igraph-help
[Top][All Lists]
Advanced
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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: Tue, 6 Nov 2012 08:57:58 +0100
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
> address@hidden (mailto:address@hidden)
> https://lists.nongnu.org/mailman/listinfo/igraph-help




_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help



_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help




--
Gabor Csardi <address@hidden>     MTA KFKI RMKI


_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help


reply via email to
[Prev in Thread] Current Thread [Next in Thread]