[med-svn] [Git][med-team/berkeley-express][master] 9 commits: New upstream version
Michael R. Crusoe
gitlab at salsa.debian.org
Sun Nov 17 16:30:07 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / berkeley-express
Commits:
6ccf0f09 by Michael R. Crusoe at 2019-11-17T15:24:33Z
New upstream version
- - - - -
b0d54647 by Michael R. Crusoe at 2019-11-17T15:24:35Z
New upstream version 1.5.3+dfsg
- - - - -
3e57c1c1 by Michael R. Crusoe at 2019-11-17T15:24:42Z
Update upstream source from tag 'upstream/1.5.3+dfsg'
Update to upstream version '1.5.3+dfsg'
with Debian dir 0710a3347101a19750b0502c450348c57e01008a
- - - - -
a4534180 by Michael R. Crusoe at 2019-11-17T15:24:43Z
debhelper-compat 12
- - - - -
f8a47474 by Michael R. Crusoe at 2019-11-17T15:24:50Z
Standards-Version: 4.4.0
- - - - -
2bb8d84a by Michael R. Crusoe at 2019-11-17T15:30:15Z
freshen patches
- - - - -
f45e901e by Michael R. Crusoe at 2019-11-17T16:12:48Z
-doc: Include the sample data
- - - - -
f7f61561 by Michael R. Crusoe at 2019-11-17T16:19:43Z
remote the version check for privacy
- - - - -
428e7ca6 by Michael R. Crusoe at 2019-11-17T16:19:43Z
upload to unstable
- - - - -
15 changed files:
- CMakeLists.txt
- + debian/berkeley-express-doc.examples
- debian/changelog
- − debian/compat
- debian/control
- debian/patches/correct-debug-flags.patch
- debian/patches/drop-zlib
- debian/patches/fix-bamtools-path
- − debian/patches/gcc-6.patch
- debian/patches/privacy-breach.patch
- debian/patches/series
- + debian/tests/control
- + debian/tests/run-tests
- src/CMakeLists.txt
- src/targets.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -6,6 +6,9 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
set(${PROJECT_NAME}_VERSION_MINOR 5)
set(${PROJECT_NAME}_VERSION_PATCH 1)
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
set(CMAKE_CXX_FLAGS "-Wall")
set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")
=====================================
debian/berkeley-express-doc.examples
=====================================
@@ -0,0 +1 @@
+sample_data/*
=====================================
debian/changelog
=====================================
@@ -1,9 +1,17 @@
-berkeley-express (1.5.2+dfsg-2) UNRELEASED; urgency=medium
+berkeley-express (1.5.3+dfsg-1) unstable; urgency=medium
+ [ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
- -- Jelmer Vernooij <jelmer at debian.org> Sat, 20 Oct 2018 13:12:49 +0000
+ [ Michael R. Crusoe ]
+ * New upstream version
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * -doc: Include the sample data
+ * remove the version check for privacy
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sun, 17 Nov 2019 17:17:25 +0100
berkeley-express (1.5.2+dfsg-1) unstable; urgency=medium
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
libboost-thread-dev,
libboost-system-dev,
libboost-filesystem-dev,
@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 11~),
cmake,
libprotobuf-dev,
protobuf-compiler
-Standards-Version: 4.1.3
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/berkeley-express
Vcs-Git: https://salsa.debian.org/med-team/berkeley-express.git
Homepage: http://bio.math.berkeley.edu/eXpress/index.html
=====================================
debian/patches/correct-debug-flags.patch
=====================================
@@ -4,11 +4,11 @@ Description: remove forced flags and set dynamic linking
Author: Gert Wollny <gw.fossdev at gmail.com>
Forwarded: no
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -6,14 +6,13 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
- set(${PROJECT_NAME}_VERSION_MINOR 5)
- set(${PROJECT_NAME}_VERSION_PATCH 1)
+--- berkeley-express.orig/CMakeLists.txt
++++ berkeley-express/CMakeLists.txt
+@@ -9,14 +9,13 @@
+ set(CMAKE_CXX_STANDARD 11)
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_FLAGS "-Wall")
+#set(CMAKE_CXX_FLAGS "-Wall")
@@ -27,9 +27,9 @@ Forwarded: no
find_package(Boost 1.39
COMPONENTS
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -10,12 +10,12 @@ add_executable(express ${sources} ${head
+--- berkeley-express.orig/src/CMakeLists.txt
++++ berkeley-express/src/CMakeLists.txt
+@@ -10,12 +10,12 @@
set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES})
if (GPERFTOOLS_TCMALLOC)
=====================================
debian/patches/drop-zlib
=====================================
@@ -1,8 +1,8 @@
Description: drop unused zlib dependency
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -57,7 +57,6 @@ else(WIN32)
+--- berkeley-express.orig/CMakeLists.txt
++++ berkeley-express/CMakeLists.txt
+@@ -60,7 +60,6 @@
message(STATUS "Do not try to find libbamtools.a")
set(BAMTOOLS_LIBRARIES bamtools)
endif()
@@ -10,13 +10,13 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
set(WIN32_INT 0)
endif(WIN32)
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -7,7 +7,7 @@ endif(PROTOBUF_FOUND)
+--- berkeley-express.orig/src/CMakeLists.txt
++++ berkeley-express/src/CMakeLists.txt
+@@ -7,7 +7,7 @@
add_executable(express ${sources} ${headers} ${PROTO_SOURCES} ${PROTO_HEADERS})
--set(LIBRARIES ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} ${BAMTOOLS_LIBRARIES})
+-set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES} ${ZLIB_LIBRARIES})
+set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES})
if (GPERFTOOLS_TCMALLOC)
=====================================
debian/patches/fix-bamtools-path
=====================================
@@ -2,9 +2,9 @@ Author: Michael R. Crusoe <mcrusoe at msu.edu>
Last-Update: Thu, 12 Feb 2015 09:21:09 +0100
Description: Fix path to Debian packaged bamtools
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -33,10 +33,11 @@ endif(GPERFTOOLS_TCMALLOC_LIB)
+--- berkeley-express.orig/CMakeLists.txt
++++ berkeley-express/CMakeLists.txt
+@@ -36,10 +36,11 @@
find_package(Protobuf)
if (PROTOBUF_FOUND)
@@ -18,7 +18,7 @@ Description: Fix path to Debian packaged bamtools
set(PROTO_INT 0)
endif(PROTOBUF_FOUND)
-@@ -52,7 +53,9 @@ else(WIN32)
+@@ -55,7 +56,9 @@
if (EXISTS "${PROJECT_SOURCE_DIR}/bamtools/lib/libbamtools.a")
set(BAMTOOLS_LIBRARIES "${PROJECT_SOURCE_DIR}/bamtools/lib/libbamtools.a")
else()
@@ -29,9 +29,9 @@ Description: Fix path to Debian packaged bamtools
endif()
find_package(ZLIB REQUIRED)
set(WIN32_INT 0)
---- a/src/mismatchmodel.cpp
-+++ b/src/mismatchmodel.cpp
-@@ -126,7 +126,7 @@ MismatchTable::MismatchTable(string para
+--- berkeley-express.orig/src/mismatchmodel.cpp
++++ berkeley-express/src/mismatchmodel.cpp
+@@ -126,7 +126,7 @@
size_t k = 0;
do {
if (k > max_indel_size) {
@@ -40,7 +40,7 @@ Description: Fix path to Debian packaged bamtools
"truncated at max indel length of %d.",
param_file_name.c_str(), max_indel_size);
break;
-@@ -143,7 +143,7 @@ MismatchTable::MismatchTable(string para
+@@ -143,7 +143,7 @@
k = 0;
do {
if (k > max_indel_size) {
=====================================
debian/patches/gcc-6.patch deleted
=====================================
@@ -1,21 +0,0 @@
-Description: Fix compilation with gcc-6
-Author: Gert Wollny <gw.fossdev at gmail.com>
-Bug-Debian: https://bugs.debian.org/811859
-
---- a/src/targets.cpp
-+++ b/src/targets.cpp
-@@ -113,12 +113,12 @@
-
- double ll = LOG_1;
- double tot_mass = mass(with_pseudo);
-- double tot_eff_len = cached_effective_length(lib.bias_table);
-+ double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table));
- if (neighbors) {
- foreach (const Target* neighbor, *neighbors) {
- tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo));
- tot_eff_len = log_add(tot_eff_len,
-- neighbor->cached_effective_length(lib.bias_table));
-+ neighbor->cached_effective_length(static_cast<bool>(lib.bias_table)));
- }
- }
- ll += tot_mass - tot_eff_len;
=====================================
debian/patches/privacy-breach.patch
=====================================
@@ -2,8 +2,8 @@ Description: avoid privace breach JS in html doc
Author: Andreas Tille <tille at debian.org>
Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
---- a/html/faq.html
-+++ b/html/faq.html
+--- berkeley-express.orig/html/faq.html
++++ berkeley-express/html/faq.html
@@ -17,9 +17,6 @@
_gaq.push(['_trackPageview']);
@@ -30,8 +30,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
}, true);
</script>
<link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/index.html
-+++ b/html/index.html
+--- berkeley-express.orig/html/index.html
++++ berkeley-express/html/index.html
@@ -17,9 +17,6 @@
_gaq.push(['_trackPageview']);
@@ -58,8 +58,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
}, true);
</script>
<link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/manual.html
-+++ b/html/manual.html
+--- berkeley-express.orig/html/manual.html
++++ berkeley-express/html/manual.html
@@ -17,9 +17,6 @@
_gaq.push(['_trackPageview']);
@@ -86,8 +86,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
}, true);
</script>
<link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/overview.html
-+++ b/html/overview.html
+--- berkeley-express.orig/html/overview.html
++++ berkeley-express/html/overview.html
@@ -17,9 +17,6 @@
_gaq.push(['_trackPageview']);
@@ -114,8 +114,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
}, true);
</script>
<link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/tutorial.html
-+++ b/html/tutorial.html
+--- berkeley-express.orig/html/tutorial.html
++++ berkeley-express/html/tutorial.html
@@ -17,9 +17,6 @@
_gaq.push(['_trackPageview']);
@@ -142,3 +142,152 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
}, true);
</script>
<link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
+--- berkeley-express.orig/src/main.cpp
++++ berkeley-express/src/main.cpp
+@@ -38,10 +38,6 @@
+ #include <boost/archive/iterators/ostream_iterator.hpp>
+ #endif
+
+-#ifndef WIN32
+- #include "update_check.h"
+-#endif
+-
+ using namespace std;
+ namespace po = boost::program_options;
+ namespace fs = boost::filesystem;
+@@ -365,12 +361,6 @@
+ expr_alpha_map = parse_priors(prior_file);
+ }
+
+-#ifndef WIN32
+- if (!vm.count("no-update-check")) {
+- check_version(PACKAGE_VERSION);
+- }
+-#endif
+-
+ return 0;
+ }
+
+--- berkeley-express.orig/src/update_check.h
++++ /dev/null
+@@ -1,120 +0,0 @@
+-/**
+- * update_check.h
+- * express
+- * Based on code from http://www.linuxhowtos.org/C_C++/socket.htm
+- * Modified by Adam Roberts on 1/18/11.
+- */
+-
+-#include <signal.h>
+-#include <strings.h>
+-#include <sys/socket.h>
+-#include <netinet/in.h>
+-#include <netdb.h>
+-
+-int NUM_SEPS = 3;
+-int CONNECT_TIMEOUT = 5;
+-
+-static int sTimeout = 0;
+-
+-static void AlarmHandler(int sig)
+-
+-{
+-
+- sTimeout = 1;
+-
+-}
+-
+-bool error(const char *msg)
+-{
+- return false;
+-}
+-
+-int parse_version_str(char* version_str)
+-{
+- int version_int = 0;
+- char* token = strtok(version_str,".");
+- for(int i = 0; i < NUM_SEPS; ++i)
+- {
+- version_int += atoi(token)*(int)pow(100.,NUM_SEPS-i);
+- }
+- return version_int;
+-}
+-
+-bool get_current_version(char* curr_version)
+-{
+- int sockfd, portno, n;
+- struct sockaddr_in serv_addr;
+- struct hostent *server;
+-
+- portno = 80;
+- sockfd = socket(AF_INET, SOCK_STREAM, 0);
+- if (sockfd < 0)
+-
+- return error("ERROR opening socket");
+-
+- server = gethostbyname("bio.math.berkeley.edu");
+- if (server == NULL)
+-
+- return error("ERROR, no such host");
+-
+- bzero((char *) &serv_addr, sizeof(serv_addr));
+- serv_addr.sin_family = AF_INET;
+- bcopy((char *)server->h_addr,
+-
+- (char *)&serv_addr.sin_addr.s_addr,
+- server->h_length);
+- serv_addr.sin_port = htons(portno);
+-
+- signal(SIGALRM, AlarmHandler);
+-
+- sTimeout = 0;
+-
+- alarm(CONNECT_TIMEOUT);
+-
+-
+- int ret;
+- ret = connect(sockfd, (struct sockaddr*)&serv_addr, sizeof(serv_addr));
+- if (ret < 0 || sTimeout)
+- {
+- return error("ERROR connecting");
+- }
+-
+- char buffer[1024];
+- strcpy(buffer, "GET /eXpress/curr_xprs_version HTTP/1.1\nHost: bio.math.berkeley.edu\n\n");
+- n = (int)write(sockfd,buffer,1024);
+-
+- if (n < 0)
+-
+- return error("ERROR writing to socket");
+- bzero(curr_version, sizeof(curr_version));
+- n = (int)read(sockfd,buffer,1024);
+- if (n < 0)
+-
+- return error("ERROR reading from socket");
+-
+- char* token;
+- token = strtok(buffer, "$");
+- token = strtok(NULL, "$");
+- if (token==NULL)
+- return error("ERROR parsing response");
+-
+- strcpy(curr_version, token);
+-
+- return true;
+-}
+-
+-void check_version(const char* this_version)
+-{
+- char curr_version[256];
+- memset(curr_version, 0, sizeof(curr_version));
+- if (get_current_version(curr_version))
+- {
+- if (strcmp(curr_version, this_version)==0) {
+- fprintf(stderr, "You are using eXpress v%s, which is the most recent release.\n\n", PACKAGE_VERSION);
+- } else {
+- fprintf(stderr, "WARNING: Your version of eXpress is not up-to-date. It is recommended that you upgrade to v%s to benefit from the most recent features and bug fixes (http://bio.math.berkeley.edu/eXpress).\n\n", curr_version);
+- }
+- } else {
+- fprintf(stderr, "WARNING: Could not connect to update server to verify current version. Please check at the eXpress website (http://bio.math.berkeley.edu/eXpress).\n\n");
+- }
+-}
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,5 @@
spelling-fixes
fix-bamtools-path
drop-zlib
-gcc-6.patch
correct-debug-flags.patch
privacy-breach.patch
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-tests
+Depends: @, bowtie, samtools, gzip
+Restrictions: allow-stderr
+
=====================================
debian/tests/run-tests
=====================================
@@ -0,0 +1,12 @@
+#!/bin/sh -ex
+pkg=berkeley-express
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+fi
+
+cd "${AUTOPKGTEST_TMP}"
+cp /usr/share/doc/${pkg}/sample_data/* .
+gunzip *
+bowtie-build --offrate 1 transcripts.fasta transcripts
+bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq | samtools view -Sb - > hits.bam
+berkeley-express transcripts.fasta hits.bam
=====================================
src/CMakeLists.txt
=====================================
@@ -7,7 +7,7 @@ endif(PROTOBUF_FOUND)
add_executable(express ${sources} ${headers} ${PROTO_SOURCES} ${PROTO_HEADERS})
-set(LIBRARIES ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} ${BAMTOOLS_LIBRARIES})
+set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES} ${ZLIB_LIBRARIES})
if (GPERFTOOLS_TCMALLOC)
set(LIBRARIES ${LIBRARIES} "libtcmalloc_minimal.a")
@@ -20,7 +20,9 @@ endif(PROTOBUF_FOUND)
if (WIN32)
target_link_libraries(express ${LIBRARIES})
-else(WIN32)
+elseif(APPLE)
+target_link_libraries(express ${LIBRARIES} pthread)
+elseif(UNIX)
target_link_libraries(express ${LIBRARIES} pthread rt)
-endif(WIN32)
+endif()
install(TARGETS express DESTINATION bin)
=====================================
src/targets.cpp
=====================================
@@ -113,12 +113,12 @@ double Target::sample_likelihood(bool with_pseudo,
double ll = LOG_1;
double tot_mass = mass(with_pseudo);
- double tot_eff_len = cached_effective_length(lib.bias_table);
+ double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table));
if (neighbors) {
foreach (const Target* neighbor, *neighbors) {
tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo));
tot_eff_len = log_add(tot_eff_len,
- neighbor->cached_effective_length(lib.bias_table));
+ neighbor->cached_effective_length(static_cast<bool>(lib.bias_table)));
}
}
ll += tot_mass - tot_eff_len;
View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/compare/71779ab29ceefea1299e706f55353bd7057795a4...428e7ca69201fc7ae521c90b942e3a0f8b02ee48
--
View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/compare/71779ab29ceefea1299e706f55353bd7057795a4...428e7ca69201fc7ae521c90b942e3a0f8b02ee48
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