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Re: [igraph] Problems compiling igraph 0.6 on MacOS X

From: Bob Pap
Subject: Re: [igraph] Problems compiling igraph 0.6 on MacOS X
Date: Thu, 15 Nov 2012 13:24:49 +0100
Hi Gabor and Tamás,

I noticed that new tarballs were added yesterday. Just to let you know that the problems with compiing on OSX (R version 2.15.2) remain. Would you know the most recent useable tarball that has the revision to alpha centrality included? Many thanks.
Kind regards,
Ivan

for 7:

interface.c: In function ‘R_igraph_get_shortest_paths’:
rinterface.c:3692: error: too few arguments to function ‘igraph_get_shortest_paths_dijkstra’
rinterface.c: In function ‘R_igraph_bipartite_game_gnp’:
rinterface.c:12012: warning: implicit declaration of function ‘igraph_bipartite_game_gnp’
rinterface.c: In function ‘R_igraph_bipartite_game_gnm’:
rinterface.c:12063: warning: implicit declaration of function ‘igraph_bipartite_game_gnm’
make: *** [rinterface.o] Error 1
ERROR: compilation failed for package ‘igraph’

For 6.1:

ld: warning: can't find atom for N_GSYM stabs logfil:G(0,6) in dseupd.o
ld: sectionForAddress(0x80) address not in any section for architecture i386
collect2: ld returned 1 exit status
make: *** [igraph.so] Error 1
ERROR: compilation failed for package ‘igraph’


On 6 November 2012 08:57, Bob Pap <address@hidden> wrote:
Hi Gábor,

Snapshot 0.7-3055 from last night fails
R CMD install ~/Downloads/igraph_nightly_0.7-3055-20121106.tar.gz 
...
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSING_R -I. -Ics -Iglpk -Iglpk/amd -Iglpk/colamd -g -O2 -I/usr/include/libxml2 -g -O2 -I/usr/include/libxml2 -DNDEBUG -DPACKAGE_VERSION=\"0.7\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -g -O2  -c rinterface.c -o rinterface.o
rinterface.c: In function ‘R_igraph_get_shortest_paths’:
rinterface.c:3692: error: too few arguments to function ‘igraph_get_shortest_paths_dijkstra’
rinterface.c: In function ‘R_igraph_bipartite_game_gnp’:
rinterface.c:12012: warning: implicit declaration of function ‘igraph_bipartite_game_gnp’
rinterface.c: In function ‘R_igraph_bipartite_game_gnm’:
rinterface.c:12063: warning: implicit declaration of function ‘igraph_bipartite_game_gnm’
make: *** [rinterface.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’

Snapshot 0.6.1-3007 also from last night also fails with a bunch of ld errors
R CMD install ~/Downloads/igraph_nightly_0.6.1-3007-20121106.tar.gz 
....
ld: warning: can't find atom for N_GSYM stabs nopx:G(0,3) in dstatn.o
ld: sectionForAddress(0x80) address not in any section for architecture i386
collect2: ld returned 1 exit status
make: *** [igraph.so] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’

Snapshot 3043 from Friday also fails with the ld problems
R CMD install ~/Downloads/igraph_nightly_0.7-3043-20121102.tar.gz 
...
ld: warning: can't find atom for N_GSYM stabs nopx:G(0,3) in dstats.o
ld: sectionForAddress(0x80) address not in any section for architecture i386
collect2: ld returned 1 exit status
make: *** [igraph.so] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’

I am using gcc 4.2.1 (plain vanilla from the lastest XCode) on the latest copy of OsX 10.8.2.  Maybe an issue of the architecture?  I am using R64 only and I see the i386 is referred to in the errors.

Kind regards,
Bob Pap

On 6 November 2012 02:13, Gábor Csárdi <address@hidden> wrote:
Hi Bob,

On Mon, Nov 5, 2012 at 6:08 PM, Bob Pap <address@hidden> wrote:
Hi Tamás,

I seem to have the same problem compiling the recent snapshot on OSX 10.8.2 (R CMD install ~/Downloads/igraph_nightly_0.7-3053-20121105.tar.gz). I get errors (not always the same) with all the recent snapshots (igraph_nightly_0.6.1-3000-20121102.tar.gz  igraph_nightly_0.6.1-3005-20121103.tar.gz  igraph_nightly_0.7-3043-20121102.tar.gz    igraph_nightly_0.7-3050-20121103.tar.gz    igraph_nightly_0.7-3053-20121105.tar.gz). Do you know which is the latest snapshot to compile without problems? Am I in the wrong direction?  Many thanks for any help.

3043 should compile, I guess. I'll fix the issue in a sec, and the next nightly after 3053 should compile, too. 

Gabor
 
Kind regards,
Bob Pap

gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSING_R -I. -Ics -Iglpk -Iglpk/amd -Iglpk/colamd -g -O2 -I/usr/include/libxml2 -g -O2 -I/usr/include/libxml2 -DNDEBUG -DPACKAGE_VERSION=\"0.7\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -g -O2  -c rinterface.c -o rinterface.o
rinterface.c: In function ‘R_igraph_get_shortest_paths’:
rinterface.c:3692: error: too few arguments to function ‘igraph_get_shortest_paths_dijkstra’
rinterface.c: In function ‘R_igraph_bipartite_game_gnp’:
rinterface.c:12012: warning: implicit declaration of function ‘igraph_bipartite_game_gnp’
rinterface.c: In function ‘R_igraph_bipartite_game_gnm’:
rinterface.c:12063: warning: implicit declaration of function ‘igraph_bipartite_game_gnm’
make: *** [rinterface.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’


On 24 April 2012 22:26, Bob Pap <address@hidden> wrote:
Perfect! Many thanks, it worked with the build from 04.13.


On Tue, Apr 24, 2012 at 10:15 PM, Tamás Nepusz <address@hidden> wrote:
Dear Bob,

Thanks for the bug report; this is an error on our side. We have recently added a new argument to igraph_community_eb_get_merges in the C core and the R interface has not been updated yet. Please try an earlier nightly snapshot; any nightly build released before 19 April 2012 would do.

Best,
--
T.


On Tuesday, 24 April 2012 at 22:07, Bob Pap wrote:

> Dear all,
>
> I get the error below compiling igraph on MacOS X 10.7.3 (with command: R CMD install ~/Downloads/igraph_nightly_0.6-2694-20120421.tar.gz ). Could a guru please maybe point me in the right direction? Any help is appreciated (I need to use weighted betweeness measure that I understand is available in th enew version).
>
> Kind regards,
> Bob
>
> gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DUSING_R -I. -Ics -Iglpk -Iglpk/amd -Iglpk/colamd -g -O2 -I/usr/include/libxml2 -g -O2 -I/usr/include/libxml2 -DNDEBUG -DPACKAGE_VERSION=\"0.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC -g -O2 -c rinterface.c -o rinterface.o
> rinterface.c: In function ‘R_SEXP_to_vector_complex_copy’:
> rinterface.c:2380: warning: passing argument 2 of ‘igraph_vector_complex_init_copy’ from incompatible pointer type
> rinterface.c: In function ‘R_SEXP_to_matrix_complex_copy’:
> rinterface.c:2393: warning: passing argument 2 of ‘igraph_vector_complex_init_copy’ from incompatible pointer type
> rinterface.c: In function ‘R_igraph_community_eb_get_merges’:
> rinterface.c:6177: warning: passing argument 3 of ‘igraph_community_eb_get_merges’ from incompatible pointer type
> rinterface.c:6177: warning: passing argument 4 of ‘igraph_community_eb_get_merges’ from incompatible pointer type
> rinterface.c:6177: error: too few arguments to function ‘igraph_community_eb_get_merges’
> make: *** [rinterface.o] Error 1
> ERROR: compilation failed for package ‘igraph’
> * removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’
> * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/igraph’
>
>
> _______________________________________________
> igraph-help mailing list
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Gabor Csardi <address@hidden>     MTA KFKI RMKI


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