '-info' ]; then
65 INFO=1
66 shift
67 fi
68
69 FORCE=0
70 if [ $1 = '-f' ]; then
71 FORCE=1
72 shift
73 fi
74 export FORCE
75
76 DELETE_TMP=0
77 if [ $1 = '-s' -o $1 = '-m' ]; then
78 DELETE_TMP=0
79 shift
80 fi
81
82 INSTALLED="$SAGE_PACKAGES/installed/"
83 PKG_NAME=`echo "$1" | sed -e "s/\.spkg$//"`
84 PKG_NAME=`basename "$PKG_NAME"`
85 PKG_SRC="$1"
86 PKG_BASE=`echo "$PKG_NAME" | sed -e "s/-.*//"`
87 # check if noclobber is set and warn about it
88 if [ $PKG_SRC == "noclobber" ]; then
89 echo "***********************************************************"
90 echo "* WARNING WARNING WARNING WARNING WARNING WARNING WARNING *"
91 echo "* *"
92 echo "* noclobber is set in .bashrc and/or .bash_profile - you *"
93 echo "* should consider disabling it. The Sage install should *"
94 echo "* continue to work, so don't worry about it too much. *"
95 echo "* *"
96 echo "* WARNING WARNING WARNING WARNING WARNING WARNING WARNING *"
97 echo "***********************************************************"
98 exit 0
99 fi
100
101 if [ ! -f "$PKG_SRC" ]; then
102 if [ -f "$SAGE_PACKAGES/standard/$PKG_NAME.spkg" ]; then
103 PKG_SRC="$SAGE_PACKAGES/standard/$PKG_NAME.spkg"
104 else
105 if [ -f "$SAGE_PACKAGES/optional/$PKG_NAME.spkg" ]; then
106 PKG_SRC="$SAGE_PACKAGES/optional/$PKG_NAME.spkg"
107 fi
108 fi
109 fi
110
111 if [ $INFO -ne 0 ]; then
112 if [ ! -f "$PKG_SRC" ]; then
113 echo "Package $PKG_NAME not found"
114 fi
115 bunzip2 -c "$PKG_SRC" 2>/dev/null | tar Ofx - $PKG_NAME/SAGE.txt 2>/dev/null
116 if [ $? -ne 0 ]; then
117 tar Ofx "$PKG_SRC" "$PKG_NAME/SAGE.txt" 2>/dev/null
118 fi
119 echo ""
120 if [ $? -ne 0 ]; then
121 echo "No file SAGE.txt in $PKG_NAME"
122 exit 1
123 fi
124 exit 0
125 fi
126
127 echo "$PKG_NAME"
128
129 echo "Machine:"
130 uname -a
131
132 if [ -f "$INSTALLED/$PKG_NAME" -a $FORCE -eq 0 ]; then
133 echo "sage: $1 is already installed"
134 touch "$INSTALLED/$PKG_NAME"
135 exit 0
136 fi
137
138 cd "$SAGE_PACKAGES/build"
139
140 if [ $DELETE_TMP -eq 1 ]; then
141 echo "Deleting directories from past builds of previous/current versions of $PKG_NAME"
142 # Make triply sure that we are in the build directory before doing
143 # a scary "rm -rf".
144 cd "$SAGE_PACKAGES/build"
145 if [ $? -ne 0 ]; then
146 echo "Unable to find build directory."
147 else
148 rm -rf "$PKG_BASE-"*
149 fi
150 else
151 echo "Moving directories from past builds of previous/current versions of $PKG_NAME to build/old"
152 mv -f "$PKG_BASE-"* old/ 2>/dev/null
153 fi
154
155 if [ ! -f "$PKG_SRC" ]; then
156
157 echo "$0: file $PKG_NAME does not exist"
158 echo "Attempting to download it."
159 CUR=`pwd`
160 cd "$SAGE_PACKAGES"
161 if [ ! -d optional ]; then
162 $MKDIR optional
163 fi
164 cd optional
165 sage-download_package "$1"
166 if [ ! -f "$PKG_NAME.spkg" ]; then
167 echo "sage: Failed to download package $PKG_NAME from $SAGE_SERVER"
168 exit 1
169 fi
170 PKG_SRC="`pwd`/$PKG_NAME.spkg"
171 cd "$CUR"
172 fi
173
174 # * The -i option below to ignore checksum errors, since
175 # I've had problems with this on Solaris.
176 # * The m option avoids clock skew problems.
177
178 echo "Extracting package $PKG_SRC ..."
179 ls -l "$PKG_SRC"
180
181 if [ -d "$PKG_NAME" ]; then
182 echo "Removing previous version."
183 rm -rf "$PKG_NAME"
184 fi
185
186 bunzip2 -c "$PKG_SRC" 2>/dev/null | tar fxv - 2>/dev/null
187 if [ ! -d "$PKG_NAME" ]; then
188 tar fxv "$PKG_SRC"
189 fi
190 echo "Finished extraction"
191
192 if [ ! -d "$PKG_NAME" ]; then
193 echo "sage: After decompressing the directory $PKG_NAME does not exist"
194 echo "This means that the corresponding .spkg needs to be downloaded"
195 echo "again."
196 sage-download_package "$PKG_NAME"
197 echo `pwd`
198 bunzip2 -c "$PKG_NAME.spkg" | tar fxv -
199 if [ ! -d "$PKG_NAME.spkg" ]; then
200 tar fxv "$PKG_NAME.spkg"
201 fi
202 if [ ! -d "$PKG_NAME" ]; then
203 echo "Second download resulted in a corrupted package."
204 exit 1
205 fi
206 fi
207
208 if [ -f "$SAGE_PACKAGES/patches/$PKG_NAME.patch" ]; then
209 echo "Applying local patches for $PKG_NAME"
210 if ! patch -p0 < "$SAGE_PACKAGES/patches/$PKG_NAME.patch"; then
211 echo "Patching failed"
212 exit 1
213 fi
214 fi
215
216 cd "$PKG_NAME"
217 if [ ! -f spkg-install ]; then
218 echo "#!/usr/bin/env bash" > spkg-install
219 echo "" >> spkg-install
220 if [ -f setup.py ]; then
221 echo "python setup.py install" >> spkg-install
222 else
223 if [ -f configure ]; then
224 echo "./configure --prefix=\$SAGE_ROOT/local/" >> spkg-install
225 echo "make" >> spkg-install
226 echo "make install" >> spkg-install
227 else
228 echo "There is no spkg-install script, no setup.py, and no configure script,"
229 echo "so I do not know how to install $PKG_SRC."
230 exit 1
231 fi
232 fi
233 fi
234
235 chmod +x spkg-install
236
237 # this is just wrong... (so don't do it)
238 #echo "TOUCHING"
239 #touch * */* */*/* */*/*/* 1>/dev/null 2>/dev/null
240
241 echo "****************************************************"
242 echo "Host system"
243 echo "uname -a:"
244 uname -a
245 if [ $? -ne 0 ]; then
246 echo "Unable to determine host system information."
247 fi
248 echo "****************************************************"
249
250 echo "****************************************************"
251 echo "CC Version"
252 echo "$CC -v"
253 $CC -v
254 if [ $? -ne 0 ]; then
255 echo "Unable to determine C compiler version."
256 fi
257 echo "****************************************************"
258
259 BASEDIR=`pwd`
260 if [ -n "$DEBIAN_RELEASE" ]; then
261 SAGE_CHECK=''
262 if [ -e ./spkg-debian ]; then
263 time ./spkg-debian
264 else
265 time sage-build-debian $BASEDIR
266 fi
267 else
268 time ./spkg-install
269 fi
270
271 if [ $? -eq 0 ]; then
272 cd $INSTALLED
273 # TURNED OFF: Remove all old packages with the same name up to the first "-":
274 # rm -f $PKG_BASE-*
275
276 # Mark that the new package has been installed.
277 # This file will eventually be a certificate like in OS X.
278 echo "PACKAGE NAME: $PKG_NAME" > "$PKG_NAME"
279 echo "INSTALL DATE: `date`" >> "$PKG_NAME"
280 echo "UNAME: `uname -a`" >> "$PKG_NAME"
281 echo "Sage VERSION: `grep Sage $SAGE_LOCAL/bin/sage-banner`" >> "$PKG_NAME"
282 echo "Successfully installed $PKG_NAME"
283
284 cd $BASEDIR
285 if [ "$SAGE_CHECK" != "" -a -f spkg-check ]; then
286 echo "Running the test suite."
287 chmod +x spkg-check
288 ./spkg-check
289 if [ $? -ne 0 ]; then
290 echo "*************************************"
291 echo "Error testing package ** $PKG_NAME **"
292 echo "*************************************"
293 rm -f $SAGE_ROOT/spkg/installed/$PKG_NAME
294 echo "sage: An error occurred while testing $PKG_NAME"
295 echo "Please email sage-devel http://groups.google.com/group/sage-devel"
296 echo "explaining the problem and send the relevant part of"
297 echo "of $SAGE_ROOT/install.log. Describe your computer, operating system, etc."
298 echo "If you want to try to fix the problem, yourself *don't* just cd to"
299 echo "`pwd` and type 'make check' or whatever is appropriate."
300 echo "Instead type \"$SAGE_ROOT/sage -sh\""
301 echo "in order to set all environment variables correctly, then cd to"
302 echo "`pwd`"
303 echo "(When you are done debugging, you can type \"exit\" to leave the"
304 echo "subshell.)"
305 exit 1
306 else
307 echo "TEST SUITE: passed" >> "$PKG_NAME"
308 fi
309 fi
310
311
312 # Delete the temporary build directory if required.
313 if [ $DELETE_TMP -eq 1 ]; then
314 echo "Now cleaning up tmp files."
315 if [ -d "$SAGE_PACKAGES/build/$PKG_NAME" ]; then
316 # the if is there only to avoid the possibility of a weird bug.
317 rm -rf "$SAGE_PACKAGES/build/$PKG_NAME"
318 fi
319 else
320 echo "You can safely delete the temporary build directory"
321 echo "$SAGE_PACKAGES/build/$PKG_NAME"
322 fi
323
324 else
325
326 echo "sage: An error occurred while installing $PKG_NAME"
327 echo "Please email sage-devel http://groups.google.com/group/sage-devel"
328 echo "explaining the problem and send the relevant part of"
329 echo "of $SAGE_ROOT/install.log. Describe your computer, operating system, etc."
330 echo "If you want to try to fix the problem, yourself *don't* just cd to"
331 echo "`pwd` and type 'make'."
332 echo "Instead type \"$SAGE_ROOT/sage -sh\""
333 echo "in order to set all environment variables correctly, then cd to"
334 echo "`pwd`"
335 echo "(When you are done debugging, you can type \"exit\" to leave the"
336 echo "subshell.)"
337 exit 1
338 fi
339
340
341 echo "Making Sage/Python scripts relocatable..."
342
343 cd "$SAGE_LOCAL"/bin
344 ./sage-make_relative
345
346 echo "Finished installing $PKG_NAME.spkg"
347
348 # It's OK if they above fails -- in fact it will until Python
349 # itself gets installed. That's fine.
350 exit 0
351 spkg/patches/ 000755 001752 001752 00000000000 11243334664 013763 5 ustar 00peter peter 000000 000000 spkg/patches/base.patch 000644 001752 001752 00000000730 11225763755 015725 0 ustar 00peter peter 000000 000000 --- spkg/base/sage-spkg~ 2009-02-21 20:38:33.000000000 +1100
352 +++ spkg/base/sage-spkg 2009-03-01 07:51:32.465298061 +1100
353 @@ -205,6 +205,14 @@
354 fi
355 fi
356
357 +if [ -f "$SAGE_PACKAGES/patches/$PKG_NAME.patch" ]; then
358 + echo "Applying local patches for $PKG_NAME"
359 + if ! patch -p0 < "$SAGE_PACKAGES/patches/$PKG_NAME.patch"; then
360 + echo "Patching failed"
361 + exit 1
362 + fi
363 +fi
364 +
365 cd "$PKG_NAME"
366 if [ ! -f spkg-install ]; then
367 echo "#!/usr/bin/env bash" > spkg-install
368 spkg/patches/r-2.6.1.p23.patch 000644 001752 001752 00000002410 11237006537 016305 0 ustar 00peter peter 000000 000000 --- r-2.6.1.p23/spkg-install~ 2009-01-20 21:22:33.000000000 +1100
369 +++ r-2.6.1.p23/spkg-install 2009-03-20 05:46:02.702566714 +1100
370 @@ -21,7 +21,7 @@
371 CUR=`pwd`
372
373 # set CPPFLAGS so that Sage's readline is picked up
374 -CPPFLAGS=-I"$SAGE_LOCAL"/inlcude; export CPPFLAGS
375 +CPPFLAGS="-I$SAGE_LOCAL/include $CPPFLAGS"; export CPPFLAGS
376
377 # copy an R file that has corrected R includes, i.e. <foo.h> vs. "foo.h"
378 cp patches/sys-std.c src/src/unix/sys-std.c
379 @@ -74,8 +74,17 @@
380
381 # These flags are *critical* so that R will be built against Sage's
382 # copy of readline and ATLAS.
383 -CFLAGS="-I$SAGE_LOCAL/include -L$SAGE_LOCAL/lib/ "$CFLAGS; export CFLAGS
384 -LDFLAGS="-L$SAGE_LOCAL/lib/ "$LDFLAGS; export LDFLAGS
385 +CFLAGS="-I$SAGE_LOCAL/include -L$SAGE_LOCAL/lib/ $CFLAGS"; export CFLAGS
386 +LDFLAGS="-L$SAGE_LOCAL/lib/ $LDFLAGS"; export LDFLAGS
387
388 +# FreeBSD needs the path to libiconv to be explicitly specified. In theory,
389 +# --with-libiconv-prefix should work but configure script is broken and
390 +# ignores that path when looking for libiconv. Hard-wire via xxFLAGS.
391 +if [ `uname` = "FreeBSD" ]; then
392 + CPPFLAGS="$CPPFLAGS -I/usr/local/include"
393 + CFLAGS="$CFLAGS -I/usr/local/include"
394 + LDFLAGS="$LDFLAGS -L/usr/local/lib"
395 +fi
396 +
397 # do not build recommended packages for now, for speed.
398
399 spkg/patches/matplotlib-0.98.5.3rc0-svn6910.p4.patch 000644 001752 001752 00000004044 11236752717 022135 0 ustar 00peter peter 000000 000000 --- matplotlib-0.98.5.3rc0-svn6910.p4/patches/setupext.py~ 2009-03-15 17:24:10.279608339 +1100
400 +++ matplotlib-0.98.5.3rc0-svn6910.p4/patches/setupext.py 2009-03-15 21:52:55.397113345 +1100
401 @@ -45,6 +45,7 @@
402 import re
403 import subprocess
404 ### FOR SAGE
405 +sage_base = os.environ['SAGE_LOCAL']
406 sage_inc = os.environ['SAGE_LOCAL'] + '/include/'
407 sage_lib = os.environ['SAGE_LOCAL'] + '/lib/'
408
409 @@ -57,6 +58,8 @@
410 'freebsd4' : ['/usr/local', '/usr'],
411 'freebsd5' : ['/usr/local', '/usr'],
412 'freebsd6' : ['/usr/local', '/usr'],
413 + 'freebsd7' : [sage_base, '/usr/local', '/usr'],
414 + 'freebsd8' : [sage_base, '/usr/local', '/usr'],
415 'sunos5' : [os.getenv('MPLIB_BASE') or '/usr/local',],
416 'gnukfreebsd5' : ['/usr/local', '/usr'],
417 'gnukfreebsd6' : ['/usr/local', '/usr'],
418 --- matplotlib-0.98.5.3rc0-svn6910.p4/src/ttconv/pprdrv.h~ 2008-05-08 05:41:26.000000000 +1000
419 +++ matplotlib-0.98.5.3rc0-svn6910.p4/src/ttconv/pprdrv.h 2009-03-19 06:00:07.875942989 +1100
420 @@ -21,6 +21,7 @@
421
422 #include <vector>
423 #include <cassert>
424 +#undef putchar /* gcc43 is broken */
425
426 /*
427 * Encapsulates all of the output to write to an arbitrary output
428 --- matplotlib-0.98.5.3rc0-svn6910.p4/src/ttconv/truetype.h~ 2008-05-02 04:24:54.000000000 +1000
429 +++ matplotlib-0.98.5.3rc0-svn6910.p4/src/ttconv/truetype.h 2009-03-19 20:13:28.247298109 +1100
430 @@ -5,6 +5,7 @@
431 */
432
433 #include <stdio.h>
434 +#undef putchar /* Broken g++43 */
435
436 /*
437 ** ~ppr/src/include/typetype.h
438 --- matplotlib-0.98.5.3rc0-svn6910.p4/src/lib/matplotlib/afm.py~ 2008-10-05 21:14:42.000000000 +1100
439 +++ matplotlib-0.98.5.3rc0-svn6910.p4/src/lib/matplotlib/afm.py 2009-03-29 08:16:04.656668429 +1100
440 @@ -165,7 +165,7 @@
441 num = _to_int(vals[0].split()[1])
442 wx = _to_float(vals[1].split()[1])
443 name = vals[2].split()[1]
444 - bbox = _to_list_of_ints(vals[3][2:])
445 + bbox = _to_list_of_floats(vals[3][2:])
446 # Workaround: If the character name is 'Euro', give it the corresponding
447 # character code, according to WinAnsiEncoding (see PDF Reference).
448 if name == 'Euro':
449 spkg/patches/sage-4.1.1.patch 000644 001752 001752 00000011111 11243354646 016357 0 ustar 00peter peter 000000 000000 --- sage-4.1.1/sage/misc/freebsd_memory_usage.c.orig 2009-08-13 16:35:40.000000000 +1000
450 +++ sage-4.1.1/sage/misc/freebsd_memory_usage.c 2009-08-13 16:36:24.000000000 +1000
451 @@ -0,0 +1,27 @@
452 +#include <sys/types.h>
453 +#include <fcntl.h>
454 +#include <kvm.h>
455 +#include <limits.h> /* for _POSIX2_LINE_MAX */
456 +#include <stdio.h>
457 +#include <unistd.h>
458 +
459 +/* Return virtual size of current process in bytes */
460 +unsigned long long freebsd_virtual_size()
461 +{
462 + static kvm_t *kvm;
463 + chat errbuf[_POSIX2_LINE_MAX];
464 + struct kinfo_proc *ki;
465 + int cnt;
466 +
467 + if (!kvm) {
468 + kvm = kvm_open(NULL, "/dev/null", NULL, O_RDONLY, errbuf);
469 + if (!kvm)
470 + return 0; /* Don't report errors */
471 + }
472 +
473 + ki = kvm_procs(kvm, KERN_PROC_PID, getpid(), &cnt);
474 + if (!ki)
475 + return 0;
476 +
477 + return ki_size
478 +}
479 --- sage-4.1.1/sage/misc/freebsd_memory_usage.h.orig 2009-08-13 16:35:40.000000000 +1000
480 +++ sage-4.1.1/sage/misc/freebsd_memory_usage.h 2009-08-13 16:37:31.000000000 +1000
481 @@ -0,0 +1,2 @@
482 +/* Return virtual size of current process in bytes */
483 +unsigned long long freebsd_virtual_size(void);
484 --- sage-4.1.1/sage/misc/freebsd_utilities.pyx.orig 2009-08-13 16:35:40.000000000 +1000
485 +++ sage-4.1.1/sage/misc/freebsd_utilities.pyx 2009-08-13 16:38:38.000000000 +1000
486 @@ -0,0 +1,30 @@
487 +# freebsd_utilities extension module built only on FreeBSD (see end of module_list.py)
488 +
489 +cdef extern from "freebsd_memory_usage.h":
490 + cdef unsigned long long freebsd_virtual_size()
491 +
492 +def freebsd_memory_usage():
493 + r"""
494 + On Freebsd, returns the virtual size of the process in bytes.
495 + This will match what "top" reports as the VSIZE.
496 + Raises on all other platforms
497 +
498 + EXAMPLES
499 + sage: uname = os.uname()
500 + sage: if uname[0] == 'FreeBSD':
501 + ... from sage.misc.freebsd_utilities import freebsd_memory_usage
502 + ... memory_usage = freebsd_memory_usage()
503 +
504 + sage: uname = os.uname()
505 + sage: if uname[0] != 'FreeBSD':
506 + ... try:
507 + ... from sage.misc.freebsd_utilities import freebsd_memory_usage
508 + ... memory_usage = freebsd_memory_usage()
509 + ... print "doctest failure!"
510 + ... print "freebsd_memory_usage() not implemented on platform %s"%uname[0]
511 + ... except ImportError:
512 + ... pass
513 +
514 +
515 + """
516 + return freebsd_virtual_size()
517 --- sage-4.1.1/sage/combinat/partitions_c.cc.orig 2009-08-01 07:45:19.000000000 +1000
518 +++ sage-4.1.1/sage/combinat/partitions_c.cc 2009-08-11 19:06:52.000000000 +1000
519 @@ -94,6 +94,11 @@
520 extern "C" long double coshl (long double);
521 extern "C" long double sinhl (long double);
522 #endif
523 +/* FreeBSD pre-8.x doesn't have sqrtl() et al. Hack around it for now
524 + * since this sage code will be changed shortly */
525 +#if defined(__FreeBSD__) && __FreeBSD__ < 8
526 +#define sqrtl(x) sqrt(x)
527 +#endif
528
529
530
531 --- sage-4.1.1/sage/ext/fast_eval.pyx.orig 2009-08-06 02:11:12.000000000 +1000
532 +++ sage-4.1.1/sage/ext/fast_eval.pyx 2009-08-11 19:06:52.000000000 +1000
533 @@ -127,13 +127,20 @@
534 double exp(double)
535 double log(double)
536 double log10(double)
537 - double log2_ "log2"(double)
538 +
539 +IF UNAME_SYSNAME != "FreeBSD":
540 + cdef extern from "math.h":
541 + double log2_ "log2"(double)
542
543
544 # This is only needed on Cygwin since log2 is a macro.
545 # If we don't do this the cygwin GCC gets very confused.
546 -cdef inline double log2(double x):
547 - return log2_(x)
548 +IF UNAME_SYSNAME != "FreeBSD":
549 + cdef inline double log2(double x):
550 + return log2_(x)
551 +ELSE:
552 + cdef inline double log2(double x):
553 + return 1.442695040888963407359924681*log(x)
554
555 cdef extern from *:
556 void* memcpy(void* dst, void* src, size_t len)
557 --- sage-4.1.1/module_list.py.orig 2009-08-01 08:46:13.000000000 +1000
558 +++ sage-4.1.1/module_list.py 2009-08-14 05:55:29.000000000 +1000
559 @@ -1325,8 +1325,8 @@
560 ]
561
562
563 -# Only include darwin_utilities on OS_X >= 10.5
564 UNAME = os.uname()
565 +# Only include darwin_utilities on OS_X >= 10.5
566 if UNAME[0] == "Darwin" and not UNAME[2].startswith('8.'):
567 ext_modules.append(
568 Extension('sage.misc.darwin_utilities',
569 @@ -1334,5 +1334,14 @@
570 'sage/misc/darwin_utilities.pyx'],
571 depends = ['sage/misc/darwin_memory_usage.h'])
572 )
573 -
574 +
575 +# Only include freebsd_utilities on FreeBSD
576 +if UNAME[0] == "FreeBSD":
577 + ext_modules.append(
578 + Extension('sage.misc.freebsd_utilities',
579 + sources = ['sage/misc/freebsd_memory_usage.c',
580 + 'sage/misc/freebsd_utilities.pyx'],
581 + depends = ['sage/misc/freebsd_memory_usage.h'],
582 + libraries = ["kvm"])
583 + )
584
585 spkg/patches/numpy-1.3.0.p1.patch 000644 001752 001752 00000002242 11237737452 017135 0 ustar 00peter peter 000000 000000 --- numpy-1.3.0.p1/patches/__init__.py~ 2008-09-26 14:02:13.000000000 +1000
586 +++ numpy-1.3.0.p1/patches/__init__.py 2009-03-09 21:38:51.369170316 +1100
587 @@ -686,6 +686,7 @@
588 ('linux.*', ('sage_fortran','gnu','intel','lahey','pg','absoft','nag','vast','compaq',
589 'intele','intelem','gnu95','g95')),
590 ('darwin.*', ('sage_fortran','nag', 'absoft', 'ibm', 'intel', 'gnu', 'gnu95', 'g95')),
591 + ('freebsd.*', ('sage_fortran','gnu','gnu95','g95')),
592 ('sunos.*', ('sage_fortran','sun','gnu','gnu95','g95')),
593 ('irix.*', ('mips','gnu','gnu95',)),
594 ('aix.*', ('ibm','gnu','gnu95',)),
595 --- numpy-1.3.0.p1/src/numpy/distutils/system_info.py~ 2008-09-26 09:10:02.000000000 +1000
596 +++ numpy-1.3.0.p1/src/numpy/distutils/system_info.py 2009-03-11 05:21:41.081498204 +1100
597 @@ -853,12 +853,8 @@
598 section = 'atlas'
599 dir_env_var = 'ATLAS'
600 _lib_names = ['f77blas','cblas']
601 - if sys.platform[:7]=='freebsd':
602 - _lib_atlas = ['atlas_r']
603 - _lib_lapack = ['alapack_r']
604 - else:
605 - _lib_atlas = ['atlas']
606 - _lib_lapack = ['lapack']
607 + _lib_atlas = ['atlas']
608 + _lib_lapack = ['lapack']
609
610 notfounderror = AtlasNotFoundError
611
612 spkg/patches/atlas-3.8.3.p7.patch 000644 001752 001752 00000002224 11243332630 017073 0 ustar 00peter peter 000000 000000 --- atlas-3.8.3.p7/src/CONFIG/src/SpewMakeInc.c~ 2009-02-19 05:47:37.000000000 +1100
613 +++ atlas-3.8.3.p7/src/CONFIG/src/SpewMakeInc.c 2009-03-01 16:24:42.131861605 +1100
614 @@ -664,6 +664,8 @@
615 fprintf(fpout, " -melf_i386");
616 else if (ptrbits == 64)
617 fprintf(fpout, " -melf_x86_64");
618 + if (OS == OSFreeBSD)
619 + fprintf(fpout, "_fbsd");
620 }
621 fprintf(fpout, "\n F77SYSLIB = %s\n", f77lib ? f77lib : "");
622 fprintf(fpout, " BC = $(ICC)\n");
623 --- atlas-3.8.3.p7/make_correct_shared.sh.orig 2009-02-03 07:22:04.000000000 +1100
624 +++ atlas-3.8.3.p7/make_correct_shared.sh 2009-03-09 20:40:10.327469958 +1100
625 @@ -26,10 +26,10 @@
626
627
628
629 -if [ `uname` = "Linux" ]; then
630 +if [ `uname` = "Linux" -o `uname` = "FreeBSD" ]; then
631 if [ `./fortran_type.pl` = "g95" ]; then
632 cd "$SAGE_LOCAL"/lib
633 lapack_command="ld -L"$f95_dir" -L"$SAGE_LOCAL"/lib -shared -soname liblapack.so -o liblapack.so --whole-archive liblapack.a --no-whole-archive -lc -lm -lf95"
634 f77blas_command="ld -L"$f95_dir" -L"$SAGE_LOCAL"/lib -shared -soname libf77blas.so -o libf77blas.so --whole-archive libf77blas.a --no-whole-archive -lc -lm -lf95"
635
636 echo $lapack_command
637 spkg/patches/sage_scripts-4.1.1.patch 000644 001752 001752 00000001154 11243332731 020123 0 ustar 00peter peter 000000 000000 --- sage_scripts-4.1.1/sage-spkg~ 2009-02-21 20:38:33.000000000 +1100
638 +++ sage_scripts-4.1.1/sage-spkg 2009-03-01 07:51:32.465298061 +1100
639 @@ -73,7 +73,7 @@
640 fi
641 export FORCE
642
643 -DELETE_TMP=1
644 +DELETE_TMP=0
645 if [ $1 = '-s' -o $1 = '-m' ]; then
646 DELETE_TMP=0
647 shift
648 @@ -205,6 +205,14 @@
649 fi
650 fi
651
652 +if [ -f "$SAGE_PACKAGES/patches/$PKG_NAME.patch" ]; then
653 + echo "Applying local patches for $PKG_NAME"
654 + if ! patch -p0 < "$SAGE_PACKAGES/patches/$PKG_NAME.patch"; then
655 + echo "Patching failed"
656 + exit 1
657 + fi
658 +fi
659 +
660 cd "$PKG_NAME"
661 if [ ! -f spkg-install ]; then
662 echo "#!/usr/bin/env bash" > spkg-install
663
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