Question: MAQ install error
gravatar for Ashley
10 weeks ago by
Ashley40 wrote:

Hello, I've been trying to install Maq onto a 64bit linux system. I've looked at the other threads that have had problems with Maq but nothing in those worked for me so I'm hoping someone might have some new answers! The ./configure step works fine, but when I try to make, I get this output:

(CDPATH="${ZSH_VERSION+.}:" && cd . && autoheader)
rm -f stamp-h1
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make all-am
make[1]: Entering directory `/home/jess28/My_Packages/maq-0.7.1'
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c -o mapcheck.o In function ‘int ma_mapcheck(int, char**)’: warning: variable ‘fpout’ set but not used [-Wunused-but-set-variable]
FILE *fp_bfa, *fpout;
In file included from
stdhash.hh: In instantiation of ‘bool hash_set_misc<keytype_t>::insert(const keytype_t&) [with keytype_t = long long unsigned int]’: required from here
**stdhash.hh:415:81: error: ‘direct_insert_aux’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]****
int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
stdhash.hh:415:81: note: declarations in dependent base ‘__lh3_hash_base_class<long long unsigned int>’ are not found by unqualified lookup
stdhash.hh:415:81: note: use ‘this->direct_insert_aux’ instead
make[1]: *** [mapcheck.o] Error 1
make[1]: Leaving directory `/home/jess28/My_Packages/maq-0.7.1'
make: *** [all] Error 2

I've tried doing ./ before configuring, but that did not help. I'm have no idea what to do to fix this! Any help would be greatly appreciated.


ADD COMMENTlink modified 10 weeks ago by h.mon23k • written 10 weeks ago by Ashley40
gravatar for h.mon
10 weeks ago by
h.mon23k wrote:

Why do you need MAQ? Its latest version is more than 10 years old - I think you would be better of using some newer program.

MAQ is really old, and by now it has problems compiling with current compilers. You can use the fpermissive flag to get it to compile:

make CFLAGS="-Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fpermissive" CXXFLAGS="-Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fpermissive"

Note I took the CFLAGS and CXXFLAGS from the Makefile, and appended -fpermissive to them. Your CFLAGS and CXXFLAGS may be different, check them before issuing make.

ADD COMMENTlink written 10 weeks ago by h.mon23k
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