[Debian-med-packaging] Bug#1114377: sift: FTBFS: Matrix_Info.c:822:1: error: number of arguments doesn't match prototype
Santiago Vila
sanvila at debian.org
Fri Sep 5 19:26:18 BST 2025
Package: src:sift
Version: 6.2.1-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:sift, so that this is still
visible in the BTS web page for this package.
Thanks.
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[...]
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ -e src/Makefile -a -e src/deps.mk ]; then make -j2 -C src prefix=/usr distclean; fi
rm -f info_on_seqs.1 SIFT_for_submitting_fasta_seq.csh.1
# remove pre-compiled binaries from bin - thanks to Michael Bienia <geser at ubuntu.com>
rm -f bin/choose_seqs_via_psiblastseedmedian
rm -f bin/clump_output_alignedseq
rm -f bin/consensus_to_seq
rm -f bin/fastaseqs
rm -f bin/info_on_seqs
rm -f bin/process_alignment
rm -f bin/psiblast_res_to_fasta_dbpairwise
[... snipped ...]
choose_seqs_via_psiblastseedmedian.c:56:52: warning: unused variable ‘dtemp’ [-Wunused-variable]
56 | int i, k, index = 0, nseqs_written; double dtemp;
| ^~~~~
choose_seqs_via_psiblastseedmedian.c:53:28: warning: unused variable ‘temp_chk_fp’ [-Wunused-variable]
53 | FILE* outfp; FILE* temp_chk_fp;
| ^~~~~~~~~~~
choose_seqs_via_psiblastseedmedian.c: In function ‘write_seqs_not_in_hash’:
choose_seqs_via_psiblastseedmedian.c:288:25: error: too many arguments to function ‘output_sequence’; expected 0, have 2
288 | output_sequence (seqs[i], outfp);
| ^~~~~~~~~~~~~~~ ~~~~~~~
/usr/include/blimps/sequences.h:253:13: note: declared here
253 | extern void output_sequence();
| ^~~~~~~~~~~~~~~
choose_seqs_via_psiblastseedmedian.c: In function ‘write_seq_to_file’:
choose_seqs_via_psiblastseedmedian.c:395:9: error: too many arguments to function ‘output_sequence’; expected 0, have 2
395 | output_sequence (seq, fp);
| ^~~~~~~~~~~~~~~ ~~~
/usr/include/blimps/sequences.h:253:13: note: declared here
253 | extern void output_sequence();
| ^~~~~~~~~~~~~~~
Matrix_Info.c: In function ‘read_multiple_polymorphism_data’:
Matrix_Info.c:1473:15: warning: unused variable ‘string_pos’ [-Wunused-variable]
1473 | char *string_pos;
| ^~~~~~~~~~
Matrix_Info.c:1470:19: warning: unused variable ‘aa_pos’ [-Wunused-variable]
1470 | int aa, i, aa_pos, pos;
| ^~~~~~
Matrix_Info.c:1470:12: warning: unused variable ‘aa’ [-Wunused-variable]
1470 | int aa, i, aa_pos, pos;
| ^~
Matrix_Info.c: In function ‘read_polymorphism_data’:
Matrix_Info.c:1539:15: warning: unused variable ‘string_pos’ [-Wunused-variable]
1539 | char *string_pos;
| ^~~~~~~~~~
Matrix_Info.c:1536:20: warning: unused variable ‘aa_pos’ [-Wunused-variable]
1536 | int aa, i, aa_pos, pos;
| ^~~~~~
Matrix_Info.c:1536:13: warning: unused variable ‘aa’ [-Wunused-variable]
1536 | int aa, i, aa_pos, pos;
| ^~
In file included from Psiblast.c:11,
from clump_output_alignedseq.c:24:
stringhash.c: In function ‘Hash’:
stringhash.c:59:19: warning: unused variable ‘temp’ [-Wunused-variable]
59 | char* temp;
| ^~~~
Psiblast.c: In function ‘initialize_Aligned_Pair’:
Psiblast.c:54:21: error: too many arguments to function ‘get_token’; expected 0, have 1
54 | stringptr = get_token (Buffer);
| ^~~~~~~~~ ~~~~~~
/usr/include/blimps/strutil.h:87:14: note: declared here
87 | extern char *get_token();
| ^~~~~~~~~
Psiblast.c: In function ‘read_4_alignment_lines’:
Psiblast.c:119:18: error: too many arguments to function ‘get_token’; expected 0, have 1
119 | strptr = get_token (Buffer);
| ^~~~~~~~~ ~~~~~~
/usr/include/blimps/strutil.h:87:14: note: declared here
87 | extern char *get_token();
| ^~~~~~~~~
Psiblast.c:121:18: error: too many arguments to function ‘get_token’; expected 0, have 1
121 | strptr = get_token (NULL);
| ^~~~~~~~~ ~~~~
/usr/include/blimps/strutil.h:87:14: note: declared here
87 | extern char *get_token();
| ^~~~~~~~~
Psiblast.c:125:18: error: too many arguments to function ‘get_token’; expected 0, have 1
125 | strptr = get_token (NULL); /* this is the alignment */
| ^~~~~~~~~ ~~~~
/usr/include/blimps/strutil.h:87:14: note: declared here
87 | extern char *get_token();
| ^~~~~~~~~
Psiblast.c:129:18: error: too many arguments to function ‘get_token’; expected 0, have 1
129 | strptr = get_token (Buffer);
| ^~~~~~~~~ ~~~~~~
/usr/include/blimps/strutil.h:87:14: note: declared here
87 | extern char *get_token();
| ^~~~~~~~~
Psiblast.c:131:18: error: too many arguments to function ‘get_token’; expected 0, have 1
131 | strptr = get_token (NULL);
| ^~~~~~~~~ ~~~~
/usr/include/blimps/strutil.h:87:14: note: declared here
87 | extern char *get_token();
| ^~~~~~~~~
Psiblast.c:135:18: error: too many arguments to function ‘get_token’; expected 0, have 1
135 | strptr = get_token (NULL); /* subject alignment */
| ^~~~~~~~~ ~~~~
/usr/include/blimps/strutil.h:87:14: note: declared here
87 | extern char *get_token();
| ^~~~~~~~~
Psiblast.c: In function ‘process_sequence_line’:
Psiblast.c:170:5: error: too many arguments to function ‘resize_sequence’; expected 0, have 1
170 | resize_sequence(seq);
| ^~~~~~~~~~~~~~~ ~~~
/usr/include/blimps/sequences.h:264:13: note: declared here
264 | extern void resize_sequence();
| ^~~~~~~~~~~~~~~
Psiblast.c:177:17: error: too many arguments to function ‘read_sequence’; expected 0, have 4
177 | num_entered = read_sequence(seq, seq->type, start_pos, buff);
| ^~~~~~~~~~~~~ ~~~
/usr/include/blimps/sequences.h:136:12: note: declared here
136 | extern int read_sequence();
| ^~~~~~~~~~~~~
Psiblast.c: In function ‘free_aligned_pair’:
Psiblast.c:192:17: error: too many arguments to function ‘free_sequence’; expected 0, have 1
192 | free_sequence (alignment->query);
| ^~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~
/usr/include/blimps/sequences.h:175:13: note: declared here
175 | extern void free_sequence();
| ^~~~~~~~~~~~~
Psiblast.c:193:17: error: too many arguments to function ‘free_sequence’; expected 0, have 1
193 | free_sequence (alignment->subject);
| ^~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~
/usr/include/blimps/sequences.h:175:13: note: declared here
175 | extern void free_sequence();
| ^~~~~~~~~~~~~
Psiblast.c: In function ‘block_to_checkpoint_file’:
Psiblast.c:209:16: error: too many arguments to function ‘PN_block_to_matrix’; expected 0, have 2
209 | pssm = PN_block_to_matrix (block, 20);
| ^~~~~~~~~~~~~~~~~~ ~~~~~
PN_convert.c:105:9: note: declared here
105 | Matrix *PN_block_to_matrix(block, conversion_method)
| ^~~~~~~~~~~~~~~~~~
Psiblast.c:226:9: error: too many arguments to function ‘free_matrix’; expected 0, have 1
226 | free_matrix (pssm);
| ^~~~~~~~~~~ ~~~~
/usr/include/blimps/matrix.h:111:13: note: declared here
111 | extern void free_matrix();
| ^~~~~~~~~~~
Psiblast.c: At top level:
Psiblast.c:272:28: warning: argument 1 of type ‘char[]’ with mismatched bound [-Warray-parameter=]
272 | formatdb_system_call (char database[])
| ~~~~~^~~~~~~~~~
In file included from Psiblast.c:8:
Psiblast.h:65:33: note: previously declared as ‘char[500]’
65 | void formatdb_system_call (char database[LARGE_BUFF_LENGTH]);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
Psiblast.c: In function ‘formatdb_system_call’:
Psiblast.c:276:14: warning: unused variable ‘makeblastdb_command’ [-Wunused-variable]
276 | char makeblastdb_command[LARGE_BUFF_LENGTH];
| ^~~~~~~~~~~~~~~~~~~
Psiblast.c:275:14: warning: unused variable ‘formatdb_command’ [-Wunused-variable]
275 | char formatdb_command[LARGE_BUFF_LENGTH];
| ^~~~~~~~~~~~~~~~
Psiblast.c: In function ‘add_sequence_to_msa’:
Psiblast.c:410:9: error: too many arguments to function ‘output_sequence’; expected 0, have 2
410 | output_sequence (seq, outfp);
| ^~~~~~~~~~~~~~~ ~~~
/usr/include/blimps/sequences.h:253:13: note: declared here
253 | extern void output_sequence();
| ^~~~~~~~~~~~~~~
In file included from Clumping.c:7,
from clump_output_alignedseq.c:25:
Clumping.h: At top level:
Clumping.h:9:9: warning: ‘MAXSEQ’ redefined
9 | #define MAXSEQ 400
| ^~~~~~
Alignment.c:20:9: note: this is the location of the previous definition
20 | #define MAXSEQ 20000
| ^~~~~~
Clumping.c: In function ‘clump_into_consensus_seqs’:
Clumping.c:244:25: error: too many arguments to function ‘pb_weights’; expected 0, have 1
244 | pb_weights (block);
| ^~~~~~~~~~ ~~~~~
PN_convert.c:48:6: note: declared here
48 | void pb_weights(/*block*/);
| ^~~~~~~~~~
Clumping.c:245:32: error: too many arguments to function ‘PN_block_to_matrix’; expected 0, have 2
245 | pssm = PN_block_to_matrix (block, 2);
| ^~~~~~~~~~~~~~~~~~ ~~~~~
PN_convert.c:105:9: note: declared here
105 | Matrix *PN_block_to_matrix(block, conversion_method)
| ^~~~~~~~~~~~~~~~~~
Clumping.c:247:25: error: too many arguments to function ‘free_block’; expected 0, have 1
247 | free_block(block); free_matrix (pssm);
| ^~~~~~~~~~ ~~~~~
/usr/include/blimps/blocks.h:101:13: note: declared here
101 | extern void free_block() ;
| ^~~~~~~~~~
Clumping.c:247:44: error: too many arguments to function ‘free_matrix’; expected 0, have 1
247 | free_block(block); free_matrix (pssm);
| ^~~~~~~~~~~ ~~~~
/usr/include/blimps/matrix.h:111:13: note: declared here
111 | extern void free_matrix();
| ^~~~~~~~~~~
Clumping.c: In function ‘print_consensus_seqs_aligned’:
Clumping.c:404:9: error: too many arguments to function ‘pb_weights’; expected 0, have 1
404 | pb_weights (block);
| ^~~~~~~~~~ ~~~~~
PN_convert.c:48:6: note: declared here
48 | void pb_weights(/*block*/);
| ^~~~~~~~~~
Clumping.c:405:16: error: too many arguments to function ‘PN_block_to_matrix’; expected 0, have 2
405 | pssm = PN_block_to_matrix (block, 2);
| ^~~~~~~~~~~~~~~~~~ ~~~~~
PN_convert.c:105:9: note: declared here
105 | Matrix *PN_block_to_matrix(block, conversion_method)
| ^~~~~~~~~~~~~~~~~~
Clumping.c:415:17: error: too many arguments to function ‘output_sequence’; expected 0, have 2
415 | output_sequence (consensus_sequence, outfp);
| ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~
/usr/include/blimps/sequences.h:253:13: note: declared here
253 | extern void output_sequence();
| ^~~~~~~~~~~~~~~
Clumping.c:425:9: error: too many arguments to function ‘free_block’; expected 0, have 1
425 | free_block (block);
| ^~~~~~~~~~ ~~~~~
/usr/include/blimps/blocks.h:101:13: note: declared here
101 | extern void free_block() ;
| ^~~~~~~~~~
Clumping.c:426:9: error: too many arguments to function ‘free_matrix’; expected 0, have 1
426 | free_matrix (pssm);
| ^~~~~~~~~~~ ~~~~
/usr/include/blimps/matrix.h:111:13: note: declared here
111 | extern void free_matrix();
| ^~~~~~~~~~~
Clumping.c:427:9: error: too many arguments to function ‘free_sequence’; expected 0, have 1
427 | free_sequence (consensus_sequence);
| ^~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~
/usr/include/blimps/sequences.h:175:13: note: declared here
175 | extern void free_sequence();
| ^~~~~~~~~~~~~
clump_output_alignedseq.c: At top level:
clump_output_alignedseq.c:28:9: warning: ‘MAXSEQ’ redefined
28 | #define MAXSEQ 20000
| ^~~~~~
Clumping.h:9:9: note: this is the location of the previous definition
9 | #define MAXSEQ 400
| ^~~~~~
clump_output_alignedseq.c: In function ‘main’:
clump_output_alignedseq.c:63:17: error: too many arguments to function ‘type_dbs’; expected 0, have 2
63 | db_type = type_dbs(seqfp, DbInfo);
| ^~~~~~~~ ~~~~~
/usr/include/blimps/sequences.h:216:12: note: declared here
216 | extern int type_dbs();
| ^~~~~~~~
clump_output_alignedseq.c:66:18: error: too many arguments to function ‘seq_type_dbs’; expected 0, have 4
66 | seq_type = seq_type_dbs(seqfp, DbInfo, db_type, seq_type);
| ^~~~~~~~~~~~ ~~~~~
/usr/include/blimps/sequences.h:232:12: note: declared here
232 | extern int seq_type_dbs();
| ^~~~~~~~~~~~
clump_output_alignedseq.c:79:29: error: too many arguments to function ‘read_a_sequence’; expected 0, have 3
79 | (seqs[nseqs] = read_a_sequence(seqfp, db_type, seq_type)) != NULL)
| ^~~~~~~~~~~~~~~ ~~~~~
/usr/include/blimps/sequences.h:110:18: note: declared here
110 | extern Sequence *read_a_sequence();
| ^~~~~~~~~~~~~~~
clump_output_alignedseq.c:53:13: warning: unused variable ‘i’ [-Wunused-variable]
53 | int i;
| ^
clump_output_alignedseq.c:52:19: warning: unused variable ‘consensus_seqs’ [-Wunused-variable]
52 | Sequence* consensus_seqs[MAXSEQ];
| ^~~~~~~~~~~~~~
clump_output_alignedseq.c:51:19: warning: unused variable ‘queryseq’ [-Wunused-variable]
51 | Sequence* queryseq;
| ^~~~~~~~
clump_output_alignedseq.c:44:41: warning: unused variable ‘queryseqfp’ [-Wunused-variable]
44 | FILE* seqfp; FILE* outfp; FILE* queryseqfp; FILE* keyoutfp;
| ^~~~~~~~~~
clump_output_alignedseq.c: In function ‘getargs’:
clump_output_alignedseq.c:137:14: warning: unused variable ‘queryfilename’ [-Wunused-variable]
137 | char queryfilename[LARGE_BUFF_LENGTH];
| ^~~~~~~~~~~~~
PN_convert.c: At top level:
PN_convert.c:1331:13: warning: ‘basic_matrix_construction’ defined but not used [-Wunused-function]
1331 | static void basic_matrix_construction(block, seq_weight, matrix)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [<builtin>: choose_seqs_via_psiblastseedmedian.o] Error 1
make[2]: *** Waiting for unfinished jobs....
PN_convert.c: At top level:
PN_convert.c:1331:13: warning: ‘basic_matrix_construction’ defined but not used [-Wunused-function]
1331 | static void basic_matrix_construction(block, seq_weight, matrix)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [<builtin>: clump_output_alignedseq.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [debian/rules:54: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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