igraph / igraph Goto Github PK

# First upgrade the vcproj as suggested by the error in vcbuild call
vcbuild igraph.vcproj "release|win32"

<Platforms>
        <Platform
            Name="x64"
        />
    </Platforms>

Name="Release|x64"

cl : Command line warning D9035 : option 'Wp64' has been deprecated and will be
removed in a future release
math.c
.\src\math.c(68) : error C4235: nonstandard extension used : '__asm' keyword not
 supported on this architecture
.\src\math.c(68) : error C2065: 'fld' : undeclared identifier
.\src\math.c(68) : error C2109: subscript requires array or pointer type
.\src\math.c(68) : error C2143: syntax error : missing ';' before '}'
.\src\math.c(69) : error C4235: nonstandard extension used : '__asm' keyword not
 supported on this architecture
.\src\math.c(69) : error C2065: 'fxtract' : undeclared identifier
.\src\math.c(69) : error C2143: syntax error : missing ';' before '}'
.\src\math.c(70) : error C4235: nonstandard extension used : '__asm' keyword not
 supported on this architecture
.\src\math.c(70) : error C2065: 'fstp' : undeclared identifier
.\src\math.c(70) : error C2146: syntax error : missing ';' before identifier 'st
'
.\src\math.c(70) : error C2065: 'st' : undeclared identifier
.\src\math.c(70) : error C2143: syntax error : missing ';' before '}'
.\src\math.c(71) : error C4235: nonstandard extension used : '__asm' keyword not
 supported on this architecture
.\src\math.c(71) : error C2065: 'fistp' : undeclared identifier
.\src\math.c(71) : error C2109: subscript requires array or pointer type
.\src\math.c(71) : error C2143: syntax error : missing ';' before '}'
Build log was saved at "file://c:\data\external\igraph-msvc\igraph-0.6.5-msvc\Re
lease\BuildLog.htm"
igraph - 16 error(s), 99 warning(s)

./bootstrap.sh
make

[...]
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -I/usr/include/libxml2 -I../include -I../include -Wall -I../optional/glpk -g -O2 -I/usr/include/libxml2 -MT libigraph_la-matching.lo -MD -MP -MF .deps/libigraph_la-matching.Tpo -c matching.c  -DDLL_EXPORT -DPIC -o .libs/libigraph_la-matching.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -I/usr/include/libxml2 -I../include -I../include -Wall -I../optional/glpk -g -O2 -I/usr/include/libxml2 -MT libigraph_la-matching.lo -MD -MP -MF .deps/libigraph_la-matching.Tpo -c matching.c -o libigraph_la-matching.o >/dev/null 2>&1
mv -f .deps/libigraph_la-matching.Tpo .deps/libigraph_la-matching.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -g -O2 -I/usr/include/libxml2 -I../include  -I../include -Wall -I../optional/glpk -g -O2 -I/usr/include/libxml2 -MT libigraph_la-lad.lo -MD -MP -MF .deps/libigraph_la-lad.Tpo -c -o libigraph_la-lad.lo `test -f 'lad.c' || echo './'`lad.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -I/usr/include/libxml2 -I../include -I../include -Wall -I../optional/glpk -g -O2 -I/usr/include/libxml2 -MT libigraph_la-lad.lo -MD -MP -MF .deps/libigraph_la-lad.Tpo -c lad.c  -DDLL_EXPORT -DPIC -o .libs/libigraph_la-lad.o
In file included from lad.c:58:
igraph_interrupt_internal.h:43: warning: `thread' attribute directive ignored
lad.c: In function `igraph_i_lad_createGraph':
lad.c:769: error: prior parameter's size depends on 'nbU'
lad.c:769: error: prior parameter's size depends on 'nbV'
lad.c:795: error: prior parameter's size depends on 'nbU'
lad.c:795: error: prior parameter's size depends on 'nbV'
lad.c:795: error: prior parameter's size depends on 'nbV'
lad.c:795: error: prior parameter's size depends on 'nbU'
lad.c:786: confused by earlier errors, bailing out
Makefile:5165: recipe for target `libigraph_la-lad.lo' failed
make[3]: *** [libigraph_la-lad.lo] Error 1
make[3]: Leaving directory `/cygdrive/c/data/external/igraph/src'
Makefile:1149: recipe for target `all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory `/cygdrive/c/data/external/igraph/src'
Makefile:418: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/data/external/igraph'
Makefile:318: recipe for target `all' failed
make: *** [all] Error 2

Hmmm, I think restarting R is not a very good solution. It is rather
ugly in the first place. But perhaps even more importantly, it can be
rather inconvenient if one has a large data set in the memory and
needs to save/load it just to reload a package that was updated in the
meanwhile.

This happens to me quite often with 20-40Gb of data, so I would really
love to have a solution for proper detach/unload.

On 19/02/2009 6:19 PM, Alex F. Bokov wrote:

    Hello. To save the hassle of quitting and restarting R every time I
    rebuild the package I'm working on (for the purposes of this question called
    "roots") I would like to write a script cleanly remove the package from my R
    session and then load it again. Of course detach("package:roots") works for
    the native R objects in the package. However, the compiled C library remains
    loaded. Using library.dynam.unload as documented results in:

    Error in library.dynam.unload("roots.so",
    "~/R/x86_64-pc-linux-gnu-library/2.8/roots/libs/") :
     shared library 'roots' was not loaded

    I also tried the above command with the file extension omitted and the
    last one and two levels of the directory path omitted. In both cases I still
    get the "not loaded" error. I've also Googled the list archives and while
    there were several questions like mine, none of them were answered by the
    list. Am I to believe that this is something hardly anybody does? Does this
    mean everybody sits around waiting for R to start up everytime they make a
    minor change to the C source?

    If there is a tutorial for doing this, I'd much appreciate the link.

This is more of an R-devel question than R-help, so if this doesn't answer
your question, please follow up there.

On Windows, the following sort of works:

    library(rgl)
    .dynLibs()

                                         Filename Dynamic.Lookup
1     F:/R/R-2.8.1/library/methods/libs/methods.dll          FALSE
2 F:/R/R-2.8.1/library/grDevices/libs/grDevices.dll          FALSE
3         F:/R/R-2.8.1/library/stats/libs/stats.dll          FALSE
4             F:/R/R-2.8.1/library/rgl/libs/rgl.dll           TRUE

    library.dynam.unload("rgl", "F:/R/R-2.8.1/library/rgl")

I say "sort of", in that I get no error messages and the dll is no longer
locked in use as it normally would be in Windows, but reloading the package
doesn't function properly. It's possible some combination of detach() and
unloadNamespace() would get a clean unload, but really, I normally just quit
R and restart.  It's pretty quick to start up, compared to the recompile
time for the package.

Duncan Murdoch

______________________________________________
<email address hidden> mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

>>> print g_giant.summary()
IGRAPH UN-- 68303 184788 -- 
+ attr: name (v)

>>> _id = 0
>>> for i in range(1,20):
>>>     print str(i) + ": " + str(g_giant.closeness(vertices=[_id], cutoff=i))
>>> print str("oo") + ": " + str(g_giant.closeness(vertices=[_id], cutoff=0))

1: [0.00018463857449137346]
2: [0.00018646324811754687]
3: [0.00019331169771785695]
4: [0.00021734321395232314]
5: [0.00040565599510438034]
6: [-0.00023178404736435846]
7: [-5.625506191677867e-05]
8: [3.432949157412304e-05]
9: [6.243362890574019e-05]
10: [0.00012521807634011635]
11: [0.0002605744451427101]
12: [0.0005577231725167555]
13: [0.001118365372989965]
14: [0.002562406848171298]
15: [0.006123525555601777]
16: [0.019109864514188588]
17: [0.03947058949304026]
18: [0.10707438394840514]
19: [0.11991032445063192]
oo: [0.11991032445063192]
def betweeness_estimate(g, p=0.2, normalized=True):
    # Betweeness: how often is the given vertex on the shortest path?
    import collections
    import random
    import itertools
    no_vertices = len(g.vs)
    sample_number = int(no_vertices*p)
    #print("sample# %s; complete: %s" % (sample_number,no_vertices))
    assert sample_number > 2, "Sample too small, specify higher number of vertices"
    sample = random.sample(range(no_vertices), sample_number)
    values = collections.defaultdict(float)
    # first get all the shortest path
    for vertex in sample:
        shortest_paths = g.get_all_shortest_paths(vertex, to=sample)
        _cache = collections.defaultdict(float)
        _cur_last = -1
        _no_paths = 0
        # Now add one for each middle vertex in the result
        for path in shortest_paths:
            if len(path) < 3:
                continue
            _no_paths += 1
            if _cur_last != path[-1]:
                # A change in the endpoint, so 
                # add the no of shortest path to the max_values cache
                for v in _cache.keys():
                    values[v] += float(_cache[v]) / _no_paths
                _cache = collections.defaultdict(float)
                _no_paths = 0
                _cur_last = path[-1]
            for i in path[1:-1]:
                _cache[i] += 1
    result = map(values.__getitem__, range(no_vertices))
    if normalized:
        _min, _max = min(result), max(result)
        result = map(lambda x: (x-_min)/(_max - _min), result)
    return result

if k is None:
    nodes = G
else:
    random.seed(seed)
    nodes = random.sample(G.nodes(), k)
for s in nodes:
    [shortest path finding]

igraph / igraph Goto Github PK

igraph's Introduction

The igraph library

Citation

igraph's People

Contributors

Stargazers

Watchers

Forkers

igraph's Issues

works fine

problem

Load the igraph package

Create and plot a small graph

Same without changing size

Code:

Docs:

IGRAPH U--- 10 0 -- Ring graph

+ attr: name (g/c), mutual (g/x), circular (g/x)

IGRAPH U--- 10 10 -- Ring graph

+ attr: name (g/c), mutual (g/x), circular (g/x), rtdev (e/n)

IGRAPH U--- 10 0 -- Ring graph

+ attr: name (g/c), mutual (g/x), circular (g/x), rtdev (e/n)

IGRAPH U--- 10 10 -- Ring graph

+ attr: name (g/c), mutual (g/x), circular (g/x), rtdev (e/n)

IGRAPH U--- 10 9 -- Ring graph

+ attr: name (g/c), mutual (g/x), circular (g/x), rtdev (e/n)

Gabor Csardi UNIL DGM

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