make step failed

[Anto]

Hi,

I'm trying to get kma installed on my computational cluster for eventually running ResFinder tool but I'm stuck at the compilation step with the below error. CentOS Linux release 7.9.2009 is being used on my cluster login node. I would appreciate if you've any ideas on fixing this error. Please fel free to get back to me if you need any additional information.

(virtualenv3) [name@loginXXX-XX-X cge]$ cd kma && make
/sw/csi/intel/2017/compilers_and_libraries/linux/bin/intel64/icc -Wall -O3 -std=c99 -c -o alnfrags.o alnfrags.c
alnfrags.c(1079): error: first argument must be a pointer to integer or enumeration type
lockTime(excludeIn, 65536);
^

alnfrags.c(1089): error: first argument must be a pointer to integer or enumeration type
unlock(excludeIn);
^

alnfrags.c(1150): error: first argument must be a pointer to integer or enumeration type
lock(excludeIn);
^

alnfrags.c(1152): error: first argument must be a pointer to integer or enumeration type
unlock(excludeIn);
^

compilation aborted for alnfrags.c (code 2)
make: *** [alnfrags.o] Error 2

[ptlcc]

Hi Anto

I have made a new branch (develop) to solve the problem, can I get you to compile on that one.

Best,
Philip

[Anto]

Thank you Philip for your response- much appreciated. I tried compiling using the new branch but keep ending up with compiling errors as below. Not sure if I’m doing something wrong/silly here. Thanks again for your kind support.

(virtualenv3) [XXXX@loginXXX-v resfinder]$ git clone https://[e-mail]/genomicepidemiology/kma.git
Cloning into 'kma'...
remote: Counting objects: 1274, done.
remote: Compressing objects: 100% (1057/1057), done.
remote: Total 1274 (delta 757), reused 0 (delta 0)
Receiving objects: 100% (1274/1274), 2.58 MiB | 3.48 MiB/s, done.
Resolving deltas: 100% (887/887), done.
(virtualenv3) [antonycp@login509-02-r resfinder]$ cd kma && make
/sw/csi/intel/2017/compilers_and_libraries/linux/bin/intel64/icc -Wall -O3 -std=c99 -c -o align.o align.c
/sw/csi/intel/2017/compilers_and_libraries/linux/bin/intel64/icc -Wall -O3 -std=c99 -c -o alnfrags.o alnfrags.c
alnfrags.c(1079): error: first argument must be a pointer to integer or enumeration type
lockTime(excludeIn, 65536);
^

alnfrags.c(1089): error: first argument must be a pointer to integer or enumeration type
unlock(excludeIn);
^

alnfrags.c(1150): error: first argument must be a pointer to integer or enumeration type
lock(excludeIn);
^

alnfrags.c(1152): error: first argument must be a pointer to integer or enumeration type
unlock(excludeIn);
^

compilation aborted for alnfrags.c (code 2)
make: *** [alnfrags.o] Error 2

‌

[ptlcc]

Hi Anto

After your git clone you should do the following:

cd kma
git checkout develop
make

To go to the develop branch and check the changes.

Best,
Philip

[Anto]

Thank you so much Philip. I’m happy to report that it is fixed now at my end. You may please close this ticket.