[med-svn] [Git][med-team/abyss][upstream] New upstream version 2.2.1
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Aug 13 11:48:03 BST 2019
Michael R. Crusoe pushed to branch upstream at Debian Med / abyss
Commits:
6e7e1b38 by Michael R. Crusoe at 2019-08-13T10:32:06Z
New upstream version 2.2.1
- - - - -
25 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
- 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])
=====================================
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.
-3. RESTRICTIONS: You acknowledge and agree that You shall not, and shall not authorize any third party to:
-(a) make copies of the Product, except as provided in Section 2 and except for a single backup copy, and any such copy together with the original must be kept in Your possession or control;
-(b) modify,, adapt, decompile, disassemble, translate into another computer language, create derivative works of, or otherwise reverse engineer the Product, or disclose any trade secrets relating to the Product, except as permitted in Section 5;
-(c) license, sublicense, distribute, sell, lease, transfer, assign, trade, rent or publish the Product or any part thereof and/or copies thereof, to any third party;
-(d) use the Product to process any data other than Your own;
-(e) use the Product or any part thereof for any commercial or for-profit purpose or any other purpose other than as permitted in Section 2; or
-(f) use, without its express permission, the name of BCCA.
-4. INTELLECTUAL PROPERTY RIGHTS: Subject to Section 5 below, all patents, copyrights, trade secrets, service marks, trademarks and other proprietary rights in or related to the Product and any improvements, modifications and enhancements thereof are and will remain the exclusive property of BCCA or its licensors. You agree that You will not, either during or after the termination of this Agreement, contest or challenge the title to or the intellectual property rights of BCCA or its licensors in the Product or any portion thereof.
-5. OWNERSHIP OF IMPROVEMENTS: In the event that the Product, in the form provided to You, includes source code (the “Source Code”), You are entitled to make improvements, modifications and enhancements to the Source Code (collectively, “Improvements”) which Improvements are to be used by You for non-profit research and educational purposes only and You shall be the owner of those Improvements that You directly make and of all intellectual property rights to such Improvements, subject to the foregoing limits on Your use and distribution of such Improvements. You hereby grant to BCCA a perpetual, non-exclusive, worldwide, fully-paid, irrevocable license to use such Improvements for any purposes whatsoever, and to sublicense such Improvements including the right for third parties to sublicense the same, in perpetuity to the extent such rights are not limited in duration under applicable law, without identifying or seeking Your consent. Notwithstanding the foregoing, You acknowledge that BCCA and its licensors will retain or own all rights in and to any pre-existing code or other technology, content and data that may be incorporated in the Improvements. For greater certainty, this Section applies solely to the Source Code and shall not give You any rights with respect to the object code or any other portion or format of the Product which use, for greater certainty, is limited as set forth in this Agreement including as set out in Section 3.(b) above. You acknowledge and agree that you will provide copies of Improvements to BCCA in such format as reasonably requested by BCCA at any time upon the request of BCCA.
-6. CONFIDENTIALITY: You acknowledge that the Product is and incorporates confidential and proprietary information developed, acquired by or licensed to BCCA. You will take all reasonable precautions necessary to safeguard the confidentiality of the Product, and will not disclose any information about the Product to any other person without BCCA’s prior written consent. You will not allow the removal or defacement of any confidential or proprietary notice placed on the Product. You acknowledge that any breach of this Section 6 will cause irreparable harm to BCCA and its licensors.
-7. NO WARRANTIES: This Product is provided to You by BCCA in order to allow You to obtain access to leading academic research. The Product is provided to you on an “as is” basis without warranty of any kind. No warranty, representation or condition either express or implied, including without limitation, any implied warranty or condition of merchantability, non-infringement, performance, durability or fitness for a particular purpose or use shall apply. BCCA does not warrant that the Product will operate on a continuous or trouble free basis.
-8. LIMITATION OF LIABILITY: To the maximum extent permitted by applicable law, in no event shall the aggregate liability of BCCA to You exceed the amount You have paid to acquire the Product (“Maximum amount”) and where You have not paid any amount for the Product then the Maximum Amount shall be deemed to be CDN$1,000. in no event shall BCCA be liable for any indirect, incidental, consequential, or special damages, including without limitation any damages for lost profits or savings, regardless of whether they have been advised of the possibility of such damage. Except to the extent that the laws of a competent jurisdiction require liabilities beyond and despite these limitations, exclusions and disclaimers, these limitations, exclusions and disclaimers shall apply whether an action, claim or demand arises from a breach of warranty or condition, breach of contract, negligence, strict liability or any other kind of civil or statutory liability connected with or arising from this Agreement. You agree that the foregoing disclaimer of warranties and limitation of liability are fair in light of the nature of the rights granted herein and the amount of fees paid by You in respect of the Product.
-9. INDEMNITY: You will indemnify, defend and hold harmless BCCA, its board of directors, staff and agents from and against any and all liability, loss, damage, action, claim or expense (including attorney’s fees and costs at trial and appellate levels) in connection with any claim, suit, action, demand or judgement (collectively, “Claim”) arising out of, connected with, resulting from, or sustained as a result of Your use of the Product or the downloading of the Product, including without limitation, any Claim relating to infringement of BCCA’s intellectual property rights or the intellectual property rights of any third party.
-10. SUPPORT AND MAINTENANCE: You acknowledge and agree that, unless and to the extent expressly agreed by BCCA in a separate written document, the Product is provided to You without any support or maintenance from BCCA and, for greater certainty, BCCA shall have no obligation to issue any update or upgrade to any Product.
-11. TERM: This Agreement is effective until terminated. You may terminate this Agreement at any time by ceasing use of the Product and destroying or deleting any copies of the Product. This Agreement will terminate immediately without notice from BCCA if You fail to comply with any provision of this Agreement. BCCA may terminate this Agreement at any time upon notice to you where BCCA determines, in its sole discretion, that any continued use of the Product could infringe the rights of any third parties. Upon termination of this Agreement, and in any event upon BCCA delivering You notice of termination, You shall immediately purge all Products from Your computer system(s), return to BCCA all copies of the Product that are in Your possession or control, and cease any further development of any Improvements. On any termination of this Agreement Sections 1, 4, 6, 7, 8, 9, 13 and 14 shall survive such termination.
-12. GOVERNMENT END USERS: Where any of the Product is used, duplicated or disclosed by or to the United States government or a government contractor or sub contractor, it is provided with RESTRICTED RIGHTS as defined in Title 48 CFR 52.227-19 and is subject to the following: Title 48 CFR 2.101, 52.227-19, 227.7201 through 227.7202-4, FAR 52.227-14, and FAR 52.227-19(c)(1-2) and (6/87), and where applicable, the customary software license, as described in Title 48 CFR 227-7202 with respect to commercial software and commercial software documentation including DFAR 252.227-7013, DFAR 252,227-7014, DFAR 252.227-7015 and DFAR 252.7018, all as applicable.
-13. USE OF THE DOWNLOAD SERVICE: You acknowledge and agree that you will be responsible for all costs, charges and taxes (where applicable) arising out of Your use of the Product and the downloading of the Product. You acknowledge that You are responsible for supplying any hardware or software necessary to use the Product pursuant to this Agreement.
-14. GENERAL PROVISIONS:
-(a) This Agreement will be governed by the laws of the Province of British Columbia, and the laws of Canada applicable therein, excluding any rules of private international law that lead to the application of the laws of any other jurisdiction. The United Nations Convention on Contracts for the International Sale of Goods (1980) does not apply to this Agreement. The courts of the Province of British Columbia shall have non-exclusive jurisdiction to hear any matter arising in connection with this Agreement.
-(b) USE OF THE PRODUCT IS PROHIBITED IN ANY JURISDICTION WHICH DOES NOT GIVE EFFECT TO THE TERMS OF THIS AGREEMENT.
-(c) You agree that no joint venture, partnership, employment, consulting or agency relationship exists between You and BCCA as a result of this Agreement or Your use of the Product.
-(d) You hereby consent to Your contact information and any other personally identifiable information that You provide to us being disclosed to and maintained and used by us and our business partners for the purposes of (i) managing and developing our respective businesses and operations; (ii) marketing products and services to You and your staff; and (iii) developing new and enhancing existing products. You further agree that we may provide this information to other persons as required to satisfy any legal requirements and to any person that acquires some or all of the assets of BCCA. Where any of the personally identifiable information that You provide to us is in respect of individuals other than Yourself (such as Your staff) then You represent and warrant to use that You have obtained all necessary consents and authorizations from such individuals in order to comply with this provision. Please see the BCCA website for further information regarding personally identifiable information.
-(e) This Agreement is the entire Agreement between You and BCCA relating to this subject matter. You will not contest the validity of this Agreement merely because it is in electronic form. No modification of this Agreement will be binding, unless in writing and accepted by an authorized representative of each party.
-(f) The provisions of this Agreement are severable in that if any provision in the Agreement is determined to be invalid or unenforceable under any controlling body of law, that will not affect the validity or enforceability of the remaining provisions of the Agreement.
-(g) You agree to print out or download a copy of this Agreement and retain it for Your records.
-(h) You consent to the use of the English language in this Agreement.
-(i) You may not assign this Agreement or any of Your rights or obligations hereunder without BCCA’s prior written consent. BCCA, at its sole discretion may assign this Agreement without notice to You.
=====================================
vendor/btl_bloomfilter/LICENSE
=====================================
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights. Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received. You must make sure that they, too, receive
+or can get the source code. And you must show them these terms so they
+know their rights.
+
+ Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+ For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software. For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+ Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so. This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software. The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable. Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products. If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+ Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary. To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU General Public License.
+
+ "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+ "The Program" refers to any copyrightable work licensed under this
+License. Each licensee is addressed as "you". "Licensees" and
+"recipients" may be individuals or organizations.
+
+ To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy. The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+ A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+ To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+ To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+ An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License. If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+ 1. Source Code.
+
+ The "source code" for a work means the preferred form of the work
+for making modifications to it. "Object code" means any non-source
+form of a work.
+
+ A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.
+
+ The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
+Major Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form. A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+
+ The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities. However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+ The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.
+
+ The Corresponding Source for a work in source code form is that
+same work.
+
+ 2. Basic Permissions.
+
+ All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+ You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force. You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright. Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.
+
+ Conveying under any other circumstances is permitted solely under
+the conditions stated below. Sublicensing is not allowed; section 10
+makes it unnecessary.
+
+ 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+ No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.
+
+ When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+
+ 4. Conveying Verbatim Copies.
+
+ You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+
+ You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
+
+ 5. Conveying Modified Source Versions.
+
+ You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:
+
+ a) The work must carry prominent notices stating that you modified
+ it, and giving a relevant date.
+
+ b) The work must carry prominent notices stating that it is
+ released under this License and any conditions added under section
+ 7. This requirement modifies the requirement in section 4 to
+ "keep intact all notices".
+
+ c) You must license the entire work, as a whole, under this
+ License to anyone who comes into possession of a copy. This
+ License will therefore apply, along with any applicable section 7
+ additional terms, to the whole of the work, and all its parts,
+ regardless of how they are packaged. This License gives no
+ permission to license the work in any other way, but it does not
+ invalidate such permission if you have separately received it.
+
+ d) If the work has interactive user interfaces, each must display
+ Appropriate Legal Notices; however, if the Program has interactive
+ interfaces that do not display Appropriate Legal Notices, your
+ work need not make them do so.
+
+ A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.
+
+ 6. Conveying Non-Source Forms.
+
+ You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
+machine-readable Corresponding Source under the terms of this License,
+in one of these ways:
+
+ a) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by the
+ Corresponding Source fixed on a durable physical medium
+ customarily used for software interchange.
+
+ b) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by a
+ written offer, valid for at least three years and valid for as
+ long as you offer spare parts or customer support for that product
+ model, to give anyone who possesses the object code either (1) a
+ copy of the Corresponding Source for all the software in the
+ product that is covered by this License, on a durable physical
+ medium customarily used for software interchange, for a price no
+ more than your reasonable cost of physically performing this
+ conveying of source, or (2) access to copy the
+ Corresponding Source from a network server at no charge.
+
+ c) Convey individual copies of the object code with a copy of the
+ written offer to provide the Corresponding Source. This
+ alternative is allowed only occasionally and noncommercially, and
+ only if you received the object code with such an offer, in accord
+ with subsection 6b.
+
+ d) Convey the object code by offering access from a designated
+ place (gratis or for a charge), and offer equivalent access to the
+ Corresponding Source in the same way through the same place at no
+ further charge. You need not require recipients to copy the
+ Corresponding Source along with the object code. If the place to
+ copy the object code is a network server, the Corresponding Source
+ may be on a different server (operated by you or a third party)
+ that supports equivalent copying facilities, provided you maintain
+ clear directions next to the object code saying where to find the
+ Corresponding Source. Regardless of what server hosts the
+ Corresponding Source, you remain obligated to ensure that it is
+ available for as long as needed to satisfy these requirements.
+
+ e) Convey the object code using peer-to-peer transmission, provided
+ you inform other peers where the object code and Corresponding
+ Source of the work are being offered to the general public at no
+ charge under subsection 6d.
+
+ A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
+
+ A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling. In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage. For a particular
+product received by a particular user, "normally used" refers to a
+typical or common use of that class of product, regardless of the status
+of the particular user or of the way in which the particular user
+actually uses, or expects or is expected to use, the product. A product
+is a consumer product regardless of whether the product has substantial
+commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.
+
+ "Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source. The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.
+
+ If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information. But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).
+
+ The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or updates
+for a work that has been modified or installed by the recipient, or for
+the User Product in which it has been modified or installed. Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.
+
+ Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.
+
+ 7. Additional Terms.
+
+ "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+ When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.
+
+ Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+
+ a) Disclaiming warranty or limiting liability differently from the
+ terms of sections 15 and 16 of this License; or
+
+ b) Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or
+
+ c) Prohibiting misrepresentation of the origin of that material, or
+ requiring that modified versions of such material be marked in
+ reasonable ways as different from the original version; or
+
+ d) Limiting the use for publicity purposes of names of licensors or
+ authors of the material; or
+
+ e) Declining to grant rights under trademark law for use of some
+ trade names, trademarks, or service marks; or
+
+ f) Requiring indemnification of licensors and authors of that
+ material by anyone who conveys the material (or modified versions of
+ it) with contractual assumptions of liability to the recipient, for
+ any liability that these contractual assumptions directly impose on
+ those licensors and authors.
+
+ All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term. If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
+not survive such relicensing or conveying.
+
+ If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.
+
+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+
+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+ An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+
+ You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+ In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+ If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+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
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+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/commit/6e7e1b38578b87f6725285595e73dbce6ef0c0cd
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/commit/6e7e1b38578b87f6725285595e73dbce6ef0c0cd
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190813/22399f54/attachment-0001.html>
More information about the debian-med-commit
mailing list