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Update PolyBoRi to upstream release 0.7-1 #11261

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alexanderdreyer mannequin opened this issue Apr 27, 2011 · 36 comments
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Update PolyBoRi to upstream release 0.7-1 #11261

alexanderdreyer mannequin opened this issue Apr 27, 2011 · 36 comments
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c: packages: standard p: major / 3 t: enhancement
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sage-4.7.2

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alexanderdreyer mannequin commented Apr 27, 2011

There was a small bugfix release of PolyBoRi.

Perhaps we can revert #11019.

Current spkg:

Upstream: None of the above - read trac for reasoning.

CC: Martin Albrecht @sagetrac-PolyBoRi @burcin

Component: packages: standard

Author: Alexander Dreyer

Reviewer: Burcin Erocal, François Bissey, Karl-Dieter Crisman

Merged: sage-4.7.2.alpha1

Issue created by migration from https://trac.sagemath.org/ticket/11261
@alexanderdreyer alexanderdreyer mannequin added this to the sage-4.7.1 milestone Apr 27, 2011
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alexanderdreyer mannequin commented Apr 29, 2011

comment:2

The package can be reviewed (independently of reverting #11019).

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alexanderdreyer mannequin commented Apr 29, 2011

comment:3

I added a small patch, that makes PolyBoRi compatible with upcoming M4RI release: http://boxen.math.washington.edu/home/dreyer/spkg/polybori-0.7.1.p1.spkg

It also fixed the issue that the while site-packages directory was recompiled.
(Both backported from upcoming PolyBoRi 0.8.)

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kiwifb commented May 12, 2011

comment:4

Probably not the proper place to report this but I have tried to compile polybori against m4ri-20100817 and it doesn't work:

gcc -o Cudd/util/pathsearch.os -c -O1 -march=native -pipe -ggdb -fPIC -DNDEBUG -DHAVE_GD -DHAVE_TR1_UNORDERED_MAP -DPACKED -DHAVE_M4RI -DHAVE_GD -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=8 -DHAVE_IEEE_754 -DBSD -I/usr/include/python2.7 -Ipolybori/include -ICudd/obj -ICudd/util -ICudd/cudd -ICudd/mtr -ICudd/st -ICudd/epd Cudd/util/pathsearch.c
In file included from PyPolyBoRi/main_wrapper.cc:25:0:
/usr/include/m4ri/packedmatrix.h:75:3: error: 'mmb_t' does not name a type
/usr/include/m4ri/packedmatrix.h:105:3: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h: In function 'void mzd_row_swap(mzd_t*, size_t, size_t)':
/usr/include/m4ri/packedmatrix.h:174:3: error: 'word' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:174:9: error: 'a' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:174:16: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:175:9: error: 'b' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:175:16: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:176:8: error: expected ';' before 'tmp'
/usr/include/m4ri/packedmatrix.h:177:8: error: expected ';' before 'mask_begin'
/usr/include/m4ri/packedmatrix.h:178:8: error: expected ';' before 'mask_end'
/usr/include/m4ri/packedmatrix.h:181:5: error: 'tmp' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:182:21: error: 'mask_begin' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:191:29: error: 'mask_end' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:195:5: error: 'tmp' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:196:21: error: 'mask_begin' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:196:56: error: 'mask_end' was not declared in this scope
/usr/include/m4ri/packedmatrix.h: In function 'void mzd_col_swap_in_rows(mzd_t*, size_t, size_t, size_t, size_t)':
/usr/include/m4ri/packedmatrix.h:242:31: error: 'RADIX' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:247:3: error: 'word' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:247:8: error: expected ';' before 'a'
/usr/include/m4ri/packedmatrix.h:252:11: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h:253:11: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h:255:7: error: 'base' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:255:18: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:256:16: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h:257:16: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h:258:15: error: 'b' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:258:21: error: 'x' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:258:26: error: 'ai' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:258:38: error: 'bi' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:263:9: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h:264:9: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h:269:7: error: 'base' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:269:17: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:270:7: error: 'a' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:271:7: error: 'b' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:273:17: error: 'b_bm' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:274:17: error: 'a_bm' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:283:7: error: 'base' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:283:17: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:284:7: error: 'a' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:285:7: error: 'b' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:287:17: error: 'b_bm' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:288:17: error: 'a_bm' was not declared in this scope
/usr/include/m4ri/packedmatrix.h: At global scope:
/usr/include/m4ri/packedmatrix.h:308:15: error: 'BIT' does not name a type
/usr/include/m4ri/packedmatrix.h:324:86: error: 'BIT' does not name a type
/usr/include/m4ri/packedmatrix.h: In function 'void mzd_write_bit(mzd_t*, size_t, size_t, int)':
/usr/include/m4ri/packedmatrix.h:326:16: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:326:42: error: 'RADIX' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:326:73: error: 'SET_BIT' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:328:16: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:328:42: error: 'RADIX' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:328:73: error: 'CLR_BIT' was not declared in this scope
/usr/include/m4ri/packedmatrix.h: In function 'void mzd_row_add_offset(mzd_t*, size_t, size_t, size_t)':
/usr/include/m4ri/packedmatrix.h:362:38: error: 'RADIX' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:364:3: error: 'word' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:364:9: error: 'src' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:364:18: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:365:9: error: 'dst' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:365:18: error: 'struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:370:8: error: expected ';' before 'temp'
/usr/include/m4ri/packedmatrix.h:372:5: error: 'temp' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:372:60: error: 'RIGHTMOST_BITS' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:373:13: error: 'temp' was not declared in this scope
/usr/include/m4ri/packedmatrix.h: At global scope:
/usr/include/m4ri/packedmatrix.h:556:1: error: 'BIT' does not name a type
/usr/include/m4ri/packedmatrix.h:738:15: error: 'word' does not name a type
/usr/include/m4ri/packedmatrix.h:772:94: error: 'word' has not been declared
/usr/include/m4ri/packedmatrix.h: In function 'void mzd_xor_bits(const mzd_t*, size_t, size_t, int, int)':
/usr/include/m4ri/packedmatrix.h:773:3: error: 'word' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:773:9: error: 'temp' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:778:23: error: 'RADIX' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:780:16: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:787:8: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:788:8: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h: At global scope:
/usr/include/m4ri/packedmatrix.h:802:94: error: 'word' has not been declared
/usr/include/m4ri/packedmatrix.h: In function 'void mzd_and_bits(const mzd_t*, size_t, size_t, int, int)':
/usr/include/m4ri/packedmatrix.h:803:3: error: 'word' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:803:9: error: 'temp' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:808:23: error: 'RADIX' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:810:16: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:817:8: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:818:8: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h: In function 'void mzd_clear_bits(const mzd_t*, size_t, size_t, int)':
/usr/include/m4ri/packedmatrix.h:832:3: error: 'word' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:832:8: error: expected ';' before 'temp'
/usr/include/m4ri/packedmatrix.h:837:23: error: 'RADIX' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:839:5: error: 'temp' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:839:16: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:843:8: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:848:8: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:848:32: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:848:51: error: 'ONE' was not declared in this scope
/usr/include/m4ri/packedmatrix.h:849:8: error: 'const struct mzd_t' has no member named 'rows'
/usr/include/m4ri/packedmatrix.h:849:32: error: 'const struct mzd_t' has no member named 'rows'

Are you meaning a later release of m4ri that will fix this?

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alexanderdreyer mannequin commented May 12, 2011

comment:5

It seems that the header m4ri/packedmatrix.h is not self-contained in that version. I'll add a patch for PolyBoRi which includes m4ri/m4ri.h instead. I'll also re-bundle the spkg with the Sage release. (Maybe #11331 could be release first.)

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alexanderdreyer mannequin commented May 12, 2011

comment:6

@kiwifb Switching to the development version at bibucket should also fix that issue.

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kiwifb commented May 12, 2011

comment:7

I didn't know about the polybori page on bitbucket, thanks for pointing it out. Actually if you make the release available on bitbucket it would be easier to automatically fetch than sourceforge.

Thanks for the patch.

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alexanderdreyer mannequin commented May 12, 2011

comment:8

I meant the bitbucket repo of m4ri, but of course you may also have a look at PolyBoRi there. The "Downloads" section of bitbucket is automatically generated from mercurial tags. I just realized that the releases 0.7.0 and 0.7.1 are missing albeit the tags do exist. Maybe I'll have to contact the support there.

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kiwifb commented May 12, 2011

comment:9

Just to be picky the patch hasn't been made with the git compatibility mode which means that "plain patch" doesn't like it. It shouldn't get in the way of merging this ticket I am just mentioning.

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alexanderdreyer mannequin commented May 12, 2011

Backporting m4ri header issue patch from upcoming PolyBoRi 0.8

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alexanderdreyer mannequin commented May 12, 2011

comment:10

Attachment: polybori-m4ri20100817.patch.gz

I hope this patch applies better.

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kiwifb commented May 12, 2011

comment:11

Thx.

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alexanderdreyer mannequin commented May 13, 2011

comment:12

This should be rebased on the spkg from #11331 when the latter is accepted.

@alexanderdreyer alexanderdreyer mannequin self-assigned this May 13, 2011
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alexanderdreyer mannequin commented Jun 8, 2011

comment:14

After Sage 4.7 being out (a while, I must admit), I rebased it the spkg to the most recent one from Sage. Please have a look at it: http://boxen.math.washington.edu/home/dreyer/spkg/polybori-0.7.1.p2.spkg

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alexanderdreyer mannequin commented Jun 10, 2011

comment:15

BTW all tests pass on a SLES 11 Linux (64 bits).

@alexanderdreyer alexanderdreyer mannequin removed their assignment Jun 10, 2011
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kiwifb commented Jun 10, 2011

comment:16

I should do some test on vanilla sage but I shamelessly decided to skip 0.7 altogether in favor of that one for sage-on-gentoo for sage-4.7 and over. Works a treat on x86 and amd64. Still an annoying problem on macos that is not mirrored in the vanilla version for some reason.

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alexanderdreyer mannequin commented Jun 10, 2011

comment:17

I have often several times that installing one package breaks some completely unrelated tests, while replacing the spkg and building all Sage from scratch works fine. Does sage -ba always suffice?

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alexanderdreyer mannequin commented Jun 17, 2011

comment:19

Attachment: plot.py.patch.gz

I backported another thing from 0.8: polybori.plot may use jinja2, where available http://boxen.math.washington.edu/home/dreyer/spkg/polybori-0.7.1.p3.spkg

See the attached patch for details.

@alexanderdreyer alexanderdreyer mannequin self-assigned this Jun 17, 2011
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comment:20

Passes relevant tests on PPC OS X 10.4.

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alexanderdreyer mannequin commented Jul 5, 2011

comment:21

To push this forward: it builds/installs on Solaris (t2) and passes all tests in sage/rings/polynomial/. (I tested it with the official Sage 4.7 build for Solaris.)

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burcin commented Jul 5, 2011

comment:22

I've also used this version for a while and it seems to work fine. Given the reports of extensive tests above, I am switching this to positive review.

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jdemeyer commented Jul 6, 2011

Reviewer: Burcin Erocal

@jdemeyer jdemeyer modified the milestones: sage-4.7.1, sage-4.7.2 Jul 6, 2011
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burcin commented Jul 6, 2011

Changed reviewer from Burcin Erocal to Burcin Erocal, Francois Bissey, Karl-Dieter Crisman

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jdemeyer commented Aug 8, 2011

comment:26

The spkg contains files which are not world-readable. In order to avoid another #11660, this should be fixed by a simple

chmod -R "og+rX" .

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jdemeyer commented Aug 8, 2011

comment:27

See also #11664 to do the same in sage-4.7.1 with polybori-0.7.

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alexanderdreyer mannequin commented Aug 9, 2011

comment:28

I rebased the package on #11664 and did the chmod here:
http://boxen.math.washington.edu/home/dreyer/spkg/polybori-0.7.1.p4.spkg

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malb commented Aug 16, 2011

comment:29

Files are world-readable now. returning to positive review.

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Merged: sage-4.7.2.alpha1

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nexttime mannequin commented Sep 23, 2011

Changed reviewer from Burcin Erocal, Francois Bissey, Karl-Dieter Crisman to Burcin Erocal, François Bissey, Karl-Dieter Crisman

@malb malb mentioned this issue Sep 12, 2011
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@alexanderdreyer alexanderdreyer mannequin mentioned this issue Aug 9, 2011
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