[med-svn] [Git][med-team/cufflinks][master] Another chunk of patches
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Dec 8 15:43:45 GMT 2025
Andreas Tille pushed to branch master at Debian Med / cufflinks
Commits:
43e1c685 by Andreas Tille at 2025-12-08T16:43:24+01:00
Another chunk of patches
- - - - -
4 changed files:
- + debian/patches/byte.patch
- debian/patches/gcc15.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/patches/byte.patch
=====================================
@@ -0,0 +1,112 @@
+--- a/src/GBase.h
++++ b/src/GBase.h
+@@ -15,6 +15,7 @@
+ #include <sys/types.h>
+ #include <sys/stat.h>
+ #include <stdint.h>
++#include <cstdint>
+
+ #if defined __WIN32__ || defined WIN32 || defined _WIN32 || defined _WIN32_
+ #ifndef __WIN32__
+@@ -72,7 +73,6 @@ typedef int16_t int16;
+ typedef uint16_t uint16;
+
+ typedef unsigned char uchar;
+-typedef unsigned char byte;
+
+ #ifndef MAXUINT
+ #define MAXUINT ((unsigned int)-1)
+--- a/src/gff.h
++++ b/src/gff.h
+@@ -43,7 +43,7 @@ extern const uint gfo_flag_DISCARDED; //
+ extern const uint gfo_flag_LST_KEEP; //GffObj from GffReader::gflst is to be kept (not deallocated)
+ //when GffReader is destroyed
+ extern const uint gfo_flag_LEVEL_MSK; //hierarchical level: 0 = no parent
+-extern const byte gfo_flagShift_LEVEL;
++extern const uint8_t gfo_flagShift_LEVEL;
+
+ extern bool gff_show_warnings;
+
+@@ -502,18 +502,18 @@ public:
+ if (v) flags |= gfo_flag_CHILDREN_PROMOTED;
+ else flags &= ~gfo_flag_CHILDREN_PROMOTED;
+ }
+- void setLevel(byte v) {
++ void setLevel(uint8_t v) {
+ if (v==0) flags &= ~gfo_flag_LEVEL_MSK;
+ else flags &= ~(((uint)v) << gfo_flagShift_LEVEL);
+ }
+- byte incLevel() {
++ uint8_t incLevel() {
+ uint v=((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL);
+ v++;
+ flags &= ~(v << gfo_flagShift_LEVEL);
+ return v;
+ }
+- byte getLevel() {
+- return ((byte)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL));
++ uint8_t getLevel() {
++ return ((uint8_t)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL));
+ }
+
+ bool isValidTranscript() {
+--- a/src/locfit/adap.c
++++ b/src/locfit/adap.c
+@@ -12,9 +12,6 @@
+
+ #include "local.h"
+
+-extern INT wdiagp(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
+-extern INT wdiag(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
+-
+ double hmin;
+
+ double acri(double lk, double t0, double t2, double pen)
+--- a/src/locfit/lffuns.h
++++ b/src/locfit/lffuns.h
+@@ -158,6 +158,7 @@ void strip();
+
+ /* wdiag.c */
+ INT wdiagp(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
++INT wdiag(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
+ INT procvhatm(design *des, lfit *lf, INT v);
+ void cwdiag(vari *v);
+
+@@ -218,10 +219,10 @@ double rpois();
+ void rseed(char *seed);
+
+ /* readfile.c */
+-extern void readfile();
++void readfile();
+
+ /* scbmax.c */
+-extern void cscbmax();
++void cscbmax();
+
+ /* vari.c */
+ #include "vari.hpp"
+--- a/src/locfit/local.h
++++ b/src/locfit/local.h
+@@ -138,10 +138,9 @@ extern double Rf_lgammafn();
+ #define ISWAP(a,b) { int zz; zz = a; a = b; b = zz; }
+ #else
+ #define ISWAP(a,b) { INT zz; zz = a; a = b; b = zz; }
+-extern INT lf_error;
+ #endif
+
+-extern INT lf_error;
++INT lf_error;
+
+ double lf_exp(double x);
+
+--- a/src/locfit/vari.hpp
++++ b/src/locfit/vari.hpp
+@@ -20,8 +20,6 @@ extern "C"
+ vari *findvar(varname name, int err, int* n);
+ vari *growvar(vari* vold, int n);
+ void *viptr(vari* v, int i);
+- void setvarname(vari* v, varname name);
+- vari *findvar(varname name, int err, int* n);
+
+ void deletevar(vari* v); /* delete variable, or top variable if NULL */
+ void deleteifhidden(vari* v);
=====================================
debian/patches/gcc15.patch
=====================================
@@ -5,21 +5,21 @@ Description: Build with gcc-15
--- a/src/locfit/lffuns.h
+++ b/src/locfit/lffuns.h
-@@ -4,17 +4,21 @@
+@@ -4,162 +4,172 @@
/* FILES IN THE src DIRECTORY */
/* adap.c */
-extern double afit(), aband2(), aband3();
-extern INT ainitband();
-+extern double afit();
-+extern double aband2(design *des, lfit *lf, double h0);
-+extern double aband3(design *des, lfit *lf, double h0);
-+extern INT ainitband(design *des, lfit *lf);
++double afit();
++double aband2(design *des, lfit *lf, double h0);
++double aband3(design *des, lfit *lf, double h0);
++INT ainitband(design *des, lfit *lf);
/* band.c */
-extern void band(), kdeselect();
-+extern void band(vari *v);
-+extern void kdeselect(double *band, double *x, INT *ind, double h0, double h1, INT *meth, INT nm, INT ker, INT n)
++void band(vari *v);
++void kdeselect(double *band, double *x, INT *ind, double h0, double h1, INT *meth, INT nm, INT ker, INT n);
/* density.c */
-extern INT densinit();
@@ -33,58 +33,299 @@ Description: Build with gcc-15
+void prresp(double *coef, double *resp, INT p);
/* dens_haz.c */
- extern void haz_init();
-@@ -86,8 +90,9 @@ extern void setstrval();
- extern INT ppwhat(), restyp();
+-extern void haz_init();
+-extern INT hazint();
++void haz_init();
++INT hazint();
+
+ /* dens_int.c */
+-extern double dens_integrate();
+-extern void dens_renorm(), dens_lscv(), lforder();
++double dens_integrate();
++void dens_renorm(), dens_lscv(), lforder();
+
+ /* dist.c */
+-extern double igamma(), ibeta();
+-extern double pf(), pchisq(), pnorm();
+-extern double df(), dchisq();
++double igamma(), ibeta();
++double pf(), pchisq(), pnorm();
++double df(), dchisq();
+
+ /* ev_atree.c */
+-extern void atree_start(), atree_grow(), atree_guessnv();
+-extern double atree_int();
++void atree_start(), atree_grow(), atree_guessnv();
++double atree_int();
+
+ /* ev_interp.c */
+-extern double dointpoint(), cubintd();
+-extern double linear_interp(), cubic_interp(), rectcell_interp();
+-extern INT exvval();
+-extern void exvvalpv(), hermite2();
++double dointpoint(), cubintd();
++double linear_interp(), cubic_interp(), rectcell_interp();
++INT exvval();
++void exvvalpv(), hermite2();
+
+ /* ev_kdtre.c */
+-extern void kdtre_start();
+-extern double kdtre_int();
++void kdtre_start();
++double kdtre_int();
+
+ /* ev_main.c */
+-extern void trchck(), guessnv();
+-extern void dataf(), gridf(), crossf(), xbarf(), preset();
+-extern INT newsplit();
+-extern int lfit_reqd(), lfit_reqi();
++void trchck(), guessnv();
++void dataf(), gridf(), crossf(), xbarf(), preset();
++INT newsplit();
++int lfit_reqd(), lfit_reqi();
+ #ifndef CVERSION
+ extern vari *createvar();
+ #endif
+
+ /* ev_trian.c */
+-extern void triang_start(), triang_grow();
+-extern double triang_int();
++void triang_start(), triang_grow();
++double triang_int();
+
+ /* family.c */
+-extern INT links(), stdlinks(), defaultlink(), validlinks();
+-extern double b2(), b3(), b4(), lf_link(), invlink();
++INT links(), stdlinks(), defaultlink(), validlinks();
++double b2(), b3(), b4(), lf_link(), invlink();
+
+ /* frend.c */
+-extern void fitfun(), degfree(), ressumm(), makecfn();
+-extern INT procv(), procvraw(), procvvord();
+-extern double base(), cens(), prwt(), resp(), getxi(), rss();
+-extern INT calcp();
++void fitfun(), degfree(), ressumm(), makecfn();
++INT procv(), procvraw(), procvvord();
++double base(), cens(), prwt(), resp(), getxi(), rss();
++INT calcp();
+
+ /* kappa0.c */
+-extern double critval(), critvalc(), tailp(), taild();
+-extern INT constants();
++double critval(), critvalc(), tailp(), taild();
++INT constants();
+
+ /* lf_dercor.c */
+-extern void dercor();
++void dercor();
+
+ /* lf_fitfun.c */
+-extern void fitfun(), designmatrix();
+-extern INT calcp(), coefnumber();
++void designmatrix();
++INT coefnumber();
+
+ /* lf_robust.c */
+-extern double median();
+-extern void lf_robust();
++double median();
++void lf_robust();
+
+ /* lfstr.c */
+-extern void setstrval();
+-extern INT ppwhat(), restyp();
++void setstrval();
++INT ppwhat(), restyp();
/* lf_vari.c */
-extern void comp_vari(), local_df();
-extern double comp_infl();
-+extern void comp_vari(lfit *lf, design *des, double *tr, double *t0);
-+extern void local_df(lfit *lf, design *des, double *tr);
-+extern double comp_infl(lfit *lf, design *des);
++void comp_vari(lfit *lf, design *des, double *tr, double *t0);
++void local_df(lfit *lf, design *des, double *tr);
++double comp_infl(lfit *lf, design *des);
/* linalg.c */
- extern void svd(), hsvdsolve();
-@@ -99,19 +104,23 @@ extern double innerprod(), m_trace();
- extern INT svdsolve();
+-extern void svd(), hsvdsolve();
+-extern void addouter(), multmatscal();
+-extern void QRupd(), QR1(), bacK(), bacT(), solve(), grsc();
+-extern void setzero(), unitvec();
+-extern void transpose();
+-extern double innerprod(), m_trace();
+-extern INT svdsolve();
++void svd(), hsvdsolve();
++void addouter(), multmatscal();
++void QRupd(), QR1(), bacK(), bacT(), solve(), grsc();
++void setzero(), unitvec();
++void transpose();
++double innerprod(), m_trace();
++INT svdsolve();
/* locfit.c or parfit.c (most) */
-extern int ident, locfit(), lf_iter();
-+extern int ident;
-+extern int locfit(lfit *lf, design *des, double h, int noit);
-+extern int lf_iter();
++int ident;
++int locfit(lfit *lf, design *des, double h, int noit);
++int lf_iter();
/* math.c */
- extern double lflgamma(), lferf(), lferfc(), lfdaws();
- extern double ptail(), logit(), expit();
+-extern double lflgamma(), lferf(), lferfc(), lfdaws();
+-extern double ptail(), logit(), expit();
++double lflgamma(), lferf(), lferfc(), lfdaws();
++double ptail(), logit(), expit();
//extern double lgamma(), erf(), erfc();
-extern int factorial();
-+extern int factorial(int n);
++int factorial(int n);
/* minmax.c */
- extern double ipower(), minmax();
+-extern double ipower(), minmax();
++double ipower(), minmax();
/* nbhd.c */
-extern double kordstat(), nbhd(), rho();
-+extern double kordstat(double *x, INT k, INT n, INT *ind);
-+extern double nbhd(lfit *lf, design *des, double fxh, INT redo, INT nn);
-+extern double rho(double *x, double *sc, INT d, INT kt, INT *sty);
++double kordstat(double *x, INT k, INT n, INT *ind);
++double nbhd(lfit *lf, design *des, double fxh, INT redo, INT nn);
++double rho(double *x, double *sc, INT d, INT kt, INT *sty);
/* odint.c */
- extern INT onedint();
-@@ -148,8 +157,9 @@ extern int stm(), pmatch(), matchlf(), m
- extern void strip();
+-extern INT onedint();
+-extern void recurint();
++INT onedint();
++void recurint();
+
+ /* pcomp.c */
+-extern double addparcomp();
+-extern void compparcomp(), subparcomp(), subparcomp2(), pcchk();
+-extern int pc_reqd();
+-extern INT noparcomp(), hasparcomp();
++double addparcomp();
++void compparcomp(), subparcomp(), subparcomp2(), pcchk();
++int pc_reqd();
++INT noparcomp(), hasparcomp();
+
+ /* preplot.c */
+-extern void preplot(), cpreplot();
+-extern INT setpppoints();
++void preplot(), cpreplot();
++INT setpppoints();
+
+ /* resid.c */
+-extern double resid();
+-extern void cfitted();
+-extern vari *vfitted(), *vresid();
++double resid();
++void cfitted();
++vari *vfitted(), *vresid();
+
+ /* scb.c */
+-extern void scb(), cscbsim();
++void scb(), cscbsim();
+
+ /* simul.c */
+-extern void liksim(), scbsim(), scbmax(), regband(), rband();
++void liksim(), scbsim(), scbmax(), regband(), rband();
+
+ /* startlf.c */
+-extern void bbox(), deschk(), startlf(), preproc(), fitdefault();
+-extern void fitoptions(), clocfit(), endfit();
+-extern INT nofit();
++void bbox(), deschk(), startlf(), preproc(), fitdefault();
++void fitoptions(), clocfit(), endfit();
++INT nofit();
+
+ /* strings.c */
+-extern int stm(), pmatch(), matchlf(), matchrt(), checkltor(), checkrtol();
+-extern void strip();
++int stm(), pmatch(), matchlf(), matchrt(), checkltor(), checkrtol();
++void strip();
/* wdiag.c */
-extern INT wdiag(), procvhatm();
-extern void cwdiag();
-+extern INT wdiagp(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
-+extern INT procvhatm(design *des, lfit *lf, INT v);
-+extern void cwdiag(vari *v);
++INT wdiagp(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
++INT procvhatm(design *des, lfit *lf, INT v);
++void cwdiag(vari *v);
/* weight.c */
- extern double W(), weight(), weightd(), Wd(), Wdd(), wint();
+-extern double W(), weight(), weightd(), Wd(), Wdd(), wint();
+-extern double Wconv(), Wconv1(), Wconv4(), Wconv5(), Wconv6(), Wikk();
+-extern INT iscompact(), wtaylor();
++double W(), weight(), weightd(), Wd(), Wdd(), wint();
++double Wconv(), Wconv1(), Wconv4(), Wconv5(), Wconv6(), Wikk();
++INT iscompact(), wtaylor();
+
+ /* arith.c */
+-extern INT arvect(), intitem();
+-extern double areval(), arith(), darith(), dareval();
+-extern vari *varith(), *saveresult(), *arbuild();
++INT arvect(), intitem();
++double areval(), arith(), darith(), dareval();
++vari *varith(), *saveresult(), *arbuild();
+
+ /* c_args.c */
+ #define argused(v,i) (((carg *)viptr(v,i))->used)
+@@ -167,42 +177,45 @@ extern vari *varith(), *saveresult(), *a
+ #define setunused(v,i) { ((carg *)viptr(v,i))->used = 0; }
+ #define argarg(v,i) (((carg *)viptr(v,i))->arg)
+ #define argvalis(v,i,z) (strcmp(argval(v,i),z)==0)
+-extern char *argval(), *getargval();
+-extern int getarg(), readilist(), getlogic();
++char *argval(), *getargval();
++int getarg(), readilist(), getlogic();
+
+ /* cmd.c */
+-extern int locfit_dispatch(char*);
+-extern void setuplf(), recondat(), cmdint();
+-extern double backtr(), docrit();
++int locfit_dispatch(char*);
++void setuplf(), recondat(), cmdint();
++double backtr(), docrit();
+
+ /* c_plot.c */
+-extern void plotdata(), plotfit(), plottrack(), plotopt(), setplot();
++void plotdata(), plotfit(), plottrack(), plotopt(), setplot();
+
+ /* help.c */
+-extern void example();
++void example();
+
+ /* lfd.c */
+-extern void doreaddata(), dosavedata(), dosavefit();
+-extern INT setfilename();
++void doreaddata(), dosavedata(), dosavefit();
++INT setfilename();
+
+ /* main.c */
+-extern void SetWinDev();
++void SetWinDev();
+
+ /* makecmd.c */
+-extern vari *getcmd();
+-extern void makecmd(), del_clines(), inc_forvar(), dec_forvar();
++vari *getcmd();
++void makecmd(), del_clines(), inc_forvar(), dec_forvar();
+
+ /* post.c */
+-extern void SetPSDev();
++void SetPSDev();
+
+ /* pout.c */
+-extern INT pretty();
+-extern void displayplot();
+-extern void plotmaple(), plotmathe(), plotmatlb(), plotgnup(), plotxwin();
++INT pretty();
++void displayplot();
++void plotmaple(), plotmathe(), plotmatlb(), plotgnup(), plotxwin();
+
+ /* random.c */
+-extern double rnorm(), rexp(), runif(), rpois();
+-extern void rseed();
++double rnorm(double mu, doubles);
++double rexp(double lb);
++double runif();
++double rpois();
++void rseed(char *seed);
+
+ /* readfile.c */
+ extern void readfile();
--- a/src/locfit/wdiag.c
+++ b/src/locfit/wdiag.c
@@ -18,11 +18,7 @@ static double *wd;
@@ -161,18 +402,18 @@ Description: Build with gcc-15
i = getarg(v,"ev",0);
--- a/src/locfit/adap.c
+++ b/src/locfit/adap.c
-@@ -11,11 +11,13 @@
- */
+@@ -12,10 +12,12 @@
#include "local.h"
+
+-static double hmin;
+extern INT wdiagp(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
+extern INT wdiag(lfit *lf, design *des, double *lx, INT deg, INT ty, INT exp);
-+extern int factorial(int n);
-
- static double hmin;
-double acri(lk,t0,t2,pen)
-double lk, t0, t2, pen;
++double hmin;
++
+double acri(double lk, double t0, double t2, double pen)
{ double y;
/* return(-2*lk/(t0*exp(pen*log(1-t2/t0)))); */
@@ -188,6 +429,15 @@ Description: Build with gcc-15
{ int i, ii, j, p, p1;
double sv, sb, *l, dp;
l = des->wd;
+@@ -43,7 +43,7 @@ design *des;
+ return(sv+sb*sb*lf->dp[DADP]*lf->dp[DADP]/(p1*p1));
+ }
+
+-static double mcp, clo, cup;
++double mcp, clo, cup;
+
+ /*
+ Initial bandwidth will be (by default)
@@ -52,9 +52,7 @@ static double mcp, clo, cup;
or DFXH components)
*/
@@ -760,3 +1010,48 @@ Description: Build with gcc-15
{ INT deg, p, i, ii, j, nnz, rnz, lset, ang, status;
double w;
+--- a/src/locfit/random.c
++++ b/src/locfit/random.c
+@@ -23,11 +23,10 @@ double runif()
+ return(((tv ^ cc) >> 1) / 2147483648.0);
+ }
+
+-void rseed(seed)
++void rseed(char *seed)
+ /*
+ Seed should be string of at least 8 characters.
+ */
+-char *seed;
+ { ss = 0;
+ tv = seed[0];
+ tv = (tv<<8) | seed[1];
+@@ -46,8 +45,7 @@ char *seed;
+ * Reference: Kinderman & Monahan, Proceedings of
+ * the ASA, Statistical Computing Section, 1975, 128-131.
+ */
+-double rnorm(mu,s)
+-double mu, s;
++double rnorm(double mu, doubles)
+ {
+ double rnormk, u, x2;
+
+@@ -59,8 +57,7 @@ double mu, s;
+ return(mu+s*rnormk);
+ }
+
+-double rexp(lb)
+-double lb;
++double rexp(double lb)
+ { return(-log(runif())/lb);
+ }
+
+@@ -71,8 +68,7 @@ double lb;
+ * to work correctly.
+ * Reference: Devroye, pages 504, 511 and 516 (with corrections!)
+ */
+-double rpois(lambda)
+-double lambda;
++double rpois(double lambda)
+ {
+ static double olambda = -1, a, mu, delta, d, c1, c2, c3, c4, c5;
+ double u, e, n, x, y, w, t, p, q;
=====================================
debian/patches/series
=====================================
@@ -12,3 +12,4 @@ gcc10.patch
no_svnversion.patch
gcc14.patch
gcc15.patch
+byte.patch
=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@ pkg := cufflinks
mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
bindir := $(CURDIR)/debian/$(pkg)/usr/bin
-export DEB_CFLAGS_MAINT_APPEND=-std=gnu11 # -std=c11
+# export DEB_CFLAGS_MAINT_APPEND=-std=gnu99 # gnu11 # -std=c11
%:
dh $@ --with python3
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/commit/43e1c6851f997784dba37a0fb8dbee9b26463a15
--
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/commit/43e1c6851f997784dba37a0fb8dbee9b26463a15
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