Installing TFMpvalue for FunSeq2
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Based on the instructions I read, running make can solve the problem of TFMpvalue installation for FunSeq2 but when I do so I get this error:
root@milad:/home/milad/funseq2-1.0# cd '/home/milad/funseq2-1.0/TFM-Pvalue'
root@milad:/home/milad/funseq2-1.0/TFM-Pvalue# make
g++ -O3 -DJASPAR=1 -DPROGRAM=0 TFMpvalue.cpp Matrix.cpp ArgumentException.cpp FileException.cpp ParseException.cpp -o TFMpvalue-pv2sc
TFMpvalue.cpp: In function ‘void arguments(int, char* const*)’:
TFMpvalue.cpp:503:45: error: ‘getopt’ was not declared in this scope
while (((option = getopt(argc,argv,options)) != EOF)) {
^
TFMpvalue.cpp:507:23: error: ‘optind’ was not declared in this scope
OPTIONS[option] = optind-1;
^
make: *** [TFMpvalue-pv2sc] Error 1
What's the problem and how can I fix it?
software-installation
edited Apr 21 at 20:25
Zanna
48k13119227
asked Apr 21 at 18:27
Milad Shademan
11
add a comment |Â
up vote
0
down vote
favorite
Based on the instructions I read, running make can solve the problem of TFMpvalue installation for FunSeq2 but when I do so I get this error:
root@milad:/home/milad/funseq2-1.0# cd '/home/milad/funseq2-1.0/TFM-Pvalue'
root@milad:/home/milad/funseq2-1.0/TFM-Pvalue# make
g++ -O3 -DJASPAR=1 -DPROGRAM=0 TFMpvalue.cpp Matrix.cpp ArgumentException.cpp FileException.cpp ParseException.cpp -o TFMpvalue-pv2sc
TFMpvalue.cpp: In function ‘void arguments(int, char* const*)’:
TFMpvalue.cpp:503:45: error: ‘getopt’ was not declared in this scope
while (((option = getopt(argc,argv,options)) != EOF)) {
^
TFMpvalue.cpp:507:23: error: ‘optind’ was not declared in this scope
OPTIONS[option] = optind-1;
^
make: *** [TFMpvalue-pv2sc] Error 1
What's the problem and how can I fix it?
software-installation
edited Apr 21 at 20:25
Zanna
48k13119227
asked Apr 21 at 18:27
Milad Shademan
11
add a comment |Â
up vote
0
down vote
favorite
up vote
0
down vote
favorite
Based on the instructions I read, running make can solve the problem of TFMpvalue installation for FunSeq2 but when I do so I get this error:
root@milad:/home/milad/funseq2-1.0# cd '/home/milad/funseq2-1.0/TFM-Pvalue'
root@milad:/home/milad/funseq2-1.0/TFM-Pvalue# make
g++ -O3 -DJASPAR=1 -DPROGRAM=0 TFMpvalue.cpp Matrix.cpp ArgumentException.cpp FileException.cpp ParseException.cpp -o TFMpvalue-pv2sc
TFMpvalue.cpp: In function ‘void arguments(int, char* const*)’:
TFMpvalue.cpp:503:45: error: ‘getopt’ was not declared in this scope
while (((option = getopt(argc,argv,options)) != EOF)) {
^
TFMpvalue.cpp:507:23: error: ‘optind’ was not declared in this scope
OPTIONS[option] = optind-1;
^
make: *** [TFMpvalue-pv2sc] Error 1
What's the problem and how can I fix it?
software-installation
edited Apr 21 at 20:25
Zanna
48k13119227
asked Apr 21 at 18:27
Milad Shademan
11
Based on the instructions I read, running make can solve the problem of TFMpvalue installation for FunSeq2 but when I do so I get this error:
root@milad:/home/milad/funseq2-1.0# cd '/home/milad/funseq2-1.0/TFM-Pvalue'
root@milad:/home/milad/funseq2-1.0/TFM-Pvalue# make
g++ -O3 -DJASPAR=1 -DPROGRAM=0 TFMpvalue.cpp Matrix.cpp ArgumentException.cpp FileException.cpp ParseException.cpp -o TFMpvalue-pv2sc
TFMpvalue.cpp: In function ‘void arguments(int, char* const*)’:
TFMpvalue.cpp:503:45: error: ‘getopt’ was not declared in this scope
while (((option = getopt(argc,argv,options)) != EOF)) {
^
TFMpvalue.cpp:507:23: error: ‘optind’ was not declared in this scope
OPTIONS[option] = optind-1;
^
make: *** [TFMpvalue-pv2sc] Error 1
What's the problem and how can I fix it?
software-installation
edited Apr 21 at 20:25
Zanna
48k13119227
asked Apr 21 at 18:27
Milad Shademan
11
edited Apr 21 at 20:25
Zanna
48k13119227
edited Apr 21 at 20:25
Zanna
48k13119227
edited Apr 21 at 20:25
Zanna
48k13119227
48k13119227
asked Apr 21 at 18:27
Milad Shademan
11
asked Apr 21 at 18:27
Milad Shademan
11
asked Apr 21 at 18:27
Milad Shademan
11
11
add a comment |Â
add a comment |Â
1 Answer
1
active
oldest
votes
up vote
0
down vote
The problem is something wrong with TFMpvalue.cpp:
sudo chown username:username TFMpvalue.cpp- Uncomment line 16 in TFMpvalue.cpp and change GetOpt.h into getopt.h
edited Jun 27 at 9:18
andrew.46
20.4k1463138
answered Jun 27 at 8:05
Yan zijun
1
add a comment |Â
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
The problem is something wrong with TFMpvalue.cpp:
sudo chown username:username TFMpvalue.cpp- Uncomment line 16 in TFMpvalue.cpp and change GetOpt.h into getopt.h
edited Jun 27 at 9:18
andrew.46
20.4k1463138
answered Jun 27 at 8:05
Yan zijun
1
add a comment |Â
up vote
0
down vote
The problem is something wrong with TFMpvalue.cpp:
sudo chown username:username TFMpvalue.cpp- Uncomment line 16 in TFMpvalue.cpp and change GetOpt.h into getopt.h
edited Jun 27 at 9:18
andrew.46
20.4k1463138
answered Jun 27 at 8:05
Yan zijun
1
add a comment |Â
up vote
0
down vote
up vote
0
down vote
The problem is something wrong with TFMpvalue.cpp:
sudo chown username:username TFMpvalue.cpp- Uncomment line 16 in TFMpvalue.cpp and change GetOpt.h into getopt.h
edited Jun 27 at 9:18
andrew.46
20.4k1463138
answered Jun 27 at 8:05
Yan zijun
1
The problem is something wrong with TFMpvalue.cpp:
sudo chown username:username TFMpvalue.cpp- Uncomment line 16 in TFMpvalue.cpp and change GetOpt.h into getopt.h
edited Jun 27 at 9:18
andrew.46
20.4k1463138
answered Jun 27 at 8:05
Yan zijun
1
edited Jun 27 at 9:18
andrew.46
20.4k1463138
edited Jun 27 at 9:18
andrew.46
20.4k1463138
edited Jun 27 at 9:18
andrew.46
20.4k1463138
20.4k1463138
answered Jun 27 at 8:05
Yan zijun
1
answered Jun 27 at 8:05
Yan zijun
1
answered Jun 27 at 8:05
Yan zijun
1
1
add a comment |Â
add a comment |Â
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