diff options
| -rw-r--r-- | sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch | 76 | ||||
| -rw-r--r-- | sci-biology/seaview/files/seaview-4.6-fno-common.patch | 110 | ||||
| -rw-r--r-- | sci-biology/seaview/seaview-4.6-r1.ebuild (renamed from sci-biology/seaview/seaview-4.6.ebuild) | 29 |
3 files changed, 203 insertions, 12 deletions
diff --git a/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch new file mode 100644 index 000000000000..c9595748e901 --- /dev/null +++ b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch @@ -0,0 +1,76 @@ +--- a/align.cxx ++++ b/align.cxx +@@ -754,7 +754,7 @@ + alignitems[clustalopt + MAX_MSA_ALGOS].label(strdup(options)); + alignitems[clustalopt + MAX_MSA_ALGOS].flags = attr; + if (view->alignment_algorithm < 2) alignitems[clustalopt + MAX_MSA_ALGOS + 3].flags = FL_MENU_INACTIVE; +- delete options; ++ delete[] options; + view->menu_align = alignitems; + view->menubar->add("Align", 0, NULL, (void*)view->menu_align, FL_SUBMENU_POINTER); + if (view->count_msa_algos >= MAX_MSA_ALGOS) (alignitems + clustalopt + MAX_MSA_ALGOS + 2)->deactivate(); +--- a/seaview.cxx ++++ b/seaview.cxx +@@ -3314,7 +3314,7 @@ + if(p != NULL) *p = 0; + if(printout_black == TEXT_ONLY) strcat(suggested, ".txt"); + else { +- strcat(suggested, "."PDF_OR_PS_EXT); ++ strcat(suggested, "." PDF_OR_PS_EXT); + } + if( view->alt_col_rank != NULL ) { + for(anerr = 0; anerr < view->tot_seqs; anerr++) +@@ -3424,7 +3424,7 @@ + + pdf_form = new Fl_Window(415, 90); + pdf_form->box(FL_FLAT_BOX); +-pdf_form->label("Set "PDF_OR_PS" output options"); ++pdf_form->label("Set " PDF_OR_PS " output options"); + + x = 5 + (int)fl_width("block size:"); y = 5; w = 50; h = 25; + sizeinput = new Fl_Input(x, y, w, h, "font size:"); +@@ -5000,10 +5000,10 @@ + {"Save prot alignmt", 0,file_menu_callback, 0, FL_MENU_INACTIVE}, + {"Save bootstrap replicates", 0,file_menu_callback, 0, FL_MENU_INACTIVE | FL_MENU_DIVIDER}, + #if !defined(__APPLE__) +- {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, 0}, +- {""PDF_OR_PS" options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, ++ {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, 0}, ++ {"" PDF_OR_PS " options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, + #else +- {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, ++ {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, + #endif + {"Concatenate", 0,file_menu_callback, 0, FL_MENU_DIVIDER}, + {"New window", FL_COMMAND | 'n', file_menu_callback, 0, 0}, +--- a/treedraw.cxx ++++ b/treedraw.cxx +@@ -210,7 +210,7 @@ + {"Save all trees", 0, file_callback, NULL, 0}, + {"Save patristic distances", 0, patristic_callback, NULL, FL_MENU_DIVIDER}, + {"Print", FL_COMMAND | 'p', file_callback, NULL, 0}, +- {"Save as "PDF_OR_PS"", 0, file_callback, NULL, 0}, ++ {"Save as " PDF_OR_PS "", 0, file_callback, NULL, 0}, + {"Save as SVG", 0, file_callback, NULL, 0}, + {"A4", 0, file_callback, NULL, FL_MENU_RADIO | 0}, + {"Letter", 0, file_callback, NULL, FL_MENU_RADIO | 0}, +--- a/xfmatpt.cxx ++++ b/xfmatpt.cxx +@@ -205,7 +205,7 @@ + compute->callback(compute_proc, fdui); + fdui->compute_butt = compute; + +-Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write "PDF_OR_PS); ++Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write " PDF_OR_PS); + fin += width; + postscript->callback(plot_button_proc, fdui); + +@@ -870,7 +870,7 @@ + #ifndef MICRO + matpt->form->hide(); Fl::flush(); // because of strange bug on 32-bit Linux only + #endif +- fl_message("Dot plot is now in file\n%s\nin "PDF_OR_PS" format", surface->outfname()); ++ fl_message("Dot plot is now in file\n%s\nin " PDF_OR_PS " format", surface->outfname()); + delete surface; + #ifndef MICRO + matpt->form->show(); Fl::flush(); diff --git a/sci-biology/seaview/files/seaview-4.6-fno-common.patch b/sci-biology/seaview/files/seaview-4.6-fno-common.patch new file mode 100644 index 000000000000..24cc28dfb3b7 --- /dev/null +++ b/sci-biology/seaview/files/seaview-4.6-fno-common.patch @@ -0,0 +1,110 @@ +--- a/csrc/dnapars.c ++++ b/csrc/dnapars.c +@@ -77,41 +77,43 @@ + /* function prototypes */ + + +-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, ++extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, + weightfilename[FNMLNGTH]; + char basechar[32]="ACMGRSVTWYHKDBNO???????????????"; +-node *root; +-long chars, col, msets, ith, njumble, jumb, maxtrees; ++extern node *root; ++extern long chars, col, msets, ith, njumble, jumb; ++long maxtrees; + /* chars = number of sites in actual sequences */ +-long inseed, inseed0; +-double threshold; +-boolean jumble, usertree, thresh, weights, thorough, rearrfirst, +- trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf, +- multf; ++extern long inseed, inseed0; ++extern double threshold; ++boolean thorough, rearrfirst, mulf, multf; ++extern boolean justwts, ancseq, weights, thresh, jumble, usertree, trout, mulsets, progress, stepbox, firstset; + steptr oldweight; +-longer seed; +-pointarray treenode; /* pointers to all nodes in tree */ +-long *enterorder; ++extern longer seed; ++extern pointarray treenode; /* pointers to all nodes in tree */ ++extern long *enterorder; + long *zeros; + + /* local variables for Pascal maketree, propagated globally for C version: */ + +-long minwhich; ++extern long minwhich; + static double like, minsteps, bestyet, bestlike, bstlike2; +-boolean lastrearr, recompute; +-double nsteps[maxuser]; +-long **fsteps; +-node *there, *oldnufork; +-long *place; +-bestelm *bestrees; +-long *threshwt; ++extern boolean lastrearr, recompute; ++extern double nsteps[maxuser]; ++extern long **fsteps; ++extern node *there; ++node *oldnufork; ++extern long *place; ++extern bestelm *bestrees; ++extern long *threshwt; + baseptr nothing; +-gbases *garbage; +-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, ++extern gbases *garbage; ++extern node *temp, *temp1; ++node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, + *tmp2, *tmp3, *tmprm, *tmpadd; +-boolean *names; ++extern boolean *names; + node *grbg; +-char *progname; ++extern char *progname; + + + static void getoptions(int arg_maxtrees, dnapars_S_option s_option) +--- a/csrc/phylip.c ++++ b/csrc/phylip.c +@@ -35,6 +35,8 @@ + + #include "phylip.h" + ++boolean javarun; ++ + #ifdef WIN32 + #include <windows.h> + /* for console code (clear screen, text color settings) */ +--- a/csrc/phylip.h ++++ b/csrc/phylip.h +@@ -342,7 +342,7 @@ + /* Lower-triangular format. */ + #define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE) + +-boolean javarun; ++extern boolean javarun; + + typedef long *steptr; + typedef long longer[6]; +@@ -363,7 +363,6 @@ + extern boolean ibmpc, ansi, tranvsp; + //extern naym *nayme; /* names of species */ + extern char* *nayme; /* names of species */ +-boolean firstplotblock; // for debugging BMP output + + #define ebcdic EBCDIC + +--- a/csrc/protpars.c ++++ b/csrc/protpars.c +@@ -127,7 +127,7 @@ + node *temp, *temp1; + Char ch; + aas tmpa; +-char *progname; ++extern char *progname; + + /* Local variables for maketree, propagated globally for c version: */ + long minwhich; diff --git a/sci-biology/seaview/seaview-4.6.ebuild b/sci-biology/seaview/seaview-4.6-r1.ebuild index 4ad8ad61b72b..469f88728120 100644 --- a/sci-biology/seaview/seaview-4.6.ebuild +++ b/sci-biology/seaview/seaview-4.6-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit eutils toolchain-funcs +inherit desktop toolchain-funcs DESCRIPTION="A graphical multiple sequence alignment editor" HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" @@ -15,19 +15,24 @@ KEYWORDS="~amd64 ~x86" IUSE="+xft" RDEPEND=" + sci-biology/clustalw:2 + sci-biology/phyml + || ( + sci-libs/libmuscle + sci-biology/muscle + ) sys-libs/zlib - x11-libs/fltk:1 + x11-libs/fltk:1[xft?] x11-libs/libX11 - xft? ( - x11-libs/libXft - x11-libs/fltk:1[xft] ) - sci-biology/clustalw:2 - || ( sci-libs/libmuscle sci-biology/muscle ) - sci-biology/phyml" -DEPEND="${RDEPEND} - virtual/pkgconfig" + xft? ( x11-libs/libXft )" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" S="${WORKDIR}/${PN}" +PATCHES=( + "${FILESDIR}"/${PN}-4.6-fno-common.patch + "${FILESDIR}"/${PN}-4.6-Wreserved-user-defined-literal.patch +) src_prepare() { default |