Installation issue

[Rr9825]

Greetings,

I have been trying to install prodigal using cygwin. However, the installation seems to just stop once it reaches a point, as shown below. How do I rectify this problem?

user@DESKTOP-2TG2OLB /cygdrive/c/Users/user/Downloads/Prodigal-2.6.3 (1)/Prodigal-2.6.3
$ make install
gcc -pedantic -Wall -O3 -c -o bitmap.o bitmap.c
gcc -pedantic -Wall -O3 -c -o dprog.o dprog.c
gcc -pedantic -Wall -O3 -c -o gene.o gene.c
gene.c: In function ‘record_gene_data’:
gene.c:298:9: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
298 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | sd_spacer[nod[ndx].rbs[0]]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:303:9: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
303 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
304 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
305 | sd_spacer[nod[ndx].rbs[1]]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:309:12: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
309 | else sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%dbp",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
310 | genes[i].gene_data, qt, nod[ndx].mot.spacer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:307:9: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
307 | sprintf(genes[i].gene_data, "%srbs_motif=None;rbs_spacer=None",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
308 | genes[i].gene_data);
| ~~~~~~~~~~~~~~~~~~~
gene.c:290:9: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
290 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
291 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | sd_spacer[nod[ndx].rbs[1]]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:286:9: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
286 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
287 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
288 | sd_spacer[nod[ndx].rbs[0]]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:312:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
312 | sprintf(genes[i].gene_data, "%s;gc_cont=%.3f", genes[i].gene_data,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
313 | nod[ndx].gc_cont);
| ~~~~~~~~~~~~~~~~~
gene.c:322:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict]
322 | sprintf(genes[i].score_data, "%stscore=%.2f;", genes[i].score_data,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
323 | nod[ndx].tscore);
| ~~~~~~~~~~~~~~~~
gene.c: In function ‘print_genes’:
gene.c:347:26: warning: ‘model="’ directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
347 | sprintf(run_data, "%smodel="%s";", run_data, mdesc);
| ^~~~~~~~
gene.c:347:5: note: ‘sprintf’ output 10 or more bytes (assuming 10009) into a destination of size 10000
347 | sprintf(run_data, "%smodel="%s";", run_data, mdesc);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:347:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘run_data’ [-Wrestrict]
gene.c:335:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here
335 | char seq_data[MAX_LINE2], run_data[MAX_LINE];
| ^~~~~~~~
gene.c:343:26: warning: ‘model="Ab initio";’ directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
343 | sprintf(run_data, "%smodel="Ab initio";", run_data);
| ^~~~~~~~~~~~~~~~~~~~
gene.c:343:5: note: ‘sprintf’ output between 19 and 10018 bytes into a destination of size 10000
343 | sprintf(run_data, "%smodel="Ab initio";", run_data);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:343:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘run_data’ [-Wrestrict]
gene.c:335:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here
335 | char seq_data[MAX_LINE2], run_data[MAX_LINE];
| ^~~~~~~~
gene.c:349:24: warning: ‘gc_cont=’ directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data,
| ^~~~~~~~
gene.c:349:21: note: assuming directive output of 4 bytes
349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:349:3: note: ‘sprintf’ output between 37 and 10366 bytes into a destination of size 10000
349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
350 | tinf->gc100.0, tinf->trans_table, tinf->uses_sd);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gene.c:349:3: warning: ‘sprintf’ argument 3 overlaps destination object ‘run_data’ [-Wrestrict]
gene.c:335:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here
335 | char seq_data[MAX_LINE2], run_data[MAX_LINE];
| ^~~~~~~~
gcc -pedantic -Wall -O3 -c -o main.o main.c
gcc -pedantic -Wall -O3 -c -o metagenomic.o metagenomic.c
gcc -pedantic -Wall -O3 -c -o node.o node.c
node.c: In function ‘write_start_file’:
node.c:1426:26: warning: ‘model="’ directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
1426 | sprintf(run_data, "%smodel="%s";", run_data, mdesc);
| ^~~~~~~~
node.c:1426:5: note: ‘sprintf’ output 10 or more bytes (assuming 10009) into a destination of size 10000
1426 | sprintf(run_data, "%smodel="%s";", run_data, mdesc);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
node.c:1426:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘run_data’ [-Wrestrict]
node.c:1414:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here
1414 | char seq_data[MAX_LINE2], run_data[MAX_LINE];
| ^~~~~~~~
node.c:1422:26: warning: ‘model="Ab initio";’ directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
1422 | sprintf(run_data, "%smodel="Ab initio";", run_data);
| ^~~~~~~~~~~~~~~~~~~~
node.c:1422:5: note: ‘sprintf’ output between 19 and 10018 bytes into a destination of size 10000
1422 | sprintf(run_data, "%smodel="Ab initio";", run_data);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
node.c:1422:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘run_data’ [-Wrestrict]
node.c:1414:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here
1414 | char seq_data[MAX_LINE2], run_data[MAX_LINE];
| ^~~~~~~~
node.c:1428:24: warning: ‘gc_cont=’ directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data,
| ^~~~~~~~
node.c:1428:21: note: assuming directive output of 4 bytes
1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
node.c:1428:3: note: ‘sprintf’ output between 37 and 10366 bytes into a destination of size 10000
1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1429 | tinf->gc100.0, tinf->trans_table, tinf->uses_sd);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
node.c:1428:3: warning: ‘sprintf’ argument 3 overlaps destination object ‘run_data’ [-Wrestrict]
node.c:1414:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here
1414 | char seq_data[MAX_LINE2], run_data[MAX_LINE];
| ^~~~~~~~
gcc -pedantic -Wall -O3 -c -o sequence.o sequence.c
gcc -pedantic -Wall -O3 -c -o training.o training.c

[Forside]

It just takes very long. If you don't need to build it yourself, you can also take the prebuilt release.