LTR_Finder:Compilation failed

[C2051]

Hi,I came across an issue on installing LTR_Finder. I don't know how to solve the problem of compilation failure because I'm a beginner. I would appreciate it if you could help me. Look forward to your reply your reply.

(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin$ git clone https://github.com/xzhub/LTR_Finder.git
Cloning into 'LTR_Finder'...
remote: Enumerating objects: 80, done.
remote: Total 80 (delta 0), reused 0 (delta 0), pack-reused 80
Unpacking objects: 100% (80/80), 3.56 MiB | 9.00 KiB/s, done.
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin$ cd LTR_
LTR_Finder/ LTR_retriever/
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin$ cd LTR_Finder/
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder$ ls
LICENSE README.md build help.pdf source
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder$ cd source
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder/source$ make
gcc -c regex.c -fomit-frame-pointer -DNDBUG -O3
regex.c: In function ‘re_match_2’:
regex.c:4015:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
4015 | if ((int) old_regend[r] >= (int) regstart[r])
| ^
regex.c:4015:56: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
4015 | if ((int) old_regend[r] >= (int) regstart[r])
| ^
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2546:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2546 | PUSH_FAILURE_ITEM (lowest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4022:21: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4022 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2549:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2549 | PUSH_FAILURE_ITEM (highest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4022:21: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4022 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2546:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2546 | PUSH_FAILURE_ITEM (lowest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4193:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4193 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2549:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2549 | PUSH_FAILURE_ITEM (highest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4193:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4193 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2546:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2546 | PUSH_FAILURE_ITEM (lowest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4251:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4251 | PUSH_FAILURE_POINT (p + mcnt, d, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2549:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2549 | PUSH_FAILURE_ITEM (highest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4251:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4251 | PUSH_FAILURE_POINT (p + mcnt, d, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2634:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
2634 | high_reg = (unsigned) POP_FAILURE_ITEM ();
| ^
regex.c:4364:17: note: in expansion of macro ‘POP_FAILURE_POINT’
4364 | POP_FAILURE_POINT (sdummy, pdummy,
| ^~~~~~~~~~~~~~~~~
regex.c:2637:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
2637 | low_reg = (unsigned) POP_FAILURE_ITEM ();
| ^
regex.c:4364:17: note: in expansion of macro ‘POP_FAILURE_POINT’
4364 | POP_FAILURE_POINT (sdummy, pdummy,
| ^~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2546:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2546 | PUSH_FAILURE_ITEM (lowest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4407:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4407 | PUSH_FAILURE_POINT (0, 0, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2549:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2549 | PUSH_FAILURE_ITEM (highest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4407:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4407 | PUSH_FAILURE_POINT (0, 0, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2546:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2546 | PUSH_FAILURE_ITEM (lowest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4423:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4423 | PUSH_FAILURE_POINT (0, 0, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2467:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2467 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
| ^
regex.c:2549:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
2549 | PUSH_FAILURE_ITEM (highest_active_reg);
| ^~~~~~~~~~~~~~~~~
regex.c:4423:13: note: in expansion of macro ‘PUSH_FAILURE_POINT’
4423 | PUSH_FAILURE_POINT (0, 0, -2);
| ^~~~~~~~~~~~~~~~~~
regex.c:2634:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
2634 | high_reg = (unsigned) POP_FAILURE_ITEM ();
| ^
regex.c:4647:13: note: in expansion of macro ‘POP_FAILURE_POINT’
4647 | POP_FAILURE_POINT (d, p,
| ^~~~~~~~~~~~~~~~~
regex.c:2637:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
2637 | low_reg = (unsigned) POP_FAILURE_ITEM ();
| ^
regex.c:4647:13: note: in expansion of macro ‘POP_FAILURE_POINT’
4647 | POP_FAILURE_POINT (d, p,
| ^~~~~~~~~~~~~~~~~
g++ -c Timing.C -fomit-frame-pointer -DNDBUG -O3
g++ -c BooleanString.C -fomit-frame-pointer -DNDBUG -O3
g++ -c LinearSuffixSort.cpp -fomit-frame-pointer -DNDBUG -O3
g++ -c lcp.c -fomit-frame-pointer -DNDBUG -O3
g++ -c stdaln.c -fomit-frame-pointer -DNDBUG -O3
stdaln.c:47:28: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
47 | char aln_nt16_rev_table = "XAGRCMSVTWKDYHBN-";
| ^~~~~~~~~~~~~~~~~~~
stdaln.c:68:27: warning: ISO C++ forbids converting a string constant to ‘char’ [-Wwrite-strings]
68 | char aln_nt4_rev_table = "AGCTN-";
| ^~~~~~~~
stdaln.c:89:26: warning: ISO C++ forbids converting a string constant to ‘char’ [-Wwrite-strings]
89 | char aln_aa_rev_table = "ARNDCQEGHILKMFPSTWYVX-";
| ^~~~~~~~~~~~~~~~~~~~~~~~~
stdaln.c:99:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
99 | char aln_trans_table_eu_char = "KKNNRRSSTTTTIMIIEEDDGGGGAAAAVVVVQQHHRRRRPPPPLLLL**YYWCCSSSSLLFFX";
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c seq.c -fomit-frame-pointer -DNDBUG -O3
g++ -c PairsFilter.cpp -fomit-frame-pointer -DNDBUG -O3
PairsFilter.cpp: In function ‘bool ExtendPairs(char*, int, stick&)’:
PairsFilter.cpp:956:48: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
956 | FindTwoChar(aln_global1, tg_pos1, tg_pos2, "TG");
| ^~~~
PairsFilter.cpp:958:48: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
958 | FindTwoChar(aln_global2, ca_pos1, ca_pos2, "CA");
| ^~~~
g++ -c PBS.cpp -fomit-frame-pointer -DNDBUG -O3
g++ -c CallPsScan.cpp -fomit-frame-pointer -DNDBUG -O3
CallPsScan.cpp: In member function ‘void CPSSCAN::init(char*)’:
CallPsScan.cpp:101:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘time_t’ {aka ‘long int’} [-Wformat=]
101 | sprintf(buf, "%d%d", getpid(), time(0));
| ^ ~~~~~~~
| | |
| int time_t {aka long int}
| %ld
g++ -c stdaln_interface.cpp -fomit-frame-pointer -DNDBUG -O3
g++ -o ltr_finder main.cpp PairsFilter.o stdaln.o seq.o LinearSuffixSort.o BooleanString.o Timing.o lcp.o PBS.o CallPsScan.o stdaln_interface.o regex.o -fomit-frame-pointer -DNDBUG -O3
main.cpp: In function ‘int main(int, char**)’:
main.cpp:819:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
819 | char *version = "1.07";
| ^~~~~~
g++ -o psearch psearch.cpp PBS.o seq.o stdaln_interface.o stdaln.o
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder/source$ cd ..
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder$ cd source/test
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder/source/test$ ./ltr_finder test/3ds_72.fa -P 3ds_72 -w2 -f /dev/stderr 2>&1 > test/3ds_72_result.txt | perl genome_plot.pl test/
Can't open perl script "genome_plot.pl": No such file or directory
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder/source/test$ cd ../..
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder$ chmod 755 source
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder$ export PATH=/anaconda3/bin/LTR_Fi
nder:$PATH
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder$ ./ltr_finder test/3ds_72.fa -P 3ds_72 -w2 -f /dev/stderr 2>&1 > test/3ds_72_result.txt | perl genome_plot.pl test/
Can't open perl script "genome_plot.pl": No such file or directory
(base) wangdan@DESKTOP-TM5M3VO:/anaconda3/bin/LTR_Finder$ cd source
(base) wangdan@DESKTOP-TM5M3VO:~/anaconda3/bin/LTR_Finder/source$ ./ltr_finder test/3ds_72.fa -P 3ds_72 -w2 -f /dev/stderr 2>&1 > test/3ds_72_result.txt | perl genome_plot.pl test/
Can't locate GD.pm in @inc (you may need to install the GD module) (@inc contains: /home/wangdan/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/wangdan/anaconda3/lib/site_perl/5.26.2 /home/wangdan/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /home/wangdan/anaconda3/lib/5.26.2 .) at genome_plot.pl line 24.
BEGIN failed--compilation aborted at genome_plot.pl line 24.