install STAR:Parameters.cpp:227:37: error: 'parametersDefault' was not declared in this scope

[Kai Wu]

Dear All,

When install the STAR in my docker container, I run the command of
STAR-STAR_2.4.1d/source# make STAR
Get the error:

Makefile:71: Depend.list: No such file or directory
make -C htslib lib-static
make[1]: Entering directory `/var/data/STAR-STAR_2.4.1d/source/htslib'
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c
.............
Parameters.cpp: In member function 'void Parameters::inputParameters(int, char**)':
Parameters.cpp:227:37: error: 'parametersDefault' was not declared in this scope
Parameters.cpp:227:55: error: 'parametersDefault_len' was not declared in this scope
make: *** [Parameters.o] Error 1

My docker container is  base on ubuntu12.04.
So, what can I fix this?

[Alexander Dobin]

Hi Kai,

this could happen if parametersDefault.xxd file gets corrupted.

Please remove this file, then run 'make clean' and 'make'.

Cheers

Alex

[GopalGunanathan Jayaraj]

Hi Alex, 

     I got a similar error and did what you suggested. However the same error persists.

g++ -c -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri Oct 16 20:31:40 IST 2015 SMLAB:/home/gopal/STAR-        STAR_2.4.2a/source"'    STAR.cpp

g++ -c -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri Oct 16 20:31:40 IST 2015 SMLAB:/home/gopal/STAR-        STAR_2.4.2a/source"'    Parameters.cpp

Parameters.cpp: In member function ‘void Parameters::inputParameters(int, char**)’:

Parameters.cpp:227:37: error: ‘parametersDefault’ was not declared in this scope

     string parString( (const char*) parametersDefault,parametersDefault_len);

                                     ^

Parameters.cpp:227:55: error: ‘parametersDefault_len’ was not declared in this scope

     string parString( (const char*) parametersDefault,parametersDefault_len);

                                                       ^

make: *** [Parameters.o] Error 1

 My OS is a Fedora 20. Kindly guide me. 

Regards,

Gopal

[Alexander Dobin]

Hi Gopal,

please remove the parametersDefault.xxd, and then run 'make clean' and 'make' .

Cheers

Alex

[John B]

I too have this problem on CentOS 6.5 even after removing the parametersDefault.xxd file, running 'make clean', and followed by 'make' doesn't resolve the issue.

[John B]

Following up on my recent comment I was able to copy and paste  parametersDefault.xxd  from ver 2.5.0a into the source/ file of ver 2.4.2a and it got past the previous point that was causing troubles, although I'm not sure it worked entirely.  Regardless, I will just used the pre-compiled binaries (our compute resources have a slightly older version of gcc and I doubt they'll upgrade soon so that's why I can't compile v2.5.0a).Thanks.