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ergo70 / pgchem_tigress

Pgchem::tigress is the chemoinformatics extension to the PostgreSQL DBMS. It enables PostgreSQL to handle molecules through SQL statements.
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obwrapper.cpp issue #1

Closed telukir closed 8 years ago

telukir commented 8 years ago

I am getting a make error as following:

g++ -fPIC -O2 -finline-functions -funroll-loops -I. -Iopenbabel-2.3.2/build/include/ -Iopenbabel-2.3.2/include/ -Iopenbabel-2.3.2/include/openbabel/ -Iopenbabel-2.3.2/build/ -I../../../src/backend/ -I. -I. -I../../../src/include -D_GNU_SOURCE -c -o obwrapper.o obwrapper.cpp obwrapper.cpp:114:12: error: '_ISOTOPE_PATTERN' does not name a type extern "C" _ISOTOPE_PATTERN * ^

: recipe for target 'obwrapper.o' failed make: **\* [obwrapper.o] Error 1 This is coming in the file obrapper.cpp `extern "C" _ISOTOPE_PATTERN * ob_molfile_to_isotope_pattern(char *molfile, int charge, double normal) { _ISOTOPE_PATTERN *retval; vector msa_mz; vector msa_abundance; vector composition; vector m; const double limit = 10e-30; OBMol mol; OBConversion conv; string tmpStr (molfile); istringstream molstream (tmpStr); double main_peak_mass=0.0, scale = 1.0, maxintensity;` is it correct or what should be changed?
ergo70 commented 8 years ago

No, this is not correct. I'll check.

ergo70 commented 8 years ago

Hm, I just cloned the repository fresh from github, added OpenBabel 2.3.2 and compiled with 'make -f Makefile.linux.x64' - no errors.

_ISOTOPE_PATTERN is defined in obwrapper.h. Wrong include path? What is the command you are using to build?