[Phylobase-devl] New phylobase build approach using static libncl (Was: Rcpp and OS X compiliation)
Peter Cowan
pdc at berkeley.edu
Sat Jan 30 21:47:49 CET 2010
Thanks Dirk, Mark, Romain, Simon and others who have worked on this. Getting this fixed has been on my wish list for a long time, but well beyond my abilities.
I recently found some time to attempt building phylobase on my mac (10.6.2) w/ 64bit R 2.10.1 and phylobase r725. I haven't been able to compile the package, it looks like it might be a configure issue, any suggestions for what I should look into changing?
Peter
a directory
* installing to library ‘/Library/Frameworks/R.framework/Resources/library’
* created lock directory ‘/Library/Frameworks/R.framework/Resources/library/00LOCK’
* build_help_types=
* DBG: R CMD INSTALL' now doing do_install
* installing *source* package ‘phylobase’ ...
** backing up earlier installation
configure command: ‘ ./configure ’
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-4.2 -arch x86_64 accepts -g... yes
checking how to run the C++ preprocessor... g++-4.2 -arch x86_64 -E
checking for R... yes
checking for Rscript... yes
configure: starting to build libncl.a in ncl
./configure: line 620: test: too many arguments
./configure: line 620: test: too many arguments
./configure: line 620: test: too many arguments
./configure: line 620: test: too many arguments
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
./configure: line 17133: sort: No such file or directory
./configure: line 17130: sed: No such file or directory
./configure: line 19694: sort: No such file or directory
./configure: line 19691: sed: No such file or directory
make all-recursive
Making all in ncl
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxsdatablock.lo -MD -MP -MF .deps/nxsdatablock.Tpo -c nxsdatablock.cpp -o nxsdatablock.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxsdistancedatum.lo -MD -MP -MF .deps/nxsdistancedatum.Tpo -c nxsdistancedatum.cpp -o nxsdistancedatum.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxsdistancesblock.lo -MD -MP -MF .deps/nxsdistancesblock.Tpo -c nxsdistancesblock.cpp -o nxsdistancesblock.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxsexception.lo -MD -MP -MF .deps/nxsexception.Tpo -c nxsexception.cpp -o nxsexception.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxspublicblocks.lo -MD -MP -MF .deps/nxspublicblocks.Tpo -c nxspublicblocks.cpp -o nxspublicblocks.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxsreader.lo -MD -MP -MF .deps/nxsreader.Tpo -c nxsreader.cpp -o nxsreader.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxstaxablock.lo -MD -MP -MF .deps/nxstaxablock.Tpo -c nxstaxablock.cpp -o nxstaxablock.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxstoken.lo -MD -MP -MF .deps/nxstoken.Tpo -c nxstoken.cpp -o nxstoken.o
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -O3 -ffast-math -MT nxsunalignedblock.lo -MD -MP -MF .deps/nxsunalignedblock.Tpo -c nxsunalignedblock.cpp -o nxsunalignedblock.o
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ranlib: file: .libs/libncl.a(nxsdistancedatum.o) has no symbols
libtool: link: ranlib .libs/libncl.a
ranlib: file: .libs/libncl.a(nxsdistancedatum.o) has no symbols
libtool: link: ( cd ".libs" && rm -f "libncl.la" && ln -s "../libncl.la" "libncl.la" )
Making all in example
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Making install in ncl
test -z "/private/tmp/tmpIdDKYW/src/ncl/../lib/ncl" || ../config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../lib/ncl"
/bin/sh ../libtool --mode=install /usr/bin/install -c 'libncl.la' '/private/tmp/tmpIdDKYW/src/ncl/../lib/ncl/libncl.la'
libtool: install: /usr/bin/install -c .libs/libncl.lai /private/tmp/tmpIdDKYW/src/ncl/../lib/ncl/libncl.la
libtool: install: /usr/bin/install -c .libs/libncl.a /private/tmp/tmpIdDKYW/src/ncl/../lib/ncl/libncl.a
libtool: install: chmod 644 /private/tmp/tmpIdDKYW/src/ncl/../lib/ncl/libncl.a
libtool: install: ranlib /private/tmp/tmpIdDKYW/src/ncl/../lib/ncl/libncl.a
ranlib: file: /private/tmp/tmpIdDKYW/src/ncl/../lib/ncl/libncl.a(nxsdistancedatum.o) has no symbols
----------------------------------------------------------------------
Libraries have been installed in:
/private/tmp/tmpIdDKYW/src/ncl/../lib/ncl
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/private/tmp/tmpIdDKYW/src/ncl/../include/ncl" || ../config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../include/ncl"
/usr/bin/install -c -m 644 'ncl.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/ncl.h'
/usr/bin/install -c -m 644 'nxsallocatematrix.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsallocatematrix.h'
/usr/bin/install -c -m 644 'nxsassumptionsblock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsassumptionsblock.h'
/usr/bin/install -c -m 644 'nxsblock.cpp' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsblock.cpp'
/usr/bin/install -c -m 644 'nxsblock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsblock.h'
/usr/bin/install -c -m 644 'nxscharactersblock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxscharactersblock.h'
/usr/bin/install -c -m 644 'nxscdiscretematrix.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxscdiscretematrix.h'
/usr/bin/install -c -m 644 'nxscxxdiscretematrix.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxscxxdiscretematrix.h'
/usr/bin/install -c -m 644 'nxsdatablock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsdatablock.h'
/usr/bin/install -c -m 644 'nxsdefs.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsdefs.h'
/usr/bin/install -c -m 644 'nxsdiscretedatum.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsdiscretedatum.h'
/usr/bin/install -c -m 644 'nxsdistancedatum.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsdistancedatum.h'
/usr/bin/install -c -m 644 'nxsdistancesblock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsdistancesblock.h'
/usr/bin/install -c -m 644 'nxsexception.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsexception.h'
/usr/bin/install -c -m 644 'nxsmultiformat.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsmultiformat.h'
/usr/bin/install -c -m 644 'nxspublicblocks.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxspublicblocks.h'
/usr/bin/install -c -m 644 'nxsreader.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsreader.h'
/usr/bin/install -c -m 644 'nxssetreader.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxssetreader.h'
/usr/bin/install -c -m 644 'nxsstring.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsstring.h'
/usr/bin/install -c -m 644 'nxstaxablock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxstaxablock.h'
/usr/bin/install -c -m 644 'nxstoken.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxstoken.h'
/usr/bin/install -c -m 644 'nxstreesblock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxstreesblock.h'
/usr/bin/install -c -m 644 'nxsunalignedblock.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsunalignedblock.h'
/usr/bin/install -c -m 644 'nxsutilcopy.h' '/private/tmp/tmpIdDKYW/src/ncl/../include/ncl/nxsutilcopy.h'
Making install in example
Making install in nclsimplest
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
Making install in ncltest
test -z "/private/tmp/tmpIdDKYW/src/ncl/../bin" || ../../config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../bin"
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'ncltest' '/private/tmp/tmpIdDKYW/src/ncl/../bin/ncltest'
libtool: install: /usr/bin/install -c ncltest /private/tmp/tmpIdDKYW/src/ncl/../bin/ncltest
make[3]: Nothing to be done for `install-data-am'.
Making install in basiccmdline
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
Making install in normalizer
test -z "/private/tmp/tmpIdDKYW/src/ncl/../bin" || ../../config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../bin"
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEXUSnormalizer' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSnormalizer'
libtool: install: /usr/bin/install -c NEXUSnormalizer /private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSnormalizer
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEXUSvalidator' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSvalidator'
libtool: install: /usr/bin/install -c NEXUSvalidator /private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSvalidator
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEXUSinspector' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSinspector'
libtool: install: /usr/bin/install -c NEXUSinspector /private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSinspector
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEX_us2ml' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEX_us2ml'
libtool: install: /usr/bin/install -c NEX_us2ml /private/tmp/tmpIdDKYW/src/ncl/../bin/NEX_us2ml
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEXUSunion' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSunion'
libtool: install: /usr/bin/install -c NEXUSunion /private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSunion
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NCLconverter' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NCLconverter'
libtool: install: /usr/bin/install -c NCLconverter /private/tmp/tmpIdDKYW/src/ncl/../bin/NCLconverter
make[3]: Nothing to be done for `install-data-am'.
Making install in basicfactory
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
Making install in patristic
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
Making install in gapcode
test -z "/private/tmp/tmpIdDKYW/src/ncl/../bin" || ../../config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../bin"
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEXUSgapcode' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSgapcode'
libtool: install: /usr/bin/install -c NEXUSgapcode /private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUSgapcode
make[3]: Nothing to be done for `install-data-am'.
Making install in splitsinfile
test -z "/private/tmp/tmpIdDKYW/src/ncl/../bin" || ../../config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../bin"
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEXUStosplits' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUStosplits'
libtool: install: /usr/bin/install -c NEXUStosplits /private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUStosplits
make[3]: Nothing to be done for `install-data-am'.
Making install in translate
test -z "/private/tmp/tmpIdDKYW/src/ncl/../bin" || ../../config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../bin"
/bin/sh ../../libtool --mode=install /usr/bin/install -c 'NEXUStranslate' '/private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUStranslate'
libtool: install: /usr/bin/install -c NEXUStranslate /private/tmp/tmpIdDKYW/src/ncl/../bin/NEXUStranslate
make[3]: Nothing to be done for `install-data-am'.
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
Making install in test
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Nothing to be done for `install-exec-am'.
test -z "/private/tmp/tmpIdDKYW/src/ncl/../lib/pkgconfig" || config/install-sh -c -d "/private/tmp/tmpIdDKYW/src/ncl/../lib/pkgconfig"
/usr/bin/install -c -m 644 'nclv2.1.pc' '/private/tmp/tmpIdDKYW/src/ncl/../lib/pkgconfig/nclv2.1.pc'
configure: finished building libncl.a in ncl
./configure: line 2579: sort: No such file or directory
./configure: line 2576: sed: No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
./configure: line 3703: sort: No such file or directory
./configure: line 3700: sed: No such file or directory
** libs
** arch - x86_64
about to run R CMD SHLIB -o phylobase.so NCLInterface.cpp ReadWithNCL.cpp ancestors.c descendants.c phyloXX.c reorderBinary.c reorderRobust.c
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I/Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64 -Iinclude/ncl -fPIC -mtune=core2 -g -O2 -c NCLInterface.cpp -o NCLInterface.o
In file included from NCLInterface.cpp:24:
include/ncl/ncl.h:89:25: error: ncl/nxsdefs.h: No such file or directory
include/ncl/ncl.h:90:27: error: ncl/nxsstring.h: No such file or directory
include/ncl/ncl.h:91:30: error: ncl/nxsexception.h: No such file or directory
include/ncl/ncl.h:92:26: error: ncl/nxstoken.h: No such file or directory
include/ncl/ncl.h:93:26: error: ncl/nxsblock.h: No such file or directory
include/ncl/ncl.h:94:27: error: ncl/nxsreader.h: No such file or directory
include/ncl/ncl.h:95:30: error: ncl/nxssetreader.h: No such file or directory
include/ncl/ncl.h:96:30: error: ncl/nxstaxablock.h: No such file or directory
include/ncl/ncl.h:97:31: error: ncl/nxstreesblock.h: No such file or directory
include/ncl/ncl.h:98:34: error: ncl/nxsdistancedatum.h: No such file or directory
include/ncl/ncl.h:99:35: error: ncl/nxsdistancesblock.h: No such file or directory
include/ncl/ncl.h:100:34: error: ncl/nxsdiscretedatum.h: No such file or directory
include/ncl/ncl.h:101:36: error: ncl/nxscharactersblock.h: No such file or directory
include/ncl/ncl.h:102:37: error: ncl/nxsassumptionsblock.h: No such file or directory
include/ncl/ncl.h:103:30: error: ncl/nxsdatablock.h: No such file or directory
include/ncl/ncl.h:104:35: error: ncl/nxsunalignedblock.h: No such file or directory
include/ncl/ncl.h:105:33: error: ncl/nxspublicblocks.h: No such file or directory
include/ncl/ncl.h:106:32: error: ncl/nxsmultiformat.h: No such file or directory
In file included from NCLInterface.cpp:25:
NCLInterface.h:75: error: expected class-name before ‘,’ token
NCLInterface.h:77: error: expected class-name before ‘{’ token
NCLInterface.h:91: error: ‘NxsString’ has not been declared
NCLInterface.h:92: error: ‘NxsString’ has not been declared
NCLInterface.h:95: error: expected ‘,’ or ‘...’ before ‘&’ token
NCLInterface.h:95: error: ISO C++ forbids declaration of ‘NxsString’ with no type
NCLInterface.h:97: error: ‘NxsString’ has not been declared
NCLInterface.h:97: error: ‘file_pos’ has not been declared
NCLInterface.h:103: error: ‘NxsString’ has not been declared
NCLInterface.h:104: error: ‘NxsString’ has not been declared
NCLInterface.h:105: error: ‘NxsString’ has not been declared
NCLInterface.h:106: error: ‘NxsString’ has not been declared
NCLInterface.h:106: error: ‘NxsString’ has not been declared
NCLInterface.h:107: error: ‘NxsToken’ has not been declared
NCLInterface.h:108: error: ‘NxsString’ does not name a type
NCLInterface.h:109: error: ‘NxsString’ does not name a type
NCLInterface.h:110: error: ‘NxsString’ has not been declared
NCLInterface.h:111: error: ‘NxsString’ has not been declared
NCLInterface.h:112: error: ‘NxsString’ has not been declared
NCLInterface.h:121: error: ‘NxsString’ does not name a type
NCLInterface.h:122: error: ISO C++ forbids declaration of ‘NxsTreesBlock’ with no type
NCLInterface.h:122: error: expected ‘;’ before ‘*’ token
NCLInterface.h:123: error: ISO C++ forbids declaration of ‘NxsTaxaBlock’ with no type
NCLInterface.h:123: error: expected ‘;’ before ‘*’ token
NCLInterface.h:124: error: ISO C++ forbids declaration of ‘NxsAssumptionsBlock’ with no type
NCLInterface.h:124: error: expected ‘;’ before ‘*’ token
NCLInterface.h:125: error: ISO C++ forbids declaration of ‘NxsDistancesBlock’ with no type
NCLInterface.h:125: error: expected ‘;’ before ‘*’ token
NCLInterface.h:126: error: ISO C++ forbids declaration of ‘NxsCharactersBlock’ with no type
NCLInterface.h:126: error: expected ‘;’ before ‘*’ token
NCLInterface.h:127: error: ISO C++ forbids declaration of ‘NxsDataBlock’ with no type
NCLInterface.h:127: error: expected ‘;’ before ‘*’ token
NCLInterface.h:129: error: ‘NxsString’ has not been declared
NCLInterface.h:131: error: ‘NxsString’ does not name a type
NCLInterface.h:133: error: ‘NxsToken’ has not been declared
NCLInterface.h:134: error: ‘NxsToken’ has not been declared
NCLInterface.h:135: error: ‘NxsToken’ has not been declared
NCLInterface.h:136: error: ‘NxsToken’ has not been declared
NCLInterface.h:137: error: ‘NxsToken’ has not been declared
NCLInterface.h:139: error: ‘NxsToken’ has not been declared
NCLInterface.h:141: error: ‘NxsString’ has not been declared
NCLInterface.h:150: error: expected class-name before ‘{’ token
NCLInterface.h:154: error: expected ‘,’ or ‘...’ before ‘&’ token
NCLInterface.h:154: error: ISO C++ forbids declaration of ‘NxsString’ with no type
NCLInterface.h:181: error: expected ‘,’ or ‘...’ before ‘&’ token
NCLInterface.h:181: error: ISO C++ forbids declaration of ‘NxsString’ with no type
NCLInterface.cpp: In constructor ‘MyNexusToken::MyNexusToken(std::istream&)’:
NCLInterface.cpp:34: error: class ‘MyNexusToken’ does not have any field named ‘NxsToken’
NCLInterface.cpp: At global scope:
NCLInterface.cpp:44: error: expected ‘,’ or ‘...’ before ‘&’ token
NCLInterface.cpp:44: error: ISO C++ forbids declaration of ‘NxsString’ with no type
NCLInterface.cpp: In member function ‘void MyNexusToken::OutputComment(int)’:
NCLInterface.cpp:46: error: ‘msg’ was not declared in this scope
NCLInterface.cpp: In constructor ‘BASICCMDLINE::BASICCMDLINE()’:
NCLInterface.cpp:56: error: ‘id’ was not declared in this scope
NCLInterface.cpp:62: error: ‘taxa’ was not declared in this scope
NCLInterface.cpp:63: error: ‘trees’ was not declared in this scope
NCLInterface.cpp:64: error: ‘assumptions’ was not declared in this scope
NCLInterface.cpp:65: error: ‘distances’ was not declared in this scope
NCLInterface.cpp:66: error: ‘characters’ was not declared in this scope
NCLInterface.cpp:67: error: ‘data’ was not declared in this scope
NCLInterface.cpp: At global scope:
NCLInterface.cpp:94: error: ‘unsigned int BASICCMDLINE::CharLabelToNumber’ is not a static member of ‘class BASICCMDLINE’
NCLInterface.cpp:94: error: ‘NxsString’ was not declared in this scope
NCLInterface.cpp:95: error: expected ‘,’ or ‘;’ before ‘{’ token
NCLInterface.cpp:106: error: ‘bool BASICCMDLINE::EnteringBlock’ is not a static member of ‘class BASICCMDLINE’
NCLInterface.cpp:106: error: ‘NxsString’ was not declared in this scope
NCLInterface.cpp:107: error: expected ‘,’ or ‘;’ before ‘{’ token
NCLInterface.cpp:121: error: variable or field ‘ExitingBlock’ declared void
NCLInterface.cpp:121: error: ‘NxsString’ was not declared in this scope
NCLInterface.cpp: In member function ‘void BASICCMDLINE::FactoryDefaults()’:
NCLInterface.cpp:133: error: ‘isEmpty’ was not declared in this scope
NCLInterface.cpp:137: error: ‘message’ was not declared in this scope
NCLInterface.cpp:139: error: ‘trees’ was not declared in this scope
NCLInterface.cpp:141: error: ‘Detach’ was not declared in this scope
NCLInterface.cpp:142: error: type ‘’ argument given to ‘delete’, expected pointer
NCLInterface.cpp:146: error: ‘taxa’ was not declared in this scope
NCLInterface.cpp:148: error: ‘Detach’ was not declared in this scope
NCLInterface.cpp:149: error: type ‘’ argument given to ‘delete’, expected pointer
NCLInterface.cpp:153: error: ‘assumptions’ was not declared in this scope
NCLInterface.cpp:155: error: ‘Detach’ was not declared in this scope
NCLInterface.cpp:156: error: type ‘’ argument given to ‘delete’, expected pointer
NCLInterface.cpp:160: error: ‘distances’ was not declared in this scope
NCLInterface.cpp:162: error: ‘Detach’ was not declared in this scope
NCLInterface.cpp:163: error: type ‘’ argument given to ‘delete’, expected pointer
NCLInterface.cpp:167: error: ‘characters’ was not declared in this scope
NCLInterface.cpp:169: error: ‘Detach’ was not declared in this scope
NCLInterface.cpp:170: error: type ‘’ argument given to ‘delete’, expected pointer
NCLInterface.cpp:174: error: ‘data’ was not declared in this scope
NCLInterface.cpp:176: error: ‘Detach’ was not declared in this scope
NCLInterface.cpp:177: error: type ‘’ argument given to ‘delete’, expected pointer
NCLInterface.cpp: At global scope:
NCLInterface.cpp:214: error: ‘NxsString’ does not name a type
NCLInterface.cpp:237: error: variable or field ‘HandleReturnData’ declared void
NCLInterface.cpp:237: error: ‘NxsToken’ was not declared in this scope
NCLInterface.cpp:237: error: ‘token’ was not declared in this scope
make: *** [NCLInterface.o] Error 1
ERROR: compilation failed for package ‘phylobase’
* removing ‘/Library/Frameworks/R.framework/Resources/library/phylobase’
* restoring previous ‘/Library/Frameworks/R.framework/Resources/library/phylobase’
On Jan 23, 2010, at 10:04 PM, Dirk Eddelbuettel wrote:
>
> Thanks to the excellent debugging work by Mark Holder, as well as some help
> from Simon Urbanek, we finally got OS X and Rcpp to be nice to each other:
> static linking lets everybody be friends.
>
> This was encoded in Rcpp 0.7.3 which was released earlier this week. So I
> figured it was time to get back to the rest of the phylobase build. And a
> few days earlier I had suggested:
>
> On 11 January 2010 at 08:55, Dirk Eddelbuettel wrote:
> | I am still game. I see a three-pronged approach:
> |
> | i) Suggestion Let's fix NCL and have a locally built version outside
> | of phylobase on all test platforms
> |
> | ii) With that, fix/simplify Rcpp usage. Should be easy
> |
> | iii) With that, get back to i) and clean up NCL's configure.
> |
> | I think it would be easier to disentangle Rcpp and NCL inside phylobase while
> | we make this more.
>
> And I just committed a simple and easy fix to phylobase's SVN on R-Forge. In
> a nutshell, we were just descending down to ncl's source directory and saying
> 'configure; make' which leaves the ncl library unfinished. The mighty libtool
> would normally run over it once more during 'make install'.
>
> So I changed it to this (and recall that this is relative to top-level
> directory for phylobase):
>
> cd src/ncl
> ./configure --quiet --enable-static --disable-shared --prefix=`pwd`/..
> make
> make install
> cd ../..
>
> So we ask for a static library (and no dynamic library), and we tell
> configure to put it simply one directory up. That works well enough! I also
> changed the CPPFLAGS and LDFLAGS accordingly: include/ncl and lib/ncl are now
> created during that new 'make install' step:
>
> ## configure include/load flags and copy sample source to inst/doc
> AC_SUBST([CPPFLAGS],["${CPPFLAGS} ${rcpp_cxxflags} -Iinclude/ncl"])
> AC_SUBST([LDFLAGS],["${LDFLAGS} ${rcpp_ldflags} -Llib/ncl -lncl"])
>
> With that phylobase builds and installs fine on my Linux machine and
> (finger's crossed!!) should do the same on other people's Linux and OS X
> boxen. So if over the next few days you have a moment, could you update from
> SVN and give it a whirl?
>
> Cheers, Dirk
>
> --
> Three out of two people have difficulties with fractions.
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