Comments (4)
Yes I was going to write it but you were faster than me :)
from bwise.
Hello, can you copy/paste the content of the file /home/igib/visanu2/BWISE/src/logCompile.txt ?
from bwise.
Sure.
`g++ -o n50.o -c N50.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o sequencesToNumbers.o -c sequencesToNumbers.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o numbersToSequences.o -c numbersToSequences.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o numbersFilter.o -c numbersFilter.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o simulator.o -c simulator.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o path_counter.o -c path_counter.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o maximal_sr.o -c Maximal_SR.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o crush_bulle.o -c crush_bulle.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
In file included from Maximal_SR.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:48: maximal_sr.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from path_counter.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:30: path_counter.o] Error 1
simulator.cpp: In function ‘uint32_t xs(uint32_t&)’:
simulator.cpp:15:33: warning: operation on ‘y’ may be undefined [-Wsequence-point]
15 | y^=(y<<13); y^=(y>>17);y=(y^=(y<<15)); return y;
| ~^~~~~~~~~~~~~
simulator.cpp:15:33: warning: operation on ‘y’ may be undefined [-Wsequence-point]
g++ -o n50 n50.o -flto -fopenmp -lz
g++ -o sequencesToNumbers sequencesToNumbers.o -flto -fopenmp -lz
g++ -o numbersToSequences numbersToSequences.o -flto -fopenmp -lz
g++ -o numbersFilter numbersFilter.o -flto -fopenmp -lz
g++ -o simulator simulator.o -flto -fopenmp -lz
g++ -o path_counter.o -c path_counter.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o maximal_sr.o -c Maximal_SR.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o crush_bulle crush_bulle.o -flto -fopenmp -lz
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [makefile:60: n50] Error 1
make: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [makefile:33: crush_bulle] Error 1
make: *** [makefile:63: simulator] Error 1
collect2: error: ld returned 1 exit status
make: *** [makefile:81: numbersFilter] Error 1
collect2: error: ld returned 1 exit status
make: *** [makefile:87: numbersToSequences] Error 1
collect2: error: ld returned 1 exit status
make: *** [makefile:69: sequencesToNumbers] Error 1
In file included from Maximal_SR.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
In file included from path_counter.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:48: maximal_sr.o] Error 1
make: *** [makefile:30: path_counter.o] Error 1
g++ -o n50 n50.o -flto -fopenmp -lz
g++ -o sequencesToNumbers sequencesToNumbers.o -flto -fopenmp -lz
g++ -o numbersToSequences numbersToSequences.o -flto -fopenmp -lz
g++ -o numbersFilter numbersFilter.o -flto -fopenmp -lz
g++ -o simulator simulator.o -flto -fopenmp -lz
g++ -o path_counter.o -c path_counter.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o maximal_sr.o -c Maximal_SR.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o crush_bulle crush_bulle.o -flto -fopenmp -lz
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld/usr/bin/ld: cannot find : cannot find -lz-lz: : No such file or directoryNo such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [makefile:33: crush_bulle] Error 1
make: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [makefile:81: numbersFilter] Error 1
make: *** [makefile:69: sequencesToNumbers] Error 1
make: *** [makefile:60: n50] Error 1
make: *** [makefile:87: numbersToSequences] Error 1
make: *** [makefile:63: simulator] Error 1
In file included from Maximal_SR.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
In file included from path_counter.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:48: maximal_sr.o] Error 1
make: *** [makefile:30: path_counter.o] Error 1
g++ -o n50 n50.o -flto -fopenmp -lz
g++ -o sequencesToNumbers sequencesToNumbers.o -flto -fopenmp -lz
g++ -o numbersToSequences numbersToSequences.o -flto -fopenmp -lz
g++ -o numbersFilter numbersFilter.o -flto -fopenmp -lz
g++ -o simulator simulator.o -flto -fopenmp -lz
g++ -o path_counter.o -c path_counter.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o maximal_sr.o -c Maximal_SR.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o crush_bulle crush_bulle.o -flto -fopenmp -lz
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld/usr/bin/ld: cannot find : cannot find -lz-lz: : No such file or directoryNo such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [makefile:69: sequencesToNumbers] Error 1
make: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
make: *** [makefile:63: simulator] Error 1
make: *** [makefile:81: numbersFilter] Error 1
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [makefile:60: n50] Error 1
make: *** [makefile:87: numbersToSequences] Error 1
collect2: error: ld returned 1 exit status
make: *** [makefile:33: crush_bulle] Error 1
In file included from path_counter.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:30: path_counter.o] Error 1
In file included from Maximal_SR.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:48: maximal_sr.o] Error 1
g++ -o n50 n50.o -flto -fopenmp -lz
g++ -o sequencesToNumbers sequencesToNumbers.o -flto -fopenmp -lz
g++ -o numbersToSequences numbersToSequences.o -flto -fopenmp -lz
g++ -o numbersFilter numbersFilter.o -flto -fopenmp -lz
g++ -o simulator simulator.o -flto -fopenmp -lz
g++ -o path_counter.o -c path_counter.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o maximal_sr.o -c Maximal_SR.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o crush_bulle crush_bulle.o -flto -fopenmp -lz
/usr/bin/ld/usr/bin/ld: cannot find : cannot find -lz-lz: : No such file or directoryNo such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [makefile:87: numbersToSequences] Error 1
make: *** Waiting for unfinished jobs....
make: *** [makefile:81: numbersFilter] Error 1
make: *** [makefile:60: n50] Error 1
make: *** [makefile:63: simulator] Error 1
make: *** [makefile:69: sequencesToNumbers] Error 1
collect2: error: ld returned 1 exit status
make: *** [makefile:33: crush_bulle] Error 1
In file included from path_counter.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
In file included from Maximal_SR.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
compilation terminated.
make: *** [makefile:48: maximal_sr.o] Error 1
make: *** [makefile:30: path_counter.o] Error 1
g++ -o n50 n50.o -flto -fopenmp -lz
g++ -o sequencesToNumbers sequencesToNumbers.o -flto -fopenmp -lz
g++ -o numbersToSequences numbersToSequences.o -flto -fopenmp -lz
g++ -o numbersFilter numbersFilter.o -flto -fopenmp -lz
g++ -o simulator simulator.o -flto -fopenmp -lz
g++ -o path_counter.o -c path_counter.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o maximal_sr.o -c Maximal_SR.cpp -Wall -Ofast -std=c++11 -flto -pipe -funit-at-a-time -Wfatal-errors -fopenmp -lz
g++ -o crush_bulle crush_bulle.o -flto -fopenmp -lz
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory/usr/bin/ld
: cannot find -lz: No such file or directory
/usr/bin/ld: cannot find -lz: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [makefile:60: n50] Error 1
make: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [makefile:69: sequencesToNumbers] Error 1
make: *** [makefile:33: crush_bulle] Error 1
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [makefile:63: simulator] Error 1
collect2: error: ld returned 1 exit status
make: *** [makefile:81: numbersFilter] Error 1
make: *** [makefile:87: numbersToSequences] Error 1
In file included from Maximal_SR.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:48: maximal_sr.o] Error 1
In file included from path_counter.cpp:12:
zstr.hpp:15:10: fatal error: zlib.h: No such file or directory
15 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [makefile:30: path_counter.o] Error 1`
from bwise.
Ok, so through this log I realized I lacked the zlib library files and upon installing them with apt-get install zlib1g-dev,
BWISE compilation was successful. Thanks!
from bwise.
Related Issues (18)
- Parameter for multi libraries HOT 1
- ZeroDivisionError: division by zero HOT 8
- Running time HOT 2
- What is the final file ? HOT 1
- BWISE stops working properly when k=220
- replace "integral information" by something like "fully uses paired-end information"
- Default output directory should be "." but is ".." instead, leading to a crash HOT 1
- add information about the output in the README
- Unable to write tipped_out.unitigs.fa file HOT 5
- Checking dependencies?
- Unexpected error during graph construction: <class 'FileNotFoundError'> HOT 1
- Create a "dev" branch separate from the "stable" branch
- Add option to crush isolated bubbles HOT 2
- Haplo contigs not generated
- Test fails at Graph3: Construction
- Please add a copy of the AGPL to the source code
- One or several files could not be generated
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from bwise.