gentoo resync : 25.11.2020

5 files changed, 206 insertions, 91 deletions

diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
index 370ccb30d448..dd7a8e73e258 100644
--- a/sci-biology/seaview/Manifest
+++ b/sci-biology/seaview/Manifest
@@ -1,5 +1,5 @@
-DIST seaview_4.5.4.tar.gz 420608 BLAKE2B 14b044706440da88987cd6b546595497f2de61e8d03615bfce4634104914a56544a464b0abedc83e6c96329697dccb2087c2b1af5a1fdbf0d9bdc26418a49a75 SHA512 a8a2e49a13f87ae4279311068147169b1e17874e9ce5787003b854c7271efc7a128db6916bb883a9b7b0b90f855fe40d83c77e9fd9f5751464e04346b9923301
+AUX seaview-4.6-Wreserved-user-defined-literal.patch 3271 BLAKE2B 695411acffed448ecc792753a9c8f969e4e88fea711b163a9b45f7b5878e44f5504d162991924958d8910c5eb7241b893ae27ea328a5efb754ba13ed0ddf7422 SHA512 fe9837a85e68e486fcc1a1903af027a71916aa70bf54d8616f5be6b13c52ca4ca7f5d2901724e3ec2e3e754c2772c59d3db78fb6e75432ef7f67e99692571bfe
+AUX seaview-4.6-fno-common.patch 3171 BLAKE2B a3dfdb8d90279cdc16489d5e304eb81d3893f63d55ec5363d86fce5d90aa87c003fb2f41dafb09f46002aa1b45871161ff5b0de6e22bd24d77c98727880818d5 SHA512 89b1d46956232b6c7a3979c804339e2bc4e9f99224c7c06091a2526c92ddd55415762a39d183e0249ae7251afada28bfb6f863bd91167ea647d76d4c548c1f6a
 DIST seaview_4.6.tar.gz 424258 BLAKE2B e958ff4b1f6bb283a2122d65917a352914f33e5c9593c34c449800fbcac74b0dd4fa98bb1f47c45e11f24e07dfebb3ced54fbd8440b2bcd2b1df32dc398d5892 SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6
-EBUILD seaview-4.5.4.ebuild 2013 BLAKE2B 91c192d7cb22411f7af4366088c1e47c657fc75855cab2a289d4a1d7cec206302b2670612117334d6c6b79d25c578daf3da5cbd053dc98602ead9033c3b90f35 SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945
-EBUILD seaview-4.6.ebuild 1997 BLAKE2B 1c7c01e0a52f943b9506954d84519c8ff09b15d307476aa659f7bb49af9de1ea02076bb74bcebaac49a571d18624455879c321faa7458f8ac2660773eb4b8706 SHA512 5768df52c205ccfaa4d2d52ec753125dd77eb91a7b0be959dbc67aca00c0a66dc3f13b125d073450a81a06eea29880503981942042c77a0c6e1bb8f19f070cb8
+EBUILD seaview-4.6-r1.ebuild 2106 BLAKE2B 6a7d4e6295285cd072db997acc3f9467fb46a813a8da640372ec55228792d85f43fce137b2c5f90d60c6e77918280192967001ad7ac6a2a80a69c390cf6ed218 SHA512 76b24794f87383ec39638569e7c61c5f500ea84a89cabb04d1bbcf101bffecc97e99729a4e29f3d4252a980c8a40889d1e4161ebea272a09946a78ecd4b75f4c
 MISC metadata.xml 621 BLAKE2B 9c56cc2099ed696942e2958926ee8c9f24be26fd273e74a7f789d368c3a222f084363ec3a4eada5e1197c4a81f533074f4b05c43d1e9c951e66261d55bc4d9e8 SHA512 7c49694ef56359e58b76b0dd7715d28615a541655c6ccaa2d7d64041c7340082bd5026fa2baa5a15e51e3aa27309d5a72ab836a5ee554366eb324406a50a09c4
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-4.5.4.ebuild b/sci-biology/seaview/seaview-4.5.4.ebuild
deleted file mode 100644
index 33ee6f65ccbd..000000000000
--- a/sci-biology/seaview/seaview-4.5.4.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib toolchain-funcs
-
-DESCRIPTION="A graphical multiple sequence alignment editor"
-HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
-SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="+xft"
-
-CDEPEND="
-	sys-libs/zlib
-	x11-libs/fltk:1
-	x11-libs/libX11
-	xft? (
-		x11-libs/libXft
-		x11-libs/fltk:1[xft] )"
-RDEPEND="${CDEPEND}
-	sci-biology/clustalw
-	|| ( sci-libs/libmuscle sci-biology/muscle )
-	sci-biology/phyml"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# respect CXXFLAGS (package uses them as CFLAGS)
-	sed \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
-		-e "s:\$(OPT):${CXXFLAGS}:" \
-		-e "s:^OPT:#OPT:" \
-		-e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
-		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
-		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
-		-e "s:^USE_XFT:#USE_XFT:" \
-		-e "s:^#HELPFILE:HELPFILE:" \
-		-e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
-		-e "s:^#PHYMLNAME:PHYMLNAME:" \
-		-e 's:-lXinerama::g' \
-		-e 's:-lpng::g' \
-		-e 's:-ljpeg::g' \
-		-e 's:-lfontconfig::g' \
-		-i Makefile || die "sed failed while editing Makefile"
-
-	if use xft; then
-		sed \
-			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
-			-e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
-			-i Makefile || die "sed failed while editing Makefile to enable xft"
-	else
-		sed -i -e "s:-lXft::" Makefile || die
-	fi
-}
-
-src_install() {
-	dobin seaview
-
-	# /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
-	insinto /usr/share/seaview
-	doins example.nxs seaview.html
-
-	insinto /usr/share/seaview/images
-	doins seaview.xpm
-
-	make_desktop_entry seaview Seaview
-
-	doman seaview.1
-}
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