[med-svn] [Git][med-team/abyss][master] 8 commits: New upstream version 2.2.1
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Aug 13 11:48:00 BST 2019
Michael R. Crusoe pushed to branch master at Debian Med / abyss
Commits:
6e7e1b38 by Michael R. Crusoe at 2019-08-13T10:32:06Z
New upstream version 2.2.1
- - - - -
365f1aa5 by Michael R. Crusoe at 2019-08-13T10:32:09Z
Update upstream source from tag 'upstream/2.2.1'
Update to upstream version '2.2.1'
with Debian dir a857d15c18397b38f3de419462bb42612310801c
- - - - -
2a10680d by Michael R. Crusoe at 2019-08-13T10:37:41Z
2.2.1-1
- - - - -
7ab1c9e0 by Michael R. Crusoe at 2019-08-13T10:38:03Z
debhelper-compat 12
- - - - -
858e1b57 by Michael R. Crusoe at 2019-08-13T10:38:08Z
Standards-Version: 4.4.0
- - - - -
46713be2 by Michael R. Crusoe at 2019-08-13T10:38:13Z
Use secure URI in debian/watch.
Fixes lintian: debian-watch-uses-insecure-uri
See https://lintian.debian.org/tags/debian-watch-uses-insecure-uri.html for more details.
- - - - -
716c8720 by Michael R. Crusoe at 2019-08-13T10:38:13Z
Set upstream metadata fields: Contact.
- - - - -
acb47509 by Michael R. Crusoe at 2019-08-13T10:40:08Z
release 2.2.1-1
- - - - -
30 changed files:
- Bloom/HashAgnosticCascadingBloom.h
- Bloom/RollingBloomDBGVisitor.h
- BloomDBG/RollingBloomDBG.h
- BloomDBG/RollingHash.h
- BloomDBG/RollingHashIterator.h
- ChangeLog
- Misc/samtobreak.hs
- Unittest/BloomDBG/HashAgnosticCascadingBloomTest.cpp
- Unittest/BloomDBG/RollingBloomDBGTest.cpp
- azure-pipelines.yml
- bin/abyss-pe
- configure.ac
- debian/changelog
- − debian/compat
- debian/control
- debian/upstream/metadata
- debian/watch
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1
- + vendor/btl_bloomfilter/.clang-format
- + vendor/btl_bloomfilter/.gitignore
- − vendor/btl_bloomfilter/COPYING
- + vendor/btl_bloomfilter/LICENSE
- vendor/btl_bloomfilter/Tests/AdHoc/BloomFilterTests.cpp
- vendor/btl_bloomfilter/azure-pipelines.yml
- vendor/btl_bloomfilter/configure.ac
- vendor/btl_bloomfilter/swig/test.pl
- vendor/btl_bloomfilter/swig/testBloom_rolling.pl
- vendor/btl_bloomfilter/swig/writeBloom_rolling.pl
Changes:
=====================================
Bloom/HashAgnosticCascadingBloom.h
=====================================
@@ -26,6 +26,7 @@
class HashAgnosticCascadingBloom
{
public:
+ typedef uint64_t hash_t;
/** Default constructor */
HashAgnosticCascadingBloom()
: m_k(0)
@@ -91,7 +92,7 @@ class HashAgnosticCascadingBloom
* Return true if the element with the given hash values
* has count >= levels.
*/
- bool contains(const std::vector<size_t>& hashes) const
+ bool contains(const std::vector<hash_t>& hashes) const
{
assert(m_data.back() != NULL);
return m_data.back()->contains(hashes);
@@ -101,14 +102,14 @@ class HashAgnosticCascadingBloom
* Return true if the element with the given hash values
* has count >= levels.
*/
- bool contains(const size_t hashes[]) const
+ bool contains(const hash_t hashes[]) const
{
assert(m_data.back() != NULL);
return m_data.back()->contains(hashes);
}
/** Add the object with the specified index to this multiset. */
- void insert(const std::vector<size_t>& hashes)
+ void insert(const std::vector<hash_t>& hashes)
{
for (unsigned i = 0; i < m_data.size(); ++i) {
assert(m_data.at(i) != NULL);
@@ -120,7 +121,7 @@ class HashAgnosticCascadingBloom
}
/** Add the object with the specified index to this multiset. */
- void insert(const size_t hashes[])
+ void insert(const hash_t hashes[])
{
for (unsigned i = 0; i < m_data.size(); ++i) {
assert(m_data.at(i) != NULL);
=====================================
Bloom/RollingBloomDBGVisitor.h
=====================================
@@ -29,6 +29,7 @@ class RollingBloomDBGVisitor : public DefaultBFSVisitor<GraphT>
typedef std::vector<std::pair<std::string, BloomFilter*>> BloomProperties;
typedef typename BloomProperties::const_iterator BloomPropertiesIt;
+ typedef uint64_t hash_t;
/** Constructor */
template<typename VertexSetT>
@@ -110,7 +111,7 @@ class RollingBloomDBGVisitor : public DefaultBFSVisitor<GraphT>
m_out << "," << it->first;
}
- size_t hashes[MAX_HASHES];
+ hash_t hashes[MAX_HASHES];
v.rollingHash().getHashes(hashes);
for (BloomPropertiesIt it = m_bloomProperties.begin(); it != m_bloomProperties.end();
=====================================
BloomDBG/RollingBloomDBG.h
=====================================
@@ -205,9 +205,10 @@ struct graph_traits< RollingBloomDBG<BF> > {
/**
* Identifier for accessing a vertex in the graph.
- * The second member of the pair (std::vector<size_t>) is
+ * The second member of the pair (std::vector<hash_t>) is
* a set of hash values associated with the k-mer.
*/
+ typedef uint64_t hash_t;
typedef RollingBloomDBGVertex vertex_descriptor;
typedef boost::directed_tag directed_category;
struct traversal_category
@@ -223,11 +224,11 @@ struct graph_traits< RollingBloomDBG<BF> > {
typedef unsigned degree_size_type;
// VertexListGraph
- typedef size_t vertices_size_type;
+ typedef uint64_t vertices_size_type;
typedef void vertex_iterator;
// EdgeListGraph
- typedef size_t edges_size_type;
+ typedef uint64_t edges_size_type;
typedef void edge_iterator;
// AdjacencyGraph
@@ -438,7 +439,8 @@ vertex_exists(
const typename graph_traits<RollingBloomDBG<BloomT> >::vertex_descriptor& u,
const RollingBloomDBG<BloomT>& g)
{
- size_t hashes[MAX_HASHES];
+ typedef uint64_t hash_t;
+ hash_t hashes[MAX_HASHES];
u.rollingHash().getHashes(hashes);
return g.m_bloom.contains(hashes);
}
=====================================
BloomDBG/RollingHash.h
=====================================
@@ -19,11 +19,13 @@ class RollingHash
{
private:
+ typedef uint64_t hash_t;
+
/**
* Determine the canonical hash value, given hash values for
* forward and reverse-complement of the same k-mer.
*/
- uint64_t canonicalHash(uint64_t hash, uint64_t rcHash) const
+ hash_t canonicalHash(hash_t hash, hash_t rcHash) const
{
return (rcHash < hash) ? rcHash : hash;
}
@@ -136,7 +138,7 @@ public:
*
* @param hashes array for returned hash values
*/
- void getHashes(size_t hashes[]) const
+ void getHashes(hash_t hashes[]) const
{
for (unsigned i = 0; i < m_numHashes; ++i)
hashes[i] = NTE64(m_hash, m_k, i);
@@ -208,12 +210,12 @@ private:
/** k-mer length */
unsigned m_k;
/** value of first hash function for current k-mer */
- uint64_t m_hash1;
+ hash_t m_hash1;
/** value of first hash function for current k-mer, after
* reverse-complementing */
- uint64_t m_rcHash1;
+ hash_t m_rcHash1;
/** current canonical hash value */
- uint64_t m_hash;
+ hash_t m_hash;
};
#endif
=====================================
BloomDBG/RollingHashIterator.h
=====================================
@@ -98,6 +98,7 @@ private:
public:
+ typedef uint64_t hash_t;
/**
* Default constructor. Creates an iterator pointing to
* the end of the iterator range.
@@ -142,7 +143,7 @@ public:
}
/** get reference to hash values for current k-mer */
- const size_t* operator*() const
+ const hash_t* operator*() const
{
assert(m_pos + m_k <= m_seq.length());
return m_hashes;
@@ -216,7 +217,7 @@ private:
/** number of hash functions */
unsigned m_numHashes;
/** hash values */
- size_t m_hashes[MAX_HASHES];
+ hash_t m_hashes[MAX_HASHES];
/** k-mer size */
unsigned m_k;
/** internal state for rolling hash */
=====================================
ChangeLog
=====================================
@@ -1,3 +1,8 @@
+2019-08-12 Johnathan Wong <jowong at bcgsc.ca>
+
+ * Release version 2.2.1
+ * Fix abyss-bloom for macOS
+
2019-08-01 Johnathan Wong <jowong at bcgsc.ca>
* Release version 2.2.0
=====================================
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) 2.2.0\n"
+ version = "abyss-samtobreak (ABySS) 2.2.1\n"
usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
\Calculate contig and scaffold contiguity and correctness metrics.\n"
=====================================
Unittest/BloomDBG/HashAgnosticCascadingBloomTest.cpp
=====================================
@@ -25,7 +25,7 @@ TEST(HashAgnosticCascadingBloom, base)
RollingHashIterator itB(b, numHashes, k);
RollingHashIterator itC(c, numHashes, k);
RollingHashIterator itD(d, numHashes, k);
- size_t hash;
+ hash_t hash;
x.insert(*itA);
EXPECT_EQ(x.popcount(), 0U);
=====================================
Unittest/BloomDBG/RollingBloomDBGTest.cpp
=====================================
@@ -11,6 +11,7 @@ using namespace boost;
typedef RollingBloomDBG<BloomFilter> Graph;
typedef graph_traits<Graph> GraphTraits;
typedef graph_traits<Graph>::vertex_descriptor V;
+typedef uint64_t hash_t;
/** Test fixture for RollingBloomDBG tests. */
class RollingBloomDBGTest : public ::testing::Test
@@ -42,7 +43,7 @@ protected:
* complements of these k-mers.
*/
- size_t hashes[MAX_HASHES];
+ hash_t hashes[MAX_HASHES];
RollingHash("CGACT", m_numHashes, m_k).getHashes(hashes);
m_bloom.insert(hashes);
RollingHash("TGACT", m_numHashes, m_k).getHashes(hashes);
@@ -156,7 +157,7 @@ TEST_F(RollingBloomDBGTest, pathTraversal)
const V GACTC("GACTC", RollingHash("GACTC", m_numHashes, m_k));
const V ACTCG("ACTCG", RollingHash("ACTCG", m_numHashes, m_k));
- size_t hashes[MAX_HASHES];
+ hash_t hashes[MAX_HASHES];
CGACT.rollingHash().getHashes(hashes);
bloom.insert(hashes);
GACTC.rollingHash().getHashes(hashes);
@@ -268,7 +269,7 @@ protected:
* any additional edges in the graph.
*/
- size_t hashes[MAX_HASHES];
+ hash_t hashes[MAX_HASHES];
RollingHash("CGACT", m_numHashes, m_k).getHashes(hashes);
m_bloom.insert(hashes);
RollingHash("TGACT", m_numHashes, m_k).getHashes(hashes);
=====================================
azure-pipelines.yml
=====================================
@@ -1,4 +1,25 @@
jobs:
+- job: linux_gcc8_32bit
+ pool:
+ vmImage: Ubuntu 16.04
+ steps:
+ - script: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq software-properties-common
+ sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+ sudo apt-get update -qq
+ sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
+ displayName: Install common
+ - script: sudo apt-get install -qq gcc-8 g++-8
+ displayName: Install gcc-8
+ - script: sudo apt-get install gcc-8-multilib g++-8-multilib
+ displayName: Install 32-bit compilation support
+ - script: |
+ ./autogen.sh
+ ./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
+
- job: linux_clang6
pool:
vmImage: Ubuntu 16.04
@@ -118,3 +139,19 @@ jobs:
displayName: Install clang-format
- script: make clang-format
displayName: Run clang-format
+
+- job: macOS_gcc8
+ pool:
+ vmImage: macOS-10.14
+ steps:
+ - script: |
+ brew update
+ brew install automake boost at 1.70 openmpi google-sparsehash make pandoc ghc
+ displayName: Install common
+ - script: brew install gcc at 8
+ displayName: Install gcc
+ - script: |
+ ./autogen.sh
+ ./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
=====================================
bin/abyss-pe
=====================================
@@ -398,7 +398,7 @@ help:
@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users at bcgsc.ca.'
version:
- @echo "abyss-pe (ABySS) 2.2.0"
+ @echo "abyss-pe (ABySS) 2.2.1"
@echo "Written by Shaun Jackman and Anthony Raymond."
@echo
@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.2.0, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.2.1, abyss-users at bcgsc.ca, abyss,
http://www.bcgsc.ca/platform/bioinfo/software/abyss)
AC_CONFIG_MACRO_DIR([m4])
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+abyss (2.2.1-1) unstable; urgency=medium
+
+ * New upstream release, should fix failing builds on 32-bit architectures.
+ * Remove unused libgtest-dev dependency, as it is unused and may be causing
+ an error on hurd
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Use secure URI in debian/watch.
+ * Set upstream metadata fields: Contact.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 13 Aug 2019 12:38:14 +0200
+
abyss (2.2.0-1) unstable; urgency=medium
* New upstream.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -4,17 +4,16 @@ Uploaders: Andreas Tille <tille at debian.org>,
Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
python-markdown,
libboost-graph-dev,
libopenmpi-dev,
libsparsehash-dev,
libtext-multimarkdown-perl,
- libgtest-dev,
libsqlite3-dev,
- pkg-config,
- help2man
-Standards-Version: 4.3.0
+ pkg-config,
+ help2man
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/abyss
Vcs-Git: https://salsa.debian.org/med-team/abyss.git
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
@@ -27,9 +26,9 @@ Depends: make,
${perl:Depends},
bsdmainutils,
# For openmpi error messages:
- openmpi-common,
+ openmpi-common,
# for /usr/bin/orted and possibly other MPI components:
- openmpi-bin
+ openmpi-bin
Description: de novo, parallel, sequence assembler for short reads
ABySS is a de novo, parallel, sequence assembler that is designed for
short reads. It may be used to assemble genome or transcriptome
=====================================
debian/upstream/metadata
=====================================
@@ -1,8 +1,7 @@
Name: ABySS
Reference:
- Author: >
- Jared T. Simpson and Kim Wong and Shaun D. Jackman and
- Jacqueline E. Schein and Steven J.M. Jones and İnanç Birol
+ Author: "Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein\
+ \ and Steven J.M. Jones and İnanç Birol\n"
Title: "ABySS: A parallel assembler for short read sequence data"
Journal: Genome Research
Year: 2009
@@ -14,9 +13,10 @@ Reference:
URL: http://genome.cshlp.org/content/19/6/1117
eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html
Registry:
- - Name: bio.tools
- Entry: ABySS
- - Name: OMICtools
- Entry: OMICS_00006
- - Name: SciCrunch
- Entry: SCR_010709
+- Name: bio.tools
+ Entry: ABySS
+- Name: OMICtools
+ Entry: OMICS_00006
+- Name: SciCrunch
+ Entry: SCR_010709
+Contact: Shaun Jackman <sjackman at gmail.com>
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
https://github.com/bcgsc/abyss/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-# http://www.bcgsc.ca/downloads/abyss/ abyss-(.+)\.tar\.gz
+# https://www.bcgsc.ca/downloads/abyss/ abyss-(.+)\.tar\.gz
=====================================
doc/ABYSS.1
=====================================
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.0" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.1" "User Commands"
.SH NAME
ABYSS \- assemble short reads into contigs
.SH SYNOPSIS
=====================================
doc/abyss-pe.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.0" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.1" "User Commands"
.SH NAME
abyss-pe - assemble reads into contigs
.SH SYNOPSIS
=====================================
doc/abyss-tofastq.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.0" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.1" "User Commands"
.SH NAME
abyss-tofastq \- convert various file formats to FASTQ format
.br
=====================================
vendor/btl_bloomfilter/.clang-format
=====================================
@@ -0,0 +1,9 @@
+BasedOnStyle: Mozilla
+AlignAfterOpenBracket: AlwaysBreak
+AlignOperands: true
+ColumnLimit: 100
+ContinuationIndentWidth: 4
+IndentCaseLabels: false
+IndentWidth: 4
+TabWidth: 4
+UseTab: ForIndentation
=====================================
vendor/btl_bloomfilter/.gitignore
=====================================
@@ -0,0 +1,29 @@
+INSTALL
+Makefile
+Makefile.in
+Tests/AdHoc/BloomFilterTests
+Tests/AdHoc/ParallelFilter
+Tests/Unit/BloomFilterTests
+aclocal.m4
+autom4te.cache
+autoscan-*.log
+autoscan.log
+compile
+config.guess
+config.h
+config.h.in
+config.status
+config.sub
+configure
+configure.scan
+depcomp
+install-sh
+missing
+stamp-h1
+test-driver
+
+*.Po
+*.Tpo
+*.log
+*.o
+*.trs
=====================================
vendor/btl_bloomfilter/COPYING deleted
=====================================
@@ -1,32 +0,0 @@
-LICENSE AGREEMENT (ACADEMIC USE)
-CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. This License Agreement (the “Agreement”) is a legal contract between you, your employer, educational institution or organization (collectively, “You”) and the BC Cancer Agency Branch (“BCCA”) with respect to the license of the [insert name of product], including all associated documentation (collectively, the “Product”).
-BCCA is willing to license the Product to You only if You accept the terms and conditions of this Agreement. By clicking on the “I ACCEPT” button, or by copying, downloading, accessing or otherwise using the Product, You automatically agree to be bound by the terms of this Agreement. If You do not wish to be bound by the terms of this Agreement, do not copy, download, access or otherwise use the Product.
-1. AUTHORITY: In the event that You are an educational institution or organization, Your representative who is clicking the “I ACCEPT” button, or otherwise copying, downloading, accessing or using the Product hereby, in their personal capacity, represents and warrants that they possess the legal authority to enter into this Agreement on Your behalf and to bind You to the terms of this Agreement.
-2. LICENSE TO USE: BCCA hereby grants to You a personal, non-exclusive, non-transferable, limited license to use the Product solely for internal, non-commercial use for non-profit research or educational purposes only on the terms and conditions contained in this Agreement. The Product may be installed on a maximum of one machine per Qualified User at Your premises only. A copy of the Product installed on a single common machine may be shared for internal use by Qualified Users only. In order to be a “Qualified User”, an individual must be a student, researcher, professor, instructor or staff member of a non-profit educational institution or organization who uses the Product solely for non-profit research or educational purposes.
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=====================================
vendor/btl_bloomfilter/LICENSE
=====================================
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
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+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
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+
+ 13. Use with the GNU Affero General Public License.
+
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+
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+
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+
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+to attach them to the start of each source file to most effectively
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+ (at your option) any later version.
+
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+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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+
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+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+
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+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
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+might be different; for a GUI interface, you would use an "about box".
+
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+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
=====================================
vendor/btl_bloomfilter/Tests/AdHoc/BloomFilterTests.cpp
=====================================
@@ -120,6 +120,8 @@ main()
cout << "premade bf tests done" << endl;
+#if __linux__
+
// memory leak tests
BloomFilter* filter3 = new BloomFilter(filterSize, 5, 20);
@@ -138,6 +140,8 @@ main()
cout << "memory leak prevention tests done" << endl;
cout << memory_usage() - memUsage << "kb" << endl;
+#endif
+
remove(filename.c_str());
// //check parallelized code speed
=====================================
vendor/btl_bloomfilter/azure-pipelines.yml
=====================================
@@ -1,18 +1,45 @@
-pool:
- vmImage: "Ubuntu 16.04"
+jobs:
+- job: linux_gcc_default
+ pool:
+ vmImage: "Ubuntu 16.04"
+ steps:
+ - script: |
+ ./autogen.sh
+ ./configure
+ make distcheck
+ displayName: "Compile btl_bloomfilter with gcc_default"
+ - script: |
+ curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
+ sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main"
+ sudo apt-get update
+ sudo apt-get install -y --no-install-recommends clang-format-8
+ sudo ln -s clang-format-8 /usr/bin/clang-format
+ displayName: Install clang-format
+ - script: make clang-format
+ displayName: Run clang-format
-steps:
-- script: |
- ./autogen.sh
- ./configure
- make distcheck
- displayName: "Compile btl_bloomfilter"
-- script: |
- curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
- sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main"
- sudo apt-get update
- sudo apt-get install -y --no-install-recommends clang-format-8
- sudo ln -s clang-format-8 /usr/bin/clang-format
- displayName: Install clang-format
-- script: make clang-format
- displayName: Run clang-format
+- job: linux_clang6
+ pool:
+ vmImage: "Ubuntu 16.04"
+ steps:
+ - script: sudo apt-get install -qq clang-6.0
+ displayName: Install clang-6.0
+ - script: |
+ ./autogen.sh
+ ./configure CC=clang-6.0 CXX=clang++-6.0
+ make distcheck
+ displayName: "Compile btl_bloomfilter with clang 6.0"
+
+- job: macOS_gcc_default
+ pool:
+ vmImage: macOS-10.14
+ steps:
+ - script: |
+ brew update
+ brew install automake
+ displayName: Install automake
+ - script: |
+ ./autogen.sh
+ ./configure
+ make distcheck
+ displayName: "Compile btl_bloomfilter with default gcc"
=====================================
vendor/btl_bloomfilter/configure.ac
=====================================
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
-AC_INIT(BLOOMFILTER, 1.2.0, cjustin at bcgsc.ca)
+AC_INIT(BLOOMFILTER, 1.2.1, cjustin at bcgsc.ca)
AC_CANONICAL_SYSTEM
AM_INIT_AUTOMAKE()
=====================================
vendor/btl_bloomfilter/swig/test.pl
=====================================
@@ -1,5 +1,7 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
+use FindBin;
+use lib "$FindBin::Bin/./";
use BloomFilter;
#Same inputs as the adhoc tests
=====================================
vendor/btl_bloomfilter/swig/testBloom_rolling.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#AUTHOR
@@ -31,6 +31,7 @@ use FindBin;
#perl 5.10.0
#use lib "/projects/rwarren_prj2/LINKS/paper/links_v1.5.2/lib/Bloom-Faster-1.7/bloom5-16-3/lib/site_perl/5.16.3/x86_64-linux";###rebuild against PERL version or replace by pre-built
#use Bloom::Faster;
+use lib "$FindBin::Bin/./";
use BloomFilter;
use Getopt::Std;
use Net::SMTP;
=====================================
vendor/btl_bloomfilter/swig/writeBloom_rolling.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#AUTHOR
@@ -31,6 +31,7 @@ use FindBin;
#perl 5.10.0
#use lib "$FindBin::Bin/../lib/Bloom-Faster-1.7/bloom5-16-3/lib/site_perl/5.16.3/x86_64-linux";###rebuild against PERL version or replace by pre-built
#use Bloom::Faster;
+use lib "$FindBin::Bin/./";
use BloomFilter;
use Getopt::Std;
use Net::SMTP;
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/030e2cb2973695b79fda1c2d99594713e5efa096...acb475098819c0d7d7a34465551fe3df2d4f9804
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/030e2cb2973695b79fda1c2d99594713e5efa096...acb475098819c0d7d7a34465551fe3df2d4f9804
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