diff options
author | Leo Famulari <leo@famulari.name> | 2021-01-25 15:21:09 -0500 |
---|---|---|
committer | Leo Famulari <leo@famulari.name> | 2021-01-25 15:40:55 -0500 |
commit | 68dd78e2e47248b3e1e7ba1807a92a8374b39097 (patch) | |
tree | d38564293f285d688a55b23e8a6424c6b26213b1 /gnu/packages/patches | |
parent | 8b55544212a90b0276df49596a3d373e5c2e8f5c (diff) | |
parent | 3f0af15131e524891df8c9f013f1be1597fe2d7e (diff) | |
download | guix-68dd78e2e47248b3e1e7ba1807a92a8374b39097.tar.gz |
Merge branch 'master' into staging
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r-- | gnu/packages/patches/freebayes-devendor-deps.patch | 152 | ||||
-rw-r--r-- | gnu/packages/patches/guile-2.2-skip-so-test.patch | 23 | ||||
-rw-r--r-- | gnu/packages/patches/idris-disable-test.patch | 19 | ||||
-rw-r--r-- | gnu/packages/patches/ipxe-reproducible-geniso.patch | 77 | ||||
-rw-r--r-- | gnu/packages/patches/mutt-CVE-2021-3181.patch | 45 | ||||
-rw-r--r-- | gnu/packages/patches/podofo-cmake-3.12.patch | 19 | ||||
-rw-r--r-- | gnu/packages/patches/r-httpuv-1.5.5-unvendor-libuv.patch (renamed from gnu/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch) | 0 | ||||
-rw-r--r-- | gnu/packages/patches/tipp10-disable-downloader.patch | 165 | ||||
-rw-r--r-- | gnu/packages/patches/tipp10-qt5.patch | 69 | ||||
-rw-r--r-- | gnu/packages/patches/vcflib-use-shared-libraries.patch | 135 |
10 files changed, 550 insertions, 154 deletions
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch new file mode 100644 index 0000000000..7e84666b85 --- /dev/null +++ b/gnu/packages/patches/freebayes-devendor-deps.patch @@ -0,0 +1,152 @@ +This patch is original to Guix, ongoing work to upstream bits as possible. + +From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001 +From: Efraim Flashner <efraim@flashner.co.il> +Date: Sun, 17 Jan 2021 13:27:17 +0200 +Subject: [PATCH] devendor-dependants + +--- + meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------ + 1 file changed, 66 insertions(+), 18 deletions(-) + +diff --git a/meson.build b/meson.build +index f6bf242..bded4af 100644 +--- a/meson.build ++++ b/meson.build +@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'], + + zlib_dep = dependency('zlib') + lzma_dep = dependency('liblzma') ++simde_dep = dependency('simde') + bzip2_dep = dependency('bz2lib', required: false) + htslib_dep = dependency('htslib', required : false) ++tabixpp_dep = dependency('tabixpp', required : false) ++fastahack_dep = dependency('fastahack', required : false) ++smithwaterman_dep = dependency('smithwaterman', required : false) ++vcflib_dep = dependency('libvcflib', required: false) + thread_dep = dependency('threads') + + if htslib_dep.found() +@@ -59,6 +64,56 @@ else + ] + endif + ++if tabixpp_dep.found() ++ tabixpp_includes = '' ++ tabixpp_src = [] ++else ++ tabixpp_includes = [ ++ 'vcflib/tabixpp', ++ ] ++ tabixpp_src = [ ++ 'vcflib/tabixpp/tabix.cpp', ++ ] ++endif ++ ++if vcflib_dep.found() ++ vcflib_includes = '' ++ vcflib_src = [] ++else ++ vcflib_includes = [ ++ 'vcflib/src', ++ 'vcflib/multichoose', ++ 'vcflib/filevercmp', ++ ] ++ vcflib_src = [ ++ 'vcflib/src/Variant.cpp', ++ ] ++endif ++ ++if fastahack_dep.found() ++ fastahack_src = [] ++else ++ fastahack_src = [ ++ 'vcflib/fastahack/Fasta.cpp', ++ 'vcflib/src/split.cpp', ++ ] ++endif ++ ++if smithwaterman_dep.found() ++ smithwaterman_includes = '' ++ smithwaterman_src = [] ++else ++ smithwaterman_includes = [ ++ 'vcflib/smithwaterman', ++ ] ++ smithwaterman_src = [ ++ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', ++ 'vcflib/smithwaterman/disorder.cpp', ++ 'vcflib/smithwaterman/Repeats.cpp', ++ 'vcflib/smithwaterman/LeftAlign.cpp', ++ 'vcflib/smithwaterman/IndelAllele.cpp', ++ ] ++endif + + + # +@@ -105,23 +160,18 @@ seqlib_src = [ + ] + + vcflib_src = [ +- 'vcflib/tabixpp/tabix.cpp', +- 'vcflib/src/Variant.cpp', +- 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', +- 'vcflib/smithwaterman/disorder.cpp', +- 'vcflib/smithwaterman/Repeats.cpp', +- 'vcflib/smithwaterman/LeftAlign.cpp', +- 'vcflib/smithwaterman/IndelAllele.cpp', ++ vcflib_src, ++ tabixpp_src, ++ smithwaterman_src, + ] + + bamleftalign_src = [ + 'src/bamleftalign.cpp', + 'src/IndelAllele.cpp', + 'contrib/SeqLib/src/BamWriter.cpp', +- 'vcflib/fastahack/Fasta.cpp', +- 'vcflib/smithwaterman/LeftAlign.cpp', +- 'vcflib/smithwaterman/IndelAllele.cpp', +- 'vcflib/src/split.cpp', ++ fastahack_src, ++ smithwaterman_src, ++ vcflib_src, + 'src/LeftAlign.cpp', + ] + +@@ -134,11 +184,9 @@ incdir = include_directories( + 'ttmath', + 'contrib', + 'contrib/SeqLib', +- 'vcflib/src', +- 'vcflib/tabixpp', +- 'vcflib/smithwaterman', +- 'vcflib/multichoose', +- 'vcflib/filevercmp') ++ tabixpp_includes, ++ smithwaterman_includes, ++ vcflib_includes) + + c_args = ['-fpermissive','-w'] + cpp_args = ['-fpermissive','-w','-Wc++14-compat'] +@@ -152,7 +200,7 @@ executable('freebayes', + include_directories : incdir, + cpp_args : cpp_args, + c_args : c_args, +- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], ++ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep], + install: true + ) + +@@ -165,7 +213,7 @@ executable('bamleftalign', + include_directories : incdir, + cpp_args : cpp_args, + c_args : c_args, +- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], ++ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep], + install: true + ) + +-- +2.30.0 + diff --git a/gnu/packages/patches/guile-2.2-skip-so-test.patch b/gnu/packages/patches/guile-2.2-skip-so-test.patch new file mode 100644 index 0000000000..e7c2594e91 --- /dev/null +++ b/gnu/packages/patches/guile-2.2-skip-so-test.patch @@ -0,0 +1,23 @@ +Skip 'test-stack-overflow' that crashes when using QEMU transparent emulation. + +--- a/test-suite/standalone/Makefile.in 1970-01-01 01:00:01.000000000 +0100 ++++ b/test-suite/standalone/Makefile.in 2021-01-11 10:59:31.606269449 +0100 +@@ -102,8 +102,7 @@ + test-scm-to-latin1-string$(EXEEXT) test-scm-values$(EXEEXT) \ + test-scm-c-bind-keyword-arguments$(EXEEXT) \ + test-srfi-4$(EXEEXT) $(am__append_6) $(am__EXEEXT_1) \ +- test-smob-mark$(EXEEXT) test-smob-mark-race$(EXEEXT) \ +- test-stack-overflow ++ test-smob-mark$(EXEEXT) test-smob-mark-race$(EXEEXT) + check_PROGRAMS = test-num2integral$(EXEEXT) test-round$(EXEEXT) \ + test-foreign-object-c$(EXEEXT) test-list$(EXEEXT) \ + test-unwind$(EXEEXT) test-conversion$(EXEEXT) \ +@@ -1938,7 +1937,7 @@ + test-command-line-encoding test-command-line-encoding2 \ + test-language test-guild-compile $(am__append_3) \ + test-foreign-object-scm test-fast-slot-ref test-mb-regexp \ +- test-use-srfi $(am__append_5) test-stack-overflow ++ test-use-srfi $(am__append_5) + BUILT_SOURCES = $(am__append_2) + EXTRA_DIST = test-import-order-a.scm test-import-order-b.scm \ + test-import-order-c.scm test-import-order-d.scm \ diff --git a/gnu/packages/patches/idris-disable-test.patch b/gnu/packages/patches/idris-disable-test.patch new file mode 100644 index 0000000000..ec8c7c8451 --- /dev/null +++ b/gnu/packages/patches/idris-disable-test.patch @@ -0,0 +1,19 @@ +The "pkg010" test output depends on the version of optparse-applicative being +used. The expected output requires optparse-applicative >= 0.15.1.0. Skip +the test for now. + +--- idris-1.3.3/test/TestData.hs 2021-01-19 23:05:24.238958262 -0600 ++++ idris-1.3.3/test/TestData.hs 2021-01-19 23:10:33.314390997 -0600 +@@ -212,8 +212,10 @@ + ( 5, ANY ), + ( 6, ANY ), + ( 7, ANY ), +- ( 8, ANY ), +- ( 10, ANY )]), ++ ( 8, ANY )]), ++-- FIXME: Expected output depends on optparse-applicative version. ++-- See https://github.com/idris-lang/Idris-dev/issues/4896 ++-- ( 10, ANY )]), + ("prelude", "Prelude", + [ ( 1, ANY )]), + ("primitives", "Primitive types", diff --git a/gnu/packages/patches/ipxe-reproducible-geniso.patch b/gnu/packages/patches/ipxe-reproducible-geniso.patch new file mode 100644 index 0000000000..ff6aa1da94 --- /dev/null +++ b/gnu/packages/patches/ipxe-reproducible-geniso.patch @@ -0,0 +1,77 @@ +From 052d24d8217c51c572c2f6cbb4a687be2e8ba52d Mon Sep 17 00:00:00 2001 +From: Brice Waegeneire <brice@waegenei.re> +Date: Fri, 5 Jun 2020 14:38:43 +0200 +Subject: [PATCH] [geniso] Make it reproducible + +Some timestamps get embedded in the generated ISO, making it +unreproducible so we overwrite those timestamps to be at the UNIX epoch. +--- + src/util/geniso | 24 +++++++++++++++++++++--- + 1 file changed, 21 insertions(+), 3 deletions(-) + +diff --git a/src/util/geniso b/src/util/geniso +index ff090d4a..e032ffb0 100755 +--- a/src/util/geniso ++++ b/src/util/geniso +@@ -11,6 +11,13 @@ function help() { + echo " -o FILE save iso image to file" + } + ++function reset_timestamp() { ++ for f in "$1"/*; do ++ touch -t 197001010100 "$f" ++ done ++ touch -t 197001010100 "$1" ++} ++ + LEGACY=0 + FIRST="" + +@@ -37,8 +44,9 @@ if [ -z "${OUT}" ]; then + exit 1 + fi + +-# There should either be mkisofs or the compatible genisoimage program +-for command in genisoimage mkisofs; do ++# There should either be mkisofs, xorriso or the compatible genisoimage ++# program ++for command in xorriso genisoimage mkisofs; do + if ${command} --version >/dev/null 2>/dev/null; then + mkisofs=(${command}) + break +@@ -46,8 +54,10 @@ for command in genisoimage mkisofs; do + done + + if [ -z "${mkisofs}" ]; then +- echo "${0}: mkisofs or genisoimage not found, please install or set PATH" >&2 ++ echo "${0}: mkisofs, xorriso or genisoimage not found, please install or set PATH" >&2 + exit 1 ++elif [ "$mkisofs" = "xorriso" ]; then ++ mkisofs+=(-as mkisofs) + fi + + dir=$(mktemp -d bin/iso.dir.XXXXXX) +@@ -115,6 +125,8 @@ case "${LEGACY}" in + exit 1 + fi + ++ reset_timestamp "$dir" ++ + # generate the iso image + "${mkisofs[@]}" -b boot.img -output ${OUT} ${dir} + ;; +@@ -127,6 +139,12 @@ case "${LEGACY}" in + cp ${LDLINUX_C32} ${dir} + fi + ++ reset_timestamp "$dir" ++ ++ if [ "${mkisofs[0]}" = "xorriso" ]; then ++ mkisofs+=(-isohybrid-mbr "$SYSLINUX_MBR_DISK_PATH") ++ fi ++ + # generate the iso image + "${mkisofs[@]}" -b isolinux.bin -no-emul-boot -boot-load-size 4 -boot-info-table -output ${OUT} ${dir} + +-- +2.26.2 diff --git a/gnu/packages/patches/mutt-CVE-2021-3181.patch b/gnu/packages/patches/mutt-CVE-2021-3181.patch new file mode 100644 index 0000000000..df5214b052 --- /dev/null +++ b/gnu/packages/patches/mutt-CVE-2021-3181.patch @@ -0,0 +1,45 @@ +Fix CVE-2021-3181: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-3181 + +Patch copied from upstream source repository: + +https://gitlab.com/muttmua/mutt/-/commit/c059e20ea4c7cb3ee9ffd3500ffe313ae84b2545 + +From c059e20ea4c7cb3ee9ffd3500ffe313ae84b2545 Mon Sep 17 00:00:00 2001 +From: Kevin McCarthy <kevin@8t8.us> +Date: Sun, 17 Jan 2021 10:40:37 -0800 +Subject: [PATCH] Fix memory leak parsing group address. + +When there was a group address terminator with no previous addresses, +an address would be allocated but not attached to the address list. + +Change this to only allocate when last exists. + +It would be more correct to not allocate at all unless we are inside a +group list, but I will address that in a separate commit to master. +--- + rfc822.c | 5 ++--- + 1 file changed, 2 insertions(+), 3 deletions(-) + +diff --git a/rfc822.c b/rfc822.c +index 7ff4eaa3..ced619f2 100644 +--- a/rfc822.c ++++ b/rfc822.c +@@ -587,11 +587,10 @@ ADDRESS *rfc822_parse_adrlist (ADDRESS *top, const char *s) + #endif + + /* add group terminator */ +- cur = rfc822_new_address (); + if (last) + { +- last->next = cur; +- last = cur; ++ last->next = rfc822_new_address (); ++ last = last->next; + } + + phraselen = 0; +-- +GitLab + diff --git a/gnu/packages/patches/podofo-cmake-3.12.patch b/gnu/packages/patches/podofo-cmake-3.12.patch deleted file mode 100644 index 0a3c19b21a..0000000000 --- a/gnu/packages/patches/podofo-cmake-3.12.patch +++ /dev/null @@ -1,19 +0,0 @@ -The build fails with cmake 3.12.0. This patch will be obsolete with the next -release. - -https://sourceforge.net/p/podofo/tickets/24/attachment/podofo-cmake-3.12.patch - - ---- a/test/TokenizerTest/CMakeLists.txt 2018-07-20 18:26:02.921494293 +0200 -+++ b/test/TokenizerTest/CMakeLists.txt 2018-07-20 18:34:53.727136443 +0200 -@@ -2,10 +2,3 @@ - TARGET_LINK_LIBRARIES(TokenizerTest ${PODOFO_LIB} ${PODOFO_LIB_DEPENDS}) - SET_TARGET_PROPERTIES(TokenizerTest PROPERTIES COMPILE_FLAGS "${PODOFO_CFLAGS}") - ADD_DEPENDENCIES(TokenizerTest ${PODOFO_DEPEND_TARGET}) -- --# Copy the test samples over to the build tree --ADD_CUSTOM_COMMAND( -- TARGET TokenizerTest -- POST_BUILD -- COMMAND "${CMAKE_COMMAND}" -E copy_directory "${CMAKE_CURRENT_SOURCE_DIR}/objects" "${CMAKE_CURRENT_BINARY_DIR}/objects" -- ) diff --git a/gnu/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch b/gnu/packages/patches/r-httpuv-1.5.5-unvendor-libuv.patch index 0947718059..0947718059 100644 --- a/gnu/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch +++ b/gnu/packages/patches/r-httpuv-1.5.5-unvendor-libuv.patch diff --git a/gnu/packages/patches/tipp10-disable-downloader.patch b/gnu/packages/patches/tipp10-disable-downloader.patch new file mode 100644 index 0000000000..4917a927f9 --- /dev/null +++ b/gnu/packages/patches/tipp10-disable-downloader.patch @@ -0,0 +1,165 @@ +https://salsa.debian.org/debian/tipp10/-/raw/debian/2.1.0-5/debian/patches/disable_downloaders.patch + +Author: Reiner Herrmann <reiner@reiner-h.de> +Description: Disable downloaders + This makes porting to Qt5 much easier, as QHttp is no longer available. + But the functionality was not enabled anyway or is no longer useful. + . + - checkversion.h/.cpp: + At startup (while loading settings), Tipp10 "phones home" to do an + update check (www.tipp10.com/update/version.tipp10v210). + For a packaged software and one that is no longer being developed, + this does not make much sense. + - updatedialog.h/.cpp: + Can download newer sqlite database (www.tipp10.com/update/sql.tipp10v210.utf), + but this file is no longer available on the server (404). + The update action has also not been enabled in the menu, so the update + functionality was currently not active: + widget/mainwindow.cpp:143: //fileMenu->addAction(updateAction); + - downloaddialog.h/.cpp: + Allows downloading lessons from user-specified location. + But the action (widget/startwidget.cpp -> lessonDownload) has not been part + of any menu, so it was also not in use. + +--- a/tipp10.pro ++++ b/tipp10.pro +@@ -15,7 +15,6 @@ + INCLUDEPATH += . + CONFIG += qt + QT += sql +-QT += network + RC_FILE += tipp10.rc + RESOURCES += tipp10.qrc + HEADERS += def/defines.h \ +@@ -36,15 +35,12 @@ + widget/settingspages.h \ + widget/lessondialog.h \ + widget/regexpdialog.h \ +- widget/downloaddialog.h \ + widget/lessonprintdialog.h \ + widget/lessonresult.h \ +- widget/updatedialog.h \ + widget/helpbrowser.h \ + widget/companylogo.h \ + widget/errormessage.h \ + widget/txtmessagedialog.h \ +- widget/checkversion.h \ + sql/connection.h \ + sql/lessontablesql.h \ + sql/chartablesql.h \ +@@ -70,15 +66,12 @@ + widget/settingspages.cpp \ + widget/lessondialog.cpp \ + widget/regexpdialog.cpp \ +- widget/downloaddialog.cpp \ + widget/lessonprintdialog.cpp \ + widget/lessonresult.cpp \ +- widget/updatedialog.cpp \ + widget/helpbrowser.cpp \ + widget/companylogo.cpp \ + widget/errormessage.cpp \ + widget/txtmessagedialog.cpp \ +- widget/checkversion.cpp \ + sql/lessontablesql.cpp \ + sql/chartablesql.cpp \ + sql/trainingsql.cpp \ +--- a/widget/mainwindow.cpp ++++ b/widget/mainwindow.cpp +@@ -41,11 +41,9 @@ + + #include "mainwindow.h" + #include "settingsdialog.h" +-#include "updatedialog.h" + #include "def/defines.h" + #include "def/errordefines.h" + #include "errormessage.h" +-#include "checkversion.h" + + MainWindow::MainWindow() { + trainingStarted = false; +@@ -214,8 +212,8 @@ + } + + void MainWindow::showUpdate() { +- UpdateDialog updateDialog(this); +- updateDialog.exec(); ++ //UpdateDialog updateDialog(this); ++ //updateDialog.exec(); + // Fill lesson list after online update + startWidget->fillLessonList(false); + } +@@ -486,6 +484,7 @@ + settings.endGroup(); + + settings.beginGroup("general"); ++#if 0 + if (settings.value("check_new_version", true).toBool()) { + + QDate lastVersionCheck = settings.value("last_version_check").toDate(); +@@ -499,6 +498,7 @@ + } + settings.setValue("last_version_check", today); + } ++#endif + settings.endGroup(); + } + +--- a/widget/settingspages.cpp ++++ b/widget/settingspages.cpp +@@ -581,7 +581,7 @@ + + // Layout of group box vertical + QVBoxLayout *layout = new QVBoxLayout; +- layout->addWidget(checkNewVersion); ++ //layout->addWidget(checkNewVersion); + layout->addSpacing(1); + layout->addWidget(checkNativeStyle); + layout->setMargin(16); +@@ -610,7 +610,6 @@ + checkIntelligence->setChecked(settings.value("check_toggle_intelligence", true).toBool()); + checkLimitLesson->setChecked(settings.value("check_limit_lesson", true).toBool()); + checkLessonPublish->setChecked(settings.value("check_lesson_publish", true).toBool()); +- checkNewVersion->setChecked(settings.value("check_new_version", true).toBool()); + checkNativeStyle->setChecked(settings.value("check_native_style", false).toBool()); + settings.endGroup(); + } +@@ -636,7 +635,6 @@ + settings.setValue("check_limit_lesson", checkLimitLesson->isChecked()); + settings.setValue("check_lesson_publish", checkLessonPublish->isChecked()); + settings.setValue("check_native_style", checkNativeStyle->isChecked()); +- settings.setValue("check_new_version", checkNewVersion->isChecked()); + settings.endGroup(); + + return requireRestart; +--- a/widget/startwidget.cpp ++++ b/widget/startwidget.cpp +@@ -43,12 +43,10 @@ + + #include "startwidget.h" + #include "sql/startsql.h" +-#include "updatedialog.h" + #include "def/defines.h" + #include "def/errordefines.h" + #include "errormessage.h" + #include "lessondialog.h" +-#include "downloaddialog.h" + #include "illustrationdialog.h" + #include "txtmessagedialog.h" + +@@ -1048,7 +1046,7 @@ + } + + void StartWidget::clickDownloadLesson() { +- ++#if 0 + QStringList lessonData; + + DownloadDialog downloadDialog(&lessonData, this); +@@ -1083,6 +1081,7 @@ + } + } + } ++#endif + } + + void StartWidget::clickEditLesson() { diff --git a/gnu/packages/patches/tipp10-qt5.patch b/gnu/packages/patches/tipp10-qt5.patch new file mode 100644 index 0000000000..34ad5cd708 --- /dev/null +++ b/gnu/packages/patches/tipp10-qt5.patch @@ -0,0 +1,69 @@ +https://salsa.debian.org/debian/tipp10/-/raw/debian/2.1.0-5/debian/patches/qt5.patch + +Author: Reiner Herrmann <reiner@reiner-h.de> +Description: Port to Qt5 +Bug-Debian: https://bugs.debian.org/875207 + +--- a/tipp10.pro ++++ b/tipp10.pro +@@ -14,6 +14,7 @@ + DEPENDPATH += . + INCLUDEPATH += . + CONFIG += qt ++QT += widgets multimedia printsupport + QT += sql + RC_FILE += tipp10.rc + RESOURCES += tipp10.qrc +--- a/main.cpp ++++ b/main.cpp +@@ -24,7 +24,6 @@ + ****************************************************************/ + + #include <QApplication> +-#include <QPlastiqueStyle> + #include <QString> + #include <QSettings> + #include <QCoreApplication> +@@ -212,7 +211,7 @@ + + // Set windows style + if (!useNativeStyle) { +- app.setStyle("plastique"); ++ app.setStyle("fusion"); + } + + // Translation +--- a/games/abcrainwidget.cpp ++++ b/games/abcrainwidget.cpp +@@ -235,8 +235,7 @@ + charballs.last()->wind = (qrand() % 8) + 2; + charballs.last()->rad = 0; + +- chartext.append(new QGraphicsTextItem(QString(characterTemp), +- charballs.last(), scene)); ++ chartext.append(new QGraphicsTextItem(QString(characterTemp), charballs.last())); + chartext.last()->setFont(QFont("Courier", 16, 100)); + chartext.last()->setPos(-(chartext.last()->boundingRect().width() / 2), -(chartext.last()->boundingRect().height() / 2)); + +--- a/sql/chartablesql.cpp ++++ b/sql/chartablesql.cpp +@@ -137,7 +137,7 @@ + sortColumn(4); + + headerview->setStretchLastSection(true); +- headerview->setResizeMode(QHeaderView::Interactive); ++ headerview->setSectionResizeMode(QHeaderView::Interactive); + headerview->setSortIndicatorShown(true); + + // Resize the columns +--- a/sql/lessontablesql.cpp ++++ b/sql/lessontablesql.cpp +@@ -202,7 +202,7 @@ + sortColumn(-1); + + headerview->setStretchLastSection(true); +- headerview->setResizeMode(QHeaderView::Interactive); ++ headerview->setSectionResizeMode(QHeaderView::Interactive); + headerview->setSortIndicatorShown(true); + + // Resize the columns diff --git a/gnu/packages/patches/vcflib-use-shared-libraries.patch b/gnu/packages/patches/vcflib-use-shared-libraries.patch deleted file mode 100644 index e198ec663c..0000000000 --- a/gnu/packages/patches/vcflib-use-shared-libraries.patch +++ /dev/null @@ -1,135 +0,0 @@ -This patch is a combination of many of the patches from Debian: -https://sources.debian.org/src/libvcflib/1.0.1+dfsg-3/debian/patches/ - ---- - Makefile | 63 +++++++++++--------------------------------------------- - 1 file changed, 12 insertions(+), 51 deletions(-) - -diff --git a/Makefile b/Makefile -index 6b13350..be85f22 100644 ---- a/Makefile -+++ b/Makefile -@@ -114,43 +114,25 @@ BIN_SOURCES = src/vcfecho.cpp \ - src/vcfnull2ref.cpp \ - src/vcfinfosummarize.cpp - --# when we can figure out how to build on mac --# src/vcfsom.cpp -- - #BINS = $(BIN_SOURCES:.cpp=) - BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=))) - SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=)) - --TABIX = tabixpp/tabix.o --FASTAHACK = fastahack/Fasta.o --SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o --REPEATS = smithwaterman/Repeats.o --INDELALLELE = smithwaterman/IndelAllele.o --DISORDER = smithwaterman/disorder.o --LEFTALIGN = smithwaterman/LeftAlign.o --FSOM = fsom/fsom.o - FILEVERCMP = filevercmp/filevercmp.o - --# Work out how to find htslib --# Use the one we ship in tabixpp unless told otherwise by the environment --HTS_LIB ?= $(VCF_LIB_LOCAL)/tabixpp/htslib/libhts.a --HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabixpp/htslib --HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread -- -- --INCLUDES = $(HTS_INCLUDES) -I$(INC_DIR) --LDFLAGS = -L$(LIB_DIR) -lvcflib $(HTS_LDFLAGS) -lpthread -lz -lm -llzma -lbz2 -+INCLUDES = -I$(INC_DIR) $(shell pkg-config --cflags htslib fastahack smithwaterman tabixpp) -+LDFLAGS = -L$(LIB_DIR) -lvcflib -lpthread -lz -lstdc++ -lm -llzma -lbz2 $(shell pkg-config --libs htslib fastahack smithwaterman tabixpp) - - - --all: $(OBJECTS) $(BINS) scriptToBin -+all: $(OBJECTS) $(BINS) scriptToBin libvcflib.a - - scriptToBin: $(BINS) - $(CP) scripts/* $(BIN_DIR) - - GIT_VERSION += $(shell git describe --abbrev=4 --dirty --always) - --CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -+CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -fPIC - #CXXFLAGS = -O2 - #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual - -@@ -168,7 +150,7 @@ profiling: - gprof: - $(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all - --$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK) -+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(FILEVERCMP) - $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && $(CP) src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ - - multichoose: pre -@@ -177,39 +159,22 @@ multichoose: pre - intervaltree: pre - cd intervaltree && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ - --$(TABIX): pre -- cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ -- --$(SMITHWATERMAN): pre -- cd smithwaterman && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/ -- --$(DISORDER): $(SMITHWATERMAN) -- --$(REPEATS): $(SMITHWATERMAN) -- --$(LEFTALIGN): $(SMITHWATERMAN) -- --$(INDELALLELE): $(SMITHWATERMAN) -- --$(FASTAHACK): pre -- cd fastahack && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/ -- --#$(FSOM): --# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm -- - $(FILEVERCMP): pre - cd filevercmp && make && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/ - - $(SHORTBINS): pre - $(MAKE) $(BIN_DIR)/$@ - --$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree -+$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP) pre intervaltree - $(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\" - --libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre -- ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX) -+libvcflib.a: $(OBJECTS) $(SSW) $(FILEVERCMP) pre -+ ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP) - $(CP) libvcflib.a $(LIB_DIR) - -+libvcflib.so: $(OBJECTS) $(SSW) $(FILEVERCMP) pre -+ $(CXX) -shared -o libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP) -+ $(CP) libvcflib.so $(LIB_DIR) - - test: $(BINS) - @prove -Itests/lib -w tests/*.t -@@ -230,16 +195,12 @@ clean: - $(RM) $(BINS) $(OBJECTS) - $(RM) ssw_cpp.o ssw.o - $(RM) libvcflib.a -+ $(RM) libvcflib.so - $(RM) -r $(BIN_DIR) - $(RM) -r $(LIB_DIR) - $(RM) -r $(INC_DIR) - $(RM) -r $(OBJ_DIR) -- $(MAKE) clean -C tabixpp -- $(MAKE) clean -C smithwaterman -- $(MAKE) clean -C fastahack - $(MAKE) clean -C multichoose -- $(MAKE) clean -C fsom -- $(MAKE) clean -C libVCFH - $(MAKE) clean -C test - $(MAKE) clean -C filevercmp - $(MAKE) clean -C intervaltree --- -2.28.0 - |