From d934827bf44b7cfcf6711964418148fa60877668 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 25 Nov 2020 22:39:15 +0000 Subject: gentoo resync : 25.11.2020 --- sci-biology/seaview/Manifest | 6 +- ...eaview-4.6-Wreserved-user-defined-literal.patch | 76 ++++++++++++++ .../seaview/files/seaview-4.6-fno-common.patch | 110 +++++++++++++++++++++ sci-biology/seaview/seaview-4.5.4.ebuild | 76 -------------- sci-biology/seaview/seaview-4.6-r1.ebuild | 82 +++++++++++++++ sci-biology/seaview/seaview-4.6.ebuild | 77 --------------- 6 files changed, 271 insertions(+), 156 deletions(-) create mode 100644 sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch create mode 100644 sci-biology/seaview/files/seaview-4.6-fno-common.patch delete mode 100644 sci-biology/seaview/seaview-4.5.4.ebuild create mode 100644 sci-biology/seaview/seaview-4.6-r1.ebuild delete mode 100644 sci-biology/seaview/seaview-4.6.ebuild (limited to 'sci-biology/seaview') 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 + /* 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-r1.ebuild b/sci-biology/seaview/seaview-4.6-r1.ebuild new file mode 100644 index 000000000000..469f88728120 --- /dev/null +++ b/sci-biology/seaview/seaview-4.6-r1.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit desktop 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" + +RDEPEND=" + sci-biology/clustalw:2 + sci-biology/phyml + || ( + sci-libs/libmuscle + sci-biology/muscle + ) + sys-libs/zlib + x11-libs/fltk:1[xft?] + x11-libs/libX11 + 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 + + # 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.ebuild deleted file mode 100644 index 4ad8ad61b72b..000000000000 --- a/sci-biology/seaview/seaview-4.6.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit eutils 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" - -RDEPEND=" - sys-libs/zlib - x11-libs/fltk:1 - 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="${RDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -src_prepare() { - default - - # 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 -} -- cgit v1.2.3