--- Begin Message ---
Source: lucy
Version: 1.20-3
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240313 ftbfs-trixie ftbfs-impfuncdef
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
This is most likely caused by a change in dpkg 1.22.6, that enabled
-Werror=implicit-function-declaration. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration
Relevant part (hopefully):
> cc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o poly.o poly.c
> done!
> qual_trim.c:10:1: warning: "/*" within comment [-Wcomment]
> 10 | /* qual_trim.c - Quality trimming algorithm which determines a "clean"
> |
> qual_trim.c:11:1: warning: "/*" within comment [-Wcomment]
> 11 | /* range for a sequence based on its phred quality values.
> |
> qual_trim.c:12:1: warning: "/*" within comment [-Wcomment]
> 12 | /*
> |
> qual_trim.c:13:1: warning: "/*" within comment [-Wcomment]
> 13 | /* Written by Michael Holmes, 4/13/99.
> |
> qual_trim.c:14:1: warning: "/*" within comment [-Wcomment]
> 14 | /*
> |
> qual_trim.c:15:1: warning: "/*" within comment [-Wcomment]
> 15 | /* 1/31/2000, Michael Holmes -- Added default_windows().
> |
> qual_trim.c:16:1: warning: "/*" within comment [-Wcomment]
> 16 | /* 2/15/2000, Michael Holmes -- Added bracket_clean_range() and
> |
> qual_trim.c:17:1: warning: "/*" within comment [-Wcomment]
> 17 | /* set_bracket().
> |
> qual_trim.c:18:1: warning: "/*" within comment [-Wcomment]
> 18 | /* 2/18/2000, Michael Holmes -- Minor change to test-mode output only.
> |
> qual_trim.c:19:1: warning: "/*" within comment [-Wcomment]
> 19 | /*
> |
> qual_trim.c:20:1: warning: "/*" within comment [-Wcomment]
> 20 | /* Copyright (C) 1999, 2000, The Institute for Genomic Research. All
> rights
> |
> qual_trim.c:21:1: warning: "/*" within comment [-Wcomment]
> 21 | /* reserved.
> |
> qual_trim.c:22:1: warning: "/*" within comment [-Wcomment]
> 22 | /*
> |
> qual_trim.c:23:1: warning: "/*" within comment [-Wcomment]
> 23 | /* Note: phred quality values are based on the log (base 10) of the
> |
> qual_trim.c:24:1: warning: "/*" within comment [-Wcomment]
> 24 | /* probability that the corresponding base call is in error:
> |
> qual_trim.c:25:1: warning: "/*" within comment [-Wcomment]
> 25 | /*
> |
> qual_trim.c:26:1: warning: "/*" within comment [-Wcomment]
> 26 | /* Q = -10 log(P_error)
> |
> qual_trim.c:27:1: warning: "/*" within comment [-Wcomment]
> 27 | /*
> |
> qual_trim.c:28:1: warning: "/*" within comment [-Wcomment]
> 28 | /* Thanks to Granger Sutton for valuable suggestions.
> |
> qual_trim.c:29:1: warning: "/*" within comment [-Wcomment]
> 29 | /*
> |
> qual_trim.c:30:1: warning: "/*" within comment [-Wcomment]
> 30 | /* The main functions of interest to external code (such as lucy) are
> |
> qual_trim.c:31:1: warning: "/*" within comment [-Wcomment]
> 31 | /* default_windows() and quality_trim(). The grim() function
> emulates the
> |
> qual_trim.c:32:1: warning: "/*" within comment [-Wcomment]
> 32 | /* interface that was used by the old quality trimmimg algorithm
> (grim),
> |
> qual_trim.c:33:1: warning: "/*" within comment [-Wcomment]
> 33 | /* but it is not called by lucy. The main() function is compiled
> only if
> |
> qual_trim.c:34:1: warning: "/*" within comment [-Wcomment]
> 34 | /* TEST_THIS_CODE is #defined.
> |
> qual_trim.c:35:1: warning: "/*" within comment [-Wcomment]
> 35 | /*
> |
> qual_trim.c:36:1: warning: "/*" within comment [-Wcomment]
> 36 | /* The calling hierarchy is:
> |
> qual_trim.c:37:1: warning: "/*" within comment [-Wcomment]
> 37 | /*
> |
> qual_trim.c:38:1: warning: "/*" within comment [-Wcomment]
> 38 | /* main()
> |
> qual_trim.c:39:1: warning: "/*" within comment [-Wcomment]
> 39 | /* grim()
> |
> qual_trim.c:40:1: warning: "/*" within comment [-Wcomment]
> 40 | /* default_windows()
> |
> qual_trim.c:41:1: warning: "/*" within comment [-Wcomment]
> 41 | /* quality_trim()
> |
> qual_trim.c:42:1: warning: "/*" within comment [-Wcomment]
> 42 | /* bracket_clean_range()
> |
> qual_trim.c:43:1: warning: "/*" within comment [-Wcomment]
> 43 | /* multi_window_trim()
> |
> qual_trim.c:44:1: warning: "/*" within comment [-Wcomment]
> 44 | /* window_trim()
> |
> qual_trim.c:45:1: warning: "/*" within comment [-Wcomment]
> 45 | /* multi_window_trim() [recursive call]
> |
> qual_trim.c:46:1: warning: "/*" within comment [-Wcomment]
> 46 | /* average_error_trim()
> |
> qual_trim.c:47:1: warning: "/*" within comment [-Wcomment]
> 47 | /*
> |
> qual_trim.c:48:1: warning: "/*" within comment [-Wcomment]
> 48 |
> /**************************************************************************/
> |
> poly.c: In function ‘poly_at_left’:
> poly.c:22:9: error: implicit declaration of function ‘abi_code’
> [-Werror=implicit-function-declaration]
> 22 | if (abi_code(*seq)==T) {
> | ^~~~~~~~
> abi.c:24:8: warning: type defaults to ‘int’ in declaration of ‘condition’
> [-Wimplicit-int]
> 24 | static condition[]={
> | ^~~~~~~~~
> abi.c: In function ‘abi_code’:
> abi.c:70:15: error: implicit declaration of function ‘random’
> [-Werror=implicit-function-declaration]
> 70 | case 5: tmp=random()%2 ? 2 : 0; break;
> | ^~~~~~
> splice.c: In function ‘splice_align_left’:
> splice.c:53:12: warning: type defaults to ‘int’ in declaration of ‘left’
> [-Wimplicit-int]
> 53 | register left, top, direc, score, i, j;
> | ^~~~
> splice.c:53:18: warning: type defaults to ‘int’ in declaration of ‘top’
> [-Wimplicit-int]
> 53 | register left, top, direc, score, i, j;
> | ^~~
> splice.c:53:23: warning: type defaults to ‘int’ in declaration of ‘direc’
> [-Wimplicit-int]
> 53 | register left, top, direc, score, i, j;
> | ^~~~~
> splice.c:53:30: warning: type defaults to ‘int’ in declaration of ‘score’
> [-Wimplicit-int]
> 53 | register left, top, direc, score, i, j;
> | ^~~~~
> splice.c:53:37: warning: type defaults to ‘int’ in declaration of ‘i’
> [-Wimplicit-int]
> 53 | register left, top, direc, score, i, j;
> | ^
> abi.c:82:5: error: implicit declaration of function ‘giveup’
> [-Werror=implicit-function-declaration]
> 82 | giveup("how can other cases happen in tag_code?");
> | ^~~~~~
> splice.c:53:40: warning: type defaults to ‘int’ in declaration of ‘j’
> [-Wimplicit-int]
> 53 | register left, top, direc, score, i, j;
> | ^
> splice.c:68:32: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 68 | Score(0,0)=max_score=match[*a][*b];
> | ^~
> splice.c:68:36: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 68 | Score(0,0)=max_score=match[*a][*b];
> | ^~
> splice.c:75:20: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 75 | score=match[a[i]][*b];
> | ~^~~
> splice.c:75:25: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 75 | score=match[a[i]][*b];
> | ^~
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:76:38: note: in expansion of macro ‘Direc’
> 76 | left=Score(i-1,0)+left_penalty[Direc(i-1,0)];
> | ^~~~~
> splice.c:90:19: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 90 | score=match[*a][b[j]];
> | ^~
> splice.c:90:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 90 | score=match[*a][b[j]];
> | ~^~~
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:91:36: note: in expansion of macro ‘Direc’
> 91 | top=Score(0,j-1)+top_penalty[Direc(0,j-1)];
> | ^~~~~
> splice.c:107:25: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 107 | score+=match[a[i]][b[j]];
> | ~^~~
> splice.c:107:31: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 107 | score+=match[a[i]][b[j]];
> | ~^~~
> splice.c:110:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 110 | score=match[a[i]][b[j]];
> | ~^~~
> splice.c:110:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 110 | score=match[a[i]][b[j]];
> | ~^~~
> abi.c: In function ‘abi_align’:
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:113:38: note: in expansion of macro ‘Direc’
> 113 | top=Score(i,j-1)+top_penalty[Direc(i,j-1)];
> | ^~~~~
> abi.c:195:18: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 195 | if (badness[a[i]][b[j]]) {
> | ~^~~
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:114:40: note: in expansion of macro ‘Direc’
> 114 | left=Score(i-1,j)+left_penalty[Direc(i-1,j)];
> | ^~~~~
> abi.c:195:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 195 | if (badness[a[i]][b[j]]) {
> | ~^~~
> splice.c:139:12: warning: suggest parentheses around assignment used as truth
> value [-Wparentheses]
> 139 | while (direc=Direc(i,j))
> | ^~~~~
> abi.c:221:18: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 221 | if (badness[a[i]][b[j]]) {
> | ~^~~
> abi.c:221:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 221 | if (badness[a[i]][b[j]]) {
> | ~^~~
> splice.c: In function ‘splice_align_right’:
> splice.c:176:12: warning: type defaults to ‘int’ in declaration of ‘left’
> [-Wimplicit-int]
> 176 | register left, top, direc, score, i, j;
> | ^~~~
> abi.c:226:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 226 | l<width && r<height && badness[a[l]][b[r]]==0
> | ~^~~
> splice.c:176:18: warning: type defaults to ‘int’ in declaration of ‘top’
> [-Wimplicit-int]
> 176 | register left, top, direc, score, i, j;
> | ^~~
> splice.c:176:23: warning: type defaults to ‘int’ in declaration of ‘direc’
> [-Wimplicit-int]
> 176 | register left, top, direc, score, i, j;
> | ^~~~~
> abi.c:226:52: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 226 | l<width && r<height && badness[a[l]][b[r]]==0
> | ~^~~
> splice.c:176:30: warning: type defaults to ‘int’ in declaration of ‘score’
> [-Wimplicit-int]
> 176 | register left, top, direc, score, i, j;
> | ^~~~~
> splice.c:176:37: warning: type defaults to ‘int’ in declaration of ‘i’
> [-Wimplicit-int]
> 176 | register left, top, direc, score, i, j;
> | ^
> splice.c:176:40: warning: type defaults to ‘int’ in declaration of ‘j’
> [-Wimplicit-int]
> 176 | register left, top, direc, score, i, j;
> | ^
> abi.c:233:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 233 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> splice.c:189:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 189 | Score(0,0)=max_score=match[*a][*b];
> | ^~
> abi.c:233:36: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 233 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> splice.c:189:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 189 | Score(0,0)=max_score=match[*a][*b];
> | ^~
> splice.c:196:18: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 196 | score=match[a[i]][*b];
> | ~^~~
> vector.c: In function ‘construct_vector_tags’:
> splice.c:196:23: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 196 | score=match[a[i]][*b];
> | ^~
> vector.c:85:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 85 | accr|=tag_code(rev_code[seq[len-k%len-1]]);
> | ~~~^~~~~~~~~~~~~
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:197:36: note: in expansion of macro ‘Direc’
> 197 | left=Score(i-1,0)+left_penalty[Direc(i-1,0)];
> | ^~~~~
> abi.c:245:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 245 | l<width && r<height && badness[a[l]][b[r]]==0
> | ~^~~
> abi.c:245:52: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 245 | l<width && r<height && badness[a[l]][b[r]]==0
> | ~^~~
> splice.c:211:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 211 | score=match[*a][b[j]];
> | ^~
> splice.c:211:22: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 211 | score=match[*a][b[j]];
> | ~^~~
> abi.c:252:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 252 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:212:34: note: in expansion of macro ‘Direc’
> 212 | top=Score(0,j-1)+top_penalty[Direc(0,j-1)];
> | ^~~~~
> abi.c:252:36: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 252 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> splice.c:228:23: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 228 | score+=match[a[i]][b[j]];
> | ~^~~
> splice.c:228:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 228 | score+=match[a[i]][b[j]];
> | ~^~~
> splice.c:231:22: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 231 | score=match[a[i]][b[j]];
> | ~^~~
> abi.c:266:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 266 | l<width && r<height && badness[a[l]][b[r]]==0
> | ~^~~
> splice.c:231:28: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 231 | score=match[a[i]][b[j]];
> | ~^~~
> abi.c:266:52: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 266 | l<width && r<height && badness[a[l]][b[r]]==0
> | ~^~~
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:234:36: note: in expansion of macro ‘Direc’
> 234 | top=Score(i,j-1)+top_penalty[Direc(i,j-1)];
> | ^~~~~
> splice.c:16:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> splice.c:235:38: note: in expansion of macro ‘Direc’
> 235 | left=Score(i-1,j)+left_penalty[Direc(i-1,j)];
> | ^~~~~
> abi.c:273:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 273 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> abi.c:273:36: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 273 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> splice.c:260:10: warning: suggest parentheses around assignment used as truth
> value [-Wparentheses]
> 260 | while (direc=Direc(i,j))
> | ^~~~~
> splice.c:276:15: warning: suggest parentheses around ‘&&’ within ‘||’
> [-Wparentheses]
> 276 | if (j>=span && j>=width-max_i || j>height/2)
> | ~~~~~~~~^~~~~~~~~~~~~~~~~
> abi.c:289:18: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 289 | if (badness[a[i]][b[j]]) {
> | ~^~~
> abi.c:289:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 289 | if (badness[a[i]][b[j]]) {
> | ~^~~
> abi.c:294:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 294 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
> | ~^~~
> abi.c:294:45: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 294 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
> | ~^~~
> abi.c:301:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 301 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> abi.c:301:36: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 301 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> abi.c:313:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 313 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
> | ~^~~
> abi.c:313:45: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 313 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
> | ~^~~
> abi.c:320:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 320 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> abi.c:320:36: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 320 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> abi.c:334:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 334 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
> | ~^~~
> abi.c:334:45: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 334 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
> | ~^~~
> abi.c:341:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 341 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> abi.c:341:36: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 341 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
> | ~^~~
> vector.c: In function ‘tag_code’:
> vector.c:44:10: warning: ‘tmp’ may be used uninitialized
> [-Wmaybe-uninitialized]
> 44 | return tmp;
> | ^~~
> vector.c:22:16: note: ‘tmp’ was declared here
> 22 | register int tmp;
> | ^~~
> lucy.c: In function ‘hashstring’:
> lucy.c:111:9: warning: suggest parentheses around assignment used as truth
> value [-Wparentheses]
> 111 | if (g = value&0xF0000000) {
> | ^
> lucy.c: In function ‘worker’:
> lucy.c:172:10: warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> 172 | int id=(int)arg;
> | ^
> lucy.c: In function ‘work_splice’:
> lucy.c:206:5: error: implicit declaration of function ‘splice_align_left’
> [-Werror=implicit-function-declaration]
> 206 | splice_align_left(id, target_seq[id],
> | ^~~~~~~~~~~~~~~~~
> qual_trim.c:214:1: warning: "/*" within comment [-Wcomment]
> 214 | /* Determines some number of candidate clean ranges using a particular
> |
> qual_trim.c:215:1: warning: "/*" within comment [-Wcomment]
> 215 | /* window size.
> |
> qual_trim.c:216:1: warning: "/*" within comment [-Wcomment]
> 216 | /*
> |
> qual_trim.c:217:1: warning: "/*" within comment [-Wcomment]
> 217 | /* Globals used:
> |
> qual_trim.c:218:1: warning: "/*" within comment [-Wcomment]
> 218 | /* double end_limit, (maximum allowed probability of error
> for bases)
> |
> qual_trim.c:219:1: warning: "/*" within comment [-Wcomment]
> 219 | /* ( at each end of clean range)
> |
> qual_trim.c:220:1: warning: "/*" within comment [-Wcomment]
> 220 | /*
> |
> qual_trim.c:332:1: warning: "/*" within comment [-Wcomment]
> 332 | /* Finds the largest subsequence of a sequence whose average
> probability
> |
> qual_trim.c:333:1: warning: "/*" within comment [-Wcomment]
> 333 | /* of error does not exceed a specified maximum.
> |
> qual_trim.c:334:1: warning: "/*" within comment [-Wcomment]
> 334 | /*
> |
> qual_trim.c:335:1: warning: "/*" within comment [-Wcomment]
> 335 | /* Globals used:
> |
> qual_trim.c:336:1: warning: "/*" within comment [-Wcomment]
> 336 | /* double max_avg_error, (maximum allowed average probability
> of error)
> |
> qual_trim.c:337:1: warning: "/*" within comment [-Wcomment]
> 337 | /* double end_limit, (maximum allowed probability of error
> for bases)
> |
> lucy.c:247:7: error: implicit declaration of function ‘splice_align_right’
> [-Werror=implicit-function-declaration]
> 247 | splice_align_right(id, target_seq[id]+seqs[i].left,
> | ^~~~~~~~~~~~~~~~~~
> qual_trim.c:338:1: warning: "/*" within comment [-Wcomment]
> 338 | /* ( at each end of clean range)
> |
> qual_trim.c:339:1: warning: "/*" within comment [-Wcomment]
> 339 | /*
> |
> lucy.c: At top level:
> lucy.c:284:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 284 | main (argc, argv)
> | ^~~~
> qual_trim.c:434:1: warning: "/*" within comment [-Wcomment]
> 434 | /* Determines a single clean range, after recursively considering all
> of
> |
> qual_trim.c:435:1: warning: "/*" within comment [-Wcomment]
> 435 | /* the specified window sizes. Calls average_error_trim to trim the
> |
> qual_trim.c:436:1: warning: "/*" within comment [-Wcomment]
> 436 | /* results of the final window based on overall average probability of
> |
> qual_trim.c:437:1: warning: "/*" within comment [-Wcomment]
> 437 | /* error.
> |
> qual_trim.c:438:1: warning: "/*" within comment [-Wcomment]
> 438 | /*
> |
> qual_trim.c:439:1: warning: "/*" within comment [-Wcomment]
> 439 | /* Globals used:
> |
> qual_trim.c:440:1: warning: "/*" within comment [-Wcomment]
> 440 | /* double max_avg_error, (maximum allowed average probability
> of error)
> |
> qual_trim.c:441:1: warning: "/*" within comment [-Wcomment]
> 441 | /* double end_limit, (maximum allowed probability of error
> for bases)
> |
> qual_trim.c:442:1: warning: "/*" within comment [-Wcomment]
> 442 | /* ( at each end of clean range)
> |
> qual_trim.c:443:1: warning: "/*" within comment [-Wcomment]
> 443 | /*
> |
> lucy.c: In function ‘main’:
> qual_trim.c:569:1: warning: "/*" within comment [-Wcomment]
> 569 | /* Sets the window size and average probability of error allowed for
> the
> |
> lucy.c:361:9: error: implicit declaration of function ‘set_bracket’
> [-Werror=implicit-function-declaration]
> 361 | set_bracket(bracket_size, bracket_err);
> | ^~~~~~~~~~~
> qual_trim.c:570:1: warning: "/*" within comment [-Wcomment]
> 570 | /* terminal windows that "bracket" the candidate clean range.
> |
> qual_trim.c:571:1: warning: "/*" within comment [-Wcomment]
> 571 | /*
> |
> qual_trim.c:572:1: warning: "/*" within comment [-Wcomment]
> 572 | /* Globals used:
> |
> qual_trim.c:573:1: warning: "/*" within comment [-Wcomment]
> 573 | /* int bracket_window, (size of terminal window)
> |
> qual_trim.c:574:1: warning: "/*" within comment [-Wcomment]
> 574 | /* double bracket_error (allowable average prob. error in
> window)
> |
> qual_trim.c:575:1: warning: "/*" within comment [-Wcomment]
> 575 | /*
> |
> qual_trim.c:587:1: warning: "/*" within comment [-Wcomment]
> 587 | /* Finds the leftmost window, and the rightmost window, which meet the
> |
> qual_trim.c:588:1: warning: "/*" within comment [-Wcomment]
> 588 | /* specified error criterion. The purpose of this function is to
> bracket
> |
> qual_trim.c:589:1: warning: "/*" within comment [-Wcomment]
> 589 | /* the portion of the sequence that is of decent quality -- i.e. to
> |
> qual_trim.c:590:1: warning: "/*" within comment [-Wcomment]
> 590 | /* eliminate the really bad quality stuff that is often found on
> either
> |
> qual_trim.c:591:1: warning: "/*" within comment [-Wcomment]
> 591 | /* end. The beginning of the first matching window, and the end of
> the
> |
> qual_trim.c:592:1: warning: "/*" within comment [-Wcomment]
> 592 | /* last, bracket the sequence range that will be looked at to find the
> |
> qual_trim.c:593:1: warning: "/*" within comment [-Wcomment]
> 593 | /* final clean range.
> |
> qual_trim.c:594:1: warning: "/*" within comment [-Wcomment]
> 594 | /*
> |
> qual_trim.c:595:1: warning: "/*" within comment [-Wcomment]
> 595 | /* This function is called before the multi_window_trim function, and
> |
> qual_trim.c:596:1: warning: "/*" within comment [-Wcomment]
> 596 | /* its results are used to limit the range of sequence that will be
> |
> qual_trim.c:597:1: warning: "/*" within comment [-Wcomment]
> 597 | /* considered by that function.
> |
> qual_trim.c:598:1: warning: "/*" within comment [-Wcomment]
> 598 | /*
> |
> lucy.c:469:5: error: implicit declaration of function ‘default_windows’
> [-Werror=implicit-function-declaration]
> 469 | default_windows();
> | ^~~~~~~~~~~~~~~
> lucy.c:531:51: warning: cast to pointer from integer of different size
> [-Wint-to-pointer-cast]
> 531 | if (pthread_create(&threads[i], NULL, worker, (void*)i))
> | ^
> qual_trim.c:678:1: warning: "/*" within comment [-Wcomment]
> 678 | /* Determines the clean range. Calls multi_window_trim, which calls
> both
> |
> qual_trim.c:679:1: warning: "/*" within comment [-Wcomment]
> 679 | /* window_trim and average_error_trim.
> |
> qual_trim.c:680:1: warning: "/*" within comment [-Wcomment]
> 680 | /*
> |
> qual_trim.c:681:1: warning: "/*" within comment [-Wcomment]
> 681 | /* Globals used:
> |
> qual_trim.c:682:1: warning: "/*" within comment [-Wcomment]
> 682 | /* int num_windows, (number of windows)
> |
> qual_trim.c:683:1: warning: "/*" within comment [-Wcomment]
> 683 | /* int *windows, (array of window sizes (largest to
> smallest))
> |
> qual_trim.c:684:1: warning: "/*" within comment [-Wcomment]
> 684 | /* double *err_limits, (array of maximum allowed average
> probability)
> |
> qual_trim.c:685:1: warning: "/*" within comment [-Wcomment]
> 685 | /* ( for each window size)
> |
> qual_trim.c:686:1: warning: "/*" within comment [-Wcomment]
> 686 | /* double max_avg_error, (maximum allowed average probability
> of error)
> |
> qual_trim.c:687:1: warning: "/*" within comment [-Wcomment]
> 687 | /* double end_limit, (maximum allowed probability of error
> for bases)
> |
> qual_trim.c:688:1: warning: "/*" within comment [-Wcomment]
> 688 | /* ( at each end of clean range)
> |
> qual_trim.c:689:1: warning: "/*" within comment [-Wcomment]
> 689 | /* int bracket_window, (size of terminal window)
> |
> lucy.c:639:7: error: implicit declaration of function ‘quality_trim’
> [-Werror=implicit-function-declaration]
> 639 | quality_trim(conf_val_raw, j, minimum, &(ptr->left),
> &(ptr->right));
> | ^~~~~~~~~~~~
> qual_trim.c:690:1: warning: "/*" within comment [-Wcomment]
> 690 | /* double bracket_error (allowable average prob. error in
> window)
> |
> qual_trim.c:691:1: warning: "/*" within comment [-Wcomment]
> 691 | /*
> |
> qual_trim.c: In function ‘quality_trim’:
> qual_trim.c:705:21: warning: unused variable ‘sum’ [-Wunused-variable]
> 705 | double err, sum;
> | ^~~
> qual_trim.c:705:16: warning: unused variable ‘err’ [-Wunused-variable]
> 705 | double err, sum;
> | ^~~
> qual_trim.c: At top level:
> qual_trim.c:792:1: warning: "/*" within comment [-Wcomment]
> 792 | /* Sets up 3 windows for quality trimming, with the average error
> allowed
> |
> qual_trim.c:793:1: warning: "/*" within comment [-Wcomment]
> 793 | /* in each window calculated from max_avg_error.
> |
> qual_trim.c:794:1: warning: "/*" within comment [-Wcomment]
> 794 | /*
> |
> lucy.c:669:5: error: implicit declaration of function ‘prepare_abi_mask’
> [-Werror=implicit-function-declaration]
> 669 | prepare_abi_mask();
> | ^~~~~~~~~~~~~~~~
> qual_trim.c:795:1: warning: "/*" within comment [-Wcomment]
> 795 | /* Globals used:
> |
> lucy.c:713:9: error: implicit declaration of function ‘abi_align’
> [-Werror=implicit-function-declaration]
> 713 | abi_align(phred_seq, ptr->len, abi_seq, bases, &left, &right);
> | ^~~~~~~~~
> qual_trim.c:796:1: warning: "/*" within comment [-Wcomment]
> 796 | /* int num_windows, (number of windows)
> |
> qual_trim.c:797:1: warning: "/*" within comment [-Wcomment]
> 797 | /* int *windows, (array of window sizes (largest to
> smallest))
> |
> qual_trim.c:798:1: warning: "/*" within comment [-Wcomment]
> 798 | /* double *err_limits, (array of maximum allowed average
> probability)
> |
> qual_trim.c:799:1: warning: "/*" within comment [-Wcomment]
> 799 | /* (for each window size)
> |
> lucy.c:792:15: warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> 792 | (i=(int)fgets(buf, BUFFER_LENGTH, spl_file)) &&
> buf[0]!='>'; ) {
> | ^
> qual_trim.c:800:1: warning: "/*" within comment [-Wcomment]
> 800 | /* double max_avg_error, (maximum allowed average probability
> of error)
> |
> qual_trim.c:801:1: warning: "/*" within comment [-Wcomment]
> 801 | /*
> |
> qual_trim.c:826:1: warning: "/*" within comment [-Wcomment]
> 826 | /* Simulates the functionality of the old grim() function, by calling
> |
> qual_trim.c:827:1: warning: "/*" within comment [-Wcomment]
> 827 | /* quality_trim().
> |
> qual_trim.c:828:1: warning: "/*" within comment [-Wcomment]
> 828 | /*
> |
> qual_trim.c:829:1: warning: "/*" within comment [-Wcomment]
> 829 | /* Globals used:
> |
> qual_trim.c:830:1: warning: "/*" within comment [-Wcomment]
> 830 | /* int num_windows, (number of windows)
> |
> qual_trim.c:831:1: warning: "/*" within comment [-Wcomment]
> 831 | /* int *windows, (array of window sizes (largest to
> smallest))
> |
> qual_trim.c:832:1: warning: "/*" within comment [-Wcomment]
> 832 | /* double *err_limits, (array of maximum allowed average
> probability)
> |
> qual_trim.c:833:1: warning: "/*" within comment [-Wcomment]
> 833 | /* (for each window size)
> |
> qual_trim.c:834:1: warning: "/*" within comment [-Wcomment]
> 834 | /* double max_avg_error, (maximum allowed average probability
> of error)
> |
> qual_trim.c:835:1: warning: "/*" within comment [-Wcomment]
> 835 | /* double end_limit, (maximum allowed probability of error
> for bases)
> |
> qual_trim.c:836:1: warning: "/*" within comment [-Wcomment]
> 836 | /* ( at each end of clean range)
> |
> qual_trim.c:837:1: warning: "/*" within comment [-Wcomment]
> 837 | /*
> |
> lucy.c:891:14: error: implicit declaration of function ‘poly_at_left’
> [-Werror=implicit-function-declaration]
> 891 | left=poly_at_left(&phred_seq[seqs[i].left],
> | ^~~~~~~~~~~~
> lucy.c:894:15: error: implicit declaration of function ‘poly_at_right’
> [-Werror=implicit-function-declaration]
> 894 | right=poly_at_right(&phred_seq[seqs[i].right],
> | ^~~~~~~~~~~~~
> abi.c: In function ‘abi_code’:
> abi.c:84:10: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized]
> 84 | return tmp;
> | ^~~
> abi.c:62:16: note: ‘tmp’ was declared here
> 62 | register int tmp;
> | ^~~
> lucy.c:934:5: error: implicit declaration of function ‘construct_vector_tags’
> [-Werror=implicit-function-declaration]
> 934 | construct_vector_tags(vec_seq, bases);
> | ^~~~~~~~~~~~~~~~~~~~~
> lucy.c:947:11: error: implicit declaration of function ‘match_vector_tags’
> [-Werror=implicit-function-declaration]
> 947 | j=match_vector_tags(phred_seq+seqs[i].left, bases);
> | ^~~~~~~~~~~~~~~~~
> cc1: some warnings being treated as errors
> lucy.c:959:5: error: implicit declaration of function ‘destroy_vector_tags’
> [-Werror=implicit-function-declaration]
> 959 | destroy_vector_tags();
> | ^~~~~~~~~~~~~~~~~~~
> make[1]: *** [<builtin>: poly.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/lucy_1.20-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
pgpqZNikUlx_P.pgp
