Forside
commented
1 year ago It just takes very long. If you don't need to build it yourself, you can also take the prebuilt release.
Open Rr9825 opened 1 year ago
Forside
commented
1 year ago It just takes very long. If you don't need to build it yourself, you can also take the prebuilt release.
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",
| ^’ [-Wrestrict]
303 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s",
| ^’ [-Wrestrict]
309 | else sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%dbp",
| ^’ [-Wrestrict]
307 | sprintf(genes[i].gene_data, "%srbs_motif=None;rbs_spacer=None",
| ^’ [-Wrestrict]
290 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s",
| ^’ [-Wrestrict]
286 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s",
| ^’ [-Wrestrict]
312 | sprintf(genes[i].gene_data, "%s;gc_cont=%.3f", genes[i].gene_data,
| ^’ [-Wrestrict]
322 | sprintf(genes[i].score_data, "%stscore=%.2f;", genes[i].score_data,
| ^
~~~~~~~~~~~~~~ 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 ‘~~~~~~~~~~~~~~ 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 ‘~~~~~~~~~~~~310 | genes[i].gene_data, qt, nod[ndx].mot.spacer); |~~~~~~~~~~~~ gene.c:307:9: warning: ‘sprintf’ argument 3 overlaps destination object ‘~~~~~~~~~~~~~~ 308 | genes[i].gene_data); |~~~~~~~ gene.c:290:9: warning: ‘sprintf’ argument 3 overlaps destination object ‘~~~~~~~~~~~~~~ 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 ‘~~~~~~~~~~~~~~ 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 ‘~~~~~~~~~~~~~313 | nod[ndx].gc_cont); |~~~~~ gene.c:322:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘~~~~~~~~~~~~~~ 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