Question: kmergenie - Error 1 - It is doesnt work when I typed 'make'
1
gravatar for margxenscienculo
2.5 years ago by
Iberian Peninsule (SouthWestern Sector - Scorching Corner )
margxenscienculo50 wrote:

Good morning.

I am trying to use kmergenie v1.6972.  But it is broken when I typed "make"

sudo make
g++ -o minia/Pool.o -c minia/Pool.cpp -O4 -pthread  -D_largeint -DKMER_PRECISION=4
make: g++: Command not found
make: *** [minia/Pool.o] Error 127

Firstly i install g++ like the next user told me. But it appears new errors. I have r-base, Rscript installed.

I show the error with make, make check and ./kmergenie

make
g++ -o minia/Pool.o -c minia/Pool.cpp -O4 -pthread  -D_largeint -DKMER_PRECISION=4
g++ -o minia/Bank.o -c minia/Bank.cpp -O4 -pthread  -D_largeint -DKMER_PRECISION=4
In file included from minia/Bank.cpp:21:0:
minia/Bank.h:13:63: fatal error: zlib.h: No such file or directory
 #include <zlib.h> // Added by Pierre Peterlongo on 02/08/2012.
                                                               ^
compilation terminated.
make: *** [minia/Bank.o] Error 1
./kmergenie /home/zhu/File.fq
running histogram estimation
Execution of specialk failed: [Errno 2] No such file or directory
fitting model to histograms to estimate best k
could not predict a best k value
Execution of decide failed (return code 0). If this is a fresh Kmergenie install, try running 'make check'.
 make check
g++ -o minia/Bank.o -c minia/Bank.cpp -O4 -pthread  -D_largeint -DKMER_PRECISION=4
In file included from minia/Bank.cpp:21:0:
minia/Bank.h:13:63: fatal error: zlib.h: No such file or directory
 #include <zlib.h> // Added by Pierre Peterlongo on 02/08/2012.
                                                               ^
compilation terminated.
make: *** [minia/Bank.o] Error 1
 


 

Regards.

kmergenie • 1.4k views
ADD COMMENTlink modified 2.4 years ago by Ram12k • written 2.5 years ago by margxenscienculo50
3
gravatar for wpwupingwp
2.5 years ago by
wpwupingwp110
China
wpwupingwp110 wrote:

sudo apt-get install g++

ADD COMMENTlink written 2.5 years ago by wpwupingwp110
3
gravatar for Neilfws
2.4 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

Whenever you see an error such as

XXX.h: No such file or directory

the solution is to search for and install a package usually (but not always) named something like XXX-dev.

So in this case

apt-cache search zlib dev
sudo apt-get install zlib1g-dev

It is always worth doing a Google search with errors like these; they are common and many people will have posted solutions to them.

ADD COMMENTlink written 2.4 years ago by Neilfws47k

Thanks. I dont know the option apt-cache. Regards.

ADD REPLYlink written 2.4 years ago by margxenscienculo50
1

Please accept the solutions that worked for you, so the question is automatically marked as solved by the system.

ADD REPLYlink written 2.4 years ago by Ram12k

It worked. I accepted. I accept. I edited the title of post.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by margxenscienculo50

Under each answer that worked, please click on the check mark. That is how you mark questions as solved, not by editing the title.

ADD REPLYlink written 2.4 years ago by Ram12k
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