Your message dated Sun, 28 Sep 2025 01:54:39 +0000
with message-id <[email protected]>
and subject line Bug#1114377: fixed in sift 6.2.1-2
has caused the Debian Bug report #1114377,
regarding sift: FTBFS: Matrix_Info.c:822:1: error: number of arguments doesn't
match prototype
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1114377: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114377
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--------------------------------------------------------------------------------
[...]
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
<[email protected]>
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
âdtempâ [-Wunused-variable]
56 | int i, k, index = 0, nseqs_written; double dtemp;
| ^~~~~
choose_seqs_via_psiblastseedmedian.c:53:28: warning: unused variable
âtemp_chk_fpâ [-Wunused-variable]
53 | FILE* outfp; FILE* temp_chk_fp;
| ^~~~~~~~~~~
choose_seqs_via_psiblastseedmedian.c: In function âwrite_seqs_not_in_hashâ:
choose_seqs_via_psiblastseedmedian.c:288:25: error: too many arguments to
function âoutput_sequenceâ; 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 âwrite_seq_to_fileâ:
choose_seqs_via_psiblastseedmedian.c:395:9: error: too many arguments to
function âoutput_sequenceâ; 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 âread_multiple_polymorphism_dataâ:
Matrix_Info.c:1473:15: warning: unused variable âstring_posâ
[-Wunused-variable]
1473 | char *string_pos;
| ^~~~~~~~~~
Matrix_Info.c:1470:19: warning: unused variable âaa_posâ [-Wunused-variable]
1470 | int aa, i, aa_pos, pos;
| ^~~~~~
Matrix_Info.c:1470:12: warning: unused variable âaaâ [-Wunused-variable]
1470 | int aa, i, aa_pos, pos;
| ^~
Matrix_Info.c: In function âread_polymorphism_dataâ:
Matrix_Info.c:1539:15: warning: unused variable âstring_posâ
[-Wunused-variable]
1539 | char *string_pos;
| ^~~~~~~~~~
Matrix_Info.c:1536:20: warning: unused variable âaa_posâ [-Wunused-variable]
1536 | int aa, i, aa_pos, pos;
| ^~~~~~
Matrix_Info.c:1536:13: warning: unused variable âaaâ [-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 âHashâ:
stringhash.c:59:19: warning: unused variable âtempâ [-Wunused-variable]
59 | char* temp;
| ^~~~
Psiblast.c: In function âinitialize_Aligned_Pairâ:
Psiblast.c:54:21: error: too many arguments to function âget_tokenâ;
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 âread_4_alignment_linesâ:
Psiblast.c:119:18: error: too many arguments to function âget_tokenâ;
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 âget_tokenâ;
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 âget_tokenâ;
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 âget_tokenâ;
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 âget_tokenâ;
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 âget_tokenâ;
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 âprocess_sequence_lineâ:
Psiblast.c:170:5: error: too many arguments to function âresize_sequenceâ;
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 âread_sequenceâ;
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 âfree_aligned_pairâ:
Psiblast.c:192:17: error: too many arguments to function âfree_sequenceâ;
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 âfree_sequenceâ;
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 âblock_to_checkpoint_fileâ:
Psiblast.c:209:16: error: too many arguments to function
âPN_block_to_matrixâ; 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 âfree_matrixâ;
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 âchar[]â 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 âchar[500]â
65 | void formatdb_system_call (char database[LARGE_BUFF_LENGTH]);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
Psiblast.c: In function âformatdb_system_callâ:
Psiblast.c:276:14: warning: unused variable âmakeblastdb_commandâ
[-Wunused-variable]
276 | char makeblastdb_command[LARGE_BUFF_LENGTH];
| ^~~~~~~~~~~~~~~~~~~
Psiblast.c:275:14: warning: unused variable âformatdb_commandâ
[-Wunused-variable]
275 | char formatdb_command[LARGE_BUFF_LENGTH];
| ^~~~~~~~~~~~~~~~
Psiblast.c: In function âadd_sequence_to_msaâ:
Psiblast.c:410:9: error: too many arguments to function âoutput_sequenceâ;
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: âMAXSEQâ 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 âclump_into_consensus_seqsâ:
Clumping.c:244:25: error: too many arguments to function âpb_weightsâ;
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
âPN_block_to_matrixâ; 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 âfree_blockâ;
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 âfree_matrixâ;
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 âprint_consensus_seqs_alignedâ:
Clumping.c:404:9: error: too many arguments to function âpb_weightsâ;
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
âPN_block_to_matrixâ; 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 âoutput_sequenceâ;
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 âfree_blockâ;
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 âfree_matrixâ;
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 âfree_sequenceâ;
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: âMAXSEQâ 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 âmainâ:
clump_output_alignedseq.c:63:17: error: too many arguments to function
âtype_dbsâ; 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
âseq_type_dbsâ; 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
âread_a_sequenceâ; 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 âiâ
[-Wunused-variable]
53 | int i;
| ^
clump_output_alignedseq.c:52:19: warning: unused variable âconsensus_seqsâ
[-Wunused-variable]
52 | Sequence* consensus_seqs[MAXSEQ];
| ^~~~~~~~~~~~~~
clump_output_alignedseq.c:51:19: warning: unused variable âqueryseqâ
[-Wunused-variable]
51 | Sequence* queryseq;
| ^~~~~~~~
clump_output_alignedseq.c:44:41: warning: unused variable âqueryseqfpâ
[-Wunused-variable]
44 | FILE* seqfp; FILE* outfp; FILE* queryseqfp; FILE* keyoutfp;
| ^~~~~~~~~~
clump_output_alignedseq.c: In function âgetargsâ:
clump_output_alignedseq.c:137:14: warning: unused variable âqueryfilenameâ
[-Wunused-variable]
137 | char queryfilename[LARGE_BUFF_LENGTH];
| ^~~~~~~~~~~~~
PN_convert.c: At top level:
PN_convert.c:1331:13: warning: âbasic_matrix_constructionâ 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: âbasic_matrix_constructionâ 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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: sift
Source-Version: 6.2.1-2
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sift, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Santiago Vila <[email protected]> (supplier of updated sift package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 28 Sep 2025 02:30:00 +0200
Source: sift
Binary: sift sift-dbgsym
Architecture: source amd64
Version: 6.2.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Description:
sift - predicts if a substitution in a protein has a phenotypic effect
Closes: 1103329 1114377
Changes:
sift (6.2.1-2) unstable; urgency=medium
.
* Team upload.
* Extract parallel from DEB_BUILD_OPTIONS without eval. Closes: #1103329.
* Build with -std=gnu17 to workaround FTBFS with GCC 15. Closes: #1114377.
* Disable Salsa CI jobs which are known not to work.
* Enable nocheck build profile job in Salsa CI.
* Update standards-version.
* Turn off DH_VERBOSE.
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Files:
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sift_6.2.1-2.dsc
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sift_6.2.1-2_amd64.deb
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