gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro
anchors.c: In function ‘anchors_getline’:cstat utils/cstat.c -Wl,-z,relro
anchors.c:232:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
232 | fgets(temp, 1024, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
order.c: In function ‘doAlign’:
order.c:409:5: error: implicit declaration of function ‘printMFAAlign’; did you mean ‘printBinAlign’? [-Werror=implicit-function-declaration]
409 | printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
| ^~~~~~~~~~~~~
| printBinAlign
order.c:411:5: error: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printTextAlign’? [-Werror=implicit-function-declaration]
411 | printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
| ^~~~~~~~~~~~~~
| printTextAlign
order.c: In function ‘readfile’:
order.c:61:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
61 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
order.c: In function ‘readSubstMatrix’:
order.c:145:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
145 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
order.c:149:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
149 | fscanf (file, "%d", &gapstart);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
order.c:150:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
150 | fscanf (file, "%d", &gapcont);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/cextract.c: In function ‘getLength’:
utils/cextract.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
16 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/cextract.c: In function ‘readfile’:
utils/cextract.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
41 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
mlagan.c: In function ‘readfile’:
mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function ‘readfile’:
prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c: In function ‘readfile’:
fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args]
357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mlagan.c: In function ‘main’:
mlagan.c:1071:5: error: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Werror=implicit-function-declaration]
1071 | printXMFAAlign(outfile, final);
| ^~~~~~~~~~~~~~
| printFASTAAlign
mlagan.c: In function ‘readfile’:
mlagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
79 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function ‘main’:
prolagan.c:1091:5: error: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Werror=implicit-function-declaration]
1091 | printXMFAAlign(outfile, final);
| ^~~~~~~~~~~~~~
| printFASTAAlign
prolagan.c: In function ‘readfile’:
prolagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
79 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:344:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
344 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
fchaos.c: In function ‘readSubstMatrix’:
fchaos.c:622:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:627:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
627 | fscanf (file, "%d", &gappenstart);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:628:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
628 | fscanf (file, "%d", &gappenext);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/
utils/cstat.c: In function ‘cntlets’:contigorder utils/contigorder.c -Wl,-z,relro
utils/cstat.c:51:10: error: implicit declaration of function ‘isspace’ [-Werror=implicit-function-declaration]
51 | if (!isspace(currchar)) {
| ^~~~~~~
utils/cstat.c:6:1: note: include ‘<ctype.h>’ or provide a declaration of ‘isspace’
5 | #include <assert.h>
+++ |+#include <ctype.h>
6 |
utils/cstat.c:52:18: error: implicit declaration of function ‘toupper’ [-Werror=implicit-function-declaration]
52 | currchar = toupper(currchar);
| ^~~~~~~
utils/cstat.c:52:18: note: include ‘<ctype.h>’ or provide a declaration of ‘toupper’
utils/cstat.c:44:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
44 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
utils/cstat.c: In function ‘readseq’:
utils/cstat.c:67:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
67 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/
utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:15:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]getbounds utils/getbounds.c -Wl,-z,relro
15 | fprintf (stderr, "contigorder: Error opening file: %s\n");
| ~^
| |
| char * utils/contigorder.c:26:25: warning: unknown conversion type character ‘&’ in format [-Wformat=]
26 | fscanf (file, "%&d", &dummy);
| ^
utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args]
26 | fscanf (file, "%&d", &dummy);
| ^~~~~
utils/contigorder.c: In function ‘getScores’:
utils/contigorder.c:52:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]
52 | fprintf (stderr, "contigorder: Error opening file: %s\n");
| ~^
| |
| char * skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/
utils/contigorder.c: In function ‘getFileInfo’:getlength utils/getlength.c -Wl,-z,relro
utils/contigorder.c:19:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
19 | fscanf (file, "numContigs = %d\n", numContigs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
20 | fscanf (file, "seqLen = %d\n", seqLen);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:26:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
26 | fscanf (file, "%&d", &dummy);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c: In function ‘getScores’:
utils/contigorder.c:56:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
56 | fscanf (file, "numContigs = %*d\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:57:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
57 | fscanf (file, "seqLen = %*d\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:63:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
63 | fscanf (file, "%d", &((*score)[i][j]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getbounds.c: In function ‘getLength’:
utils/getbounds.c:18:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
18 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro
utils/getlength.c: In function ‘main’:
utils/getlength.c:20:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
20 | fgets (buffer, BUF_SIZE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc1: some warnings being treated as errors
make[2]: *** [Makefile:28: ../utils/cstat] Error 1
tag -1 pendingBug #1066580 [src:lagan] lagan: FTBFS: order.c:409:5: error: implicit declaration of function ‘printMFAAlign’; did you mean ‘printBinAlign’? [-Werror=implicit-function-declaration]
Sysop: | Keyop |
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