From e91c30bf4c54633dbb7af87af86877180e721049 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Tue, 13 Aug 2019 09:49:58 -0700 Subject: [PATCH 1/6] change size_t to uint64_t --- Map/index.cc | 2 +- Map/map.cc | 2 +- Map/overlap.cc | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Map/index.cc b/Map/index.cc index cb5beb889..c8ba9a399 100644 --- a/Map/index.cc +++ b/Map/index.cc @@ -146,7 +146,7 @@ static void buildFMIndex(FMIndex& fm, const string& path) std::vector s; readFile(path.c_str(), s); - size_t MAX_SIZE = numeric_limits::max(); + uint64_t MAX_SIZE = numeric_limits::max(); if (s.size() > MAX_SIZE) { std::cerr << PROGRAM << ": `" << path << "', " << toSI(s.size()) diff --git a/Map/map.cc b/Map/map.cc index af9166e31..15e2b6f67 100644 --- a/Map/map.cc +++ b/Map/map.cc @@ -505,7 +505,7 @@ static void buildFMIndex(FMIndex& fm, const char* path) std::vector s; readFile(path, s); - size_t MAX_SIZE = numeric_limits::max(); + uint64_t MAX_SIZE = numeric_limits::max(); if (s.size() > MAX_SIZE) { std::cerr << PROGRAM << ": `" << path << "', " << toSI(s.size()) diff --git a/Map/overlap.cc b/Map/overlap.cc index 1c0cd9f03..283391f0a 100644 --- a/Map/overlap.cc +++ b/Map/overlap.cc @@ -293,7 +293,7 @@ static void buildFMIndex(FMIndex& fm, const char* path) std::vector s; readFile(path, s); - size_t MAX_SIZE = numeric_limits::max(); + uint64_t MAX_SIZE = numeric_limits::max(); if (s.size() > MAX_SIZE) { std::cerr << PROGRAM << ": `" << path << "', " << toSI(s.size()) From 609c0de8de50970dfc2990c108f9c79d18020c07 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Tue, 13 Aug 2019 11:56:32 -0700 Subject: [PATCH 2/6] Azure: add DISTCHECK_CONFIGURE_FLAGS --- azure-pipelines.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 3463a3fb4..8c9452321 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -16,6 +16,7 @@ jobs: displayName: Install 32-bit compilation support - script: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=\"gcc-8 -m32\" CXX=\"g++-8 -m32\" --build=i386-linux-gnu" ./configure CC=gcc-8 CXX=g++-8 --build=i686-linux-gnu "CFLAGS=-m32" "CXXFLAGS=-m32" "LDFLAGS=-m32" --with-mpi=/usr/lib/openmpi make -j12 distcheck displayName: Compiling ABySS with gcc-8 @@ -35,6 +36,7 @@ jobs: displayName: Install clang-6.0 - script: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0" ./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi make -j12 distcheck displayName: Compiling ABySS with clang 6.0 @@ -54,6 +56,7 @@ jobs: displayName: Install gcc-5 - script: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5" ./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi make -j12 distcheck displayName: Compiling ABySS with gcc-5 @@ -73,6 +76,7 @@ jobs: displayName: Install gcc-6 - script: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6" ./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi make -j12 distcheck displayName: Compiling ABySS with gcc-6 @@ -92,6 +96,7 @@ jobs: displayName: Install gcc-7 - script: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7" ./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi make -j12 distcheck displayName: Compiling ABySS with gcc-7 @@ -111,6 +116,7 @@ jobs: displayName: Install gcc-8 - script: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8" ./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi make -j12 distcheck displayName: Compiling ABySS with gcc-8 @@ -152,6 +158,7 @@ jobs: displayName: Install gcc - script: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8" ./configure CC=gcc-8 CXX=g++-8 --with-boost=/usr/local/Cellar/boost/1.70.0/include/ --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2/ CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include/ make -j12 distcheck displayName: Compiling ABySS with gcc 8 From 853c10a1100bda839b319f6d0c8c78265ae54041 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Tue, 13 Aug 2019 11:58:19 -0700 Subject: [PATCH 3/6] Circle: add DISTCHECK_CONFIGURE_FLAGS --- .circleci/config.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 8d8c88368..b73a6865e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -21,6 +21,7 @@ jobs: - checkout - run: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0" ./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi - run: make -j12 distcheck @@ -34,6 +35,7 @@ jobs: - checkout - run: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5" ./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi - run: make -j12 distcheck @@ -47,6 +49,7 @@ jobs: - checkout - run: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6" ./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi - run: make -j12 distcheck @@ -60,6 +63,7 @@ jobs: - checkout - run: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7" ./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi - run: make -j12 distcheck @@ -73,6 +77,7 @@ jobs: - checkout - run: | ./autogen.sh + export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8" ./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi - run: make -j12 distcheck From 03ea55b038fca324211aeefd2391081d3dac8ee5 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Wed, 14 Aug 2019 08:47:54 -0700 Subject: [PATCH 4/6] Azure: revert CI removal --- azure-pipelines.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 8c9452321..396f26534 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -146,7 +146,7 @@ jobs: - script: make clang-format displayName: Run clang-format -- job: macOS_gcc8 +- job: macOS_default_gcc pool: vmImage: macOS-10.14 steps: @@ -154,11 +154,8 @@ jobs: brew update brew install automake boost@1.70 openmpi google-sparsehash make pandoc ghc displayName: Install common - - script: brew install gcc@8 - displayName: Install gcc - script: | ./autogen.sh - export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8" - ./configure CC=gcc-8 CXX=g++-8 --with-boost=/usr/local/Cellar/boost/1.70.0/include/ --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2/ CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include/ + ./configure --with-boost=/usr/local/Cellar/boost/1.70.0/include/ --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2/ CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include/ make -j12 distcheck - displayName: Compiling ABySS with gcc 8 + displayName: Compiling ABySS with default gcc From c5132f417a7e4e2eb23f0e7472fc3e3a85442a54 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 16 Aug 2019 08:33:38 -0700 Subject: [PATCH 5/6] change 2.2.1 to 2.2.2 --- ChangeLog | 5 +++++ bin/abyss-pe | 2 +- configure.ac | 2 +- doc/ABYSS.1 | 2 +- doc/abyss-pe.1 | 2 +- doc/abyss-tofastq.1 | 2 +- 6 files changed, 10 insertions(+), 5 deletions(-) diff --git a/ChangeLog b/ChangeLog index 0619064dc..9c8c44779 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,8 @@ +2019-08-16 Johnathan Wong + + * Release version 2.2.2 + * Fix abyss-overlap for 32-bit systems + 2019-08-12 Johnathan Wong * Release version 2.2.1 diff --git a/bin/abyss-pe b/bin/abyss-pe index 1d5804af8..4888cd4d4 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -398,7 +398,7 @@ help: @echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.' version: - @echo "abyss-pe (ABySS) 2.2.1" + @echo "abyss-pe (ABySS) 2.2.2" @echo "Written by Shaun Jackman and Anthony Raymond." @echo @echo "Copyright 2012 Canada's Michael Smith Genome Science Centre" diff --git a/configure.ac b/configure.ac index b3c0968e3..0857c3c6f 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 2.2.1, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 2.2.2, abyss-users@bcgsc.ca, abyss, http://www.bcgsc.ca/platform/bioinfo/software/abyss) AC_CONFIG_MACRO_DIR([m4]) diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index 1dce22566..bffb10d92 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.1" "User Commands" +.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.2" "User Commands" .SH NAME ABYSS \- assemble short reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1 index e2b1d32a8..584132c51 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.1" "User Commands" +.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.2" "User Commands" .SH NAME abyss-pe - assemble reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1 index 694ef6baf..bdd9bbd38 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.1" "User Commands" +.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.2" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br From 188efb1246ffaed0d86fb20d02ae50ac2743b1d6 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 16 Aug 2019 08:40:34 -0700 Subject: [PATCH 6/6] samtobreak.hs: change 2.2.1 to 2.2.2 --- Misc/samtobreak.hs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Misc/samtobreak.hs b/Misc/samtobreak.hs index 875b42c7d..ac533e140 100644 --- a/Misc/samtobreak.hs +++ b/Misc/samtobreak.hs @@ -279,7 +279,7 @@ parseArgs = do where help = putStr (usageInfo usage options) >> exitSuccess tryHelp = "Try 'abyss-samtobreak --help' for more information." - version = "abyss-samtobreak (ABySS) 2.2.1\n" + version = "abyss-samtobreak (ABySS) 2.2.2\n" usage = "Usage: samtobreak [OPTION]... [FILE]...\n\ \Calculate contig and scaffold contiguity and correctness metrics.\n"