UPDATE: 20 May 2016 – With thanks to OrthoDB's very own Fredrik Tegenfeldt, here's a more distro-complete fix for the Makefile.rules file.
# BRH flags ifeq ($(USE_BRH),1) BRH_DIR = $(BASE_DIR) CPPFLAGS += -I$(BRH_DIR)/src ifeq ($(WITH_RPATH),1) LDFLAGS += -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR) else LDFLAGS += -L$(LIB_DIR) endif LDLIBS += -lbrh endif ifeq ($(USE_BOOST_THREAD),1) CPPFLAGS += -pthread -DHAS_BOOST_THREADS LDFLAGS += -pthread LDLIBS += -L$(DIR_BOOST_LIB) -lboost_system -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD) -lpthread endif
And Happy New Year,
Yet another random Ubuntu-centric bioinformatics aside in the event others run into the same build issues (with errors included below, as you likely googled those first). For those wondering…
The Hierarchical Catalog of Orthologs v8
Orthology (website, download) is the cornerstone of comparative genomics and gene function prediction. OrthoDB aims to classify protein-coding genes from the increasing number of available sequenced genomes into groups of orthologs descended from a single gene of the last common ancestor (LCA) of each clade of species. Applying this concept to the hierarchy of LCAs along the species phylogeny results in multiple levels of orthology: the more closely-related the species, the more finely-resolved the orthologous relations.
The build here was on a fresh installation of 64-bit Ubuntu 14.04 (Trusty Tahr). All of the errors produced come from running on that clean install, meaning you'll run into dumb errors (like missing build-essential), didn't-know-we-needed-that errors (boost), and that's-probbly-an-Ubuntu-oddity errors (with a modified Makefile.rules file with explicit boost calls linked to below; I suspect the developers are working on a non-Ubuntu distro).
Relevant apt-get's
sudo apt-get install build-essential libboost-all-dev
Relevant Downloads
* tclap (1.2.1) – tclap.sourceforge.net/
Stage 1 – Just Trying The Easy Install
I build everything in /opt by default and propose you do the same (whatever). First steps included.
username@ubuntu:~$ cd Downloads/ username@ubuntu:~/Downloads$ sudo mv OrthoDB_soft_1.6.tgz /opt/ username@ubuntu:~/Downloads$ cd /opt/ username@ubuntu:/opt$ sudo tar xvf OrthoDB_soft_1.6.tgz OrthoDB_soft_1.6/ OrthoDB_soft_1.6/BRHCLUS-1.12.7/ ... OrthoDB_soft_1.6/README OrthoDB_soft_1.6/LICENSE
username@ubuntu:/opt$ cd OrthoDB_soft_1.6/ username@ubuntu:/opt/OrthoDB_soft_1.6$ sudo make WITH_RPATH=1 prefix=$(pwd) all make: *** No rule to make target `all'. Stop.
If you read the README file, you figure out to move to the BRHCLUS folder, then discover the need for the boost libraries, available via an apt-get:
username@ubuntu:/opt/OrthoDB_soft_1.6$ cd BRHCLUS-1.12.7/ username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh FATAL: cannot find boost libraries! - Is boost installed (boost_system) ? - Is boost installed in any of the search paths ? If not, add the path to PATH_SEARCH_LIB at the top of this script.
Stage 2 – sudo apt-get install libboost-all-dev
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo apt-get install libboost-all-dev Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: account-plugin-windows-live libupstart1 Use 'apt-get autoremove' to remove them. The following extra packages will be installed: icu-devtools libboost-atomic-dev libboost-atomic1.54-dev libboost-atomic1.54.0 libboost-chrono-dev libboost-chrono1.54-dev ... libxml2-dev mpi-default-bin mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common zlib1g-dev 0 upgraded, 102 newly installed, 0 to remove and 14 not upgraded. Need to get 46.7 MB of archives. After this operation, 262 MB of additional disk space will be used. Do you want to continue? [Y/n] Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main libboost-atomic1.54.0 amd64 1.54.0-4ubuntu3.1 [8,076 B] Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main libboost-chrono1.54.0 amd64 1.54.0-4ubuntu3.1 [12.5 kB] Get:3 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/universe libboost-context1.54.0 amd64 1.54.0-4ubuntu3.1 [8,028 B] Get:4 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main libboost-filesystem1.54.0 amd64 1.54.0-4ubuntu3.1 [34.2 kB] ... Setting up libboost-wave-dev:amd64 (1.54.0.1ubuntu1) ... Setting up libboost-all-dev (1.54.0.1ubuntu1) ... Setting up libhwloc-plugins (1.8-1ubuntu1.14.04.1) ... Processing triggers for libc-bin (2.19-0ubuntu6.6) ...
The configure stage now works…
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh OK - boost libraries OK - boost thread libraries OK - boost include dir OK - tclap include dir OK - thread pool include dir Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created
But, right off the bat, a clean install is missing build tools.
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make WITH_RPATH=1 prefix=$(pwd) all Compiling brh_version.cpp /bin/sh: 1: g++: not found make[2]: *** [.linux/brh_version.o] Error 127 make[1]: *** [src] Error 2 make: *** [all] Error 2
Stage 3 – sudo apt-get install build-essential
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo apt-get install build-essential Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: account-plugin-windows-live libupstart1 ... 0 upgraded, 9 newly installed, 0 to remove and 14 not upgraded. Need to get 15.9 MB of archives. After this operation, 27.9 MB of additional disk space will be used. Do you want to continue? [Y/n] Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main g++-4.8 amd64 4.8.4-2ubuntu1~14.04 [15.0 MB] Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty/main g++ amd64 4:4.8.2-1ubuntu6 [1,490 B] Get:3 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main dpkg-dev all 1.17.5ubuntu5.5 [726 kB] Get:4 http://us.archive.ubuntu.com/ubuntu/ trusty/main build-essential amd64 11.6ubuntu6 [4,838 B] ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libalgorithm-diff-perl (1.19.02-3) ... Setting up libalgorithm-diff-xs-perl (0.04-2build4) ... Setting up libalgorithm-merge-perl (0.08-2) ...
And the build process now takes steps forward.
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make WITH_RPATH=1 prefix=$(pwd) all Compiling brh_version.cpp Compiling brh_common.cpp Compiling pairdataset.cpp Compiling brh_functions.cpp Compiling keymap.cpp Compiling inparalog.cpp Compiling clusterdata.cpp Compiling cluster.cpp Compiling clusterize.cpp Compiling cluster_functions.cpp Compiling modularity.cpp Compiling tri4algo.cpp Linking libbrh.so Compiling brhclus.cpp Linking brhclus .linux/brhclus.o: In function `__static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:222: undefined reference to `boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference to `boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:224: undefined reference to `boost::system::system_category()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::get_current_thread_data()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::disable_interruption()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::interruption_point()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::start_thread_noexcept()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::interrupt()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::hiden::sleep_until(timespec const&)' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::join_noexcept()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `vtable for boost::detail::thread_data_base' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::thread_data_base::~thread_data_base()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::native_handle()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::detach()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::~disable_interruption()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `typeinfo for boost::detail::thread_data_base' collect2: error: ld returned 1 exit status make[2]: *** [/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin/brhclus] Error 1 make[1]: *** [tools/brhclus] Error 2 make: *** [all] Error 2
Stage 4 – tclap Install
A quick google search produces the following from info.circ.rochester.edu/BlueHive/Software/Bioinformatics/orthodb.html indicating that tclap is an OrthoDB dependency that needs to be satisfied. The version I've built below (1.2.1) can be downloaded from tclap.sourceforge.net
username@ubuntu:/opt$ ls OrthoDB_soft_1.6 OrthoDB_soft_1.6.tgz tclap-1.2.1.tar.gz
Extract and expand.
username@ubuntu:/opt$ sudo tar xvf tclap-1.2.1.tar.gz tclap-1.2.1/ tclap-1.2.1/aclocal.m4 tclap-1.2.1/AUTHORS tclap-1.2.1/ChangeLog ... tclap-1.2.1/config/Makefile.am tclap-1.2.1/config/Makefile.in tclap-1.2.1/config/missing tclap-1.2.1/config/mkinstalldirs
The build process goes without issue.
username@ubuntu:/opt$ cd tclap-1.2.1/ username@ubuntu:/opt/tclap-1.2.1$ sudo ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk ... config.status: creating tests/Makefile config.status: creating config/config.h config.status: executing depfiles commands config.status: executing default commands
Onto make…
username@ubuntu:/opt/tclap-1.2.1$ sudo make Making all in include make[1]: Entering directory `/opt/tclap-1.2.1/include' Making all in tclap make[2]: Entering directory `/opt/tclap-1.2.1/include/tclap' make[2]: Nothing to be done for `all'. ... make[1]: Leaving directory `/opt/tclap-1.2.1/config' make[1]: Entering directory `/opt/tclap-1.2.1' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/opt/tclap-1.2.1'
And make install…
username@ubuntu:/opt/tclap-1.2.1$ sudo make install Making install in include make[1]: Entering directory `/opt/tclap-1.2.1/include' Making install in tclap make[2]: Entering directory `/opt/tclap-1.2.1/include/tclap' ... test -z "/usr/local/lib/pkgconfig" || /bin/mkdir -p "/usr/local/lib/pkgconfig" /usr/bin/install -c -m 644 'tclap.pc' '/usr/local/lib/pkgconfig/tclap.pc' make[2]: Leaving directory `/opt/tclap-1.2.1' make[1]: Leaving directory `/opt/tclap-1.2.1'
Stage 5 – Re-attempt The OrthoDB Build
The configure goes without issue again…
username@ubuntu:/opt$ cd OrthoDB_soft_1.6/ username@ubuntu:/opt/OrthoDB_soft_1.6$ cd BRHCLUS-1.12.7/ username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make clean username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh OK - boost libraries OK - boost thread libraries OK - boost include dir OK - tclap include dir OK - thread pool include dir Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created
But there's still an error at the make stage.
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make all Compiling brh_version.cpp Compiling brh_common.cpp Compiling pairdataset.cpp Compiling brh_functions.cpp Compiling keymap.cpp Compiling inparalog.cpp Compiling clusterdata.cpp Compiling cluster.cpp Compiling clusterize.cpp Compiling cluster_functions.cpp Compiling modularity.cpp Compiling tri4algo.cpp Linking libbrh.so Compiling brhclus.cpp Linking brhclus .linux/brhclus.o: In function `__static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:222: undefined reference to `boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference to `boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:224: undefined reference to `boost::system::system_category()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::get_current_thread_data()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::disable_interruption()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::interruption_point()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::start_thread_noexcept()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::interrupt()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::hiden::sleep_until(timespec const&)' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::join_noexcept()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `vtable for boost::detail::thread_data_base' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::thread_data_base::~thread_data_base()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::native_handle()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::detach()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::~disable_interruption()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `typeinfo for boost::detail::thread_data_base' collect2: error: ld returned 1 exit status make[2]: *** [/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin/brhclus] Error 1 make[1]: *** [tools/brhclus] Error 2 make: *** [all] Error 2
Stage 6 – Google Says Make Some Symbolic Links
A first fix for the boost error was to make symbolic links for libboost_thread.so and libboost_timer.so in /usr/lib.
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ cd /usr/lib/x86_64-linux-gnu/ username@ubuntu:/usr/lib/x86_64-linux-gnu$ sudo ln -s libboost_thread.so /usr/lib username@ubuntu:/usr/lib/x86_64-linux-gnu$ sudo ln -s libboost_timer.so /usr/lib username@ubuntu:/usr/lib/x86_64-linux-gnu$ cd /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/ username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make clean username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh OK - boost libraries OK - boost thread libraries OK - boost include dir OK - tclap include dir OK - thread pool include dir Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created
But this didn't work either.
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make all Compiling brh_version.cpp Compiling brh_common.cpp Compiling pairdataset.cpp Compiling brh_functions.cpp Compiling keymap.cpp Compiling inparalog.cpp Compiling clusterdata.cpp Compiling cluster.cpp Compiling clusterize.cpp Compiling cluster_functions.cpp Compiling modularity.cpp Compiling tri4algo.cpp Linking libbrh.so Compiling brhclus.cpp Linking brhclus .linux/brhclus.o: In function `__static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:222: undefined reference to `boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference to `boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:224: undefined reference to `boost::system::system_category()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::get_current_thread_data()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::disable_interruption()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::interruption_point()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::start_thread_noexcept()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::interrupt()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::hiden::sleep_until(timespec const&)' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::join_noexcept()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `vtable for boost::detail::thread_data_base' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::thread_data_base::~thread_data_base()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::native_handle()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::detach()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::~disable_interruption()' /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `typeinfo for boost::detail::thread_data_base' collect2: error: ld returned 1 exit status make[2]: *** [/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin/brhclus] Error 1 make[1]: *** [tools/brhclus] Error 2 make: *** [all] Error 2
Stage 7 – The Boost Issue May Be Ubuntu-Specific
The final solution was to modify the Makefile.rules file to explicitly call on boost in Ubuntu. Make a backup copy of the Makefile.rules in the OrthoDB folder, then place this new Makefile.rules file into the same folder. The modified Makefile.rules is below for copy+paste, else you can download it here: 2016mar25_orthodb_Makefile_rules.txt (just rename the file and place into OrthoDB_soft_1.6/BRHCLUS-1.12.7).
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo nano Makefile.rules
#
# Build rules
#
# Keep secondary files
.SECONDARY:
include $(ROOT_DIR)/Makefile.config
ifeq ($(strip $(DIR_TCLAP)),)
$(error "Build requires TCLAP package (http://tclap.sourceforge.net)")
endif
# if install, read build details
ifeq "$(MAKE-TARGET)" "install"
include $(ROOT_DIR)/.makefile.build
endif
# Object directory
OBJ_DIR = .linux
# Use gcc4
CXX = g++
# Use rpath or not
WITH_RPATH ?= 1
LDFLAGS =
ifeq "$(MAKE-TARGET)" "static"
WITH_RPATH = 0
LDFLAGS += -static -lboost_system -lboost_thread -lpthread
endif
# check BOOST
USE_BOOST ?= 1
# check boost threads
USE_BOOST_THREAD ?= 1
ifeq ($(strip $(LIB_BOOST_THREAD)),)
USE_BOOST_THREAD = 0
USE_THREADPOOL = 0
endif
ifeq ($(strip $(DIR_THREADPOOL)),)
USE_THREADPOOL = 0
endif
# Library and binary directories
BASE_DIR := $(shell cd $(ROOT_DIR) ; pwd)
# Install directories
# With rpath, enforce install dir same as build
# Without, use same as build as default
# prefix - install topdir
# libdir/bindir - install lib/bin
# BASE_DIR - build top dir
# LIB_DIR/BIN_DIR - build top dir
#
# with rpath :
# build and install dirs are the same
# default top is BASE_DIR
# else :
# build is always under BASE_DIR
# install under prefix (default BASE_DIR)
#
#ifeq ($(WITH_RPATH),1)
#prefix ?= $(BASE_DIR)
#libdir = $(prefix)/lib
#bindir = $(prefix)/bin
##LIB_DIR := $(shell mkdir -p $(libdir) ; cd $(libdir) ; pwd)
##BIN_DIR := $(shell mkdir -p $(bindir) ; cd $(bindir) ; pwd)
#LIB_DIR := $(libdir)
#BIN_DIR := $(bindir)
#else
#LIB_DIR := $(shell mkdir -p $(BASE_DIR)/lib ; cd $(BASE_DIR)/lib ; pwd)
#BIN_DIR := $(shell mkdir -p $(BASE_DIR)/bin ; cd $(BASE_DIR)/bin ; pwd)
#prefix ?= $(BASE_DIR)
#libdir ?= $(LIB_DIR)
#bindir ?= $(BIN_DIR)
#endif
LIB_DIR := $(shell mkdir -p $(BASE_DIR)/lib ; cd $(BASE_DIR)/lib ; pwd)
BIN_DIR := $(shell mkdir -p $(BASE_DIR)/bin ; cd $(BASE_DIR)/bin ; pwd)
prefix ?= $(BASE_DIR)
libdir ?= $(LIB_DIR)
bindir ?= $(BIN_DIR)
LIB_INSTDIR := $(prefix)/lib
BIN_INSTDIR := $(prefix)/bin
# Install user/group
INST_USR = $(shell whoami)
INST_GRP ?= $(shell groups | cut -f 1 -d ' ' )
# Establish install command
# if rpath -> always chown
# else
# if targetdir==installdir -> chown
# else install
# endif
#ifeq ($(WITH_RPATH),1)
#INST_CMD = chown $(INST_USR).$(INST_GRP)
#else
TARGET_DIR = $(dir $(TARGET))
rpTARGET = $(realpath $(firstword $(TARGET_DIR)))
rpINSTDIR = $(realpath $(prefix)/$(INSTDIR))
ifeq ($(rpTARGET),$(rpINSTDIR))
INST_CMD = chown $(INST_USR).$(INST_GRP)
else
INST_CMD = mkdir -p $(prefix)/$(INSTDIR); install -D -m 755 -g $(INST_GRP) -t $(prefix)/$(INSTDIR)
endif
#endif
# Definitions concerning build environment
CPPFLAGS += -DBRH_BUILD_ENV="\"$(shell uname -s -r -v -m -i -p -o)\""
CPPFLAGS += -DBRH_BUILD_TIME="\"$(shell date)\""
# Default pre-processor flags
CPPFLAGS += -DBASE_DIR="\"$(BASE_DIR)\""
CPPFLAGS += -D_REENTRANT
CPPFLAGS += -D_XOPEN_SOURCE
# c++ standard
CPPFLAGS += -std=c++11
CXXFLAGS += -std=c++11
# debug flag
ifeq ($(USE_DEBUG),3)
CXXFLAGS += -fno-inline -fbounds-check
else ifeq ($(USE_DEBUG),2)
CPPFLAGS += -DBRH_DEBUG
CXXFLAGS += -fno-inline -fbounds-check
else ifeq ($(USE_DEBUG),1)
CPPFLAGS += -DBRH_CHECK_IT
CXXFLAGS += -finline-functions -fbounds-check
else
CXXFLAGS += -finline-functions
endif
# Default compiler flags
CXXFLAGS += -fPIC
CXXFLAGS += -MMD
CXXFLAGS += -g
CXXFLAGS += -Wall -Werror
CXXFLAGS += -fexceptions
#CXXFLAGS += -fno-inline
CXXFLAGS += -O3
#CXXFLAGS += -O0
CXXFLAGS += -I$(BASE_DIR)/src
#CXXFLAGS += -std=c++11
#CXXFLAGS += -pg
#LDFLAGS += -pg
# BRH flags
ifeq ($(USE_BRH),1)
BRH_DIR = $(BASE_DIR)
CPPFLAGS += -I$(BRH_DIR)/src
ifeq ($(WITH_RPATH),1)
LDFLAGS += -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR) -lboost_system -lboost_thread -lpthread
else
LDFLAGS += -L$(LIB_DIR) -lboost_system -lboost_thread -lpthread
endif
LDLIBS += -lbrh -lboost_system -lboost_thread -lpthread
endif
ifeq ($(USE_BOOST_THREAD),1)
CPPFLAGS += -pthread -DHAS_BOOST_THREADS
LDFLAGS += -pthread -L$(DIR_BOOST_LIB) -lboost_system -lboost_thread -lpthread -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD)
endif
ifeq ($(USE_THREADPOOL),1)
CPPFLAGS += -DHAS_BOOST_THREADPOOL
CPPFLAGS += -I$(DIR_THREADPOOL)
endif
ifeq ($(USE_BOOST),1)
CPPFLAGS += -I$(DIR_BOOST_INC)
endif
# TCLAP flags
ifeq ($(USE_TCLAP),1)
CPPFLAGS += -I$(DIR_TCLAP)
endif
# BOOST flags
ifeq ($(USE_THREAD),1)
endif
# Check file type
ifeq ($(suffix $(firstword $(SOURCES))),.cpp)
IS_CPP = 1
else
IS_CPP = 0
endif
# List of objects
ifeq ($(IS_CPP),1)
OBJECTS = $(SOURCES:%.cpp=$(OBJ_DIR)/%.o)
endif
# Default build
default: all
ifeq ($(IS_CPP),1)
# Build a binary
$(BIN_DIR)/%: $(OBJECTS) Makefile $(BASE_DIR)/Makefile.rules
@echo " Linking $(@F)"
@mkdir -p $(@D)
@$(LINK.cc) $(LDFLAGS) -o $@ $(OBJECTS) $(LDLIBS)
# Build a shared library
$(LIB_DIR)/%.so: $(OBJECTS) Makefile $(BASE_DIR)/Makefile.rules
@echo " Linking $(@F)"
@mkdir -p $(@D)
@$(LINK.cc) -shared -o $@ $(OBJECTS) $(LDLIBS)
# Build a static library
$(LIB_DIR)/%.a: $(OBJECTS) Makefile $(BASE_DIR)/Makefile.rules
@echo " Linking $(@F)"
@mkdir -p $(@D)
@ar rcs $@ $(OBJECTS)
# Include dependency files
-include $(OBJECTS:%.o=%.d)
# Build an object file
$(OBJ_DIR)/%.o: %.cpp Makefile
@echo " Compiling $< "
@mkdir -p $(@D)
@$(COMPILE.cc) -o $@ $<
else
$(BIN_DIR)/%.py: %.py
@echo " Copying $< to target dir"
@cp -f $< $@
endif
# Main targets are phony
.PHONY: default all clean_target clean_obj doc clean_doc clean install static
# Build target
all: $(TARGET)
static: $(TARGET)
# Clean objects
clean_obj:
@$(RM) -r $(OBJ_DIR)
# Clean build
clean_target:
@$(RM) -r $(OBJ_DIR) $(TARGET)
# Build documentation
doc:
@$(MAKE) -C $(BASE_DIR) $@
# Clean build
clean: clean_target
# Install
install:
# @echo "rpT : $(rpTARGET)"
# @echo "rpI : $(rpINSTDIR)"
# @echo "rpath : $(WITH_RPATH)"
# @echo "inst : $(INST_CMD) $(TARGET)"
@target="$(TARGET)"; \
[ $${#target} -gt 0 ] || target="$(OUTPUT)"; \
for f in $${target}; do \
fname=`basename $$f`; \
if [ -f $$f ]; then \
echo "Installing in $(prefix)/$(INSTDIR) <$$fname>"; \
$(INST_CMD) $$f; \
fi; \
done
The configure step runs fine…
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make clean username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh OK - boost libraries OK - boost thread libraries OK - boost include dir OK - tclap include dir OK - thread pool include dir Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created
…and the build itself runs fine.
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make all Compiling brh_version.cpp Compiling brh_common.cpp Compiling pairdataset.cpp Compiling brh_functions.cpp Compiling keymap.cpp Compiling inparalog.cpp Compiling clusterdata.cpp Compiling cluster.cpp Compiling clusterize.cpp Compiling cluster_functions.cpp Compiling modularity.cpp Compiling tri4algo.cpp Linking libbrh.so Compiling brhclus.cpp Linking brhclus Compiling evolrate.cpp Linking evolrate Compiling statbrh.cpp Linking statbrh Compiling brh2x.cpp Linking brh2x Compiling statclus.cpp Linking statclus Compiling cmpclus.cpp Linking cmpclus Compiling getclus.cpp Linking getclus Compiling cmpbrh.cpp Linking cmpbrh Compiling cmpinpar.cpp Linking cmpinpar Compiling renumclus.cpp Linking renumclus Compiling getinpar.cpp Linking getinpar Compiling mergeinpar.cpp Linking mergeinpar Compiling align2brh.cpp Linking align2brh Compiling findbrh.cpp Linking findbrh Copying parsedump.py to target dir Copying getbrh.py to target dir Copying plot_brhclus_progress.py to target dir
Stage 8 – Build The Tests
Just to make sure all is working, make globaltest.
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make globaltest
------------------------------------------------------------- Binary dir : /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin Library dir : /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib ------------------------------------------------------------- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST MACHINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ uname [ Linux ubuntux 3.16.0-59-generic #79~14.04.1-Ubuntu SMP Mon Jan 18 15:41:27...] cpu [ Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz] mem [ MemTotal: 3949740 kB] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS with option --single ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------ run default setup ------------------------------ ------------------------------ run with harder e-value cuts ------------------------------ ------------------------------ run with soft e-value cuts ------------------------------ ------------------------------ Check output files ------------------------------ default [OK] hard_e-val [OK] soft_e-val [OK] ------------------------------ Check timing ------------------------------ default [16 %] hard_e-val [-8 %] soft_e-val [10 %] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS, resume function with option --single ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ resume [OK, contents same but clids or seqs differ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS with option --nostringent ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------ run default setup ------------------------------ ------------------------------ run with harder e-value cuts ------------------------------ ------------------------------ run with soft e-value cuts ------------------------------ ------------------------------ Check output files ------------------------------ default [OK] hard_e-val [OK] soft_e-val [OK] ------------------------------ Check timing ------------------------------ default [18 %] hard_e-val [10 %] soft_e-val [2 %] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS, resume function with option --nostringent ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ resume [OK, contents same but clids or seqs differ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------ run default setup ------------------------------ ------------------------------ run with harder e-value cuts ------------------------------ ------------------------------ run with soft e-value cuts ------------------------------ ------------------------------ Check output files ------------------------------ default [OK] hard_e-val [OK] soft_e-val [OK] ------------------------------ Check timing ------------------------------ default [7 %] hard_e-val [8 %] soft_e-val [12 %] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS, resume function ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ resume [OK, contents same but clids or seqs differ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS with option --lowmem ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------ run default setup ------------------------------ ------------------------------ run with harder e-value cuts ------------------------------ ------------------------------ run with soft e-value cuts ------------------------------ ------------------------------ Check output files ------------------------------ default [OK] hard_e-val [OK] soft_e-val [OK] ------------------------------ Check timing ------------------------------ default [6 %] hard_e-val [8 %] soft_e-val [7 %] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS, resume function with option --lowmem ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ resume [OK, contents same but clids or seqs differ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST BRHCLUS merge BRHs into an existing cluster configuration ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mergebrh [OK] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST STATCLUS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ default [OK] hard_e-val [OK] soft_e-val [OK] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST CMPCLUS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exact_match [OK] mis-match [OK] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST CMPCLUS related groups ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ default [OK] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TEST MERGEINPAR ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ clusters [OK] unresolved [OK] ------------------------------------------ Warnings (4) were detected. ------------------------------------------ Most likely this is of not concern and the probable origin are messages like [OK, contents same but clids or seqs differ] They may be caused by rounding errors on different architectures/versions of the software.