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@claczny
Created September 14, 2017 07:13
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Error message when installing lotus v.1.57
doneCompiling sdm..
make: Entering directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o Demultipl.o Demultipl.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o containers.o containers.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o IO.o IO.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o InputStream.o InputStream.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o DNAconsts.o DNAconsts.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 Demultipl.o containers.o IO.o InputStream.o DNAconsts.o -lz -o sdm
make: Leaving directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
Installing sdm:
/home/cedric/apps/software/lotus_pipeline_1.57//sdm
doneCompiling LCA..
make: Entering directory '/home/cedric/apps/software/lotus_pipeline_1.57/LCA_src'
g++ -Wall -O3 -std=c++0x -lz -D__USE_XOPEN2K8 -c -o RefTax.o RefTax.cpp
In file included from RefTax.h:2:0,
from RefTax.cpp:1:
libload.h:53:12: warning: ‘__default_depth’ defined but not used [-Wunused-variable]
static int __default_depth = 7;
^
g++ -Wall -O3 -std=c++0x -lz -D__USE_XOPEN2K8 -c -o Matrix.o Matrix.cpp
In file included from Matrix.h:2:0,
from Matrix.cpp:1:
libload.h:53:12: warning: ‘__default_depth’ defined but not used [-Wunused-variable]
static int __default_depth = 7;
^
g++ -Wall -O3 -std=c++0x -lz -D__USE_XOPEN2K8 -c -o LCA.o LCA.cpp
g++ -Wall -O3 -std=c++0x -lz -D__USE_XOPEN2K8 -c -o options.o options.cpp
In file included from options.cpp:1:0:
options.h: In constructor ‘options::options(int, char**, int)’:
options.h:32:17: warning: ‘options::Taxlvls’ will be initialized after [-Wreorder]
vector<string> Taxlvls;
^
options.h:25:7: warning: ‘bool options::reportBestHit’ [-Wreorder]
bool reportBestHit; //reports best hit, if higher than required %id
^
options.cpp:33:1: warning: when initialized here [-Wreorder]
options::options(int argc, char **argv,int defDep):
^
In file included from options.h:2:0,
from options.cpp:1:
libload.h: At global scope:
libload.h:53:12: warning: ‘__default_depth’ defined but not used [-Wunused-variable]
static int __default_depth = 7;
^
g++ -Wall -O3 -std=c++0x -lz -D__USE_XOPEN2K8 -c -o LCAimpl.o LCAimpl.cpp
LCAimpl.cpp: In function ‘TaxObj* LCA(std::__cxx11::list<BlastRes*>, RefTax*, options*)’:
LCAimpl.cpp:10:9: warning: variable ‘bestScore’ set but not used [-Wunused-but-set-variable]
double bestScore(0.f);
^
g++ -Wall -O3 -std=c++0x -lz -D__USE_XOPEN2K8 RefTax.o Matrix.o LCA.o options.o LCAimpl.o -o LCA
RefTax.o: In function `BlastReader::BlastReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
RefTax.cpp:(.text+0x16b4): undefined reference to `gzopen'
RefTax.cpp:(.text+0x18f4): undefined reference to `gzwrite'
RefTax.cpp:(.text+0x1912): undefined reference to `gzclose'
RefTax.o: In function `gzstreambuf::underflow()':
RefTax.cpp:(.text._ZN11gzstreambuf9underflowEv[_ZN11gzstreambuf9underflowEv]+0x87): undefined reference to `gzread'
RefTax.o: In function `gzstreambuf::sync()':
RefTax.cpp:(.text._ZN11gzstreambuf4syncEv[_ZN11gzstreambuf4syncEv]+0x28): undefined reference to `gzwrite'
RefTax.o: In function `gzstreambuf::overflow(int)':
RefTax.cpp:(.text._ZN11gzstreambuf8overflowEi[_ZN11gzstreambuf8overflowEi]+0x42): undefined reference to `gzwrite'
RefTax.o: In function `igzstream::~igzstream()':
RefTax.cpp:(.text._ZN9igzstreamD0Ev[_ZN9igzstreamD0Ev]+0x46): undefined reference to `gzclose'
RefTax.cpp:(.text._ZN9igzstreamD0Ev[_ZN9igzstreamD0Ev]+0x7c): undefined reference to `gzwrite'
RefTax.cpp:(.text._ZN9igzstreamD0Ev[_ZN9igzstreamD0Ev]+0x9a): undefined reference to `gzclose'
RefTax.cpp:(.text._ZN9igzstreamD0Ev[_ZN9igzstreamD0Ev]+0xe5): undefined reference to `gzwrite'
RefTax.o: In function `gzstreambuf::~gzstreambuf()':
RefTax.cpp:(.text._ZN11gzstreambufD2Ev[_ZN11gzstreambufD5Ev]+0x38): undefined reference to `gzwrite'
RefTax.cpp:(.text._ZN11gzstreambufD2Ev[_ZN11gzstreambufD5Ev]+0x56): undefined reference to `gzclose'
RefTax.o: In function `gzstreambuf::~gzstreambuf()':
RefTax.cpp:(.text._ZN11gzstreambufD0Ev[_ZN11gzstreambufD5Ev]+0x38): undefined reference to `gzwrite'
RefTax.cpp:(.text._ZN11gzstreambufD0Ev[_ZN11gzstreambufD5Ev]+0x56): undefined reference to `gzclose'
RefTax.o: In function `igzstream::~igzstream()':
RefTax.cpp:(.text._ZN9igzstreamD1Ev[_ZN9igzstreamD1Ev]+0x46): undefined reference to `gzclose'
RefTax.cpp:(.text._ZN9igzstreamD1Ev[_ZN9igzstreamD1Ev]+0x7c): undefined reference to `gzwrite'
RefTax.cpp:(.text._ZN9igzstreamD1Ev[_ZN9igzstreamD1Ev]+0x9a): undefined reference to `gzclose'
RefTax.cpp:(.text._ZN9igzstreamD1Ev[_ZN9igzstreamD1Ev]+0xdd): undefined reference to `gzwrite'
RefTax.o: In function `gzstreambase::~gzstreambase()':
RefTax.cpp:(.text._ZN12gzstreambaseD2Ev[_ZN12gzstreambaseD2Ev]+0x46): undefined reference to `gzclose'
RefTax.cpp:(.text._ZN12gzstreambaseD2Ev[_ZN12gzstreambaseD2Ev]+0x7c): undefined reference to `gzwrite'
RefTax.cpp:(.text._ZN12gzstreambaseD2Ev[_ZN12gzstreambaseD2Ev]+0x9a): undefined reference to `gzclose'
RefTax.cpp:(.text._ZN12gzstreambaseD2Ev[_ZN12gzstreambaseD2Ev]+0xc5): undefined reference to `gzwrite'
collect2: error: ld returned 1 exit status
Makefile:25: recipe for target 'LCA' failed
make: *** [LCA] Error 1
make: Leaving directory '/home/cedric/apps/software/lotus_pipeline_1.57/LCA_src'
=================
Compilation of LCA failed (please contact falk.hildebrand@gmail.com).
A general prupose LCA binary is being used, but this is not recommended
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