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 --------------------------------------------------------------------------------
