[med-svn] [Git][med-team/ncbi-tools6][master] 5 commits: Start work on ncbi-tools6 6.1.20170106+dfsg2-7.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Mon Dec 29 03:33:06 GMT 2025
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
493cb13f by Aaron M. Ucko at 2025-12-28T21:11:40-05:00
Start work on ncbi-tools6 6.1.20170106+dfsg2-7.
- - - - -
a903b994 by Aaron M. Ucko at 2025-12-28T22:16:08-05:00
Always return a value from non-void functions (#1123553).
* biostruc/cdd/thrd*.[ch] (bwfi, cp[alr]l, cxei, salu, sgoi, slou,
spe[al], spni, ttb0, zsc): Correct return type to void to match
implementation and usage.
* demo/debruijn.c ([Nlm_]Main): Return 0 when not bailing.
* tools/taxblast.c (RDTaxLookupReset): Return tax_looxup, modified
in place.
- - - - -
9f6e8426 by Aaron M. Ucko at 2025-12-28T22:24:32-05:00
debian/.ncbirc: [BLAST]BLASTDB=/usr/share/ncbi/data (see #1117994).
- - - - -
f69725a8 by Aaron M. Ucko at 2025-12-28T22:26:53-05:00
Standards-Version: 4.7.3 (routine-update)
- - - - -
f9dc7296 by Aaron M. Ucko at 2025-12-28T22:30:14-05:00
Finalize ncbi-tools6 6.1.20170106+dfsg2-7 for unstable.
- - - - -
19 changed files:
- biostruc/cdd/thrdbwfi.c
- biostruc/cdd/thrdcpal.c
- biostruc/cdd/thrdcpll.c
- biostruc/cdd/thrdcprl.c
- biostruc/cdd/thrdcxei.c
- biostruc/cdd/thrddecl.h
- biostruc/cdd/thrdsalu.c
- biostruc/cdd/thrdsgoi.c
- biostruc/cdd/thrdslou.c
- biostruc/cdd/thrdspea.c
- biostruc/cdd/thrdspel.c
- biostruc/cdd/thrdspni.c
- biostruc/cdd/thrdttb0.c
- biostruc/cdd/thrdzsc.c
- debian/.ncbirc
- debian/changelog
- debian/control
- demo/debruijn.c
- tools/taxblast.c
Changes:
=====================================
biostruc/cdd/thrdbwfi.c
=====================================
@@ -51,7 +51,7 @@
#include <thrddecl.h>
#include <math.h>
-float bwfi(Thd_Tbl* ttb, Gib_Scd* gsp, Thd_Tst* tts) {
+void bwfi(Thd_Tbl* ttb, Gib_Scd* gsp, Thd_Tst* tts) {
/*---------------------------------------------------------*/
/* ttb: Table holding results of Gibbs sampled threading */
/* gsp: Various control parameters for Gibb's sampling */
=====================================
biostruc/cdd/thrdcpal.c
=====================================
@@ -62,7 +62,7 @@
/* that the same reference state sum may be used for core segment aligment */
/* location sampling. */
-int cpal(Rcx_Ptl* pmf, Cxl_Los** cpr, Cur_Loc* sli, Cxl_Als** cpa) {
+void cpal(Rcx_Ptl* pmf, Cxl_Los** cpr, Cur_Loc* sli, Cxl_Als** cpa) {
/*-------------------------------------------------------*/
/* pmf: Potential of mean force as a 3-d lookup table */
/* cpr: Contacts by segment, largest possible set */
=====================================
biostruc/cdd/thrdcpll.c
=====================================
@@ -57,7 +57,7 @@
/* n- or c-terminal offsets of a segment. They contain pointers to the */
/* energies of each contact, as well as distance intervals. */
-int cpll(Cor_Def* cdf, Rcx_Ptl* pmf, Qry_Seq* qsq, Cxl_Los** cpr,
+void cpll(Cor_Def* cdf, Rcx_Ptl* pmf, Qry_Seq* qsq, Cxl_Los** cpr,
Cur_Aln* sai, Cxl_Los** cpl) {
/*-----------------------------------------------------*/
/* cdf: Core segment locations and loop length limits */
=====================================
biostruc/cdd/thrdcprl.c
=====================================
@@ -58,7 +58,7 @@
/* similar list. Organize residue-fixed environment contacts as a list of */
/* indices and types. */
-int cprl(Fld_Mtf* mtf, Cor_Def* cdf, Rcx_Ptl* pmf, Cxl_Los** cpr, int ct) {
+void cprl(Fld_Mtf* mtf, Cor_Def* cdf, Rcx_Ptl* pmf, Cxl_Los** cpr, int ct) {
/*--------------------------------------------------------*/
/* mtf: Contact matrices defining the folding motif */
/* cdf: contains min/max segment locations */
=====================================
biostruc/cdd/thrdcxei.c
=====================================
@@ -67,7 +67,8 @@
/* side-chain to fixed-residue contacts are stored in cxe. Pairwise and */
/* hydrophobic components of the potential are included in the sums. */
-int cxei(Seg_Nsm* spn, Seg_Cmp* spc, Rcx_Ptl* pmf, Cur_Loc* sli, Seq_Mtf* psm, Cor_Def* cdf, Thd_Cxe* cxe) {
+void cxei(Seg_Nsm* spn, Seg_Cmp* spc, Rcx_Ptl* pmf, Cur_Loc* sli,
+ Seq_Mtf* psm, Cor_Def* cdf, Thd_Cxe* cxe) {
/*--------------------------------------------------------*/
/* spn: Partial sums of contact counts by segment pair */
/* spc: Residue type composition of current threaded seq */
=====================================
biostruc/cdd/thrddecl.h
=====================================
@@ -94,11 +94,11 @@ int atd(Fld_Mtf* mtf, Cor_Def* cdf, Qry_Seq* qsq, Rcx_Ptl* pmf,
Gib_Scd* gsp, Thd_Tbl* ttb, Seq_Mtf* psm, float* trg, int zscs,
double ScalingFactor, float PSSM_Weight);
-int cprl(Fld_Mtf* mtf, Cor_Def* cdf, Rcx_Ptl* pmf, Cxl_Los** cpr, int ct);
+void cprl(Fld_Mtf* mtf, Cor_Def* cdf, Rcx_Ptl* pmf, Cxl_Los** cpr, int ct);
-int ttb0(Thd_Tbl* ttb);
+void ttb0(Thd_Tbl* ttb);
-int sgoi(int is, int it, Rnd_Smp* pvl, Seg_Ord* sgo);
+void sgoi(int is, int it, Rnd_Smp* pvl, Seg_Ord* sgo);
int slo0(Fld_Mtf* mtf, Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli,
int cs, int ct, int* mn, int* mx);
@@ -112,43 +112,43 @@ int sal0(Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli, Cur_Aln* sai,
int spci(Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli, Cur_Aln* sai,
int n, Seg_Cmp* spc);
-int spni(Cxl_Los** cpl, Cur_Loc* sli, int n, Seg_Nsm* spn);
+void spni(Cxl_Los** cpl, Cur_Loc* sli, int n, Seg_Nsm* spn);
-int cxei(Seg_Nsm* spn, Seg_Cmp* spc, Rcx_Ptl* pmf, Cur_Loc* sli, Seq_Mtf* psm, Cor_Def* cdf, Thd_Cxe* cxe);
+void cxei(Seg_Nsm* spn, Seg_Cmp* spc, Rcx_Ptl* pmf, Cur_Loc* sli, Seq_Mtf* psm, Cor_Def* cdf, Thd_Cxe* cxe);
-int cpll(Cor_Def* cdf, Rcx_Ptl* pmf, Qry_Seq* qsq, Cxl_Los** cpr,
- Cur_Aln* sai, Cxl_Los** cpl);
+void cpll(Cor_Def* cdf, Rcx_Ptl* pmf, Qry_Seq* qsq, Cxl_Los** cpr,
+ Cur_Aln* sai, Cxl_Los** cpl);
-int spel(Cxl_Los** cpl, Cur_Aln* sai, Cur_Loc* sli, int cs, Seg_Gsm* spe,
- Cor_Def* cdf, Seq_Mtf* psm, Seg_Cmp* spc);
+void spel(Cxl_Los** cpl, Cur_Aln* sai, Cur_Loc* sli, int cs, Seg_Gsm* spe,
+ Cor_Def* cdf, Seq_Mtf* psm, Seg_Cmp* spc);
int ttbi(Cur_Aln* sai, Cur_Loc* sli, Thd_Gsm* tdg, Thd_Tbl* ttb,
int nrs, int o);
-int cpal(Rcx_Ptl* pmf, Cxl_Los** cpr, Cur_Loc* sli, Cxl_Als** cpa);
+void cpal(Rcx_Ptl* pmf, Cxl_Los** cpr, Cur_Loc* sli, Cxl_Als** cpa);
-int spea(Cor_Def* cdf, Cxl_Als** cpa, Cur_Aln* sai, Cur_Loc* sli,
- int n, int h, Seg_Gsm* spe, Seq_Mtf* psm, Seg_Cmp* spc);
+void spea(Cor_Def* cdf, Cxl_Als** cpa, Cur_Aln* sai, Cur_Loc* sli,
+ int n, int h, Seg_Gsm* spe, Seq_Mtf* psm, Seg_Cmp* spc);
int salr(Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli, Cur_Aln* sai,
int cs, int* mn, int* mx);
-int salu(Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli,
- int cs, int al, Cur_Aln* sai);
+void salu(Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli,
+ int cs, int al, Cur_Aln* sai);
int algs(Rnd_Smp* pvl, int tm);
int slor(Fld_Mtf* mtf, Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli, Cur_Aln* sai,
int cs, int ct, int* mn, int*mx);
-int slou(Fld_Mtf* mtf, Cor_Def* cdf, int cs, int ct, int of, Cur_Loc* sli,
- Cur_Aln* sai, Qry_Seq* qsq);
+void slou(Fld_Mtf* mtf, Cor_Def* cdf, int cs, int ct, int of, Cur_Loc* sli,
+ Cur_Aln* sai, Qry_Seq* qsq);
-float bwfi(Thd_Tbl* ttb, Gib_Scd* gsp, Thd_Tst* tts);
+void bwfi(Thd_Tbl* ttb, Gib_Scd* gsp, Thd_Tst* tts);
-float zsc(Thd_Tbl* ttb, Seq_Mtf* psm, Qry_Seq* qsq, Cxl_Los** cpr,
- Cor_Def* cdf, Rcx_Ptl* pmf, Seg_Gsm* spe, Cur_Aln* sai, Rnd_Smp* pvl,
- double ScalingFactor);
+void zsc(Thd_Tbl* ttb, Seq_Mtf* psm, Qry_Seq* qsq, Cxl_Los** cpr,
+ Cor_Def* cdf, Rcx_Ptl* pmf, Seg_Gsm* spe, Cur_Aln* sai, Rnd_Smp* pvl,
+ double ScalingFactor);
int g(Seg_Gsm* spe, Seq_Mtf* psm, Thd_Gsm* tdg);
=====================================
biostruc/cdd/thrdsalu.c
=====================================
@@ -52,7 +52,8 @@
#include <thrdatd.h>
#include <thrddecl.h>
-int salu(Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli, int cs, int al, Cur_Aln* sai) {
+void salu(Cor_Def* cdf, Qry_Seq* qsq, Cur_Loc* sli, int cs, int al,
+ Cur_Aln* sai) {
/*-------------------------------------------------------*/
/* cdf: Core segment locations and loop length limits */
/* qsq: Sequence to thread with alignment contraints */
=====================================
biostruc/cdd/thrdsgoi.c
=====================================
@@ -52,7 +52,7 @@
#include <thrdatd.h>
#include <thrddecl.h>
-int sgoi(int is, int it, Rnd_Smp* pvl, Seg_Ord* sgo) {
+void sgoi(int is, int it, Rnd_Smp* pvl, Seg_Ord* sgo) {
/*----------------------------------------------------*/
/* is: Code to determine order of segment sampling */
/* it: Code to determine order of terminus sampling */
=====================================
biostruc/cdd/thrdslou.c
=====================================
@@ -52,7 +52,7 @@
#include <thrdatd.h>
#include <thrddecl.h>
-int slou(Fld_Mtf* mtf, Cor_Def* cdf, int cs, int ct, int of, Cur_Loc* sli,
+void slou(Fld_Mtf* mtf, Cor_Def* cdf, int cs, int ct, int of, Cur_Loc* sli,
Cur_Aln* sai, Qry_Seq* qsq) {
/*--------------------------------------------------------*/
/* mtf: Contact matrices defining the folding motif */
=====================================
biostruc/cdd/thrdspea.c
=====================================
@@ -64,8 +64,8 @@
/* components, and side-chain to fixed-residue pairwise and hydrohobic */
/* components. */
-int spea(Cor_Def* cdf, Cxl_Als** cpa, Cur_Aln* sai, Cur_Loc* sli,
- int n, int h, Seg_Gsm* spe, Seq_Mtf* psm, Seg_Cmp* spc) {
+void spea(Cor_Def* cdf, Cxl_Als** cpa, Cur_Aln* sai, Cur_Loc* sli,
+ int n, int h, Seg_Gsm* spe, Seq_Mtf* psm, Seg_Cmp* spc) {
/*--------------------------------------------------------*/
/* cpa: Contacts by segment, given current location */
/* sli: Current locations of core segments in the motif */
=====================================
biostruc/cdd/thrdspel.c
=====================================
@@ -62,8 +62,8 @@
/* of side-chain to peptide contact potential. The "profile" term contains */
/* only the sum of side-chain to fixed-residue contact potential. */
-int spel(Cxl_Los** cpl, Cur_Aln* sai, Cur_Loc* sli, int cs, Seg_Gsm* spe,
- Cor_Def* cdf, Seq_Mtf* psm, Seg_Cmp* spc) {
+void spel(Cxl_Los** cpl, Cur_Aln* sai, Cur_Loc* sli, int cs, Seg_Gsm* spe,
+ Cor_Def* cdf, Seq_Mtf* psm, Seg_Cmp* spc) {
/*--------------------------------------------------------*/
/* cpl: Contacts by segment, given current location */
/* sai: Current alignment of query sequence with core */
=====================================
biostruc/cdd/thrdspni.c
=====================================
@@ -53,7 +53,7 @@
/* Sum contact counts for the n-th core segment. Use these sums to recompute */
/* total contact counts. */
-int spni(Cxl_Los** cpl, Cur_Loc* sli, int n, Seg_Nsm* spn) {
+void spni(Cxl_Los** cpl, Cur_Loc* sli, int n, Seg_Nsm* spn) {
/*-------------------------------------------------------*/
/* cpl: Contacts by segment, given current alignment */
/* sli: Current locations of core segments in the motif */
=====================================
biostruc/cdd/thrdttb0.c
=====================================
@@ -50,7 +50,7 @@
/* Initialize thread table, a linked list containing the minimum energy */
/* threads found in sampling */
-int ttb0(Thd_Tbl* ttb) {
+void ttb0(Thd_Tbl* ttb) {
/*---------------------------------------------------------*/
/* ttb: Tables to hold Results of Gibbs sampled threading */
/*---------------------------------------------------------*/
=====================================
biostruc/cdd/thrdzsc.c
=====================================
@@ -61,8 +61,8 @@
/* Sorts the stored energies in descending order, picks up the alignment.
Calculates the Z-score by shuffling the aliged region 10000 times. */
-float zsc(Thd_Tbl* ttb, Seq_Mtf* psm, Qry_Seq* qsq, Cxl_Los** cpr, Cor_Def* cdf,
- Rcx_Ptl* pmf, Seg_Gsm* spe, Cur_Aln* sai, Rnd_Smp* pvl, double ScalingFactor) {
+void zsc(Thd_Tbl* ttb, Seq_Mtf* psm, Qry_Seq* qsq, Cxl_Los** cpr, Cor_Def* cdf,
+ Rcx_Ptl* pmf, Seg_Gsm* spe, Cur_Aln* sai, Rnd_Smp* pvl, double ScalingFactor) {
/*---------------------------------------------------------*/
/* ttb: Tables to hold Results of Gibbs sampled threading */
/* qsq: Sequence to thread with alignment contraints */
=====================================
debian/.ncbirc
=====================================
@@ -73,4 +73,5 @@ DISPLAY=Courier,10
FETCHED=Times,14
[BLAST]
+BLASTDB=/usr/share/ncbi/data
IGDATA=/usr/share/ncbi/igblast
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+ncbi-tools6 (6.1.20170106+dfsg2-7) unstable; urgency=medium
+
+ * debian/.ncbirc: Belatedly set [BLAST]BLASTDB to /usr/share/ncbi/data.
+ (See #1117994.)
+ * Always return a value from non-void functions. (Closes: #1123553.)
+ - biostruc/cdd/thrd*.[ch] (bwfi, cp[alr]l, cxei, salu, sgoi, slou,
+ spe[al], spni, ttb0, zsc): Correct return type to void to match
+ implementation and usage.
+ - demo/debruijn.c ([Nlm_]Main): Return 0 when not bailing.
+ - tools/taxblast.c (RDTaxLookupReset): Return tax_looxup, modified
+ in place.
+ * Standards-Version: 4.7.3 (routine-update)
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 28 Dec 2025 22:30:14 -0500
+
ncbi-tools6 (6.1.20170106+dfsg2-6) unstable; urgency=medium
* Fix or work around build-order assumptions caught by
=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends-Arch: csh | c-shell,
libxmu-dev
Build-Depends-Indep: icoutils,
imagemagick
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-tools6
Vcs-Git: https://salsa.debian.org/med-team/ncbi-tools6.git
Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/
=====================================
demo/debruijn.c
=====================================
@@ -106,4 +106,6 @@ Int2 Main(void)
puts(output);
free(output);
+
+ return 0;
}
=====================================
tools/taxblast.c
=====================================
@@ -2046,7 +2046,8 @@ RDBTaxLookupPtr RDTaxLookupReset(RDBTaxLookupPtr tax_lookup)
}
tax_lookup->tax_array[i] = tnames = NULL;
}
- tax_lookup->taxids_in_db = 0;
+ tax_lookup->taxids_in_db = 0;
+ return tax_lookup;
}
void RDTaxLookupClose(RDBTaxLookupPtr tax_lookup)
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/compare/0041f9d77d0748c3233a70fbdf7863f0393da463...f9dc7296833a033b3afe029f1d780c02487a0445
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/compare/0041f9d77d0748c3233a70fbdf7863f0393da463...f9dc7296833a033b3afe029f1d780c02487a0445
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