diff --git a/.gitignore b/.gitignore index d0a90d7..865ec36 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ -/ugene-free-*.tar.gz +/ugene-1.*.tar.gz +/ugene-33.0.tar.gz diff --git a/create-ugene-free-tarball.sh b/create-ugene-free-tarball.sh deleted file mode 100644 index b07b9af..0000000 --- a/create-ugene-free-tarball.sh +++ /dev/null @@ -1,46 +0,0 @@ -#!/bin/bash - -set -e -set -x - -umask 0022 - -VERSION=${VERSION:-40.1} -FEDORA_TAR_VERSION=${VERSION} - -REPONAME=ugene -TARNAME=${REPONAME} - -SOURCE_TOP_URL=https://github.com/ugeneunipro/${REPONAME}/archive/ - -CURRENT_DIR=$(pwd) -TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX) - - -pushd $TMPDIR - -TARBALL_NAME=${TARNAME}-${FEDORA_TAR_VERSION}.tar.gz -SOURCE_URL=${SOURCE_TOP_URL}/${VERSION}/${TARBALL_NAME} - -wget -N ${SOURCE_URL} -rm -rf ${TARNAME}-${VERSION} -tar xzf ${TARBALL_NAME} - -pushd ${TARNAME}-${VERSION} - -echo "Removing nonfree code" -for NONFREE in \ - src/plugins_3rdparty/psipred -do - rm -rf $NONFREE -done - -echo "done" -popd - -tar czf ${TARNAME}-free-${FEDORA_TAR_VERSION}.tar.gz ${TARNAME}-${VERSION}/ -mv ${TARNAME}-free-${FEDORA_TAR_VERSION}.tar.gz ${CURRENT_DIR}/ - -popd -rm -rf $TMPDIR - diff --git a/create-ugene-git-bare-tarball.sh b/create-ugene-git-bare-tarball.sh deleted file mode 100644 index e1c57aa..0000000 --- a/create-ugene-git-bare-tarball.sh +++ /dev/null @@ -1,49 +0,0 @@ -#!/bin/bash - -set -x -set -e - -REPONAME=ugene -GITURL=https://github.com/ugeneunipro/${REPONAME}.git - -DATE=$(date '+%Y%m%d') -TIME=$(date '+%H%M') - -TARNAME=${REPONAME}-free-${DATE}T${TIME}.tar.gz - -PWDDIR=$(pwd) -TMPDIR=$(mktemp -d $(pwd)/tmp-${REPONAME}-XXXXXX) -pushd $TMPDIR - -git clone --depth 30 --no-single-branch --mirror $GITURL - -pushd ${REPONAME}.git - -git log 2>&1 | head -n 5 > git-log-orig.txt -#grep version README.md - -# remove non-free part -for NONFREE in \ - src/plugins_3rdparty/psipred -do - env FILTER_BRANCH_SQUELCH_WARNING=1 \ - git filter-branch --index-filter "git rm -r --cached --ignore-unmatch $NONFREE" -- --all -done - -# And again show git head info -git log 2>&1 | head -n 5 -#grep version README.md -echo - -# Here again show original git head infob -cat git-log-orig.txt -echo -rm -f git-log-orig.txt - -popd - -tar czf ${TARNAME} ${REPONAME}.git/ - -cp -p ${TARNAME} $PWDDIR -popd -rm -rf $TMPDIR diff --git a/sources b/sources index 76e7d22..5622a2a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-53.0.tar.gz) = 233c857d9a0ea42005efaa53e5ba5162e76a149f01d7406a73bd9215b96c096b3c379cc3b14c7d7b83c61df5ea2435412f6d43c71aef84b23d1d683d5a172b30 +SHA512 (ugene-33.0.tar.gz) = 5e02a1845d7626c1287002a25bfa1551234fc94312963aef2981bdfe70af1959d5b1c4289af0138dfa9ba44846454ba2d4d9cd96f029bac1ab262ed2bc583d87 diff --git a/ugene-1.31.0.patch b/ugene-1.31.0.patch new file mode 100644 index 0000000..a478a52 --- /dev/null +++ b/ugene-1.31.0.patch @@ -0,0 +1,24 @@ +diff --git a/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp b/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp +index a2541b880..f806afef7 100644 +--- a/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp ++++ b/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp +@@ -20,6 +20,7 @@ + */ + + #include ++#include + + #include "LengthSettingsWidget.h" + #include "LineEditHighlighter.h" +diff --git a/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp b/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp +index 00ecfef09..bce841083 100644 +--- a/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp ++++ b/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp +@@ -19,6 +19,7 @@ + * MA 02110-1301, USA. + */ + ++#include + #include + + #include "QualitySettingsWidget.h" diff --git a/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch b/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch deleted file mode 100644 index cf06c23..0000000 --- a/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch +++ /dev/null @@ -1,183 +0,0 @@ ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/thread_info.cc.port 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/thread_info.cc 2021-11-09 11:04:57.375470034 +0900 -@@ -270,9 +270,19 @@ void ThreadInfo::FillCPUContext(RawConte - out->float_save.fir = mcontext.fpc_eir; - #endif - } -+ -+#else -+uintptr_t ThreadInfo::GetInstructionPointer() const { -+ return 0; -+} -+ -+void ThreadInfo::FillCPUContext(RawContextCPU* out) const { -+} -+ - #endif // __mips__ - - void ThreadInfo::GetGeneralPurposeRegisters(void** gp_regs, size_t* size) { -+#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) - assert(gp_regs || size); - #if defined(__mips__) - if (gp_regs) -@@ -285,9 +295,11 @@ void ThreadInfo::GetGeneralPurposeRegist - if (size) - *size = sizeof(regs); - #endif -+#endif - } - - void ThreadInfo::GetFloatingPointRegisters(void** fp_regs, size_t* size) { -+#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) - assert(fp_regs || size); - #if defined(__mips__) - if (fp_regs) -@@ -300,6 +312,7 @@ void ThreadInfo::GetFloatingPointRegiste - if (size) - *size = sizeof(fpregs); - #endif -+#endif - } - - } // namespace google_breakpad ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/ucontext_reader.cc.port 2021-11-09 12:13:14.526068539 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/ucontext_reader.cc 2021-11-09 12:13:47.079160354 +0900 -@@ -254,6 +254,16 @@ void UContextReader::FillCPUContext(RawC - out->float_save.fir = uc->uc_mcontext.fpc_eir; // Unused. - #endif - } -+ -+#else -+uintptr_t UContextReader::GetStackPointer(const ucontext_t* uc) { -+ return 0; -+} -+uintptr_t UContextReader::GetInstructionPointer(const ucontext_t* uc) { -+ return 0; -+} -+void UContextReader::FillCPUContext(RawContextCPU* out, const ucontext_t* uc) { -+} - #endif - - } // namespace google_breakpad ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc.port 2021-11-09 11:04:57.135469882 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc 2021-11-09 12:06:47.875738562 +0900 -@@ -442,6 +442,7 @@ int ExceptionHandler::ThreadEntry(void* - // This function runs in a compromised context: see the top of the file. - // Runs on the crashing thread. - bool ExceptionHandler::HandleSignal(int /*sig*/, siginfo_t* info, void* uc) { -+#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) - if (filter_ && !filter_(callback_context_)) - return false; - -@@ -483,6 +484,9 @@ bool ExceptionHandler::HandleSignal(int - } - } - return GenerateDump(&g_crash_context_); -+#else -+ return false; -+#endif - } - - // This is a public interface to HandleSignal that allows the client to -@@ -661,6 +665,7 @@ bool ExceptionHandler::WriteMinidump(con - __attribute__((optimize("no-omit-frame-pointer"))) - #endif - bool ExceptionHandler::WriteMinidump() { -+#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) - if (!IsOutOfProcess() && !minidump_descriptor_.IsFD() && - !minidump_descriptor_.IsMicrodumpOnConsole()) { - // Update the path of the minidump so that this can be called multiple times -@@ -735,6 +740,9 @@ bool ExceptionHandler::WriteMinidump() { - #endif - - return GenerateDump(&context); -+#else -+ return false; -+#endif - } - - void ExceptionHandler::AddMappingInfo(const string& name, ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/microdump_writer/microdump_writer.cc.port 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/microdump_writer/microdump_writer.cc 2021-11-09 12:20:24.529281407 +0900 -@@ -338,7 +338,7 @@ class MicrodumpWriter { - # error "This mips ABI is currently not supported (n32)" - #endif - #else --#error "This code has not been ported to your platform yet" -+ const char kArch[] = "unknown"; - #endif - - LogAppend("O "); -@@ -409,11 +409,15 @@ class MicrodumpWriter { - void DumpCPUState() { - RawContextCPU cpu; - my_memset(&cpu, 0, sizeof(RawContextCPU)); -+#if !defined(__i386__) && !defined(__x86_64) && !defined(__aarch64__) -+ UContextReader::FillCPUContext(&cpu, ucontext_); -+#else - #if !defined(__ARM_EABI__) && !defined(__mips__) - UContextReader::FillCPUContext(&cpu, ucontext_, float_state_); - #else - UContextReader::FillCPUContext(&cpu, ucontext_); - #endif -+#endif - LogAppend("C "); - LogAppend(&cpu, sizeof(cpu)); - LogCommitLine(); ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_dumper.h.port 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_dumper.h 2021-11-09 11:04:57.384470040 +0900 -@@ -63,6 +63,7 @@ namespace google_breakpad { - (defined(__mips__) && _MIPS_SIM == _ABIO32) - typedef Elf32_auxv_t elf_aux_entry; - #elif defined(__x86_64) || defined(__aarch64__) || \ -+ defined(__powerpc64__) || defined(__s390x__) || \ - (defined(__mips__) && _MIPS_SIM != _ABIO32) - typedef Elf64_auxv_t elf_aux_entry; - #endif ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_ptrace_dumper.cc.port 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_ptrace_dumper.cc 2021-11-09 11:04:57.384470040 +0900 -@@ -198,6 +198,7 @@ bool LinuxPtraceDumper::ReadRegisters(Th - // these members are set to -1. Returns true iff all three members are - // available. - bool LinuxPtraceDumper::GetThreadInfoByIndex(size_t index, ThreadInfo* info) { -+#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) - if (index >= threads_.size()) - return false; - -@@ -304,6 +305,9 @@ bool LinuxPtraceDumper::GetThreadInfoByI - info->stack_pointer = reinterpret_cast(stack_pointer); - - return true; -+#else -+ return false; -+#endif - } - - bool LinuxPtraceDumper::IsPostMortem() const { ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/minidump_writer.cc.port 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/minidump_writer.cc 2021-11-09 12:20:06.954231835 +0900 -@@ -468,11 +468,15 @@ class MinidumpWriter { - if (!cpu.Allocate()) - return false; - my_memset(cpu.get(), 0, sizeof(RawContextCPU)); -+#if !defined(__i386__) && !defined(__x86_64) && !defined(__aarch64__) -+ UContextReader::FillCPUContext(cpu.get(), ucontext_); -+#else - #if !defined(__ARM_EABI__) && !defined(__mips__) - UContextReader::FillCPUContext(cpu.get(), ucontext_, float_state_); - #else - UContextReader::FillCPUContext(cpu.get(), ucontext_); - #endif -+#endif - thread.thread_context = cpu.location(); - crashing_thread_context_ = cpu.location(); - } else { -@@ -1206,7 +1210,7 @@ class MinidumpWriter { - return true; - } - #else --# error "Unsupported CPU" -+ bool WriteCPUInformation(MDRawSystemInfo* sys_info) { return false; } - #endif - - bool WriteFile(MDLocationDescriptor* result, const char* filename) { diff --git a/ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch b/ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch deleted file mode 100644 index 10bcf83..0000000 --- a/ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/raw_context_cpu.h.unwind 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/raw_context_cpu.h 2021-11-08 20:15:01.057998601 +0900 -@@ -45,7 +45,7 @@ typedef MDRawContextARM64_Old RawContext - #elif defined(__mips__) - typedef MDRawContextMIPS RawContextCPU; - #else --#error "This code has not been ported to your platform yet." -+typedef unsigned long RawContextCPU; - #endif - - } // namespace google_breakpad diff --git a/ugene-40.1-qbswap-bigendian-workaround.patch b/ugene-40.1-qbswap-bigendian-workaround.patch deleted file mode 100644 index baa1c50..0000000 --- a/ugene-40.1-qbswap-bigendian-workaround.patch +++ /dev/null @@ -1,45 +0,0 @@ ---- ugene-40.1/src/corelibs/U2Core/src/io/ZlibAdapter.cpp.char_bigen 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/corelibs/U2Core/src/io/ZlibAdapter.cpp 2021-11-09 16:41:07.802412220 +0900 -@@ -29,6 +29,12 @@ - - #include "LocalFileAdapter.h" - -+QT_BEGIN_NAMESPACE -+#if defined(Q_BYTE_ORDER) && Q_BYTE_ORDER == Q_BIG_ENDIAN -+template <> inline Q_DECL_CONSTEXPR char qbswap(char source) { return source; } -+#endif -+QT_END_NAMESPACE -+ - namespace U2 { - - class GzipUtil { ---- ugene-40.1/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp.char_bigen 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp 2021-11-09 14:55:12.703372481 +0900 -@@ -31,6 +31,12 @@ - #include - #include - -+QT_BEGIN_NAMESPACE -+#if defined(Q_BYTE_ORDER) && Q_BYTE_ORDER == Q_BIG_ENDIAN -+template <> inline Q_DECL_CONSTEXPR char qbswap(char source) { return source; } -+#endif -+QT_END_NAMESPACE -+ - namespace U2 { - - const QString DNAChromatogramSerializer::ID = "chroma_1.14"; ---- ugene-40.1/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp.char_bigen 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp 2021-11-09 16:40:41.872455587 +0900 -@@ -27,6 +27,12 @@ - #include - #include - -+QT_BEGIN_NAMESPACE -+#if defined(Q_BYTE_ORDER) && Q_BYTE_ORDER == Q_BIG_ENDIAN -+template <> inline Q_DECL_CONSTEXPR char qbswap(char source) { return source; } -+#endif -+QT_END_NAMESPACE -+ - extern "C" { - #include "samtools_core/htslib/cram/cram_samtools.h" - } diff --git a/ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch b/ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch deleted file mode 100644 index 5497653..0000000 --- a/ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch +++ /dev/null @@ -1,105 +0,0 @@ ---- ugene-40.1/src/libs_3rdparty/breakpad/src/common/memory_allocator.h.sys_mmap 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/common/memory_allocator.h 2021-11-08 22:21:13.962461668 +0900 -@@ -42,11 +42,14 @@ - #include - #endif - --#ifdef __APPLE__ -+#if defined(__APPLE__) || defined(__linux__) - #define sys_mmap mmap - #define sys_munmap munmap -+#if !defined(__linux__) - #define MAP_ANONYMOUS MAP_ANON --#else -+#endif -+#endif -+#if ! defined(__APPLE__) - #include "third_party/lss/linux_syscall_support.h" - #endif - ---- ugene-42.x/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h.sys_mmap 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-42.x/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h 2021-11-09 00:46:06.363362301 +0900 -@@ -86,10 +86,7 @@ - * on Linux. - * Porting to other related platforms should not be difficult. - */ --#if (defined(__i386__) || defined(__x86_64__) || defined(__ARM_ARCH_3__) || \ -- defined(__mips__) || defined(__PPC__) || defined(__ARM_EABI__) || \ -- defined(__aarch64__) || defined(__s390__) || defined(__e2k__)) \ -- && (defined(__linux) || defined(__ANDROID__)) -+#if defined(__linux) || defined(__ANDROID__) - - #ifndef SYS_CPLUSPLUS - #ifdef __cplusplus -@@ -108,15 +105,21 @@ extern "C" { - #include - #include - #include --#include - #include - #include - #include -+#include - #include -+#include - #include - #include -+#include - #include - -+#ifndef __linux__ -+#ifndef __linux__ -+#ifndef __linux__ -+ - #ifdef __mips__ - /* Include definitions of the ABI currently in use. */ - #ifdef __ANDROID__ -@@ -4859,6 +4862,48 @@ struct kernel_statfs { - #pragma pop_macro("pwrite64") - #pragma pop_macro("getdents64") - -+#endif -+#endif -+#endif -+#ifdef __linux__ -+#define sys_open open -+#define sys_close close -+#define sys_lseek lseek -+#define sys_write ::write -+#define sys_read read -+#define sys_pipe pipe -+#define sys_tgkill tgkill -+#define sys_gettid gettid -+#define sys_prctl prctl -+#define sys_clone clone -+#define sys_waitpid waitpid -+#define sys_sigaltstack sigaltstack -+#define sys_getpid getpid -+#define sys_ptrace(a,b,c,d) ptrace((enum __ptrace_request)a,b,c,d) -+#define sys_stat stat -+#define sys_sendmsg sendmsg -+#define sys_getdents getdents64 -+#define sys_readlink readlink -+#define sys_fstat fstat -+#define sys_fstat64 fstat64 -+#define sys_mmap mmap -+#define sys_munmap munmap -+#define kernel_iovec iovec -+#define kernel_msghdr msghdr -+#define kernel_stat stat -+#define kernel_stat64 stat64 -+#define kernel_dirent linux_dirent64 -+ -+struct linux_dirent64 { -+ ino64_t d_ino; /* 64-bit inode number */ -+ off64_t d_off; /* 64-bit offset to next structure */ -+ unsigned short d_reclen; /* Size of this dirent */ -+ unsigned char d_type; /* File type */ -+ char d_name[]; /* Filename (null-terminated) */ -+}; -+ -+#endif -+ - #if defined(__cplusplus) && !defined(SYS_CPLUSPLUS) - } - #endif diff --git a/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch deleted file mode 100644 index 7ba07ff..0000000 --- a/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2 2021-11-11 15:42:19.591500062 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp 2021-11-11 15:42:26.385496818 +0900 -@@ -23,6 +23,7 @@ - * MA 02110-1301, USA. - */ - -+#if defined(__SSE2__) - #include - #include - -@@ -1214,3 +1215,4 @@ - } - - } // namespace U2 -+#endif ---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-11-11 15:42:19.592500061 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-11 15:42:26.385496818 +0900 -@@ -21,6 +21,7 @@ - - #pragma once - -+#if defined(__SSE2__) - #include - - #include "SmithWatermanAlgorithm.h" -@@ -52,3 +53,4 @@ - }; - - } // namespace U2 -+#endif diff --git a/ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch b/ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch deleted file mode 100644 index 974f41c..0000000 --- a/ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp.sse 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp 2021-11-09 01:34:30.052988784 +0900 -@@ -81,7 +81,9 @@ - QWidget* w = createController->getWidget(); - auto l = qobject_cast(layout()); - l->insertWidget(1, w); -+#if defined (__SSE2__) - algoCombo->addItem(tr("SSE optimized"), HMMSearchAlgo_SSEOptimized); -+#endif - algoCombo->addItem(tr("Conservative"), HMMSearchAlgo_Conservative); - - okButton = buttonBox->button(QDialogButtonBox::Ok); ---- ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.sse 2022-03-09 15:37:14.586340751 +0900 -+++ ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp 2022-03-09 15:47:23.559077800 +0900 -@@ -1,4 +1,5 @@ - #include -+#if defined (__SSE2__) - #include - #include - -@@ -488,3 +489,4 @@ QList sseScoring(unsigned char* d - - return results; - } -+#endif ---- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.h.sse 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.h 2021-11-09 01:34:30.052988784 +0900 -@@ -1,6 +1,8 @@ - #ifndef __HMMSEARCH_SSE_H__ - #define __HMMSEARCH_SSE_H__ - -+#if defined(__SSE2__) - QList sseScoring(unsigned char* dsq, int seqlen, plan7_s* hmm, HMMSeqGranulation* gr, U2::TaskStateInfo& ti); -+#endif - - #endif // __HMMSEARCH_SSE_H__ diff --git a/ugene-49.1-narrowing-for-unsigned-char.patch b/ugene-49.1-narrowing-for-unsigned-char.patch deleted file mode 100644 index a37bc35..0000000 --- a/ugene-49.1-narrowing-for-unsigned-char.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ugene-49.1/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h.orig 2023-11-26 02:17:11.000000000 +0900 -+++ ugene-49.1/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h 2024-01-22 16:42:22.536722206 +0900 -@@ -37,7 +37,7 @@ namespace BALL - { - namespace __private - { -- extern const char BALL_EXPORT neighbour_table_[27][3]; -+ extern const signed char BALL_EXPORT neighbour_table_[27][3]; - } - - template class HashGrid3; ---- ugene-49.1/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp.orig 2023-11-26 02:17:11.000000000 +0900 -+++ ugene-49.1/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp 2024-01-22 16:42:28.199724474 +0900 -@@ -9,7 +9,7 @@ namespace BALL - { - namespace __private - { -- const char neighbour_table_[27][3] = -+ const signed char neighbour_table_[27][3] = - { - { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, - { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/ugene-50.x-aarch64-neon-impl-not-yet.patch b/ugene-50.x-aarch64-neon-impl-not-yet.patch deleted file mode 100644 index d21b04b..0000000 --- a/ugene-50.x-aarch64-neon-impl-not-yet.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -index be907d85b..820d43cf0 100644 ---- a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -+++ b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -@@ -1068,8 +1068,8 @@ unsigned char *(*rans_enc_func(int do_simd, int order)) - if (do_simd) { - if ((rans_cpu & RANS_CPU_ENC_NEON) && have_neon()) - return order & 1 -- ? rans_compress_O1_32x16_neon -- : rans_compress_O0_32x16_neon; -+ ? rans_compress_O1_32x16 -+ : rans_compress_O0_32x16; - else - return order & 1 - ? rans_compress_O1_32x16 -@@ -1091,8 +1091,8 @@ unsigned char *(*rans_dec_func(int do_simd, int order)) - if (do_simd) { - if ((rans_cpu & RANS_CPU_DEC_NEON) && have_neon()) - return order & 1 -- ? rans_uncompress_O1_32x16_neon -- : rans_uncompress_O0_32x16_neon; -+ ? rans_uncompress_O1_32x16 -+ : rans_uncompress_O0_32x16; - else - return order & 1 - ? rans_uncompress_O1_32x16 diff --git a/ugene-52.1.x-RegionSelectorController-overload.patch b/ugene-52.1.x-RegionSelectorController-overload.patch deleted file mode 100644 index ebc5ad2..0000000 --- a/ugene-52.1.x-RegionSelectorController-overload.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp -index f052b9122..d0fdfeb0d 100644 ---- a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp -+++ b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp -@@ -339,7 +339,7 @@ void RegionSelectorController::connectSlots() { - - connect(gui.startLineEdit, &QLineEdit::textEdited, this, &RegionSelectorController::sl_onRegionChanged); - connect(gui.endLineEdit, &QLineEdit::textEdited, this, &RegionSelectorController::sl_onRegionChanged); -- connect(gui.presetsComboBox, &QComboBox::activated, this, &RegionSelectorController::sl_onPresetChanged); -+ connect(gui.presetsComboBox, QOverload::of(&QComboBox::activated), this, &RegionSelectorController::sl_onPresetChanged); - - if (settings.selection != nullptr) { - connect(settings.selection, SIGNAL(si_onSelectionChanged(GSelection*)), SLOT(sl_onSelectionChanged(GSelection*))); diff --git a/ugene-52.x-s390x-platform-macro.patch b/ugene-52.x-s390x-platform-macro.patch deleted file mode 100644 index 72ca2de..0000000 --- a/ugene-52.x-s390x-platform-macro.patch +++ /dev/null @@ -1,27 +0,0 @@ -diff --git a/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h b/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h -index a4695a261..ec063f1ee 100644 ---- a/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h -+++ b/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h -@@ -407,6 +407,13 @@ - #define WTF_CPU_RISCV32 1 - #endif - -+/* CPU(IBM z system) */ -+#if defined(__s390x__) || defined(__s390__) -+#define WTF_CPU_S390X 1 -+#define WTF_CPU_BIG_ENDIAN 1 -+#endif -+ -+ - /* ==== OS() - underlying operating system; only to be used for mandated low-level services like - virtual memory, not to choose a GUI toolkit ==== */ - -@@ -960,6 +967,8 @@ - #if !defined(WTF_USE_JSVALUE64) && !defined(WTF_USE_JSVALUE32) && !defined(WTF_USE_JSVALUE32_64) - #if (CPU(X86_64) && !CPU(X32) && (OS(UNIX) || OS(WINDOWS) || OS(SOLARIS) || OS(HPUX))) || (CPU(IA64) && !CPU(IA64_32)) || CPU(ALPHA) || CPU(AIX64) || CPU(SPARC64) || CPU(MIPS64) || CPU(AARCH64) || CPU(RISCV64) - #define WTF_USE_JSVALUE64 1 -+#elif (CPU(S390X)) -+#define WTF_USE_JSVALUE64 1 - #elif CPU(ARM) || CPU(PPC64) || CPU(RISCV32) - #define WTF_USE_JSVALUE32 1 - #elif OS(WINDOWS) && COMPILER(MINGW) diff --git a/ugene.spec b/ugene.spec index 7390734..6cd56f4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,118 +1,40 @@ -%global use_release_branch 0 - -%if 0%{?use_release_branch} < 1 -# master -%global gitdate 20251211 -%global gitcommit b50ca792f254939978f0ffd3126e3d9ab770a10a -# New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 7e674061492924b3dfbc884c4c9503ecab9887b2 -%else -# currently 41.0 branch -%global gitdate 20250313 -%global gitcommit c0dffab5a15e01c026f80cf0a7033b08112a355f -# New git commit with non-free part using "git filter-branch" -%global gitcommit_free b0631c54cc0603a88793ed5d6ee02dec196b823e -%endif - - -%global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) -%global git_version %{gitdate}git%{shortcommit} - -%global tarballdate 20251211 -%global tarballtime 2210 - -%global use_release 1 -%global use_gitbare 0 - -%if 0%{?use_gitbare} < 1 -# force -%global use_release 1 -%endif - -%if 0%{?use_release} >= 1 -%global GIT true -%else -%global GIT git -%endif - -%global mainver 53.0 -%undefine prever - -%if 0%{?use_release} >= 1 -%global fedoraver %{mainver}%{?prever:~%{prerpmver}} -%endif -%if 0%{?use_gitbare} >= 1 -%global fedoraver %{mainver}%{?git_version:^%{git_version}} -%endif - - -Name: ugene -Summary: Integrated bioinformatics toolkit - -Version: %{fedoraver} -Release: 1%{?dist} - +Name: ugene +Summary: Integrated bioinformatics toolkit +Version: 33.0 +Release: 11%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 #files in src/plugins_3rdparty/script_debuger/src/qtscriptdebug/ which are GPLv2 -# Automatically converted from old format: GPLv2+ and GPLv2 - review is highly recommended. -License: GPL-2.0-or-later AND GPL-2.0-only -URL: http://ugene.net -%if 0%{?use_release} >= 1 -#Source0: https://github.com/ugeneunipro/ugene/archive/%{mainver}.tar.gz/#/%{name}-%{mainver}.tar.gz -# Removing non-free part -Source0: %{name}-free-%{mainver}.tar.gz -# Source0 is created by # env VERSION=%%{mainver} source ./%{SOURCE1} -%endif -%if 0%{?use_gitbare} >= 1 -Source0: %{name}-free-%{tarballdate}T%{tarballtime}.tar.gz -%endif -Source1: create-ugene-free-tarball.sh -Source2: create-%{name}-git-bare-tarball.sh -# This is not installed -Source10: ugene.wrapper -Patch1: ugene-49.1-narrowing-for-unsigned-char.patch -Patch3: ugene-52.1.x-RegionSelectorController-overload.patch -# Currently distro-specific -Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch -Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch -Patch104: ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch -Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch -Patch106: ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch -Patch107: ugene-40.1-qbswap-bigendian-workaround.patch -Patch109: ugene-50.x-aarch64-neon-impl-not-yet.patch -Patch110: ugene-52.x-s390x-platform-macro.patch +License: GPLv2+ and GPLv2 +URL: http://ugene.net +Source0: http://ugene.net/downloads/%{name}-%{version}.tar.gz +#Patch0: ugene-1.31.0.patch -BuildRequires: make -BuildRequires: gcc-c++ -BuildRequires: desktop-file-utils +BuildRequires: desktop-file-utils +BuildRequires: mesa-libGLU-devel +BuildRequires: qt5-qtbase-devel qt5-qtbase-private-devel +BuildRequires: qt5-qtbase-mysql +BuildRequires: qt5-qtmultimedia-devel +BuildRequires: qt5-qtscript-devel +BuildRequires: qt5-qtsensors-devel +BuildRequires: qt5-qtsvg-devel +BuildRequires: qt5-qttools-devel +BuildRequires: qt5-qtwebchannel-devel +BuildRequires: qt5-qtwebkit-devel +BuildRequires: qt5-qtxmlpatterns-devel +BuildRequires: qt5-qtwebengine-devel +BuildRequires: qt5-qtwebsockets-devel +BuildRequires: qt5-qtwebchannel-devel +BuildRequires: zlib-devel -%if 0%{?use_gitbare} >= 1 -BuildRequires: %{_bindir}/git -%endif +BuildConflicts: qt-devel -BuildRequires: cmake(Qt5Core) -BuildRequires: cmake(Qt5Gui) -BuildRequires: cmake(Qt5LinguistTools) -BuildRequires: cmake(Qt5Network) -BuildRequires: cmake(Qt5NetworkAuth) -BuildRequires: cmake(Qt5PrintSupport) -BuildRequires: cmake(Qt5Script) -BuildRequires: cmake(Qt5ScriptTools) -BuildRequires: cmake(Qt5Sql) -BuildRequires: cmake(Qt5Svg) -BuildRequires: cmake(Qt5Test) -BuildRequires: cmake(Qt5WebSockets) -BuildRequires: cmake(Qt5Widgets) -BuildRequires: cmake(Qt5Xml) +#We need strict versions of qt for correct work of src/libs_3rdparty/qtbindings_* +%{?_qt5:Requires: %{_qt5}%{?_isa} = %{_qt5_version}} -BuildRequires: pkgconfig(gl) -BuildRequires: pkgconfig(glu) -BuildRequires: pkgconfig(sqlite3) -BuildRequires: pkgconfig(xtst) -BuildRequires: pkgconfig(zlib) - -Provides: bundled(samtools) = 0.1.18 +Provides: bundled(sqlite) +Provides: bundled(samtools) +ExclusiveArch: %{ix86} x86_64 %description Unipro UGENE is a cross-platform visual environment for DNA and protein @@ -122,306 +44,45 @@ complex analysis of the genomic data. One of the main features of UGENE is a designer for custom bioinformatics workflows. %prep -%if 0%{?use_release} >= 1 %setup -q -%endif - -%if 0%{?use_gitbare} >= 1 -%setup -q -c -n %{name}-%{mainver}%{?git_version:-%{git_version}} -T -a 0 -git clone ./%{name}.git/ -cd %{name} -cp -a [A-Z]* .. - -git checkout -b %{mainver}-fedora %{gitcommit_free} -git config user.name "%{name} Fedora maintainer" -git config user.email "%{name}-maintainers@fedoraproject.org" -%endif -%patch -P1 -p1 -b .narrow - %GIT commit -m "Fix narrowing on arch where default char is unsigned" -a -%patch -P3 -p1 -b .include - %GIT commit -m "RegionSelectorController: specify overloaded function" -a -%patch -P102 -p1 -b .sys_mmap -Z - %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a -%patch -P103 -p1 -b .unwind -Z - %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not supporting unwind" -a -%patch -P104 -p1 -b .sse -Z - %GIT commit -m "plugins_3rdparty/hmm2: support architecture not supporting SSE2" -a -%patch -P105 -p1 -b .port -Z - %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not ported by the upstream" -a -%patch -P106 -p1 -b .sse_2 -Z - %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a -%patch -P107 -p1 -b .char_bigen -Z - %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a -%if 1 -%patch -P109 -p1 -b .neon -Z - %GIT commit -m "neon impl not yet available" -a -%endif -%patch -P110 -p1 -b .s390x_macro -Z - %GIT commit -m "define s390x related macro" -a - -# Kill system-provided 3rd-party libs -sed -i CMakeLists.txt \ - -e '\@add_subdirectory.*libs_3rdparty/sqlite3@d' \ - -e '\@add_subdirectory.*libs_3rdparty/zlib@d' \ - %{nil} -rm -rf src/libs_3rdparty/{sqlite3,zlib} -rm -rf src/include/3rdparty/{sqlite3,zlib} - %GIT rm -r -f src/libs_3rdparty/{sqlite3,zlib} || true - %GIT rm -r -f src/include/3rdparty/{sqlite3,zlib} || true - %GIT commit -m "kill system-provided 3rd-party libs" -a -grep -rl --exclude-dir=.git 3rdparty/zlib/zlib.h . | \ - xargs sed -i 's|3rdparty/zlib/zlib.h|zlib.h|' -grep -rl --exclude-dir=.git 3rdparty/sqlite3/sqlite3.h . | \ - xargs sed -i 's|3rdparty/sqlite3/sqlite3.h|sqlite3.h|' -find . -name CMakeLists.txt | \ - xargs sed -i \ - -e 's|zlib|z|' \ - -e 's|ugenedb|sqlite3|' \ - %{nil} - %GIT commit -m "fix system provided header path" -a - -sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' - %GIT commit -m "remove nonfree code" -a - -# Remove -Werror -sed -i CMakeLists.txt -e '\@" -Werror=@d' - %GIT commit -m "remove -Werror" -a - -# Enable some deprecated API -sed -i CMakeLists.txt -e '\@QT_DISABLE_DEPRECATED_BEFORE=@s|0x050F00|0x050000|' - %GIT commit -m "enable some deprecated API" -a +#%patch0 -p1 -b .qt510 %build -%if 0%{?use_gitbare} >= 1 -cd %{name} +# workaround FTBFS (https://bugzilla.redhat.com/show_bug.cgi?id=1736931) +export CXXFLAGS="-fpermissive %{optflags}" + +%{qmake_qt5} -r \ + INSTALL_BINDIR=%{_bindir} \ + INSTALL_LIBDIR=%{_libdir} \ + INSTALL_DATADIR=%{_datadir} \ + INSTALL_MANDIR=%{_mandir} \ +%if 0%{?_ugene_with_non_free} + UGENE_WITHOUT_NON_FREE=0 \ +%else + UGENE_WITHOUT_NON_FREE=1 \ %endif + UGENE_EXCLUDE_LIST_ENABLED=1 -export QT_DIR=%{_libdir}/qt5 -export LD_LIBRARY_PATH=$(pwd)/%{_vpath_builddir}/dist -%cmake \ - -DCMAKE_SKIP_RPATH=TRUE \ - %{nil} -%cmake_build +make %{?_smp_mflags} %install -%if 0%{?use_gitbare} >= 1 -cd %{name} -%endif - -%cmake_install - -# Install all files manually... -# 0. Documents -cp -a \ - LICENSE.3rd_party.txt \ - LICENSE.txt \ - .. - -pushd %_vpath_builddir - -# 1-0 bindir -mkdir -p %{buildroot}%{_bindir} -install -cpm 0755 %{SOURCE10} %{buildroot}%{_bindir}/%{name} - -# 1-1 libraries -mkdir -p %{buildroot}%{_libdir}/%{name} -cp -a dist/* %{buildroot}%{_libdir}/%{name}/ -rm -f %{buildroot}%{_libdir}/%{name}/*.a - -# Back to the top directory -popd - -# 1-2 data files -mkdir -p %{buildroot}%{_datadir}/%{name}/ -cp -a data %{buildroot}%{_datadir}/%{name} -ln -sf ../../../%{_datadir}/%{name}/data %{buildroot}%{_libdir}/%{name}/data - -pushd ./etc/shared -# 1-11 hicolor -mkdir -p %{buildroot}%{_datadir}/icons/hicolor/32x32/mimetypes/ -cp -p application-x-ugene-ext.png %{buildroot}/%{_datadir}/icons/hicolor/32x32/mimetypes/ - -# 1-12 mime -mkdir -p %{buildroot}%{_datadir}/mime/packages -cp -p application-x-ugene.xml %{buildroot}/%{_datadir}/mime/packages - -# 1-13 man file -mkdir -p %{buildroot}%{_mandir}/man1 -cp -p %{name}.1* %{buildroot}/%{_mandir}/man1 - -# 1-14 desktop files -mkdir -p %{buildroot}%{_datadir}/applications/ -cp -p %{name}.desktop %{buildroot}/%{_datadir}/applications/ - -# 1-15 icons -mkdir -p %{buildroot}%{_datadir}/pixmaps -cp -p %{name}.{png,xpm} %{buildroot}%{_datadir}/pixmaps -popd - -%check -desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop +make install INSTALL_ROOT=%{buildroot} +desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %files -%license LICENSE.txt -%license LICENSE.3rd_party.txt - -%{_bindir}/%{name} - -%dir %{_libdir}/%{name}/ -%{_libdir}/%{name}/lib*.so - -%dir %{_libdir}/%{name}/plugins/ -%{_libdir}/%{name}/plugins/*.license -%{_libdir}/%{name}/plugins/*.plugin -%{_libdir}/%{name}/plugins/lib*.so - -%{_libdir}/%{name}/transl_*.qm - -%{_libdir}/%{name}/%{name} -%{_libdir}/%{name}/%{name}cl -%{_libdir}/%{name}/%{name}m -%{_libdir}/%{name}/%{name}ui -%{_libdir}/%{name}/plugins_checker - -%dir %{_datadir}/%{name}/ -%{_datadir}/%{name}/data/ -%{_libdir}/%{name}/data - +%{!?_licensedir:%global license %%doc} +%license LICENSE.txt LICENSE.3rd_party.txt +%{_bindir}/* +%{_libdir}/%{name}/ %{_datadir}/applications/%{name}.desktop %{_datadir}/pixmaps/ugene.* -%{_datadir}/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png - +%{_datadir}/icons/hicolor/*/*/* %{_datadir}/mime/packages/*.xml -%{_mandir}/man1/%{name}.1* +%{_datadir}/%{name}/ +%{_mandir}/man1/* %changelog -* Sun Nov 30 2025 Mamoru TASAKA - 53.0-1 -- 53.0 - -* Fri Jul 25 2025 Fedora Release Engineering - 52.1-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild - -* Fri Jul 18 2025 Mamoru TASAKA - 52.1-2 -- Fix data files symlink - -* Thu May 08 2025 Mamoru TASAKA - 52.1-1 -- 52.1 - -* Fri Jan 24 2025 Mamoru TASAKA - 52.0-1 -- 52.0 - -* Fri Jan 17 2025 Mamoru TASAKA - 51.0-2 -- Support C23 strict function prototype - -* Thu Sep 26 2024 Mamoru TASAKA - 51.0-1 -- 51.0 - -* Wed Aug 7 2024 Miroslav Suchý - 50.0-3 -- convert license to SPDX - -* Sat Jul 20 2024 Fedora Release Engineering - 50.0-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild - -* Sun Apr 14 2024 Mamoru TASAKA - 50.0-1 -- 50.0 - -* Sat Jan 27 2024 Fedora Release Engineering - 49.1-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild - -* Mon Jan 22 2024 Mamoru TASAKA - 49.1-2 -- Fix -Wnarrowing on non x86(-64) arch detected by gcc14 - -* Tue Nov 28 2023 Mamoru TASAKA - 49.1-1 -- 49.1 - -* Thu Nov 9 2023 Mamoru TASAKA - 49.0-1 -- 49.0 - -* Tue Sep 5 2023 Mamoru TASAKA - 48.1-1 -- 48.1 - -* Thu Aug 10 2023 Mamoru TASAKA - 48.0-1 -- 48.0 - -* Sat Jul 22 2023 Mamoru TASAKA - 47.0-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild - -* Tue May 23 2023 Mamoru TASAKA - 47.0-1 -- 47.0 - -* Fri Feb 24 2023 Mamoru TASAKA - 46.0-1 -- 46.0 - -* Sat Jan 21 2023 Fedora Release Engineering - 45.1-2.1 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild - -* Wed Jan 18 2023 Mamoru TASAKA - 45.1-2 -- Header file inclusion fix for gcc13 - -* Sun Jan 1 2023 Mamoru TASAKA - 45.1-1 -- A Happy New Year 45.1 release - -* Tue Dec 20 2022 Florian Weimer - 45.0-2 -- Apply upstream patch to fix C99 compatibility issue - -* Sun Nov 20 2022 Mamoru TASAKA - 45.0-1 -- 45.0 - -* Sun Aug 21 2022 Mamoru TASAKA - 44.0-1 -- 44.0 - -* Sat Jul 23 2022 Fedora Release Engineering - 43.0-2.1 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild - -* Mon Jun 6 2022 Mamoru TASAKA - 43.0-1 -- 43.0 - -* Wed Mar 9 2022 Mamoru TASAKA - 42.0-1 -- 42.0 - -* Sat Jan 22 2022 Fedora Release Engineering - 41.0-1.1 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild - -* Sat Dec 4 2021 Mamoru TASAKA - 41.0-1 -- 41.0 - -* Wed Nov 17 2021 Mamoru TASAKA - 40.1-2 -- Surely remove nonfree code from tarball - -* Tue Nov 9 2021 Mamoru TASAKA - 40.1-1 -- 40.1 - -* Fri Jul 23 2021 Fedora Release Engineering - 34.0-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild - -* Wed Jan 27 2021 Fedora Release Engineering - 34.0-6 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild - -* Mon Nov 23 07:55:33 CET 2020 Jan Grulich - 34.0-5 -- rebuild (qt5) - -* Sun Oct 18 2020 Jeff Law - 34.0-4 -- Fix missing #includes for gcc-11 - -* Fri Sep 11 2020 Jan Grulich - 34.0-3 -- rebuild (qt5) - -* Wed Jul 29 2020 Fedora Release Engineering - 34.0-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Wed Apr 15 2020 Rex Dieter - 34.0-1 -- ugene-34.0 -- update Source0 URL -- no longer uses qt5 private api (yay) -- use %%check - -* Mon Apr 06 2020 Rex Dieter - 33.0-13 -- rebuild (qt5) - -* Fri Jan 31 2020 Fedora Release Engineering - 33.0-12 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - * Mon Dec 09 2019 Jan Grulich - 33.0-11 - rebuild (qt5) @@ -450,7 +111,7 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop * Thu Oct 25 2018 Yuliya Algaer - 1.31.1-1 - New upstream release -* Fri Aug 24 2018 Yuliya Algaer - 1.31.0-6 +* Thu Aug 24 2018 Yuliya Algaer - 1.31.0-6 - New upstream release * Sat Jul 14 2018 Fedora Release Engineering - 1.30.0-25 diff --git a/ugene.wrapper b/ugene.wrapper deleted file mode 100644 index 00f8788..0000000 --- a/ugene.wrapper +++ /dev/null @@ -1,4 +0,0 @@ -#!/usr/bin/bash -LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/ugene -export LD_LIBRARY_PATH -/usr/lib64/ugene/ugene "$@"