diff options
Diffstat (limited to 'examples/dragmap')
| -rw-r--r-- | examples/dragmap/Makefile | 6 | ||||
| -rw-r--r-- | examples/dragmap/README.md | 47 | ||||
| -rwxr-xr-x | examples/dragmap/config.mk | 15 | ||||
| -rwxr-xr-x | examples/dragmap/run.sh | 11 | ||||
| -rwxr-xr-x | examples/dragmap/test1.sh | 3 | ||||
| -rwxr-xr-x | examples/dragmap/test2.sh | 5 | ||||
| -rwxr-xr-x | examples/dragmap/test3.sh | 7 |
7 files changed, 94 insertions, 0 deletions
diff --git a/examples/dragmap/Makefile b/examples/dragmap/Makefile new file mode 100644 index 0000000..31dd118 --- /dev/null +++ b/examples/dragmap/Makefile @@ -0,0 +1,6 @@ +include config.mk +$(info BOOST_ROOT is $(BOOST_ROOT)) +$(info BOOST_INCLUDEDIR is $(BOOST_INCLUDEDIR)) +$(info BOOST_LIBRARYDIR is $(BOOST_LIBRARYDIR)) +$(info CPPFLAGS is $(CPPFLAGS)) +$(info LDFLAGS is $(LDFLAGS)) diff --git a/examples/dragmap/README.md b/examples/dragmap/README.md new file mode 100644 index 0000000..29ba382 --- /dev/null +++ b/examples/dragmap/README.md @@ -0,0 +1,47 @@ +# README + +Trying to build [DRAGMAP](https://github.com/Illumina/DRAGMAP) using updated +[Boost libraries](https://www.boost.org/). But the building process seems to be +using the outdated system Boost libraries in `/usr/include/boost/`. This is because I keep getting these errors: + + /usr/include/boost/program_options/detail/value_semantic.hpp:170: undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)' + +Here I examine the behaviour of the following environment variables: + +* `BOOST_ROOT` +* `BOOST_INCLUDEDIR` +* `BOOST_LIBRARYDIR` + +The required Boost libraries are: + + BOOST_LIBRARIES := system filesystem date_time thread iostreams regex program_options + +They reside in `/usr/include/boost169/boost/`; for example: + + /usr/include/boost169/boost/system + /usr/include/boost169/boost/filesystem + +Use `./run.sh` to run all the test scripts. + +## Notes + +* The `CPPFLAGS` macro is the one to use to specify `#include` directories. +* The `LDFLAGS` is normally set to contain options that are passed through to + the linker (so may include required libraries). + +[Probably the same +problem](https://stackoverflow.com/questions/62280304/yum-using-boost-1-69-instead-of-default-1-53-version-on-centos) +but I do not want to manually manipulate the symlinks by changing: + + /lib64/libboost_system.so -> libboost_system.so.1.53.0 + +to: + + /lib64/libboost_system.so -> libboost_system.so.1.69.0 + +## Fix + +Do not include `boost` in the DIR. For example: + + export BOOST_INCLUDEDIR=/usr/include/boost169 + export BOOST_LIBRARYDIR=/usr/lib64/boost169 diff --git a/examples/dragmap/config.mk b/examples/dragmap/config.mk new file mode 100755 index 0000000..433163a --- /dev/null +++ b/examples/dragmap/config.mk @@ -0,0 +1,15 @@ +BOOST_LIBRARIES := system filesystem date_time thread iostreams regex program_options + +ifneq (,$(BOOST_ROOT)) +BOOST_INCLUDEDIR?=$(BOOST_ROOT)/include +BOOST_LIBRARYDIR?=$(BOOST_ROOT)/lib +endif # ifneq (,$(BOOST_ROOT)) + +ifneq (,$(BOOST_INCLUDEDIR)) +CPPFLAGS += -I $(BOOST_INCLUDEDIR) +endif + +ifneq (,$(BOOST_LIBRARYDIR)) +LDFLAGS += -L $(BOOST_LIBRARYDIR) +endif +LDFLAGS += $(BOOST_LIBRARIES:%=-lboost_%) diff --git a/examples/dragmap/run.sh b/examples/dragmap/run.sh new file mode 100755 index 0000000..dcb38fd --- /dev/null +++ b/examples/dragmap/run.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash + +>&2 echo -e "Running test1\n" +./test1.sh +>&2 echo +>&2 echo -e "Running test2\n" +./test2.sh +>&2 echo +>&2 echo -e "Running test3\n" +./test3.sh +>&2 echo diff --git a/examples/dragmap/test1.sh b/examples/dragmap/test1.sh new file mode 100755 index 0000000..d9eae58 --- /dev/null +++ b/examples/dragmap/test1.sh @@ -0,0 +1,3 @@ +#!/usr/bin/env bash + +make diff --git a/examples/dragmap/test2.sh b/examples/dragmap/test2.sh new file mode 100755 index 0000000..8bbc6ff --- /dev/null +++ b/examples/dragmap/test2.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +export BOOST_ROOT=/usr/include/boost169/boost/ + +make diff --git a/examples/dragmap/test3.sh b/examples/dragmap/test3.sh new file mode 100755 index 0000000..99aca0d --- /dev/null +++ b/examples/dragmap/test3.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +export BOOST_ROOT=/usr/include/boost169/ +export BOOST_INCLUDEDIR=/usr/include/boost169 +export BOOST_LIBRARYDIR=/usr/lib64/boost169 + +make |