Dear fink programmers,
I have encountered the following problem when updating fink packages:
Linking CXX static library libGraphMol_static.a
[ 37%] Built target GraphMol_static
[ 38%] [FLEX][SmartsL] Building scanner with flex 2.5.35
[ 38%] [BISON][SmilesY] Building parser with bison 3.0
smiles.yy:1.1-12: Warnung: deprecated directive, use „%pure-parser“
[-Wdeprecated]
%pure_parser
^^^^^^^^^^^^
[ 38%] [BISON][SmartsY] Building parser with bison 3.0
smarts.yy:1.1-12: Warnung: deprecated directive, use „%pure-parser“
[-Wdeprecated]
%pure_parser
^^^^^^^^^^^^
smarts.yy: Warnung: 86 shift/reduce conflicts [-Wconflicts-sr]
[ 38%] [FLEX][SmilesL] Building scanner with flex 2.5.35
Scanning dependencies of target SmilesParse
[ 38%] Building CXX object
Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o
[ 38%] Building CXX object
Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o
[ 38%] Building CXX object
Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o
[ 39%] Building CXX object
Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o
[ 39%] Building CXX object
Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o
smiles.yy:25:1: warning: "YYDEBUG" redefined
In file included from smiles.yy:21:
/sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.hpp:37:1:
warning: this is the location of the previous definition
smiles.yy: In function 'int yysmiles_parse(const char*,
std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >*, std::list<unsigned
int, std::allocator<unsigned int> >*, void*)':
smiles.yy:23: error: too few arguments to function 'int yysmiles_lex(YYSTYPE*,
void*)'
/sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.cpp:1245:
error: at this point in file
make[2]: ***
[Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o] Error 1
make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error 2
make: *** [all] Error 2
### execution of /tmp/fink.tFAYE failed, exit code 2
### execution of /tmp/fink.35L3b failed, exit code 2
Removing runtime build-lock...
Removing build-lock package...
/sw64/bin/dpkg-lockwait -r fink-buildlock-rdkit-2013.06.1-5
(Reading database ... 220471 files and directories currently installed.)
Removing fink-buildlock-rdkit-2013.06.1-5 ...
Failed: phase compiling: rdkit-2013.06.1-5 failed
Package manager version: 0.35.1
Distribution version: selfupdate-cvs Wed Sep 25 10:20:40 2013, 10.6, x86_64
Trees: local/main stable/main stable/crypto unstable/main unstable/crypto
Xcode.app: 3.2.6
Xcode command-line tools: 3.2.6
Max. Fink build jobs: 1
I have updated fink via selfupdate, but the problem persists.
Thank you for your help.
Kind regards,
Magdalena
---------------------------
Magdalena Schacherl, Ph.D.
Cologne University
Institute of Biochemistry
Structural biology / Group Prof. Baumann
Otto-Fischer-Str. 14
50674 Köln
Germany
+49 221 470 3212 (phone)
+49 221 470 5066 (fax)
[email protected]
www.px.uni-koeln.de
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