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September 14, 2017 07:13
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Error message when installing lotus v.1.57
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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 [email protected]). | |
A general prupose LCA binary is being used, but this is not recommended |
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