diff options
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/Manifest.gz | bin | 19002 -> 19009 bytes | |||
-rw-r--r-- | sci-biology/bowtie/Manifest | 2 | ||||
-rw-r--r-- | sci-biology/bowtie/bowtie-2.5.1.ebuild | 2 | ||||
-rw-r--r-- | sci-biology/treeviewx/Manifest | 10 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch | 11 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch | 40 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch | 77 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch | 30 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch | 16 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch | 66 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch | 34 | ||||
-rw-r--r-- | sci-biology/treeviewx/files/treeviewx-wxt.patch | 50 | ||||
-rw-r--r-- | sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild | 42 |
13 files changed, 2 insertions, 378 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 8cc25fa0210a..b5ebc28c5f01 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index d8a1aac4fceb..147f1a2052f5 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,5 +1,5 @@ DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f EBUILD bowtie-2.4.4.ebuild 1215 BLAKE2B 4d88c3ff6149289019301cbdf5b682da576feabe5a51f2a83fceccf2b2475e81ae69a9318e64453d16c4c2b713dc7858bf4f5c3e9306004e418d34f10099ac71 SHA512 2da6db5d4d96ea3e5eba3fb992e8ef350becdbd24ba4d0844a2c6127a357f458fb709ea833bb06bf464001872f45530f9fdc6b5682801aab7ac400641c42e1b1 -EBUILD bowtie-2.5.1.ebuild 1542 BLAKE2B b927f815c929a324c607df93479833079a0e5a8dd9b723755ad19d528e35601b796cdb0618c5d7787ce591c0d8e5c0be5b5d7217fc1a0393f070049451c3d9db SHA512 1ea410f3b1c0b5be41369f1f001f92f366cd3fec9f1518bfc9da32bda8f88c9b2bb57b73e6f2ec71e9144844cca7db47c747e4193ff243c78ca1304d4897b176 +EBUILD bowtie-2.5.1.ebuild 1542 BLAKE2B 313f1f87d691a258d7bd3e6e2cea1d7de49dbbb12ae1c380648a69eb4aaae2b593b263b25107cfe367adc9971f8aa49e2e540e7dda4c9f7158d8367a5f5184b2 SHA512 94635590d0ec1d31ae520d2e231735834f03c6b25d2dbc1613fc98a2055dc6be4f596b57f7ec3e0a27f1c25ac6686ab14f5d7ad8051244a4535f5bba6ecbf0bb MISC metadata.xml 342 BLAKE2B 7f98f1707e3f53e7c2e532427d6935c692cdcf45304701d28d245ba13b62e752d14d5c3a96925fdf5bceb87a9c291edad0ce715339a5bf92ca6de7ee839adced SHA512 b7f0359b22f70ab25737565bda08e500f6a79bf33052d39fe2013b085c3f636122d0f373430ce3f0b56f95051db9571cb6c79b6f58e30658f45ef752ec708df6 diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild index b30a2b920f4e..a2b75d6b9880 100644 --- a/sci-biology/bowtie/bowtie-2.5.1.ebuild +++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{10..12} ) inherit python-single-r1 toolchain-funcs diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest index 0eea86b7ad45..c331c63113b8 100644 --- a/sci-biology/treeviewx/Manifest +++ b/sci-biology/treeviewx/Manifest @@ -1,16 +1,6 @@ -AUX treeviewx-0.5.1-70_choose_tree.patch 347 BLAKE2B deb36ebad2fce531b353376d3e115bafad9a21ee7ac62ea7cc9571733e2565903f85e733fc27cef306bb82b038e2bd16c7a69a7666af2aa9c7a04ea04319f244 SHA512 8e83180f7619e61ab6a6cdce7a576820a8e12fc2c0caf73b68c3943a98c7e618fcf0d477276b976039b594d60388a80a24f0502ebbc45ec1be371946f5c0cf1e AUX treeviewx-0.5.1-AM_PROG_AR.patch 239 BLAKE2B efd6bd8e5c2b7e609e5e5184e3f31ecbd639a6c1ee4bdfa10a6c4f7d7f0c1b1cfb29efe95ef8ec886a6290858a009222b41739b0e8473ff5daa23b8930cddd31 SHA512 198c1158006ac01c1c3a1e0f35eb19c39fdf1e05ddf22908a640c1b74eb6779958fa086b7987e86582cee16ea086f64ae1083f2aeaf5b3abb6251e21870c1447 -AUX treeviewx-0.5.1-fix_loading_crash.patch 951 BLAKE2B 7fb391335a57114a9f8ee707ffe908839a064bbe6aeab05fe0b1af8928ccb0504d91ce9e25cc55a7762422f71978e28f1479adae11293249a8a67ce8536f8d05 SHA512 9c205520dce7851520b24532f88348906c4d5a7f0fe392348099ee9f7377b778792170620856d533a275251a024756482bbd4b83d1da8281b84c39cdf2b3a711 -AUX treeviewx-0.5.1-gcc4.3.patch 2601 BLAKE2B 740a3efb736389fa0de40b0f2344e2767450809547189ef6cf659b05b6d80954550b5d5688e03a904ce6f8ec45866dff174cda0dbdbee5b0baff8cef86992240 SHA512 4629ad00ca712163fccbdb029dbb42970d432b2bcaf6b6345a7bf3dca2331ab988742a6dfbc8874e2624988c699b4ba1fff8032dda53afcffbd8264df62b480b -AUX treeviewx-0.5.1-svg.patch 1181 BLAKE2B b647b33738af0a933d0a946aa15d02f67b87175c4845813e9f01578dad6a3052902cc946b2f13dfe19451595364094094e388d8838c6c67b1448f8a32a832a65 SHA512 d71ee136f4f47792ce98826d8f7bca18320f404937abd90cdacd2685f62ed28f48601a105dd1cfb9717891a8930be339b6a663b11784f305d03af0cba24b4c4f -AUX treeviewx-0.5.1-treeview-xpm-not-xbm.patch 519 BLAKE2B 33a73602f4da18a723e292b0903a695add936697fbfd29ef978267f5e2ae1e1aa6dd49754c21900fabaf6259f732d7531f4d571f85ee544bc3d18f99961a31d4 SHA512 324b77dc43a99b55be45e1b561e528c8bb2f56ec4b1c7162987c848d0e6ea034efe262d910ee67fddcf0137b6eaeedfb50f26b8b2106b0459582942f5eccfbd4 -AUX treeviewx-0.5.1-wx30.patch 1722 BLAKE2B bc7d24b8b3953316ea4f8cb9eb26ab78fb7aee2adfce63f1ad6a758eb7d061badbcaf305d913c23fbf84773ead36242ec6995b476a1b795eb4110bc67ed4d135 SHA512 3efeea31429d623c65c958fc0ec859918e8e8b52d83973f7c7a131e47894093a2cbaafbb69c9a962ba12c0cf1ad733f2bf6d605888800d42a784d7bf3535c071 -AUX treeviewx-0.5.1-wxstring-maxlen.patch 1438 BLAKE2B a2dc6fe39c0312559628b61d86975a21db846e4c7cc3a0bb5739dd971417abd3ab9187ea56ef44d37c0394b28d4017981073eb4d890622d0d929f7a4d428950f SHA512 6e02ac59e8a28da8e94d5d6fdea71b3db9bc4501d9becf2d7aa6472d3f9f9b571fe68730390fd4cf6e1e422d618c21c40d86442d6b710e8395db107fc3445392 -AUX treeviewx-wxt.patch 1716 BLAKE2B f869d1d90dd23a7f0e242d9c1d0b0b97e0e053b5b2f00b283073f6e7f2d714cd2bf23656e65af1f3496bef0bf681ebb0618024f259b7f4d6dea777b048a438e4 SHA512 97d074e9501000099d0c5b3e3f56a796b1526499d4ccb44ef6f0b851bde1c27fc78bbc64f439ba5ecd3afa531b752c69148d7cd3b1e5a08a01566ad6155ce25c DIST treeviewx-0.5.1.20100823_p4.tar.gz 358644 BLAKE2B 3b7291415ab536230ac95decdc028dfdf60edcd986c91f76f7dacf5ec65fc31234c4d7023a9ec0fa420b68c9fe85278f8ae25106daa050872750dc5127362c46 SHA512 aec1351cfe58e1d11053c8bd3edbdf2ca74fb4bb5453bde72aa2a1b14623c69540fe7cef20f506291dad0b9358f6c37ea59feb493376b20dbdf3f7fb7df9844e DIST treeviewx_0.5.1+git20100823.7e4d0e9-4.debian.tar.xz 13880 BLAKE2B 6ab73fa79fe9a07dde17ae771edcee8d4f4e1aa25aef5fff66de4a86ee8e24c0edf9c8a4b721c12e1675083b493c65fadfff8bc79d50f28cb54a5b2cd47104a4 SHA512 4e3dbf0fd0383a0a07f924d2e59e9ed74b20c03fe57edc8e728f99dfff0a28f1c366f8a38f52f637d104b1abf98f8023abcdaff7394045642e53f5d7bb6723fd DIST treeviewx_128.png 16298 BLAKE2B 4a5f08352cd21f30e69f77403ecb79d95e8610e672979bbc46b72059bfe02edb711206260bb0b11eb733c544d584df7c9e778fe20ab2f768f18c49362cb72f11 SHA512 4986f86b7a0d4f57bd16aecb504a743ae060c2c5d3015ab2a6057e9df52ab132e6d071b5f992fc2de88529b5166f119654cbfb6c952e16d7e02d18f6d6143ee8 -DIST tv-0.5.1.tar.gz 426745 BLAKE2B 080c4e09f441fd83da3406990bbe97f9e29fa531f47a65533ca887580f8a3ec561bb4766e66e2ef4764f68eee86fdabf48481cece56ddda90f9ffdc3c80b3a1a SHA512 45a7ac6dff5b22771e4428d6b1ee528c0039956a462658d28d4f588b6df32620d8f69b3bcf5ca23643e2bdd5361da00625fcb1495bcf4f74d44ee22022c63143 -EBUILD treeviewx-0.5.1-r3.ebuild 957 BLAKE2B 6ce825eb0c8fe77bcf255d9a8f17f368f099263dd7c394703045f649246d3e44e2a18ef35c2f30bde461a1d05f0e6c197141a6ec3ff8a54d68084f0eb8868037 SHA512 d2e3f159cfa0e3c32bdfbbf464ca426c6f8db4aac39a53447b1d49015cb29d732429f3deeaadfd7de059cb3a779dca21818d54890aa136258997b672c3810033 EBUILD treeviewx-0.5.1.20100823_p4.ebuild 1170 BLAKE2B 7dcdea82488298e13d4df1853c2fcd8dcafbb0f90a46abbf61459b62229219d38b32d47db565ae72b849bcfd1709986e31cd1cef08a686e256eed85a53face72 SHA512 bcd92d43afef546a1c4da54e24e16367601cfbd2c460ffaa262bd0c8f002a015948f368508fb2354c065233f6ec1a7084cb6dc1283216f35cdebc00db55d88d5 MISC metadata.xml 613 BLAKE2B c3d6181a503990ef30c7dfb8166c2aaefa6709e78f482a45ff182825b7af7ebab6af100efba4dd51159d2e165979085559c4315f1ecc05e1947571843c7a8a73 SHA512 54eb1882193d526a2452804822140028bcad6157edc1f8fc7ca5a7757fca26e4afae7f50434a34dc401a0f1a68f54b0cdfb7727f79c7d2af0fa625accd284157 diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch deleted file mode 100644 index 7a614edff72e..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/tview.cpp -+++ b/tview.cpp -@@ -208,7 +208,7 @@ - pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), - wxSAVE|wxOVERWRITE_PROMPT); - -- if (dialog.ShowModal() == wxID_OK) -+ if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) - { - wxSVGFileDC pictureDC (dialog.GetPath(), 600, 650) ; - OnDraw (&pictureDC); diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch deleted file mode 100644 index c136539726a3..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch +++ /dev/null @@ -1,40 +0,0 @@ -Bug: http://code.google.com/p/treeviewx/issues/detail?id=1 -Description: fix crash on loading tree file. -Author: Tim Booth ---- tv-0.5.orig/tview.cpp -+++ tv-0.5/tview.cpp -@@ -278,7 +278,7 @@ - char buf[256]; - strcpy (buf, p->GetLabel().c_str()); - wchar_t wbuf[256]; -- mbstowcs (wbuf, buf, size_t(wbuf)); -+ mbstowcs (wbuf, buf, 256); - s << wbuf; - #else - s << p->GetLabel().c_str(); -@@ -563,7 +563,7 @@ - char buf[256]; - strcpy (buf, t.GetName().c_str()); - wchar_t wbuf[256]; -- mbstowcs (wbuf, buf, size_t(wbuf)); -+ mbstowcs (wbuf, buf, 256); - txt << wbuf; - #else - txt << t.GetName().c_str(); -@@ -712,7 +712,7 @@ - char buf[256]; - strcpy (buf, p.GetIthTreeName(i).c_str()); - wchar_t wbuf[256]; -- mbstowcs (wbuf, buf, size_t(wbuf)); -+ mbstowcs (wbuf, buf, 256); - - std::wstring tname = wbuf; - -@@ -1046,6 +1046,7 @@ - void MyCanvas::OnSize(wxSizeEvent& event) - { - Resize (); -+ Refresh(); - event.Skip(); - } - diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch deleted file mode 100644 index 33bd3b1741f6..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch +++ /dev/null @@ -1,77 +0,0 @@ -diff -Naur tv-0.5.1/TreeLib/Parse.cpp tv-0.5.1.new/TreeLib/Parse.cpp ---- tv-0.5.1/TreeLib/Parse.cpp 2002-02-23 07:22:32.000000000 -0500 -+++ tv-0.5.1.new/TreeLib/Parse.cpp 2008-06-17 06:08:24.000000000 -0400 -@@ -24,6 +24,11 @@ - #include <ctype.h> - #include "Parse.h" - -+ -+ -+ -+#include <cstring> -+ - // Return the next token in the string - tokentype Parser::NextToken () - { -diff -Naur tv-0.5.1/TreeLib/TreeLib.cpp tv-0.5.1.new/TreeLib/TreeLib.cpp ---- tv-0.5.1/TreeLib/TreeLib.cpp 2004-05-13 08:22:11.000000000 -0400 -+++ tv-0.5.1.new/TreeLib/TreeLib.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -24,6 +24,8 @@ - #include "TreeLib.h" - #include "Parse.h" - -+ -+#include <cstdlib> - #include <vector> - - -diff -Naur tv-0.5.1/TreeLib/treereader.cpp tv-0.5.1.new/TreeLib/treereader.cpp ---- tv-0.5.1/TreeLib/treereader.cpp 2003-09-10 08:58:16.000000000 -0400 -+++ tv-0.5.1.new/TreeLib/treereader.cpp 2008-06-17 06:07:15.000000000 -0400 -@@ -28,6 +28,9 @@ - #include <stdlib.h> - #endif - -+#include <cstring> -+#include <cstdlib> -+ - //------------------------------------------------------------------------------ - TreeReader::TreeReader (Tokeniser &p) : parser (p) - { -diff -Naur tv-0.5.1/ncl-2.0/src/charactersblock.cpp tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp ---- tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2002-12-10 06:35:49.000000000 -0500 -+++ tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,5 @@ -+ -+#include <cstring> - #include "nexusdefs.h" - #include "xnexus.h" - #include "nexustoken.h" -diff -Naur tv-0.5.1/ncl-2.0/src/nexus.cpp tv-0.5.1.new/ncl-2.0/src/nexus.cpp ---- tv-0.5.1/ncl-2.0/src/nexus.cpp 2002-12-10 06:35:50.000000000 -0500 -+++ tv-0.5.1.new/ncl-2.0/src/nexus.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,5 @@ -+ -+#include <cstring> - #include "nexusdefs.h" - #include "xnexus.h" - #include "nexustoken.h" -diff -Naur tv-0.5.1/ncl-2.0/src/nexustoken.cpp tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp ---- tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2005-04-29 10:28:17.000000000 -0400 -+++ tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,5 @@ -+ -+#include <cstring> - #include "nexusdefs.h" - #include "xnexus.h" - #include "nexustoken.h" -diff -Naur tv-0.5.1/ncl-2.0/src/nxsstring.cpp tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp ---- tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2001-02-02 07:55:40.000000000 -0500 -+++ tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,6 @@ -+ -+#include <cstring> -+ - #ifdef __BORLANDC__ - // Undefine __MINMAX_DEFINED so that min and max are correctly defined - #ifdef __MINMAX_DEFINED diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch deleted file mode 100644 index 67a62179bb87..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch +++ /dev/null @@ -1,30 +0,0 @@ -Author: Olly Betts <olly@survex.com> -Description: Update configure.in to match what it must have said when configure was generated. - One thing I should probably explain about the patch as my change may - seem odd otherwise - upstream's configure.in says "USE_SVG=0" but the - generated configure says "USE_SVG=1", so I've simply updated - configure.in to match what it must have said when configure was - generated. -Forwarded: no ---- tv-0.5.orig/configure.in -+++ tv-0.5/configure.in -@@ -66,7 +66,9 @@ - case "$wx_version" in - 2.4.*) WX_SVG_LIB=[`$WX_CONFIG --basename`_dcsvg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] - ;; -- *) WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] -+ 2.*) WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] -+ ;; -+ *) WX_SVG_LIB= - ;; - esac - -@@ -76,7 +78,7 @@ - - if test "$USE_SVG" = 1 ; then - CXXFLAGS="$CXXFLAGS -DUSE_SVG" -- LIBS="$LIBS -l$WX_SVG_LIB" -+ test -n "$WX_SVG_LIB" && LIBS="$LIBS -l$WX_SVG_LIB" - fi - - AC_OUTPUT(Makefile ncl-2.0/Makefile ncl-2.0/src/Makefile TreeLib/Makefile tv.spec) diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch deleted file mode 100644 index a57ae19aaf26..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch +++ /dev/null @@ -1,16 +0,0 @@ -Description: Fix the extension of the icon -Author: Olly Betts <olly@survex.com> -Last-Update: 2014-06-21 -Forwarded: http://code.google.com/p/treeviewx/issues/detail?id=4 - ---- tv-0.5.orig/tv.cpp -+++ tv-0.5/tv.cpp -@@ -215,7 +215,7 @@ - frame->SetIcon(wxIcon("app")); // use the name of the icon in the resource file - #endif - #if defined(__WXGTK__) || defined(__WXMOTIF__) -- frame->SetIcon(wxIcon(wxT("bitmaps/treeview.xbm"))); -+ frame->SetIcon(wxIcon(wxT("/usr/share/pixmaps/treeviewx.xpm"))); - #endif - - #ifdef __WXMAC__ diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch deleted file mode 100644 index a1cfd906f176..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch +++ /dev/null @@ -1,66 +0,0 @@ ---- a/tv.cpp -+++ b/tv.cpp -@@ -163,9 +163,9 @@ - { - // Optional command line argument is name of file to open - #if wxUSE_UNICODE -- wchar_t *InputFile = NULL; -+ const wchar_t *InputFile = NULL; - #else -- char *InputFile = NULL; -+ const char *InputFile = NULL; - #endif - // Read input/output files - if (argc > 1) ---- a/tview.cpp -+++ b/tview.cpp -@@ -62,9 +62,13 @@ - #ifdef __WXMSW__ - #else - #ifdef USE_SVG -+#if wxMAJOR_VERSION >= 3 -+ #include <wx/dcsvg.h> -+#else - #include <wx/svg/dcsvg.h> - #endif - #endif -+#endif - - // GUI interface - #include "tv.h" -@@ -186,7 +190,7 @@ - wxFrame *f = GetMainFrame(); - wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), - pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), -- wxSAVE|wxOVERWRITE_PROMPT); -+ wxFD_SAVE|wxFD_OVERWRITE_PROMPT); - - if (dialog.ShowModal() == wxID_OK) - { -@@ -206,7 +210,7 @@ - #endif - wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), - pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), -- wxSAVE|wxOVERWRITE_PROMPT); -+ wxFD_SAVE|wxFD_OVERWRITE_PROMPT); - - if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) - { -@@ -361,7 +365,7 @@ - - // Clear the canvas in case we're in single-window mode, - // and the canvas stays. --#if (wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated -+#if (wxMAJOR_VERSION >= 3 || wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated - canvas->ClearBackground(); - #else - canvas->Clear(); -@@ -686,7 +690,7 @@ - wxFontData data; - data.SetInitialFont (LeafFont); - --#ifdef __WXMAC__ -+#if wxMAJOR_VERSION >= 3 || defined __WXMAC__ - wxFontDialog dialog((wxWindow *)GetFrame(), data); - #else - wxFontDialog dialog((wxWindow *)GetMainFrame(), &data); diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch deleted file mode 100644 index 2c5179f778ca..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch +++ /dev/null @@ -1,34 +0,0 @@ -Description: Remove wxSTRING_MAXLEN (removed in wx3.0) and incomp. definition. - The definition wxSTRING_MAXLEN was removed from the public API of wxWidgets. - Its meaning was basically "take all the string", whenever a string length was - expected. The missing definition didn't raise a compilation error because - TreeLib's treedrawer.h contained a fall-back definition, which is however - incompatible with the original definition of wxWidgets and therefore is - interpreted by wxWidgets as a number representing the real string length. - This patch gets rid of the dangerous fall-back definition and of all of its - uses by using alternative wxString constructors that achieve the same - behavior. -Author: Martin Steghöfer <martin@steghoefer.eu> -Last-Update: Sun, 10 Aug 2014 14:06:42 +0200 -Bug-Debian: http://bugs.debian.org/751255 - ---- tv-0.5.orig/TreeLib/treedrawer.cpp -+++ tv-0.5/TreeLib/treedrawer.cpp -@@ -245,7 +245,7 @@ - // error in gcc, which is probably a gcc bug - { - wxCoord w, h, descent; -- wxString s (formatedString.c_str(), wxSTRING_MAXLEN); -+ wxString s (formatedString.c_str()); - pt.x += dc->GetCharWidth(); - pt.y -= dc->GetCharHeight()/2; - dc->DrawText (s, (int)pt.x, (int)pt.y); -@@ -566,7 +566,7 @@ - - #if USE_WXWINDOWS - wxCoord w, h; -- wxString s (buf, wxSTRING_MAXLEN); -+ wxString s (buf); - dc->GetTextExtent (s, &w, &h); - int x = (int)pt2.x; - int y = (int)pt2.y; diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch deleted file mode 100644 index a971e1a85074..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-wxt.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- a/tv.cpp -+++ b/tv.cpp -@@ -312,11 +312,15 @@ - { - #ifdef __WXMSW__ - file_menu->AppendSeparator(); -- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile"); -+ file_menu->Append(SAVEAS_PICTURE_CMD, -+ wxT("Save As Picture...")), -+ wxT("Save picture of tree to metafile"); - #else - #ifdef USE_SVG - file_menu->AppendSeparator(); -- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file"); -+ file_menu->Append(SAVEAS_PICTURE_CMD, -+ wxT("Save As Picture...")), -+ wxT("Save picture of tree to SVG file"); - #endif - #endif - file_menu->AppendSeparator(); ---- a/tview.cpp -+++ b/tview.cpp -@@ -184,10 +184,10 @@ - wxString pictureFileName = GetFrame()->GetTitle(); - pictureFileName += wxT(".emf"); - wxFrame *f = GetMainFrame(); -- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, -- "Enhanced metafile (*.emf)|*.emf", -- wxSAVE|wxOVERWRITE_PROMPT); -- -+ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), -+ pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), -+ wxSAVE|wxOVERWRITE_PROMPT); -+ - if (dialog.ShowModal() == wxID_OK) - { - wxMetafileDC pictureDC (dialog.GetPath(), 600, 650) ; -@@ -204,9 +204,9 @@ - #else - wxFrame *f = GetMainFrame(); - #endif -- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, -- "SVG vector picture files (*.svg)|*.svg", -- wxSAVE|wxOVERWRITE_PROMPT); -+ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), -+ pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), -+ wxSAVE|wxOVERWRITE_PROMPT); - - if (dialog.ShowModal() == wxID_OK) - { diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild deleted file mode 100644 index ada60056715e..000000000000 --- a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -WX_GTK_VER="3.0" -inherit autotools wxwidgets - -DESCRIPTION="A phylogenetic tree viewer" -HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" -SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/$(ver_cut 1-2)/tv-${PV}.tar.gz" -S="${WORKDIR}/tv-${PV}" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ~x86" - -RDEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-wxt.patch - "${FILESDIR}"/${P}-gcc4.3.patch - "${FILESDIR}"/${P}-70_choose_tree.patch - "${FILESDIR}"/${P}-fix_loading_crash.patch - "${FILESDIR}"/${P}-wx30.patch - "${FILESDIR}"/${P}-svg.patch - "${FILESDIR}"/${P}-treeview-xpm-not-xbm.patch - "${FILESDIR}"/${P}-wxstring-maxlen.patch - "${FILESDIR}"/${P}-AM_PROG_AR.patch -) - -src_prepare() { - default - mv configure.{in,ac} || die - eautoreconf -} - -src_configure() { - setup-wxwidgets - default -} |