Re: [sage-devel] Re: sage-6.4 fallout: optional ore_algebra package now broken due to change in Sage (?) (Re: downloading Ore_algebra package to sagemath)

2014-11-17 Thread Konstantin Ziegler 
> Note also that
> http://www.risc.jku.at/research/combinat/software/ore_algebra/ suggests
> that  
>> Right now you are using Version 0.2 last updated on November 16, 2014,
> developed for Sage 6.3.
> 
> So maybe we just need to update our package?
> 
> ore_algebra-0.1 . not installed

I just installed ore_algebra version 0.2 on a bleeding-edge Sage
(Version 6.5.beta0, Release Date: 2014-11-16) and it works just fine:

ore_algebra-0.1 . installed version: 0.2

Is there anything else I can help with?

Best,
Konstantin


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[sage-devel] Re: sage-6.4 fallout: optional ore_algebra package now broken due to change in Sage (?) (Re: downloading Ore_algebra package to sagemath)

2014-11-17 Thread Konstantin Ziegler 
This is Trac Ticket #17205 . John 
Palmieri gave a quick fix in comment #2. 

Note that I'm not one of the developers of this package -- merely a happy 
user. :-)

Best,
Konstantin

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Re: [sage-devel] Error building bzip2 for Sage 5.3 on Ubuntu 12.04

2012-10-01 Thread Konstantin Ziegler 
Found the cause of the error.  The environment variable BZIP2 was set by

export BZIP2="-9"

in my .profile.  According to bzip2's man page this is possible to specify 
default options, but the bzip's make process does not seem to like that.  
After "unset BZIP2" the installation ran straight through.  Should I file a 
trac ticket or is this something I should have been aware of when setting 
the variable?

Cheers
Konstantin

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Re: [sage-devel] Error building bzip2 for Sage 5.3 on Ubuntu 12.04

2012-09-28 Thread Konstantin Ziegler 
Sorry, I meant bzip2's Makefile in 

> /home/zieglerk/local/share/sage/spkg/build/bzip2-1.0.6/src 
>

Here it is.

# --
# This file is part of bzip2/libbzip2, a program and library for
# lossless, block-sorting data compression.
#
# bzip2/libbzip2 version 1.0.6 of 6 September 2010
# Copyright (C) 1996-2010 Julian Seward 
#
# Please read the WARNING, DISCLAIMER and PATENTS sections in the 
# README file.
#
# This program is released under the terms of the license contained
# in the file LICENSE.
# --

SHELL=/bin/sh

# To assist in cross-compiling
CC=gcc
AR=ar
RANLIB=ranlib
LDFLAGS=

BIGFILES=-D_FILE_OFFSET_BITS=64
CFLAGS=-Wall -Winline -O2 -g $(BIGFILES)

# Where you want it installed when you do 'make install'
PREFIX=/usr/local


OBJS= blocksort.o  \
  huffman.o\
  crctable.o   \
  randtable.o  \
  compress.o   \
  decompress.o \
  bzlib.o

all: libbz2.a bzip2 bzip2recover test

bzip2: libbz2.a bzip2.o
$(CC) $(CFLAGS) $(LDFLAGS) -o bzip2 bzip2.o -L. -lbz2

bzip2recover: bzip2recover.o
$(CC) $(CFLAGS) $(LDFLAGS) -o bzip2recover bzip2recover.o

libbz2.a: $(OBJS)
rm -f libbz2.a
$(AR) cq libbz2.a $(OBJS)
@if ( test -f $(RANLIB) -o -f /usr/bin/ranlib -o \
-f /bin/ranlib -o -f /usr/ccs/bin/ranlib ) ; then \
echo $(RANLIB) libbz2.a ; \
$(RANLIB) libbz2.a ; \
fi

check: test
test: bzip2
@cat words1
./bzip2 -1  < sample1.ref > sample1.rb2
./bzip2 -2  < sample2.ref > sample2.rb2
./bzip2 -3  < sample3.ref > sample3.rb2
./bzip2 -d  < sample1.bz2 > sample1.tst
./bzip2 -d  < sample2.bz2 > sample2.tst
./bzip2 -ds < sample3.bz2 > sample3.tst
cmp sample1.bz2 sample1.rb2 
cmp sample2.bz2 sample2.rb2
cmp sample3.bz2 sample3.rb2
cmp sample1.tst sample1.ref
cmp sample2.tst sample2.ref
cmp sample3.tst sample3.ref
@cat words3

install: bzip2 bzip2recover
if ( test ! -d $(PREFIX)/bin ) ; then mkdir -p $(PREFIX)/bin ; fi
if ( test ! -d $(PREFIX)/lib ) ; then mkdir -p $(PREFIX)/lib ; fi
if ( test ! -d $(PREFIX)/man ) ; then mkdir -p $(PREFIX)/man ; fi
if ( test ! -d $(PREFIX)/man/man1 ) ; then mkdir -p $(PREFIX)/man/man1 
; fi
if ( test ! -d $(PREFIX)/include ) ; then mkdir -p $(PREFIX)/include ; 
fi
cp -f bzip2 $(PREFIX)/bin/bzip2
cp -f bzip2 $(PREFIX)/bin/bunzip2
cp -f bzip2 $(PREFIX)/bin/bzcat
cp -f bzip2recover $(PREFIX)/bin/bzip2recover
chmod a+x $(PREFIX)/bin/bzip2
chmod a+x $(PREFIX)/bin/bunzip2
chmod a+x $(PREFIX)/bin/bzcat
chmod a+x $(PREFIX)/bin/bzip2recover
cp -f bzip2.1 $(PREFIX)/man/man1
chmod a+r $(PREFIX)/man/man1/bzip2.1
cp -f bzlib.h $(PREFIX)/include
chmod a+r $(PREFIX)/include/bzlib.h
cp -f libbz2.a $(PREFIX)/lib
chmod a+r $(PREFIX)/lib/libbz2.a
cp -f bzgrep $(PREFIX)/bin/bzgrep
ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzegrep
ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzfgrep
chmod a+x $(PREFIX)/bin/bzgrep
cp -f bzmore $(PREFIX)/bin/bzmore
ln -s -f $(PREFIX)/bin/bzmore $(PREFIX)/bin/bzless
chmod a+x $(PREFIX)/bin/bzmore
cp -f bzdiff $(PREFIX)/bin/bzdiff
ln -s -f $(PREFIX)/bin/bzdiff $(PREFIX)/bin/bzcmp
chmod a+x $(PREFIX)/bin/bzdiff
cp -f bzgrep.1 bzmore.1 bzdiff.1 $(PREFIX)/man/man1
chmod a+r $(PREFIX)/man/man1/bzgrep.1
chmod a+r $(PREFIX)/man/man1/bzmore.1
chmod a+r $(PREFIX)/man/man1/bzdiff.1
echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzegrep.1
echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzfgrep.1
echo ".so man1/bzmore.1" > $(PREFIX)/man/man1/bzless.1
echo ".so man1/bzdiff.1" > $(PREFIX)/man/man1/bzcmp.1

clean: 
rm -f *.o libbz2.a bzip2 bzip2recover \
sample1.rb2 sample2.rb2 sample3.rb2 \
sample1.tst sample2.tst sample3.tst

blocksort.o: blocksort.c
@cat words0
$(CC) $(CFLAGS) -c blocksort.c
huffman.o: huffman.c
$(CC) $(CFLAGS) -c huffman.c
crctable.o: crctable.c
$(CC) $(CFLAGS) -c crctable.c
randtable.o: randtable.c
$(CC) $(CFLAGS) -c randtable.c
compress.o: compress.c
$(CC) $(CFLAGS) -c compress.c
decompress.o: decompress.c
$(CC) $(CFLAGS) -c decompress.c
bzlib.o: bzlib.c
$(CC) $(CFLAGS) -c bzlib.c
bzip2.o: bzip2.c
$(CC) $(CFLAGS) -c bzip2.c
bzip2recover.o: bzip2recover.c
$(CC) $(CFLAGS) -c bzip2recover.c


distclean: clean
rm -f manual.ps manual.html manual.pdf

DISTNAME=bzip2-1.0.6
dist: check manual
rm -f $(DISTNAME)
ln -s -f . $(DISTNAME)
tar cvf $(DISTNAME).tar \
   $(DISTNAME)/blocksort.c \
   $(DISTNAME)/huffman.c \
   $(DISTNAME)/crctable.c \
   $(DISTNAME)/randtable.c \
   $(DISTNAME)/compress.c \
   $(DISTNAME)/decompress.c \
   $(DISTNAME)/bzlib.c \
   $(DISTNAME)/bzip2.c \
   $(DISTNAME)/bzip2recover.c \
   $(DISTNAME)/bzlib.h \
   $(DISTNAME)/bzlib_private.h \
   $(DISTN

Re: [sage-devel] Error building bzip2 for Sage 5.3 on Ubuntu 12.04

2012-09-28 Thread Konstantin Ziegler 
On Friday, September 28, 2012 12:08:57 PM UTC+2, François wrote:
>
> Could you attach the makefile. 


Sure. 

Google Groups would not let me attach the Makefile ("The uploaded file 
Makefile of type application/octet-stream is not allowed."), so I have to 
go with copy and paste.  Sorry about the size.

# Main Makefile for Sage.

# The default target ("all") builds Sage and the whole (HTML) documentation.
#
# Target "build" just builds Sage.
# 
# See below for targets to build the documentation in other formats,
# to run various types of test suites, and to remove parts of the build etc.

PIPE = spkg/pipestatus


all: start doc  # indirectly depends on build

build:
cd spkg && \
"../$(PIPE)" \
"env SAGE_PARALLEL_SPKG_BUILD='$(SAGE_PARALLEL_SPKG_BUILD)' ./install all 
2>&1" \
"tee -a ../install.log"
./sage -b

build-serial: SAGE_PARALLEL_SPKG_BUILD = no
build-serial: build

# Start Sage if the file local/lib/sage-started.txt does not exist
# (i.e. when we just installed Sage for the first time)
start: build
[ -f local/lib/sage-started.txt ] || local/bin/sage-starts

# You can choose to have the built HTML version of the documentation link to
# the PDF version. To do so, you need to build both the HTML and PDF 
versions.
# To have the HTML version link to the PDF version, do
#
# $ ./sage --docbuild all html
# $ ./sage --docbuild all pdf
#
# For more information on the docbuild utility, do
#
# $ ./sage --docbuild -H
doc: doc-html

doc-html: build
$(PIPE) "./sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS) 
2>&1" "tee -a dochtml.log"

doc-html-jsmath: build
$(PIPE) "./sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS) 
2>&1" "tee -a dochtml.log"

doc-pdf: build
$(PIPE) "./sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a 
docpdf.log"

doc-clean:
@echo "Deleting devel/sage/doc/output..."
rm -rf devel/sage/doc/output

clean:
@echo "Deleting spkg/build..."
rm -rf spkg/build
@echo "Deleting spkg/archive..."
rm -rf spkg/archive

distclean: clean
@echo "Deleting all remaining traces of builds, tests etc. ..."
rm -rf local
rm -f spkg/Makefile
rm -rf spkg/installed
rm -rf spkg/logs
rm -rf spkg/optional
rm -f install.log
rm -f dochtml.log docpdf.log
rm -f test.log testall.log testlong.log ptest.log ptestlong.log
rm -f start.log
rm -f spkg/parallel_make.cfg
rm -rf data
rm -rf dist
rm -rf devel
rm -rf doc
rm -rf examples
rm -rf sage-python
rm -rf matplotlibrc
rm -rf tmp
rm -f .BUILDSTART

micro_release:
bash -c ". spkg/bin/sage-env && local/bin/sage-micro_release"

text-expand:
./spkg/bin/text-expand

text-collapse:
./spkg/bin/text-collapse

TESTPRELIMS = local/bin/sage-starts
# The [a-z][a-z] matches all directories whose names consist of two
# lower-case letters, to match the language directories.
TESTDIRS = devel/sage/doc/common devel/sage/doc/[a-z][a-z] devel/sage/sage

test: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -t --sagenb $(TESTDIRS) 2>&1" "tee -a test.log"

check: test

testall: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -t --sagenb --optional $(TESTDIRS) 2>&1" "tee -a 
testall.log"

testlong: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -t --sagenb --long $(TESTDIRS) 2>&1" "tee -a testlong.log"

testalllong: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -t --sagenb --optional --long $(TESTDIRS) 2>&1" "tee -a 
testalllong.log"

ptest: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -tp --sagenb $(TESTDIRS) 2>&1" "tee -a ptest.log"

ptestall: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -tp --sagenb --optional $(TESTDIRS) 2>&1" "tee -a 
ptestall.log"

ptestlong: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -tp --sagenb --long $(TESTDIRS) 2>&1" "tee -a ptestlong.log"

ptestalllong: all # i.e. build and doc
$(TESTPRELIMS)
$(PIPE) "./sage -tp --sagenb --optional --long $(TESTDIRS) 2>&1" "tee -a 
ptestalllong.log"


testoptional: testall # just an alias

testoptionallong: testalllong # just an alias

ptestoptional: ptestall # just an alias

ptestoptionallong: ptestalllong # just an alias


install:
echo "Experimental use only!"
if [ "$(DESTDIR)" = "" ]; then \
echo >&2 "Set the environment variable DESTDIR to the install path."; \
exit 1; \
fi
# Make sure we remove only an existing directory. If $(DESTDIR)/sage is
# a file instead of a directory then the mkdir statement later will fail
if [ -d "$(DESTDIR)"/sage ]; then \
rm -rf "$(DESTDIR)"/sage; \
fi
mkdir -p "$(DESTDIR)"/sage
mkdir -p "$(DESTDIR)"/bin
cp -Rp * "$(DESTDIR)"/sage
rm -f "$(DESTDIR)"/bin/sage
ln -s ../sage/sage "$(DESTDIR)"/bin/sage
"$(DESTDIR)"/bin/sage -c # Run sage-location


.PHONY: all build build-serial start install \
doc doc-html doc-html-jsmath doc-pdf \
doc-clean clean distclean \
test check testoptional testall testlong testoptionallong testallong \
ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong

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Re: [sage-devel] Error building bzip2 for Sage 5.3 on Ubuntu 12.04

2012-09-28 Thread Konstantin Ziegler 
On Friday, September 28, 2012 11:34:06 AM UTC+2, François wrote:
>
> I am quite intrigued by your error message actually. 
>
> > ./bzip2 -1  < sample1.ref > sample1.rb2 
> > bzip2: Can't open input file bzip2-1.0.6: No such file or directory. 
> > make[2]: *** [test] Error 1 
>
> Are you running make in parallel (make -jxx)? 


Yes, I ran
$ export SAGE_PARALLEL_SPKG_BUILD="yes"
$ export MAKE="make -j4 -l6"

But even, if I omit that and just "make" (after a "make distclean" and 
clearing the variables) the error persists.

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Re: [sage-devel] Error building bzip2 for Sage 5.3 on Ubuntu 12.04

2012-09-28 Thread Konstantin Ziegler 

>
> Do you get the same error message with 
>
(sage-sh) $ ./bzip2 -1  < sample1.ref > sample1.rb2 
> (sage-sh) $ bzip2 -1  < sample1.ref > sample1.rb2 
> (sage-sh) $ ./bzip2 < sample1.ref > sample1.rb2 
> (sage-sh) $ ./bzip2 -1 sample1.rb2 
>
 
No errors for any of them. 

And what's the output of: 
> (sage-sh) $ file ./bzip2 
>

./bzip2: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), 
dynamically linked (uses shared libs), for GNU/Linux 2.6.24, 
BuildID[sha1]=0x80a576bae0936fe867fa78e85a012880d1241742, not stripped 
 

> (sage-sh) $ ldd ./bzip2 
>

linux-gate.so.1 =>  (0xb77ab000)
libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb75e9000)
/lib/ld-linux.so.2 (0xb77ac000)
 
 

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[sage-devel] Error building bzip2 for Sage 5.3 on Ubuntu 12.04

2012-09-28 Thread Konstantin Ziegler 
Hi,

Building Sage 5.3 on my 32-bit Ubuntu 12.04 fails early.  The process 
aborts during the tests for building bzip2.  I ran into the same error 
message when I first tried upgrading from Sage 4.8 and also later trying to 
build Sage 5.2 for comparison.  So, it may be just some misconfiguration on 
my machine.

The relevant part of the log-file reads as follows and I manually checked 
that the sample files are present in the directory 
$SAGE/spkg/build/bzip2-1.0.6.

bzip2-1.0.6

Extracting package /home/zieglerk/local/share/sage/spkg/standard/bzip2-1.0.
6.spkg
-rw-r--r-- 1 zieglerk zieglerk 796422 May 14 14:56 /home/zieglerk/local/
share/sage/spkg/standard/bzip2-1.0.6.spkg
Finished extraction

Host system:
Linux ulysses 3.2.0-31-generic-pae #50-Ubuntu SMP Fri Sep 7 16:39:45 UTC 
2012 i686 i686 i386 GNU/Linux

C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 
4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs 
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr 
--program-suffix=-4.6 --enable-shared --enable-linker-build-id 
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext 
--enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 
--libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu 
--enable-libstdcxx-debug --enable-libstdcxx-time=yes 
--enable-gnu-unique-object --enable-plugin --enable-objc-gc 
--enable-targets=all --disable-werror --with-arch-32=i686 
--with-tune=generic --enable-checking=release --build=i686-linux-gnu 
--host=i686-linux-gnu --target=i686-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) 

make[2]: Entering directory 
`/home/zieglerk/local/share/sage/spkg/build/bzip2-1.0.6/src'
gcc -fPIC -O2 -g  -c huffman.c
gcc -fPIC -O2 -g  -c blocksort.c
gcc -fPIC -O2 -g  -c crctable.c
gcc -fPIC -O2 -g  -c randtable.c
gcc -fPIC -O2 -g  -c compress.c
gcc -fPIC -O2 -g  -c decompress.c
gcc -fPIC -O2 -g  -c bzlib.c
gcc -fPIC -O2 -g  -c bzip2.c
bzip2.c: In function ‘applySavedFileAttrToOutputFile’:
bzip2.c:1073:4: warning: ignoring return value of ‘fchown’, declared with 
attribute warn_unused_result [-Wunused-result]
gcc -fPIC -O2 -g  -c bzip2recover.c
gcc -fPIC -O2 -g   -o bzip2recover bzip2recover.o
rm -f libbz2.a
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o 
decompress.o bzlib.o
ranlib libbz2.a
gcc -fPIC -O2 -g   -o bzip2 bzip2.o -L. -lbz2

Doing 6 tests (3 compress, 3 uncompress) ...
If there's a problem, things might stop at this point.
 
./bzip2 -1  < sample1.ref > sample1.rb2
bzip2: Can't open input file bzip2-1.0.6: No such file or directory.
make[2]: *** [test] Error 1
make[2]: Leaving directory `/home/zieglerk/local/share/sage/spkg/build/bzip2
-1.0.6/src'
Error building bzip2

Error installing package bzip2-1.0.6


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