[Matplotlib-users] All kinds of issues inslalling basemap under
Ubuntu 8.10 64bit [SEC=UNCLASSIFIED]
From: Scott C. <S.C...@bo...> - 2009-01-07 10:51:15
|
Greetings... I have been using basemap extensively to do presentation graphics under quite a wide variety of platforms but I got a new 64bit dual core laptop recently and have been having all kinds of problems installing it... I am using (K)ubuntu 8.10 and have tried to install it two ways... This is a 64bit system (1) using the pre-compiles libgeos 3.0.0: this is installed using the libgeos-dev package under ubuntu The package (seems) to install ok I then grab the latest source and do the usual python setup.py build jobbo and get a massive raft of errors eg: ...... src/_proj.c:2353: error: '__pyx_kp_4' undeclared here (not in a function) src/_proj.c:2353: warning: excess elements in struct initializer src/_proj.c:2353: warning: (near initialization for '__pyx_string_tab[19]') src/_proj.c:2353: warning: excess elements in struct initializer src/_proj.c:2353: warning: (near initialization for '__pyx_string_tab[19]') src/_proj.c:2353: warning: excess elements in struct initializer .. .. src/_proj.c:3155: error: expected ')' before '*' token src/_proj.c:3170: error: expected ')' before '*' token src/_proj.c:3185: error: expected ')' before '*' token src/_proj.c:3200: error: expected ')' before '*' token src/_proj.c:3215: error: expected ')' before '*' token src/_proj.c:3230: error: expected ')' before '*' token error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Isrc -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/include/python2.5 -c src/_proj.c -o build/temp.linux-x86_64-2.5/src/_proj.o" failed with exit status 1 (2) building libgeos from source... I get the same error for 2.2.3 (a version I have had no problems compiling on centos5 64bit machines in the past) and 3.0.0 make[3]: Entering directory `/home/scollis/geos-3.0.0/source/index/quadtree' if /bin/bash ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I../../../source/headers -I../../../source/headers/geos -I../../../source/headers -g -O2 -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo -MD -MP -MF ".deps/DoubleBits.Tpo" -c -o DoubleBits.lo DoubleBits.cpp; \ then mv -f ".deps/DoubleBits.Tpo" ".deps/DoubleBits.Plo"; else rm -f ".deps/DoubleBits.Tpo"; exit 1; fi g++ -DHAVE_CONFIG_H -I. -I. -I../../../source/headers -I../../../source/headers/geos -I../../../source/headers -g -O2 -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo -MD -MP -MF .deps/DoubleBits.Tpo -c DoubleBits.cpp -fPIC -DPIC -o .libs/DoubleBits.o DoubleBits.cpp: In static member function 'static double geos::index::quadtree::DoubleBits::powerOf2(int)': DoubleBits.cpp:51: error: 'memcpy' was not declared in this scope DoubleBits.cpp: In constructor 'geos::index::quadtree::DoubleBits::DoubleBits(double)': DoubleBits.cpp:94: error: 'memcpy' was not declared in this scope make[3]: *** [DoubleBits.lo] Error 1 make[3]: Leaving directory `/home/scollis/geos-3.0.0/source/index/quadtree' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/scollis/geos-3.0.0/source/index' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/scollis/geos-3.0.0/source' make: *** [all-recursive] Error 1 ANY help very very very welcome! I am some what at a loss as I have managed to compile both libgeos and basemap under much more "user unfriendly" distros before... Dr Scott Collis Postdoctoral Researcher Centre for Australian Weather and Climate Research (CAWCR) Atmosphere and Land Observation and Assessment Group Australian Bureau of Meteorology Room 9.57 Level 9 700 Collins Street Docklands 3008 Office: (03) 9669 4766 MB: 0412177550 http://www.bom.gov.au/bmrc/wefor/staff/scollis/ |
From: Jeff W. <js...@fa...> - 2009-01-07 12:44:56
|
Scott Collis wrote: > Greetings... > I have been using basemap extensively to do presentation graphics > under quite a wide variety of platforms but I got a new 64bit dual > core laptop recently and have been having all kinds of problems > installing it... > I am using (K)ubuntu 8.10 and have tried to install it two ways... > This is a 64bit system > (1) using the pre-compiles libgeos 3.0.0: > this is installed using the libgeos-dev package under ubuntu > The package (seems) to install ok > I then grab the latest source and do the usual python setup.py build jobbo > and get a massive raft of errors eg: > ...... > src/_proj.c:2353: error: ‘__pyx_kp_4’ undeclared here (not in a function) > src/_proj.c:2353: warning: excess elements in struct initializer > src/_proj.c:2353: warning: (near initialization for > ‘__pyx_string_tab[19]’) > src/_proj.c:2353: warning: excess elements in struct initializer > src/_proj.c:2353: warning: (near initialization for > ‘__pyx_string_tab[19]’) > src/_proj.c:2353: warning: excess elements in struct initializer > .. > .. > src/_proj.c:3155: error: expected ‘)’ before ‘*’ token > src/_proj.c:3170: error: expected ‘)’ before ‘*’ token > src/_proj.c:3185: error: expected ‘)’ before ‘*’ token > src/_proj.c:3200: error: expected ‘)’ before ‘*’ token > src/_proj.c:3215: error: expected ‘)’ before ‘*’ token > src/_proj.c:3230: error: expected ‘)’ before ‘*’ token > error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv > -O2 -Wall -Wstrict-prototypes -fPIC -Isrc > -I/usr/lib/python2.5/site-packages/numpy/core/include > -I/usr/include/python2.5 -c src/_proj.c -o > build/temp.linux-x86_64-2.5/src/_proj.o" failed with exit status 1 > (2) building libgeos from source... > I get the same error for 2.2.3 (a version I have had no problems > compiling on centos5 64bit machines in the past) and 3.0.0 > make[3]: Entering directory > `/home/scollis/geos-3.0.0/source/index/quadtree' > if /bin/bash ../../../libtool --tag=CXX --mode=compile g++ > -DHAVE_CONFIG_H -I. -I. -I../../../source/headers > -I../../../source/headers/geos -I../../../source/headers -g -O2 > -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo > -MD -MP -MF ".deps/DoubleBits.Tpo" -c -o DoubleBits.lo DoubleBits.cpp; \ > then mv -f ".deps/DoubleBits.Tpo" ".deps/DoubleBits.Plo"; else rm -f > ".deps/DoubleBits.Tpo"; exit 1; fi > g++ -DHAVE_CONFIG_H -I. -I. -I../../../source/headers > -I../../../source/headers/geos -I../../../source/headers -g -O2 > -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo > -MD -MP -MF .deps/DoubleBits.Tpo -c DoubleBits.cpp -fPIC -DPIC -o > .libs/DoubleBits.o > DoubleBits.cpp: In static member function 'static double > geos::index::quadtree::DoubleBits::powerOf2(int)': > DoubleBits.cpp:51: error: 'memcpy' was not declared in this scope > DoubleBits.cpp: In constructor > 'geos::index::quadtree::DoubleBits::DoubleBits(double)': > DoubleBits.cpp:94: error: 'memcpy' was not declared in this scope > make[3]: *** [DoubleBits.lo] Error 1 > make[3]: Leaving directory > `/home/scollis/geos-3.0.0/source/index/quadtree' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/home/scollis/geos-3.0.0/source/index' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/scollis/geos-3.0.0/source' > make: *** [all-recursive] Error 1 > ANY help very very very welcome! I am some what at a loss as I have > managed to compile both libgeos and basemap under much more "user > unfriendly" distros before... > Dr Scott Collis > Postdoctoral Researcher > Centre for Australian Weather and Climate Research (CAWCR) > Atmosphere and Land Observation and Assessment Group > Australian Bureau of Meteorology Room 9.57 Level 9 700 Collins Street > Docklands 3008 > Office: (03) 9669 4766 > MB: 0412177550 > http://www.bom.gov.au/bmrc/wefor/staff/scollis/ > Scott: I don't think the error compiling _proj.c has anything to do with libgeos, my guess is it can't find Python.h - perhaps you have to install a python-dev package? The geos compile error (can't find "memcpy") suggest that all your C header files are not found (I think that function is in "string.h"), which suggests that you haven't installed all the necessary gcc packages. -Jeff |
From: Jeff W. <js...@fa...> - 2009-01-07 16:18:10
|
Scott Collis wrote: > Greetings... > I have been using basemap extensively to do presentation graphics > under quite a wide variety of platforms but I got a new 64bit dual > core laptop recently and have been having all kinds of problems > installing it... > I am using (K)ubuntu 8.10 and have tried to install it two ways... > This is a 64bit system > (1) using the pre-compiles libgeos 3.0.0: > this is installed using the libgeos-dev package under ubuntu > The package (seems) to install ok > I then grab the latest source and do the usual python setup.py build jobbo > and get a massive raft of errors eg: > ...... > src/_proj.c:2353: error: ‘__pyx_kp_4’ undeclared here (not in a function) > src/_proj.c:2353: warning: excess elements in struct initializer > src/_proj.c:2353: warning: (near initialization for > ‘__pyx_string_tab[19]’) > src/_proj.c:2353: warning: excess elements in struct initializer > src/_proj.c:2353: warning: (near initialization for > ‘__pyx_string_tab[19]’) > src/_proj.c:2353: warning: excess elements in struct initializer > .. > .. > src/_proj.c:3155: error: expected ‘)’ before ‘*’ token > src/_proj.c:3170: error: expected ‘)’ before ‘*’ token > src/_proj.c:3185: error: expected ‘)’ before ‘*’ token > src/_proj.c:3200: error: expected ‘)’ before ‘*’ token > src/_proj.c:3215: error: expected ‘)’ before ‘*’ token > src/_proj.c:3230: error: expected ‘)’ before ‘*’ token > error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv > -O2 -Wall -Wstrict-prototypes -fPIC -Isrc > -I/usr/lib/python2.5/site-packages/numpy/core/include > -I/usr/include/python2.5 -c src/_proj.c -o > build/temp.linux-x86_64-2.5/src/_proj.o" failed with exit status 1 > (2) building libgeos from source... > I get the same error for 2.2.3 (a version I have had no problems > compiling on centos5 64bit machines in the past) and 3.0.0 > make[3]: Entering directory > `/home/scollis/geos-3.0.0/source/index/quadtree' > if /bin/bash ../../../libtool --tag=CXX --mode=compile g++ > -DHAVE_CONFIG_H -I. -I. -I../../../source/headers > -I../../../source/headers/geos -I../../../source/headers -g -O2 > -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo > -MD -MP -MF ".deps/DoubleBits.Tpo" -c -o DoubleBits.lo DoubleBits.cpp; \ > then mv -f ".deps/DoubleBits.Tpo" ".deps/DoubleBits.Plo"; else rm -f > ".deps/DoubleBits.Tpo"; exit 1; fi > g++ -DHAVE_CONFIG_H -I. -I. -I../../../source/headers > -I../../../source/headers/geos -I../../../source/headers -g -O2 > -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo > -MD -MP -MF .deps/DoubleBits.Tpo -c DoubleBits.cpp -fPIC -DPIC -o > .libs/DoubleBits.o > DoubleBits.cpp: In static member function 'static double > geos::index::quadtree::DoubleBits::powerOf2(int)': > DoubleBits.cpp:51: error: 'memcpy' was not declared in this scope > DoubleBits.cpp: In constructor > 'geos::index::quadtree::DoubleBits::DoubleBits(double)': > DoubleBits.cpp:94: error: 'memcpy' was not declared in this scope > make[3]: *** [DoubleBits.lo] Error 1 > make[3]: Leaving directory > `/home/scollis/geos-3.0.0/source/index/quadtree' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/home/scollis/geos-3.0.0/source/index' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/scollis/geos-3.0.0/source' > make: *** [all-recursive] Error 1 > ANY help very very very welcome! I am some what at a loss as I have > managed to compile both libgeos and basemap under much more "user > unfriendly" distros before... Scott: Could you try this modification to DoubleBits.cpp and let me know if it fixes the geos-2.2.3 compilation? I think you must be using gcc 4.3, which is much pickier than earlier versions about such things. Index: source/index/quadtree/DoubleBits.cpp =================================================================== --- source/index/quadtree/DoubleBits.cpp (revision 6729) +++ source/index/quadtree/DoubleBits.cpp (working copy) @@ -15,6 +15,7 @@ #include <geos/indexQuadtree.h> #include <geos/util.h> +#include <string> #include <cstring> Thanks, -Jeff > Dr Scott Collis > Postdoctoral Researcher > Centre for Australian Weather and Climate Research (CAWCR) > Atmosphere and Land Observation and Assessment Group > Australian Bureau of Meteorology Room 9.57 Level 9 700 Collins Street > Docklands 3008 > Office: (03) 9669 4766 > MB: 0412177550 > http://www.bom.gov.au/bmrc/wefor/staff/scollis/ > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Check out the new SourceForge.net Marketplace. > It is the best place to buy or sell services for > just about anything Open Source. > http://p.sf.net/sfu/Xq1LFB > ------------------------------------------------------------------------ > > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users > -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-113 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg |
From: Scott C. <S.C...@bo...> - 2009-01-07 21:12:42
|
Thanks Jeff or all your help (and Scott too... and all the people that have posted to this list over the years... it is an amazing source of information... A great example of why open source works so well for those in the scientific community) Jeff's libgeos mod worked... after some massaging.. I needed to put #include <cstring> in: ../source/io/StringTokenizer.cpp ../source/io/ByteOrderValues.cpp ../source/capi/geos_c.cpp (and #include <string> must be retained) ../source/io/markup/MarkupSTL.cpp (also inserted #include <string>) ../source/io/markup/MarkupSTL.h libgeos then compiled and I was able install basemap (tested by running the garp.py example...) fingers crossed the rest of my code works.. As noted it seems to be an issue with gcc4.3 requiring more explicit coding... Dr Scott Collis Postdoctoral Researcher Centre for Australian Weather and Climate Research (CAWCR) Atmosphere and Land Observation and Assessment Group Australian Bureau of Meteorology Room 9.57 Level 9 700 Collins Street Docklands 3008 Office: (03) 9669 4766 MB: 0412177550 http://www.bom.gov.au/bmrc/wefor/staff/scollis/ ________________________________ From: Jeff Whitaker [mailto:js...@fa...] Sent: Thu 8/01/2009 3:16 AM To: Scott Collis Cc: mat...@li... Subject: Re: [Matplotlib-users] All kinds of issues inslalling basemap under Ubuntu 8.10 64bit [SEC=UNCLASSIFIED] Scott Collis wrote: > Greetings... > I have been using basemap extensively to do presentation graphics > under quite a wide variety of platforms but I got a new 64bit dual > core laptop recently and have been having all kinds of problems > installing it... > I am using (K)ubuntu 8.10 and have tried to install it two ways... > This is a 64bit system > (1) using the pre-compiles libgeos 3.0.0: > this is installed using the libgeos-dev package under ubuntu > The package (seems) to install ok > I then grab the latest source and do the usual python setup.py build jobbo > and get a massive raft of errors eg: > ...... > src/_proj.c:2353: error: '__pyx_kp_4' undeclared here (not in a function) > src/_proj.c:2353: warning: excess elements in struct initializer > src/_proj.c:2353: warning: (near initialization for > '__pyx_string_tab[19]') > src/_proj.c:2353: warning: excess elements in struct initializer > src/_proj.c:2353: warning: (near initialization for > '__pyx_string_tab[19]') > src/_proj.c:2353: warning: excess elements in struct initializer > .. > .. > src/_proj.c:3155: error: expected ')' before '*' token > src/_proj.c:3170: error: expected ')' before '*' token > src/_proj.c:3185: error: expected ')' before '*' token > src/_proj.c:3200: error: expected ')' before '*' token > src/_proj.c:3215: error: expected ')' before '*' token > src/_proj.c:3230: error: expected ')' before '*' token > error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv > -O2 -Wall -Wstrict-prototypes -fPIC -Isrc > -I/usr/lib/python2.5/site-packages/numpy/core/include > -I/usr/include/python2.5 -c src/_proj.c -o > build/temp.linux-x86_64-2.5/src/_proj.o" failed with exit status 1 > (2) building libgeos from source... > I get the same error for 2.2.3 (a version I have had no problems > compiling on centos5 64bit machines in the past) and 3.0.0 > make[3]: Entering directory > `/home/scollis/geos-3.0.0/source/index/quadtree' > if /bin/bash ../../../libtool --tag=CXX --mode=compile g++ > -DHAVE_CONFIG_H -I. -I. -I../../../source/headers > -I../../../source/headers/geos -I../../../source/headers -g -O2 > -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo > -MD -MP -MF ".deps/DoubleBits.Tpo" -c -o DoubleBits.lo DoubleBits.cpp; \ > then mv -f ".deps/DoubleBits.Tpo" ".deps/DoubleBits.Plo"; else rm -f > ".deps/DoubleBits.Tpo"; exit 1; fi > g++ -DHAVE_CONFIG_H -I. -I. -I../../../source/headers > -I../../../source/headers/geos -I../../../source/headers -g -O2 > -DGEOS_INLINE -Wall -ansi -pedantic -Wno-long-long -MT DoubleBits.lo > -MD -MP -MF .deps/DoubleBits.Tpo -c DoubleBits.cpp -fPIC -DPIC -o > .libs/DoubleBits.o > DoubleBits.cpp: In static member function 'static double > geos::index::quadtree::DoubleBits::powerOf2(int)': > DoubleBits.cpp:51: error: 'memcpy' was not declared in this scope > DoubleBits.cpp: In constructor > 'geos::index::quadtree::DoubleBits::DoubleBits(double)': > DoubleBits.cpp:94: error: 'memcpy' was not declared in this scope > make[3]: *** [DoubleBits.lo] Error 1 > make[3]: Leaving directory > `/home/scollis/geos-3.0.0/source/index/quadtree' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/home/scollis/geos-3.0.0/source/index' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/scollis/geos-3.0.0/source' > make: *** [all-recursive] Error 1 > ANY help very very very welcome! I am some what at a loss as I have > managed to compile both libgeos and basemap under much more "user > unfriendly" distros before... Scott: Could you try this modification to DoubleBits.cpp and let me know if it fixes the geos-2.2.3 compilation? I think you must be using gcc 4.3, which is much pickier than earlier versions about such things. Index: source/index/quadtree/DoubleBits.cpp =================================================================== --- source/index/quadtree/DoubleBits.cpp (revision 6729) +++ source/index/quadtree/DoubleBits.cpp (working copy) @@ -15,6 +15,7 @@ #include <geos/indexQuadtree.h> #include <geos/util.h> +#include <string> #include <cstring> Thanks, -Jeff > Dr Scott Collis > Postdoctoral Researcher > Centre for Australian Weather and Climate Research (CAWCR) > Atmosphere and Land Observation and Assessment Group > Australian Bureau of Meteorology Room 9.57 Level 9 700 Collins Street > Docklands 3008 > Office: (03) 9669 4766 > MB: 0412177550 > http://www.bom.gov.au/bmrc/wefor/staff/scollis/ > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Check out the new SourceForge.net Marketplace. > It is the best place to buy or sell services for > just about anything Open Source. > http://p.sf.net/sfu/Xq1LFB > ------------------------------------------------------------------------ > > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users > -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-113 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg |