s4hts / HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

https://s4hts.github.io/HTStream/

Apache License 2.0

49 stars 9 forks source link

Problem when insalling the program #148

Closed efratushava closed 5 years ago

efratushava commented 5 years ago

Hello,

I was trying to install the program, as written here, in my linux system:

wget -O 1_60.tar.bz2 https://sourceforge.net/projects/boost/files/boost/1.60.0/boost_1_60_0.tar.bz2/download tar --bzip2 -xf 1_60.tar.bz2 cd boost_1_60_0 ./bootstrap.sh ./b2 # This will take a while. BOOST_INCLUDE=$(pwd) BOOST_INCLUDE_LIB=$(pwd)/stage/lib

I ran all the command until "./b2". Then, I run "./b2" I couldn't attach my "./b2" command output, so I copied it in the bottom of this post. I run the next two commands, and then I tried to use the program, for example "hts_SuperDeduper -h", and I get: -bash: hts_SuperDeduper: command not found

What can I do?

My ./b2 output: Performing configuration checks

- 32-bit                   : no  (cached)
- 64-bit                   : yes (cached)
- arm                      : no  (cached)
- mips1                    : no  (cached)
- power                    : no  (cached)
- sparc                    : no  (cached)
- x86                      : yes (cached)

Building the Boost C++ Libraries.

- symlinks supported       : yes (cached)
- lockfree boost::atomic_flag : yes (cached)
- has_icu builds           : yes (cached)

warning: Graph library does not contain MPI-based parallel components. note: to enable them, add "using mpi ;" to your user-config.jam

zlib : yes (cached)
iconv (libc) : yes (cached)
icu : yes (cached)
compiler-supports-visibility : yes (cached)
compiler-supports-ssse3 : yes (cached)
compiler-supports-avx2 : no (cached)
gcc visibility : yes (cached)
long double support : yes (cached) warning: skipping optional Message Passing Interface (MPI) library. note: to enable MPI support, add "using mpi ;" to user-config.jam. note: to suppress this message, pass "--without-mpi" to bjam. note: otherwise, you can safely ignore this message.
zlib : yes (cached)

Component configuration:

- atomic                   : building
- chrono                   : building
- container                : building
- context                  : building
- coroutine                : building
- coroutine2               : building
- date_time                : building
- exception                : building
- filesystem               : building
- graph                    : building
- graph_parallel           : building
- iostreams                : building
- locale                   : building
- log                      : building
- math                     : building
- mpi                      : building
- program_options          : building
- python                   : building
- random                   : building
- regex                    : building
- serialization            : building
- signals                  : building
- system                   : building
- test                     : building
- thread                   : building
- timer                    : building
- type_erasure             : building
- wave                     : building

...patience... ...patience... ...patience... ...patience... ...patience... ...patience... ...found 13863 targets... ...updating 152 targets... common.mkdir bin.v2/libs/atomic common.mkdir bin.v2/libs/atomic/build common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7 common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi gcc.compile.c++ bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi/lockpool.o gcc.link.dll bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi/libboost_atomic.so.1.60.0 common.copy stage/lib/libboost_atomic.so.1.60.0 ln-UNIX stage/lib/libboost_atomic.so common.mkdir bin.v2/libs/chrono common.mkdir bin.v2/libs/chrono/build common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7 common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/chrono.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/thread_clock.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/process_cpu_clocks.o gcc.link.dll bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/libboost_chrono.so.1.60.0 common.copy stage/lib/libboost_chrono.so.1.60.0 ln-UNIX stage/lib/libboost_chrono.so common.mkdir bin.v2/libs/container common.mkdir bin.v2/libs/container/build common.mkdir bin.v2/libs/container/build/gcc-4.4.7 common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi gcc.compile.c bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/alloc_lib.o In file included from libs/container/src/alloc_lib.c:19: libs/container/src/dlmalloc_ext_2_8_6.c: In function ‘boost_cont_malloc_stats’: libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$in_use_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$in_use_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$system_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$max_system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$max_system_bytes’ was declared here gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/dlmalloc.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/global_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/monotonic_buffer_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o libs/container/src/pool_resource.cpp:35: error: declaration of ‘typedef class boost::container::pmr::block_slist_base boost::container::pmr::pool_data_t::block_slist_base’ ./boost/container/detail/block_slist.hpp:67: error: changes meaning of ‘block_slist_base’ from ‘class boost::container::pmr::block_slist_base’

"g++"  -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pthread -fPIC -m64  -DBOOST_ALL_NO_LIB=1 -DBOOST_CONTAINER_DYN_LINK=1 -DNDEBUG  -I"." -c -o "bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o" "libs/container/src/pool_resource.cpp"

...failed gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o... gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/synchronized_pool_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/unsynchronized_pool_resource.o ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>libboost_container.so.1.60.0 for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>pool_resource.o... ...skipped <pstage/lib>libboost_container.so.1.60.0 for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>libboost_container.so.1.60.0... ...skipped <pstage/lib>libboost_container.so for lack of <pstage/lib>libboost_container.so.1.60.0... common.mkdir bin.v2/libs/context common.mkdir bin.v2/libs/context/build common.mkdir bin.v2/libs/context/build/gcc-4.4.7 common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm/make_x86_64_sysv_elf_gas.o gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm/jump_x86_64_sysv_elf_gas.o common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/posix gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/posix/stack_traits.o gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/execution_context.o gcc.link.dll bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/libboost_context.so.1.60.0 common.copy stage/lib/libboost_context.so.1.60.0 ln-UNIX stage/lib/libboost_context.so common.mkdir bin.v2/libs/coroutine common.mkdir bin.v2/libs/coroutine/build common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7 common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/detail gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/detail/coroutine_context.o gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/exceptions.o common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/posix gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/posix/stack_traits.o gcc.link.dll bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/libboost_coroutine.so.1.60.0 common.copy stage/lib/libboost_coroutine.so.1.60.0 ln-UNIX stage/lib/libboost_coroutine.so common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7 common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/greg_month.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/greg_weekday.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/date_generators.o gcc.link.dll bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/libboost_date_time.so.1.60.0 common.copy stage/lib/libboost_date_time.so.1.60.0 ln-UNIX stage/lib/libboost_date_time.so gcc.link.dll bin.v2/libs/locale/build/gcc-4.4.7/release/threading-multi/libboost_locale.so.1.60.0 common.copy stage/lib/libboost_locale.so.1.60.0 ln-UNIX stage/lib/libboost_locale.so gcc.link.dll bin.v2/libs/log/build/gcc-4.4.7/release/build-no/log-api-unix/threading-multi/libboost_log.so.1.60.0 common.copy stage/lib/libboost_log.so.1.60.0 ln-UNIX stage/lib/libboost_log.so gcc.link.dll bin.v2/libs/log/build/gcc-4.4.7/release/build-no/log-api-unix/threading-multi/libboost_log_setup.so.1.60.0 common.copy stage/lib/libboost_log_setup.so.1.60.0 ln-UNIX stage/lib/libboost_log_setup.so gcc.link.dll bin.v2/libs/timer/build/gcc-4.4.7/release/threading-multi/libboost_timer.so.1.60.0 common.copy stage/lib/libboost_timer.so.1.60.0 ln-UNIX stage/lib/libboost_timer.so gcc.link.dll bin.v2/libs/test/build/gcc-4.4.7/release/threading-multi/libboost_prg_exec_monitor.so.1.60.0 common.copy stage/lib/libboost_prg_exec_monitor.so.1.60.0 ln-UNIX stage/lib/libboost_prg_exec_monitor.so common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/chrono.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/thread_clock.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/process_cpu_clocks.o gcc.archive bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/libboost_chrono.a common.copy stage/lib/libboost_chrono.a gcc.link.dll bin.v2/libs/test/build/gcc-4.4.7/release/threading-multi/libboost_unit_test_framework.so.1.60.0 common.copy stage/lib/libboost_unit_test_framework.so.1.60.0 ln-UNIX stage/lib/libboost_unit_test_framework.so gcc.link.dll bin.v2/libs/type_erasure/build/gcc-4.4.7/release/threading-multi/libboost_type_erasure.so.1.60.0 common.copy stage/lib/libboost_type_erasure.so.1.60.0 ln-UNIX stage/lib/libboost_type_erasure.so gcc.link.dll bin.v2/libs/wave/build/gcc-4.4.7/release/threading-multi/libboost_wave.so.1.60.0 ...on 100th target... common.copy stage/lib/libboost_wave.so.1.60.0 ln-UNIX stage/lib/libboost_wave.so common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c++ bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi/lockpool.o gcc.archive bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi/libboost_atomic.a common.copy stage/lib/libboost_atomic.a common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/alloc_lib.o In file included from libs/container/src/alloc_lib.c:19: libs/container/src/dlmalloc_ext_2_8_6.c: In function ‘boost_cont_malloc_stats’: libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$in_use_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$in_use_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$system_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$max_system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$max_system_bytes’ was declared here gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/dlmalloc.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/global_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/monotonic_buffer_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o libs/container/src/pool_resource.cpp:35: error: declaration of ‘typedef class boost::container::pmr::block_slist_base boost::container::pmr::pool_data_t::block_slist_base’ ./boost/container/detail/block_slist.hpp:67: error: changes meaning of ‘block_slist_base’ from ‘class boost::container::pmr::block_slist_base’

"g++"  -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pthread -m64  -DBOOST_ALL_NO_LIB=1 -DBOOST_CONTAINER_STATIC_LINK=1 -DNDEBUG  -I"." -c -o "bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o" "libs/container/src/pool_resource.cpp"

...failed gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o... gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/synchronized_pool_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/unsynchronized_pool_resource.o ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a(clean) for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>pool_resource.o... ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>pool_resource.o... ...skipped <pstage/lib>libboost_container.a for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a... common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm/make_x86_64_sysv_elf_gas.o gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm/jump_x86_64_sysv_elf_gas.o common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/posix gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/posix/stack_traits.o gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/execution_context.o gcc.archive bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/libboost_context.a common.copy stage/lib/libboost_context.a common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/detail gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/detail/coroutine_context.o gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/exceptions.o common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/posix gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/posix/stack_traits.o gcc.archive bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/libboost_coroutine.a common.copy stage/lib/libboost_coroutine.a common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/greg_month.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/greg_weekday.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/date_generators.o gcc.archive bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/libboost_date_time.a common.copy stage/lib/libboost_date_time.a ...failed updating 2 targets... ...skipped 6 targets... ...updated 144 targets...

joe-angell commented 5 years ago

This is an old boost bug that appears to have been fixed 3 years ago: https://svn.boost.org/trac10/ticket/11856 I recommend you build a newer version of boost, latest is 1.69.

joe

On Sun, Dec 30, 2018 at 10:48 AM efratushava notifications@github.com wrote:

Hello,

I was trying to install the program, as written here https://ibest.github.io/HTStream/, in my linux system:

wget -O 1_60.tar.bz2 https://sourceforge.net/projects/boost/files/boost/1.60.0/boost_1_60_0.tar.bz2/download tar --bzip2 -xf 1_60.tar.bz2 cd boost_1_60_0 ./bootstrap.sh ./b2 # This will take a while. BOOST_INCLUDE=$(pwd) BOOST_INCLUDE_LIB=$(pwd)/stage/lib

I ran all the command until "./b2". Then, I run "./b2" I couldn't attach my "./b2" command output, so I copied it in the bottom of this post. I run the next two commands, and then I tried to use the program, for example "hts_SuperDeduper -h", and I get: -bash: hts_SuperDeduper: command not found

What can I do?

My ./b2 output: Performing configuration checks

32-bit : no (cached)

64-bit : yes (cached)

arm : no (cached)

mips1 : no (cached)

power : no (cached)

sparc : no (cached)

x86 : yes (cached)

Building the Boost C++ Libraries.

symlinks supported : yes (cached)

lockfree boost::atomic_flag : yes (cached)

has_icu builds : yes (cached)

warning: Graph library does not contain MPI-based parallel components. note: to enable them, add "using mpi ;" to your user-config.jam

zlib : yes (cached)

iconv (libc) : yes (cached)

icu : yes (cached)

compiler-supports-visibility : yes (cached)

compiler-supports-ssse3 : yes (cached)

compiler-supports-avx2 : no (cached)

gcc visibility : yes (cached)

long double support : yes (cached) warning: skipping optional Message Passing Interface (MPI) library. note: to enable MPI support, add "using mpi ;" to user-config.jam. note: to suppress this message, pass "--without-mpi" to bjam. note: otherwise, you can safely ignore this message.

zlib : yes (cached)

Component configuration:

atomic : building

chrono : building

container : building

context : building

coroutine : building

coroutine2 : building

date_time : building

exception : building

filesystem : building

graph : building

graph_parallel : building

iostreams : building

locale : building

log : building

math : building

mpi : building

program_options : building

python : building

random : building

regex : building

serialization : building

signals : building

system : building

test : building

thread : building

timer : building

type_erasure : building

wave : building

...patience... ...patience... ...patience... ...patience... ...patience... ...patience... ...found 13863 targets... ...updating 152 targets... common.mkdir bin.v2/libs/atomic common.mkdir bin.v2/libs/atomic/build common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7 common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi gcc.compile.c++ bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi/lockpool.o gcc.link.dll bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi/libboost_atomic.so.1.60.0 common.copy stage/lib/libboost_atomic.so.1.60.0 ln-UNIX stage/lib/libboost_atomic.so common.mkdir bin.v2/libs/chrono common.mkdir bin.v2/libs/chrono/build common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7 common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/chrono.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/thread_clock.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/process_cpu_clocks.o gcc.link.dll bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/libboost_chrono.so.1.60.0 common.copy stage/lib/libboost_chrono.so.1.60.0 ln-UNIX stage/lib/libboost_chrono.so common.mkdir bin.v2/libs/container common.mkdir bin.v2/libs/container/build common.mkdir bin.v2/libs/container/build/gcc-4.4.7 common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi gcc.compile.c bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/alloc_lib.o In file included from libs/container/src/alloc_lib.c:19: libs/container/src/dlmalloc_ext_2_8_6.c: In function ‘boost_cont_malloc_stats’: libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$in_use_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$in_use_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$system_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$max_system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$max_system_bytes’ was declared here gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/dlmalloc.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/global_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/monotonic_buffer_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o libs/container/src/pool_resource.cpp:35: error: declaration of ‘typedef class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header boost::container::pmr::pool_data_t::block_slist_base’ ./boost/container/detail/block_slist.hpp:67: error: changes meaning of ‘block_slist_base’ from ‘class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header’

"g++" -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pthread -fPIC -m64 -DBOOST_ALL_NO_LIB=1 -DBOOST_CONTAINER_DYN_LINK=1 -DNDEBUG -I"." -c -o "bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o" "libs/container/src/pool_resource.cpp"

...failed gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o... gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/synchronized_pool_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/unsynchronized_pool_resource.o ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>libboost_container.so.1.60.0 for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>pool_resource.o... ...skipped <pstage/lib>libboost_container.so.1.60.0 for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>libboost_container.so.1.60.0... ...skipped <pstage/lib>libboost_container.so for lack of <pstage/lib>libboost_container.so.1.60.0... common.mkdir bin.v2/libs/context common.mkdir bin.v2/libs/context/build common.mkdir bin.v2/libs/context/build/gcc-4.4.7 common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm/make_x86_64_sysv_elf_gas.o gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm/jump_x86_64_sysv_elf_gas.o common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/posix gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/posix/stack_traits.o gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/execution_context.o gcc.link.dll bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/libboost_context.so.1.60.0 common.copy stage/lib/libboost_context.so.1.60.0 ln-UNIX stage/lib/libboost_context.so common.mkdir bin.v2/libs/coroutine common.mkdir bin.v2/libs/coroutine/build common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7 common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/detail gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/detail/coroutine_context.o gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/exceptions.o common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/posix gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/posix/stack_traits.o gcc.link.dll bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/libboost_coroutine.so.1.60.0 common.copy stage/lib/libboost_coroutine.so.1.60.0 ln-UNIX stage/lib/libboost_coroutine.so common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7 common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/greg_month.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/greg_weekday.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/date_generators.o gcc.link.dll bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/libboost_date_time.so.1.60.0 common.copy stage/lib/libboost_date_time.so.1.60.0 ln-UNIX stage/lib/libboost_date_time.so gcc.link.dll bin.v2/libs/locale/build/gcc-4.4.7/release/threading-multi/libboost_locale.so.1.60.0 common.copy stage/lib/libboost_locale.so.1.60.0 ln-UNIX stage/lib/libboost_locale.so gcc.link.dll bin.v2/libs/log/build/gcc-4.4.7/release/build-no/log-api-unix/threading-multi/libboost_log.so.1.60.0 common.copy stage/lib/libboost_log.so.1.60.0 ln-UNIX stage/lib/libboost_log.so gcc.link.dll bin.v2/libs/log/build/gcc-4.4.7/release/build-no/log-api-unix/threading-multi/libboost_log_setup.so.1.60.0 common.copy stage/lib/libboost_log_setup.so.1.60.0 ln-UNIX stage/lib/libboost_log_setup.so gcc.link.dll bin.v2/libs/timer/build/gcc-4.4.7/release/threading-multi/libboost_timer.so.1.60.0 common.copy stage/lib/libboost_timer.so.1.60.0 ln-UNIX stage/lib/libboost_timer.so gcc.link.dll bin.v2/libs/test/build/gcc-4.4.7/release/threading-multi/libboost_prg_exec_monitor.so.1.60.0 common.copy stage/lib/libboost_prg_exec_monitor.so.1.60.0 ln-UNIX stage/lib/libboost_prg_exec_monitor.so common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/chrono.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/thread_clock.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/process_cpu_clocks.o gcc.archive bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/libboost_chrono.a common.copy stage/lib/libboost_chrono.a gcc.link.dll bin.v2/libs/test/build/gcc-4.4.7/release/threading-multi/libboost_unit_test_framework.so.1.60.0 common.copy stage/lib/libboost_unit_test_framework.so.1.60.0 ln-UNIX stage/lib/libboost_unit_test_framework.so gcc.link.dll bin.v2/libs/type_erasure/build/gcc-4.4.7/release/threading-multi/libboost_type_erasure.so.1.60.0 common.copy stage/lib/libboost_type_erasure.so.1.60.0 ln-UNIX stage/lib/libboost_type_erasure.so gcc.link.dll bin.v2/libs/wave/build/gcc-4.4.7/release/threading-multi/libboost_wave.so.1.60.0 ...on 100th target... common.copy stage/lib/libboost_wave.so.1.60.0 ln-UNIX stage/lib/libboost_wave.so common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c++ bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi/lockpool.o gcc.archive bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi/libboost_atomic.a common.copy stage/lib/libboost_atomic.a common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/alloc_lib.o In file included from libs/container/src/alloc_lib.c:19: libs/container/src/dlmalloc_ext_2_8_6.c: In function ‘boost_cont_malloc_stats’: libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$in_use_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$in_use_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$system_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$max_system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$max_system_bytes’ was declared here gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/dlmalloc.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/global_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/monotonic_buffer_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o libs/container/src/pool_resource.cpp:35: error: declaration of ‘typedef class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header boost::container::pmr::pool_data_t::block_slist_base’ ./boost/container/detail/block_slist.hpp:67: error: changes meaning of ‘block_slist_base’ from ‘class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header’

"g++" -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pthread -m64 -DBOOST_ALL_NO_LIB=1 -DBOOST_CONTAINER_STATIC_LINK=1 -DNDEBUG -I"." -c -o "bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o" "libs/container/src/pool_resource.cpp"

...failed gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o... gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/synchronized_pool_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/unsynchronized_pool_resource.o ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a(clean) for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>pool_resource.o... ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>pool_resource.o... ...skipped <pstage/lib>libboost_container.a for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a... common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm/make_x86_64_sysv_elf_gas.o gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm/jump_x86_64_sysv_elf_gas.o common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/posix gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/posix/stack_traits.o gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/execution_context.o gcc.archive bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/libboost_context.a common.copy stage/lib/libboost_context.a common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/detail gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/detail/coroutine_context.o gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/exceptions.o common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/posix gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/posix/stack_traits.o gcc.archive bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/libboost_coroutine.a common.copy stage/lib/libboost_coroutine.a common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/greg_month.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/greg_weekday.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/date_generators.o gcc.archive bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/libboost_date_time.a common.copy stage/lib/libboost_date_time.a ...failed updating 2 targets... ...skipped 6 targets... ...updated 144 targets...

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyYWeHeTqAPReTWESYQE-Ym6xZKfeks5u-QqKgaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

samhunter commented 5 years ago

Additional alternatives:

If you are using a version of Linux with a package management system (deb, rpm, etc), Boost is almost certainly included.

E.g. for Ubuntu sudo apt install libboost-dev libboost-system-dev libboost-program-options-dev libboost-iostreams-dev libboost-filesystem-dev

Or, you could try to just download the pre-compiled and statically linked executable files, these work on many Linux systems: wget https://github.com/ibest/HTStream/releases/download/v1.0.0-release/HTStream_1.0.0-release.tar.gz tar xvf HTStream_1.0.0-release.tar.gz ./hts_Stats --version

efratushava commented 5 years ago

This is an old boost bug that appears to have been fixed 3 years ago: https://svn.boost.org/trac10/ticket/11856 I recommend you build a newer version of boost, latest is 1.69. joe … On Sun, Dec 30, 2018 at 10:48 AM efratushava @.***> wrote: Hello, I was trying to install the program, as written here https://ibest.github.io/HTStream/, in my linux system: wget -O 1_60.tar.bz2 https://sourceforge.net/projects/boost/files/boost/1.60.0/boost_1_60_0.tar.bz2/download tar --bzip2 -xf 1_60.tar.bz2 cd boost_1_60_0 ./bootstrap.sh ./b2 # This will take a while. BOOST_INCLUDE=$(pwd) BOOST_INCLUDE_LIB=$(pwd)/stage/lib I ran all the command until "./b2". Then, I run "./b2" I couldn't attach my "./b2" command output, so I copied it in the bottom of this post. I run the next two commands, and then I tried to use the program, for example "hts_SuperDeduper -h", and I get: -bash: hts_SuperDeduper: command not found What can I do? ------------------------------ My ./b2 output: Performing configuration checks - 32-bit : no (cached) - 64-bit : yes (cached) - arm : no (cached) - mips1 : no (cached) - power : no (cached) - sparc : no (cached) - x86 : yes (cached) Building the Boost C++ Libraries. - symlinks supported : yes (cached) - lockfree boost::atomic_flag : yes (cached) - has_icu builds : yes (cached) warning: Graph library does not contain MPI-based parallel components. note: to enable them, add "using mpi ;" to your user-config.jam - zlib : yes (cached) - iconv (libc) : yes (cached) - icu : yes (cached) - compiler-supports-visibility : yes (cached) - compiler-supports-ssse3 : yes (cached) - compiler-supports-avx2 : no (cached) - gcc visibility : yes (cached) - long double support : yes (cached) warning: skipping optional Message Passing Interface (MPI) library. note: to enable MPI support, add "using mpi ;" to user-config.jam. note: to suppress this message, pass "--without-mpi" to bjam. note: otherwise, you can safely ignore this message. - zlib : yes (cached) Component configuration: - atomic : building - chrono : building - container : building - context : building - coroutine : building - coroutine2 : building - date_time : building - exception : building - filesystem : building - graph : building - graph_parallel : building - iostreams : building - locale : building - log : building - math : building - mpi : building - program_options : building - python : building - random : building - regex : building - serialization : building - signals : building - system : building - test : building - thread : building - timer : building - type_erasure : building - wave : building ...patience... ...patience... ...patience... ...patience... ...patience... ...patience... ...found 13863 targets... ...updating 152 targets... common.mkdir bin.v2/libs/atomic common.mkdir bin.v2/libs/atomic/build common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7 common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi gcc.compile.c++ bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi/lockpool.o gcc.link.dll bin.v2/libs/atomic/build/gcc-4.4.7/release/threading-multi/libboost_atomic.so.1.60.0 common.copy stage/lib/libboost_atomic.so.1.60.0 ln-UNIX stage/lib/libboost_atomic.so common.mkdir bin.v2/libs/chrono common.mkdir bin.v2/libs/chrono/build common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7 common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/chrono.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/thread_clock.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/process_cpu_clocks.o gcc.link.dll bin.v2/libs/chrono/build/gcc-4.4.7/release/threading-multi/libboost_chrono.so.1.60.0 common.copy stage/lib/libboost_chrono.so.1.60.0 ln-UNIX stage/lib/libboost_chrono.so common.mkdir bin.v2/libs/container common.mkdir bin.v2/libs/container/build common.mkdir bin.v2/libs/container/build/gcc-4.4.7 common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi gcc.compile.c bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/alloc_lib.o In file included from libs/container/src/alloc_lib.c:19: libs/container/src/dlmalloc_ext_2_8_6.c: In function ‘boost_cont_malloc_stats’: libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$in_use_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$in_use_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$system_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$max_system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$max_system_bytes’ was declared here gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/dlmalloc.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/global_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/monotonic_buffer_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o libs/container/src/pool_resource.cpp:35: error: declaration of ‘typedef class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header boost::container::pmr::pool_data_t::block_slist_base’ ./boost/container/detail/block_slist.hpp:67: error: changes meaning of ‘block_slist_base’ from ‘class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header’ "g++" -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pthread -fPIC -m64 -DBOOST_ALL_NO_LIB=1 -DBOOST_CONTAINER_DYN_LINK=1 -DNDEBUG -I"." -c -o "bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o" "libs/container/src/pool_resource.cpp" ...failed gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/pool_resource.o... gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/synchronized_pool_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/threading-multi/unsynchronized_pool_resource.o ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>libboost_container.so.1.60.0 for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>pool_resource.o... ...skipped <pstage/lib>libboost_container.so.1.60.0 for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/threading-multi>libboost_container.so.1.60.0... ...skipped <pstage/lib>libboost_container.so for lack of <pstage/lib>libboost_container.so.1.60.0... common.mkdir bin.v2/libs/context common.mkdir bin.v2/libs/context/build common.mkdir bin.v2/libs/context/build/gcc-4.4.7 common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm/make_x86_64_sysv_elf_gas.o gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/asm/jump_x86_64_sysv_elf_gas.o common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/posix gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/posix/stack_traits.o gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/execution_context.o gcc.link.dll bin.v2/libs/context/build/gcc-4.4.7/release/threading-multi/libboost_context.so.1.60.0 common.copy stage/lib/libboost_context.so.1.60.0 ln-UNIX stage/lib/libboost_context.so common.mkdir bin.v2/libs/coroutine common.mkdir bin.v2/libs/coroutine/build common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7 common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/detail gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/detail/coroutine_context.o gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/exceptions.o common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/posix gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/posix/stack_traits.o gcc.link.dll bin.v2/libs/coroutine/build/gcc-4.4.7/release/threading-multi/libboost_coroutine.so.1.60.0 common.copy stage/lib/libboost_coroutine.so.1.60.0 ln-UNIX stage/lib/libboost_coroutine.so common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7 common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/greg_month.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/greg_weekday.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/gregorian/date_generators.o gcc.link.dll bin.v2/libs/date_time/build/gcc-4.4.7/release/threading-multi/libboost_date_time.so.1.60.0 common.copy stage/lib/libboost_date_time.so.1.60.0 ln-UNIX stage/lib/libboost_date_time.so gcc.link.dll bin.v2/libs/locale/build/gcc-4.4.7/release/threading-multi/libboost_locale.so.1.60.0 common.copy stage/lib/libboost_locale.so.1.60.0 ln-UNIX stage/lib/libboost_locale.so gcc.link.dll bin.v2/libs/log/build/gcc-4.4.7/release/build-no/log-api-unix/threading-multi/libboost_log.so.1.60.0 common.copy stage/lib/libboost_log.so.1.60.0 ln-UNIX stage/lib/libboost_log.so gcc.link.dll bin.v2/libs/log/build/gcc-4.4.7/release/build-no/log-api-unix/threading-multi/libboost_log_setup.so.1.60.0 common.copy stage/lib/libboost_log_setup.so.1.60.0 ln-UNIX stage/lib/libboost_log_setup.so gcc.link.dll bin.v2/libs/timer/build/gcc-4.4.7/release/threading-multi/libboost_timer.so.1.60.0 common.copy stage/lib/libboost_timer.so.1.60.0 ln-UNIX stage/lib/libboost_timer.so gcc.link.dll bin.v2/libs/test/build/gcc-4.4.7/release/threading-multi/libboost_prg_exec_monitor.so.1.60.0 common.copy stage/lib/libboost_prg_exec_monitor.so.1.60.0 ln-UNIX stage/lib/libboost_prg_exec_monitor.so common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/chrono.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/thread_clock.o gcc.compile.c++ bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/process_cpu_clocks.o gcc.archive bin.v2/libs/chrono/build/gcc-4.4.7/release/link-static/threading-multi/libboost_chrono.a common.copy stage/lib/libboost_chrono.a gcc.link.dll bin.v2/libs/test/build/gcc-4.4.7/release/threading-multi/libboost_unit_test_framework.so.1.60.0 common.copy stage/lib/libboost_unit_test_framework.so.1.60.0 ln-UNIX stage/lib/libboost_unit_test_framework.so gcc.link.dll bin.v2/libs/type_erasure/build/gcc-4.4.7/release/threading-multi/libboost_type_erasure.so.1.60.0 common.copy stage/lib/libboost_type_erasure.so.1.60.0 ln-UNIX stage/lib/libboost_type_erasure.so gcc.link.dll bin.v2/libs/wave/build/gcc-4.4.7/release/threading-multi/libboost_wave.so.1.60.0 ...on 100th target... common.copy stage/lib/libboost_wave.so.1.60.0 ln-UNIX stage/lib/libboost_wave.so common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c++ bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi/lockpool.o gcc.archive bin.v2/libs/atomic/build/gcc-4.4.7/release/link-static/threading-multi/libboost_atomic.a common.copy stage/lib/libboost_atomic.a common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi gcc.compile.c bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/alloc_lib.o In file included from libs/container/src/alloc_lib.c:19: libs/container/src/dlmalloc_ext_2_8_6.c: In function ‘boost_cont_malloc_stats’: libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$in_use_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$in_use_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$system_bytes’ was declared here libs/container/src/dlmalloc_ext_2_8_6.c:1095: warning: ‘ret$max_system_bytes’ may be used uninitialized in this function libs/container/src/dlmalloc_ext_2_8_6.c:1095: note: ‘ret$max_system_bytes’ was declared here gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/dlmalloc.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/global_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/monotonic_buffer_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o libs/container/src/pool_resource.cpp:35: error: declaration of ‘typedef class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header boost::container::pmr::pool_data_t::block_slist_base’ ./boost/container/detail/block_slist.hpp:67: error: changes meaning of ‘block_slist_base’ from ‘class boost::container::pmr::block_slist_baseboost::container::pmr::block_slist_header’ "g++" -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pthread -m64 -DBOOST_ALL_NO_LIB=1 -DBOOST_CONTAINER_STATIC_LINK=1 -DNDEBUG -I"." -c -o "bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o" "libs/container/src/pool_resource.cpp" ...failed gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/pool_resource.o... gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/synchronized_pool_resource.o gcc.compile.c++ bin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi/unsynchronized_pool_resource.o ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a(clean) for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>pool_resource.o... ...skipped <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>pool_resource.o... ...skipped <pstage/lib>libboost_container.a for lack of <pbin.v2/libs/container/build/gcc-4.4.7/release/link-static/threading-multi>libboost_container.a... common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm/make_x86_64_sysv_elf_gas.o gcc.compile.asm bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/asm/jump_x86_64_sysv_elf_gas.o common.mkdir bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/posix gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/posix/stack_traits.o gcc.compile.c++ bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/execution_context.o gcc.archive bin.v2/libs/context/build/gcc-4.4.7/release/link-static/threading-multi/libboost_context.a common.copy stage/lib/libboost_context.a common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/detail gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/detail/coroutine_context.o gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/exceptions.o common.mkdir bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/posix gcc.compile.c++ bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/posix/stack_traits.o gcc.archive bin.v2/libs/coroutine/build/gcc-4.4.7/release/link-static/threading-multi/libboost_coroutine.a common.copy stage/lib/libboost_coroutine.a common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi common.mkdir bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/greg_month.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/greg_weekday.o gcc.compile.c++ bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/gregorian/date_generators.o gcc.archive bin.v2/libs/date_time/build/gcc-4.4.7/release/link-static/threading-multi/libboost_date_time.a common.copy stage/lib/libboost_date_time.a ...failed updating 2 targets... ...skipped 6 targets... ...updated 144 targets... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#148>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyYWeHeTqAPReTWESYQE-Ym6xZKfeks5u-QqKgaJpZM4ZlCQv . -- --------------- Joe Angell cell: (720) 260-2190

How can

Additional alternatives:

If you are using a version of Linux with a package management system (deb, rpm, etc), Boost is almost certainly included.

E.g. for Ubuntu sudo apt install libboost-dev libboost-system-dev libboost-program-options-dev libboost-iostreams-dev libboost-filesystem-dev

Or, you could try to just download the pre-compiled and statically linked executable files, these work on many Linux systems: wget https://github.com/ibest/HTStream/releases/download/v1.0.0-release/HTStream_1.0.0-release.tar.gz tar xvf HTStream_1.0.0-release.tar.gz ./hts_Stats --version

When I did that I downloaded, and untar the file, and the ran ./hts_Stats --version I got: FATAL: kernel too old Aborted (core dumped)

samhunter commented 5 years ago

Hum, that is unfortunate. If you have server admins who can help you get a recent version of boost installed (or point you to a recent version that may already be installed) that might be easiest.

You could try to compile a more recent version of Boost as @joe-angell suggested like this: wget -O 1_68.tar.bz2 https://sourceforge.net/projects/boost/files/boost/1.68.0/boost_1_68_0.tar.bz2/download tar --bzip2 -xf 1_68.tar.bz2 cd boost_1_68_0 ./bootstrap.sh ./b2 # This will take a while. BOOST_INCLUDE=$(pwd) BOOST_INCLUDE_LIB=$(pwd)/stage/lib

If you do try this, please let us know whether it works.

Sam

efratushava commented 5 years ago

Hi @samhunter , after trying the above boost, I still get this error: FATAL: kernel too old Aborted (core dumped)

What can I do?

efratushava commented 5 years ago

@samhunter I figured out it's a problem in our machine. I'll ask the admins.

Thank you!

efratushava commented 5 years ago

ello,

I was trying to install the program, as written here, in my linux system:

git clone https://github.com/ibest/HTStream.git cd HTStream mkdir build cd build cmake ..

When using an alternative Boost install:

cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB ..

To specify an install location use -DCMAKE_INSTALL_PREFIX=

make make install #install to /usr/local/bin with sudo access (or location specified with not sudo access)

I ran all the commands until "make". My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs ..

The make command has an error, and stop: sr/bin/ld: warning: liblzma.so.0, needed by /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found (try using -rpath or -rpath-link) /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_stream_decoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference tolzma_easy_encoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_code' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference tolzma_end' collect2: error: ld returned 1 exit status make[2]: [hts_Stats/hts_Stats] Error 1 make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 make: *** [all] Error 2

I'm using CentOS7, gcc-5.2.0

How can I fix the problem?

joe-angell commented 5 years ago

So you built boost successfully, but htstream fails to build now? If that is the case can you do "make VERBOSE=1" and paste the output? If not please clarify.

On Wed, Jan 2, 2019 at 6:02 AM efratushava notifications@github.com wrote:

ello,

I was trying to install the program, as written here, in my linux system:

git clone https://github.com/ibest/HTStream.git cd HTStream mkdir build cd build cmake ..

When using an alternative Boost install:

cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE

-DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB ..

To specify an install location use -DCMAKE_INSTALL_PREFIX=

make make install #install to /usr/local/bin with sudo access (or location specified with not sudo access)

I ran all the commands until "make". My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs ..

The make command has an error, and stop: sr/bin/ld: warning: liblzma.so.0, needed by /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found (try using -rpath or -rpath-link) /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_stream_decoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_easy_encoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_code' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_end' collect2: error: ld returned 1 exit status make[2]: [hts_Stats/hts_Stats] Error 1 make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 make: *** [all] Error 2

I'm using CentOS7, gcc-5.2.0

How can I fix the problem?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-450870522, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyVJjkrbhYC5hdoowRnhINvdqI7Arks5u_LvagaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

joe-angell commented 5 years ago

The problem might be that you don't have xz-libs installed, what is the output of "yum list installed | grep xz" You will need xz-libs package installed.

On Wed, Jan 2, 2019 at 10:40 AM Joe Angell joe.d.angell@gmail.com wrote:

So you built boost successfully, but htstream fails to build now? If that is the case can you do "make VERBOSE=1" and paste the output? If not please clarify.

On Wed, Jan 2, 2019 at 6:02 AM efratushava notifications@github.com wrote:

ello,

I was trying to install the program, as written here, in my linux system:

git clone https://github.com/ibest/HTStream.git cd HTStream mkdir build cd build cmake ..

When using an alternative Boost install:

cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE

-DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB ..

To specify an install location use -DCMAKE_INSTALL_PREFIX=

make make install #install to /usr/local/bin with sudo access (or location specified with not sudo access)

I ran all the commands until "make". My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs ..

The make command has an error, and stop: sr/bin/ld: warning: liblzma.so.0, needed by /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found (try using -rpath or -rpath-link) /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_stream_decoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_easy_encoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_code' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_end' collect2: error: ld returned 1 exit status make[2]: [hts_Stats/hts_Stats] Error 1 make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 make: *** [all] Error 2

I'm using CentOS7, gcc-5.2.0

How can I fix the problem?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-450870522, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyVJjkrbhYC5hdoowRnhINvdqI7Arks5u_LvagaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

--

Joe Angell cell: (720) 260-2190

samhunter commented 5 years ago

Hi @efratushava, could you try "uname -a" on your CentOS server? We are running CentOS 7.5.1804 on our servers with kernel 3.10 and the static builds I have made available work fine there. I'm wondering how old of a kernel you have?

efratushava commented 5 years ago

So you built boost successfully, but htstream fails to build now? If that is the case can you do "make VERBOSE=1" and paste the output? If not please clarify. … On Wed, Jan 2, 2019 at 6:02 AM efratushava @.> wrote: ello, I was trying to install the program, as written here, in my linux system: git clone https://github.com/ibest/HTStream.git cd HTStream mkdir build cd build cmake .. #When using an alternative Boost install: #cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB .. #To specify an install location use -DCMAKE_INSTALL_PREFIX= make make install #install to /usr/local/bin with sudo access (or location specified with not sudo access) I ran all the commands until "make". My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs .. The make command has an error, and stop: sr/bin/ld: warning: liblzma.so.0, needed by /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found (try using -rpath or -rpath-link) /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_stream_decoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_easy_encoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_code' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_end' collect2: error: ld returned 1 exit status make[2]: [hts_Stats/hts_Stats] Error 1 make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 make: [all] Error 2 I'm using CentOS7, gcc-5.2.0 How can I fix the problem? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#148 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyVJjkrbhYC5hdoowRnhINvdqI7Arks5u_LvagaJpZM4ZlCQv . -- --------------- Joe Angell cell: (720) 260-2190

[ekushele@alu10 build]$ make VERBOSE=1 /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -H/home/alu/ekushele/HTStream -B/home/alu/ekushele/HTStream/build --check-build-system CMakeFiles/Makefile.cmake 0 /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_progress_start /home/alu/ekushele/HTStream/build/CMakeFiles /home/alu/ekushele/HTStream/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory /home/alu/ekushele/HTStream/build' make -f CMakeFiles/googletest.dir/build.make CMakeFiles/googletest.dir/depend make[2]: Entering directory/home/alu/ekushele/HTStream/build' cd /home/alu/ekushele/HTStream/build && /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/alu/ekushele/HTStream /home/alu/ekushele/HTStream /home/alu/ekushele/HTStream/build /home/alu/ekushele/HTStream/build /home/alu/ekushele/HTStream/build/CMakeFiles/googletest.dir/DependInfo.cmake --color= make[2]: Leaving directory /home/alu/ekushele/HTStream/build' make -f CMakeFiles/googletest.dir/build.make CMakeFiles/googletest.dir/build make[2]: Entering directory/home/alu/ekushele/HTStream/build' make[2]: Nothing to be done for CMakeFiles/googletest.dir/build'. make[2]: Leaving directory/home/alu/ekushele/HTStream/build' [ 14%] Built target googletest make -f common/CMakeFiles/hts_common.dir/build.make common/CMakeFiles/hts_common.dir/depend make[2]: Entering directory /home/alu/ekushele/HTStream/build' cd /home/alu/ekushele/HTStream/build && /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/alu/ekushele/HTStream /home/alu/ekushele/HTStream/common /home/alu/ekushele/HTStream/build /home/alu/ekushele/HTStream/build/common /home/alu/ekushele/HTStream/build/common/CMakeFiles/hts_common.dir/DependInfo.cmake --color= make[2]: Leaving directory/home/alu/ekushele/HTStream/build' make -f common/CMakeFiles/hts_common.dir/build.make common/CMakeFiles/hts_common.dir/build make[2]: Entering directory /home/alu/ekushele/HTStream/build' make[2]: Nothing to be done forcommon/CMakeFiles/hts_common.dir/build'. make[2]: Leaving directory /home/alu/ekushele/HTStream/build' [ 22%] Built target hts_common make -f common/CMakeFiles/hts_common_test.dir/build.make common/CMakeFiles/hts_common_test.dir/depend make[2]: Entering directory/home/alu/ekushele/HTStream/build' cd /home/alu/ekushele/HTStream/build && /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/alu/ekushele/HTStream /home/alu/ekushele/HTStream/common /home/alu/ekushele/HTStream/build /home/alu/ekushele/HTStream/build/common /home/alu/ekushele/HTStream/build/common/CMakeFiles/hts_common_test.dir/DependInfo.cmake --color= make[2]: Leaving directory /home/alu/ekushele/HTStream/build' make -f common/CMakeFiles/hts_common_test.dir/build.make common/CMakeFiles/hts_common_test.dir/build make[2]: Entering directory/home/alu/ekushele/HTStream/build' make[2]: Nothing to be done for common/CMakeFiles/hts_common_test.dir/build'. make[2]: Leaving directory/home/alu/ekushele/HTStream/build' [ 33%] Built target hts_common_test make -f hts_Stats/CMakeFiles/hts_Stats.dir/build.make hts_Stats/CMakeFiles/hts_Stats.dir/depend make[2]: Entering directory /home/alu/ekushele/HTStream/build' cd /home/alu/ekushele/HTStream/build && /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/alu/ekushele/HTStream /home/alu/ekushele/HTStream/hts_Stats /home/alu/ekushele/HTStream/build /home/alu/ekushele/HTStream/build/hts_Stats /home/alu/ekushele/HTStream/build/hts_Stats/CMakeFiles/hts_Stats.dir/DependInfo.cmake --color= make[2]: Leaving directory/home/alu/ekushele/HTStream/build' make -f hts_Stats/CMakeFiles/hts_Stats.dir/build.make hts_Stats/CMakeFiles/hts_Stats.dir/build make[2]: Entering directory /home/alu/ekushele/HTStream/build' [ 35%] Linking CXX executable hts_Stats cd /home/alu/ekushele/HTStream/build/hts_Stats && /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/hts_Stats.dir/link.txt --verbose=1 /home/alu/ekushele/gcc-5.2.0/bin/g++ -std=c++11 -Wall CMakeFiles/hts_Stats.dir/src/hts_Stats.cpp.o -o hts_Stats -L/home/alu/ekushele/HTStream/build/common -rdynamic ../common/libhts_common.a -lboost_system -lboost_program_options -lboost_iostreams -lboost_filesystem -Wl,-rpath,/home/alu/ekushele/HTStream/build/common: /usr/bin/ld: warning: liblzma.so.0, needed by /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found (try using -rpath or -rpath-link) /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference tolzma_stream_decoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_easy_encoder' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference tolzma_code' /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_end' collect2: error: ld returned 1 exit status make[2]: *** [hts_Stats/hts_Stats] Error 1 make[2]: Leaving directory/home/alu/ekushele/HTStream/build' make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 make[1]: Leaving directory `/home/alu/ekushele/HTStream/build' make: [all] Error 2

efratushava commented 5 years ago

Hi @efratushava, could you try "uname -a" on your CentOS server? We are running CentOS 7.5.1804 on our servers with kernel 3.10 and the static builds I have made available work fine there. I'm wondering how old of a kernel you have?

Linux alu10 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

efratushava commented 5 years ago

The problem might be that you don't have xz-libs installed, what is the output of "c You will need xz-libs package installed. … On Wed, Jan 2, 2019 at 10:40 AM Joe Angell @.> wrote: So you built boost successfully, but htstream fails to build now? If that is the case can you do "make VERBOSE=1" and paste the output? If not please clarify. On Wed, Jan 2, 2019 at 6:02 AM efratushava @.> wrote: > ello, > > I was trying to install the program, as written here, in my linux system: > > git clone https://github.com/ibest/HTStream.git > cd HTStream > mkdir build > cd build > cmake .. > #When using an alternative Boost install: > #cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE > -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB .. > #To specify an install location use -DCMAKE_INSTALL_PREFIX= > make > make install #install to /usr/local/bin with sudo access (or location > specified with not sudo access) > > I ran all the commands until "make". > My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE > -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 > -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs .. > > The make command has an error, and stop: sr/bin/ld: warning: > liblzma.so.0, needed by > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found > (try using -rpath or -rpath-link) > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_stream_decoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined > reference to lzma_easy_encoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_code' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined > reference to lzma_end' > collect2: error: ld returned 1 exit status > make[2]: [hts_Stats/hts_Stats] Error 1 > make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 > make: *** [all] Error 2 > > I'm using CentOS7, gcc-5.2.0 > > How can I fix the problem? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#148 (comment)>, > or mute the thread > https://github.com/notifications/unsubscribe-auth/AHveyVJjkrbhYC5hdoowRnhINvdqI7Arks5u_LvagaJpZM4ZlCQv > . > -- --------------- Joe Angell cell: (720) 260-2190 -- --------------- Joe Angell cell: (720) 260-2190

running this command, "yum list installed | grep xz" I get: xz.x86_64 5.2.2-1.el7 @anaconda xz-devel.x86_64 5.2.2-1.el7 @base xz-libs.i686 5.2.2-1.el7 @base xz-libs.x86_64 5.2.2-1.el7 @anaconda

joe-angell commented 5 years ago

Ok try "ldd /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so" That should give you the path to liblzma.so.0 and then you can add that path to -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB:PATH_HERE when you run cmake.

joe

On Wed, Jan 2, 2019 at 10:20 PM efratushava notifications@github.com wrote:

The problem might be that you don't have xz-libs installed, what is the output of "c You will need xz-libs package installed. … <#m_-4630643976193133307_m6639933426523777355> On Wed, Jan 2, 2019 at 10:40 AM Joe Angell @.> wrote: So you built boost successfully, but htstream fails to build now? If that is the case can you do "make VERBOSE=1" and paste the output? If not please clarify. On Wed, Jan 2, 2019 at 6:02 AM efratushava @.> wrote: > ello, > > I was trying to install the program, as written here, in my linux system: > > git clone https://github.com/ibest/HTStream.git > cd HTStream

mkdir build > cd build > cmake .. > #When using an alternative Boost install: > #cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE > -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB .. > #To specify an install location use -DCMAKE_INSTALL_PREFIX= > make > make install #install to /usr/local/bin with sudo access (or location > specified with not sudo access) > > I ran all the commands until "make". > My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE > -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 > -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs .. > > The make command has an error, and stop: sr/bin/ld: warning: > liblzma.so.0, needed by > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found > (try using -rpath or -rpath-link) > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_stream_decoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_easy_encoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_code' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_end' > collect2: error: ld returned 1 exit status > make[2]: [hts_Stats/hts_Stats] Error 1 > make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 > make: *** [all] Error 2

I'm using CentOS7, gcc-5.2.0 > > How can I fix the problem? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#148 (comment) https://github.com/ibest/HTStream/issues/148#issuecomment-450870522>, > or mute the thread > https://github.com/notifications/unsubscribe-auth/AHveyVJjkrbhYC5hdoowRnhINvdqI7Arks5u_LvagaJpZM4ZlCQv . > -- --------------- Joe Angell cell: (720) 260-2190 -- --------------- Joe Angell cell: (720) 260-2190

running this command, "yum list installed | grep xz" I get: xz.x86_64 5.2.2-1.el7 @anaconda https://github.com/anaconda xz-devel.x86_64 5.2.2-1.el7 @base https://github.com/base xz-libs.i686 5.2.2-1.el7 @base https://github.com/base xz-libs.x86_64 5.2.2-1.el7 @anaconda https://github.com/anaconda

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-451063545, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyRn0jezi362iHyJNJ1MKPJDEFm_Oks5u_aFFgaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

Ok try "ldd /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so" That should give you the path to liblzma.so.0 and then you can add that path to -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB:PATHHERE when you run cmake. joe On Wed, Jan 2, 2019 at 10:20 PM efratushava notifications@github.com wrote: … The problem might be that you don't have xz-libs installed, what is the output of "c You will need xz-libs package installed. … <#m-4630643976193133307_m6639933426523777355> On Wed, Jan 2, 2019 at 10:40 AM Joe Angell @.> wrote: So you built boost successfully, but htstream fails to build now? If that is the case can you do "make VERBOSE=1" and paste the output? If not please clarify. On Wed, Jan 2, 2019 at 6:02 AM efratushava @.> wrote: > ello, > > I was trying to install the program, as written here, in my linux system: > > git clone https://github.com/ibest/HTStream.git > cd HTStream > mkdir build > cd build > cmake .. > #When using an alternative Boost install: > #cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE > -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB .. > #To specify an install location use -DCMAKE_INSTALL_PREFIX= > make > make install #install to /usr/local/bin with sudo access (or location > specified with not sudo access) > > I ran all the commands until "make". > My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE > -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 > -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs .. > > The make command has an error, and stop: sr/bin/ld: warning: > liblzma.so.0, needed by > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found > (try using -rpath or -rpath-link) > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_stream_decoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined > reference to lzma_easy_encoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_code' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined > reference to lzma_end' > collect2: error: ld returned 1 exit status > make[2]: [hts_Stats/hts_Stats] Error 1 > make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 > make: *** [all] Error 2 > > I'm using CentOS7, gcc-5.2.0 > > How can I fix the problem? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#148 (comment) <#148 (comment)>>, > or mute the thread > https://github.com/notifications/unsubscribe-auth/AHveyVJjkrbhYC5hdoowRnhINvdqI7Arks5u_LvagaJpZM4ZlCQv > . > -- --------------- Joe Angell cell: (720) 260-2190 -- --------------- Joe Angell cell: (720) 260-2190 running this command, "yum list installed | grep xz" I get: xz.x86_64 5.2.2-1.el7 @anaconda https://github.com/anaconda xz-devel.x86_64 5.2.2-1.el7 @base https://github.com/base xz-libs.i686 5.2.2-1.el7 @base https://github.com/base xz-libs.x86_64 5.2.2-1.el7 @anaconda https://github.com/anaconda — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#148 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyRn0jezi362iHyJNJ1MKPJDEFm_Oks5u_aFFgaJpZM4ZlCQv . -- --------------- Joe Angell cell: (720) 260-2190

This is my output: [ekushele@alu10 ~]$ ldd /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so) linux-vdso.so.1 => (0x00007ffd7ccd1000) librt.so.1 => /lib64/librt.so.1 (0x00007f1b3166e000) libz.so.1 => /lib64/libz.so.1 (0x00007f1b31458000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f1b31248000) liblzma.so.0 => not found libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f1b30f41000) libm.so.6 => /lib64/libm.so.6 (0x00007f1b30c3f000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f1b30a29000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f1b3080d000) libc.so.6 => /lib64/libc.so.6 (0x00007f1b30440000) /lib64/ld-linux-x86-64.so.2 (0x00007f1b31a9100

joe-angell commented 5 years ago

You have some non standard setup, :P.

Try:

find / -name "liblzma.so.0"

That should reveal it's hidden location and you can add it to the path as i said above.

joe

On Thu, Jan 3, 2019 at 11:04 AM efratushava notifications@github.com wrote:

Ok try "ldd /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so" That should give you the path to liblzma.so.0 and then you can add that path to -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB:PATHHERE when you run cmake. joe On Wed, Jan 2, 2019 at 10:20 PM efratushava notifications@github.com wrote: … <#m-9038168628458356419> The problem might be that you don't have xz-libs installed, what is the output of "c You will need xz-libs package installed. … <#m-4630643976193133307_m6639933426523777355> On Wed, Jan 2, 2019 at 10:40 AM Joe Angell @.> wrote: So you built boost successfully, but htstream fails to build now? If that is the case can you do "make VERBOSE=1" and paste the output? If not please clarify. On Wed, Jan 2, 2019 at 6:02 AM efratushava @.> wrote: > ello, > > I was trying to install the program, as written here, in my linux system: > > git clone https://github.com/ibest/HTStream.git > cd HTStream > mkdir build > cd build > cmake .. > #When using an alternative Boost install: > #cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE > -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB .. > #To specify an install location use -DCMAKE_INSTALL_PREFIX= > make > make install #install to /usr/local/bin with sudo access (or location > specified with not sudo access) > > I ran all the commands until "make". > My cmake command: cmake -DBoost_NO_SYSTEM_PATHS=TRUE > -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 > -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs .. > > The make command has an error, and stop: sr/bin/ld: warning: > liblzma.so.0, needed by > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so, not found > (try using -rpath or -rpath-link) > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_stream_decoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined

reference to lzma_easy_encoder' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: > undefined reference to lzma_code' > /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: undefined reference to lzma_end' > collect2: error: ld returned 1 exit status > make[2]: [hts_Stats/hts_Stats] Error 1 > make[1]: [hts_Stats/CMakeFiles/hts_Stats.dir/all] Error 2 > make: *** [all] Error 2

I'm using CentOS7, gcc-5.2.0 > > How can I fix the problem? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#148 https://github.com/ibest/HTStream/issues/148 (comment) <#148 (comment) https://github.com/ibest/HTStream/issues/148#issuecomment-450870522>>, or mute the thread > https://github.com/notifications/unsubscribe-auth/AHveyVJjkrbhYC5hdoowRnhINvdqI7Arks5u_LvagaJpZM4ZlCQv . > -- --------------- Joe Angell cell: (720) 260-2190 -- --------------- Joe Angell cell: (720) 260-2190 running this command, "yum list installed | grep xz" I get: xz.x86_64 5.2.2-1.el7 @anaconda https://github.com/anaconda https://github.com/anaconda xz-devel.x86_64 5.2.2-1.el7 @base https://github.com/base https://github.com/base xz-libs.i686 5.2.2-1.el7 @base https://github.com/base https://github.com/base xz-libs.x86_64 5.2.2-1.el7 @anaconda https://github.com/anaconda https://github.com/anaconda — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#148 (comment) https://github.com/ibest/HTStream/issues/148#issuecomment-451063545>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyRn0jezi362iHyJNJ1MKPJDEFm_Oks5u_aFFgaJpZM4ZlCQv . -- --------------- Joe Angell cell: (720) 260-2190

This is my output: [ekushele@alu10 ~]$ ldd /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/alu/ekushele/boost_1_68_0/stage/lib/libboost_iostreams.so) linux-vdso.so.1 => (0x00007ffd7ccd1000) librt.so.1 => /lib64/librt.so.1 (0x00007f1b3166e000) libz.so.1 => /lib64/libz.so.1 (0x00007f1b31458000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f1b31248000) liblzma.so.0 => not found libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f1b30f41000) libm.so.6 => /lib64/libm.so.6 (0x00007f1b30c3f000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f1b30a29000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f1b3080d000) libc.so.6 => /lib64/libc.so.6 (0x00007f1b30440000) /lib64/ld-linux-x86-64.so.2 (0x00007f1b31a9100

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-451243999, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyb_j8OYFiA_id7WCqXmvBsqx25Mjks5u_lRCgaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

So I found: /usr/lib64/liblzma.so.0.0.0 /usr/lib64/liblzma.so.0

So I run: cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs:/usr/lib64/liblzma.so.0 ..

I got: CMake Warning: Manually-specified variables were not used by the project:

CMAKE_LIBRARY_PATH

-- Build files have been written to: /home/alu/ekushele/HTStream/build

Than "make" command had errors...

joe-angell commented 5 years ago

try: cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/stage/lib:/usr/lib64 ...

On Sun, Jan 6, 2019 at 8:46 AM efratushava notifications@github.com wrote:

So I found: /usr/lib64/liblzma.so.0.0.0 /usr/lib64/liblzma.so.0

So I run: cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=/home/alu/ekushele/boost_1_68_0 -DCMAKE_LIBRARY_PATH=/home/alu/ekushele/boost_1_68_0/libs:/usr/lib64/liblzma.so.0 ..

I got: CMake Warning: Manually-specified variables were not used by the project:

CMAKE_LIBRARY_PATH

-- Build files have been written to: /home/alu/ekushele/HTStream/build

Than "make" command had errors...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-451756003, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyeNx-n3XbA1x9XzYpZprIRAya-3lks5vAih8gaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

"cmake" runs well.

make didn't run well. But somehow-I can't attach a file to the commend, so I'll just paste the head and tail of the output:

head: [ekushele@alu10 build]$ make [ 1%] Creating directories for 'googletest' [ 3%] Performing download step (download, verify and extract) for 'googletest' -- downloading... src='https://github.com/google/googletest/archive/release-1.7.0.tar.gz' dst='/home/alu/ekushele/HTStream/build/src/release-1.7.0.tar.gz' timeout='none' -- downloading... done -- verifying file... file='/home/alu/ekushele/HTStream/build/src/release-1.7.0.tar.gz' -- verifying file... warning: did not verify file - no URL_HASH specified? -- extracting... src='/home/alu/ekushele/HTStream/build/src/release-1.7.0.tar.gz' dst='/home/alu/ekushele/HTStream/build/src/googletest' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 5%] No patch step for 'googletest' [ 7%] No update step for 'googletest' [ 9%] Performing configure step for 'googletest' -- Configuring done -- Generating done -- Build files have been written to: /home/alu/ekushele/HTStream/build/src/googletest-build [ 11%] Performing build step for 'googletest' [ 50%] Built target gtest [100%] Built target gtest_main [ 12%] No install step for 'googletest' [ 14%] Completed 'googletest' [ 14%] Built target googletest [ 16%] Building CXX object common/CMakeFiles/hts_common.dir/src/ioHandler.cpp.o [ 18%] Building CXX object common/CMakeFiles/hts_common.dir/src/read.cpp.o [ 20%] Building CXX object common/CMakeFiles/hts_common.dir/src/utils.cpp.o [ 22%] Linking CXX static library libhts_common.a [ 22%] Built target hts_common [ 24%] Building CXX object common/CMakeFiles/hts_common_test.dir/test/testIO.cpp.o [ 25%] Building CXX object common/CMakeFiles/hts_common_test.dir/test/testRead.cpp.o [ 27%] Building CXX object common/CMakeFiles/hts_common_test.dir/src/ioHandler.cpp.o [ 29%] Building CXX object common/CMakeFiles/hts_common_test.dir/src/read.cpp.o [ 31%] Building CXX object common/CMakeFiles/hts_common_test.dir/src/utils.cpp.o [ 33%] Linking CXX executable hts_common_test CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::internal::PrintTo(std::string const&, std::ostream*)': testIO.cpp:(.text._ZN7testing8internal7PrintToERKSsPSo[_ZN7testing8internal7PrintToERKSsPSo]+0x1f): undefined reference totesting::internal::PrintStringTo(std::string const&, std::ostream)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function boost::system::generic_category()': testIO.cpp:(.text._ZN5boost6system16generic_categoryEv[_ZN5boost6system16generic_categoryEv]+0x5): undefined reference toboost::system::detail::generic_category_ncx()' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function `testing::AssertionResult testing::internal::CmpHelperEQ<char [26], std::string>(char const, char const, char const (&) [26], std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0[_ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0]+0x94): undefined reference to `testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function `testing::AssertionResult testing::internal::CmpHelperEQ<char [10], std::string>(char const, char const, char const (&) [10], std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQIA10_cSsEENS_15AssertionResultEPKcS5_RKTRKT0[_ZN7testing8internal11CmpHelperEQIA10_cSsEENS_15AssertionResultEPKcS5_RKTRKT0]+0x94): undefined reference to `testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function `testing::AssertionResult testing::internal::CmpHelperEQ<unsigned long, int>(char const, char const, unsigned long const&, int const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQImiEENS_15AssertionResultEPKcS4_RKTRKT0[_ZN7testing8internal11CmpHelperEQImiEENS_15AssertionResultEPKcS4_RKTRKT0]+0x91): undefined reference to `testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function `testing::AssertionResult testing::internal::CmpHelperEQ<std::string, std::string>(char const, char const, std::string const&, std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQISsSsEENS_15AssertionResultEPKcS4_RKTRKT0[_ZN7testing8internal11CmpHelperEQISsSsEENS_15AssertionResultEPKcS4_RKTRKT0]+0x94): undefined reference to `testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testRead.cpp.o: In function `testing::AssertionResult testing::internal::CmpHelperEQ<int, double>(char const, char const, int const&, double const&)': testRead.cpp:(.text._ZN7testing8internal11CmpHelperEQIidEENS_15AssertionResultEPKcS4_RKTRKT0[_ZN7testing8internal11CmpHelperEQIidEENS_15AssertionResultEPKcS4_RKTRKT0]+0x9b): undefined reference to `testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testRead.cpp.o:testRead.cpp:(.text._ZN7testing8internal11CmpHelperEQIN5boost8optionalINS2_14dynamic_bitsetImSaImEEEEES7_EENS_15AssertionResultEPKcSA_RKTRKT0[_ZN7testing8internal11CmpHelperEQIN5boost8optionalINS2_14dynamic_bitsetImSaImEEEEES7_EENS_15AssertionResultEPKcSA_RKTRKT0]+0x94): more undefined references to `testing::internal::EqFailure(char const, char const*, std::string const&, std::string const&, bool)' follow /home/alu/ekushele/HTStream/build/src/googletest-buil

Than it keeps going, and write many errors, and then: tail: /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function __gnu_cxx::__enable_if<std::__is_char<char>::__value, bool>::__type std::operator==<char>(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> > const&)': gtest-all.cc:(.text._ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_[_ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_]+0x1b): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::size() const' gtest-all.cc:(.text._ZSteqIcEN9__gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE[_ZSteqIcEN9gnu_cxx11__enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE]+0x2a): undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::size() const' gtest-all.cc:(.text._ZSteqIcEN9gnu_cxx11__enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE[_ZSteqIcEN9__gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE]+0x3b): undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const' gtest-all.cc:(.text._ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_[_ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_]+0x4a): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::data() const' gtest-all.cc:(.text._ZSteqIcEN9__gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE[_ZSteqIcEN9gnu_cxx11__enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE]+0x59): undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::data() const' /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >* std::__copy_move_backward<false, false, std::random_access_iterator_tag>::__copy_move_b<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*>(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)': gtest-all.cc:(.text._ZNSt20__copy_move_backwardILb0ELb0ESt26random_access_iterator_tagE13__copy_move_bIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EET0_T_SB_SA_[_ZNSt20__copy_move_backwardILb0ELb0ESt26random_access_iterator_tagE13__copy_move_bIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EET0_T_SB_SA_]+0x4a): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function void std::_Construct<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char const*>(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, char const* const&)': gtest-all.cc:(.text._ZSt10_ConstructINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKcEvPT_RKT0_[_ZSt10_ConstructINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKcEvPT_RKT0_]+0x4f): undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::basic_string(char const*, std::allocator const&)' /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function testing::internal::XmlUnitTestResultPrinter::~XmlUnitTestResultPrinter()': gtest-all.cc:(.text._ZN7testing8internal24XmlUnitTestResultPrinterD2Ev[_ZN7testing8internal24XmlUnitTestResultPrinterD5Ev]+0x25): undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::~basic_string()' collect2: error: ld returned 1 exit status make[2]: [common/hts_common_test] Error 1 make[1]: [common/CMakeFiles/hts_common_test.dir/all] Error 2 make: *** [all] Error 2

joe-angell commented 5 years ago

try: make clean && make VERBOSE=1

On Sun, Jan 6, 2019 at 9:43 AM efratushava notifications@github.com wrote:

"cmake" runs well.

make didn't run well. But somehow-I can't attach a file to the commend, so I'll just paste the head and tail of the output:

head: [ekushele@alu10 build]$ make [ 1%] Creating directories for 'googletest' [ 3%] Performing download step (download, verify and extract) for 'googletest' -- downloading... src='https://github.com/google/googletest/archive/release-1.7.0.tar.gz' dst='/home/alu/ekushele/HTStream/build/src/release-1.7.0.tar.gz' timeout='none' -- downloading... done -- verifying file... file='/home/alu/ekushele/HTStream/build/src/release-1.7.0.tar.gz' -- verifying file... warning: did not verify file - no URL_HASH specified? -- extracting... src='/home/alu/ekushele/HTStream/build/src/release-1.7.0.tar.gz' dst='/home/alu/ekushele/HTStream/build/src/googletest' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 5%] No patch step for 'googletest' [ 7%] No update step for 'googletest' [ 9%] Performing configure step for 'googletest' -- Configuring done -- Generating done -- Build files have been written to: /home/alu/ekushele/HTStream/build/src/googletest-build [ 11%] Performing build step for 'googletest' [ 50%] Built target gtest [100%] Built target gtest_main [ 12%] No install step for 'googletest' [ 14%] Completed 'googletest' [ 14%] Built target googletest [ 16%] Building CXX object common/CMakeFiles/hts_common.dir/src/ioHandler.cpp.o [ 18%] Building CXX object common/CMakeFiles/hts_common.dir/src/read.cpp.o [ 20%] Building CXX object common/CMakeFiles/hts_common.dir/src/utils.cpp.o [ 22%] Linking CXX static library libhts_common.a [ 22%] Built target hts_common [ 24%] Building CXX object common/CMakeFiles/hts_common_test.dir/test/testIO.cpp.o [ 25%] Building CXX object common/CMakeFiles/hts_common_test.dir/test/testRead.cpp.o [ 27%] Building CXX object common/CMakeFiles/hts_common_test.dir/src/ioHandler.cpp.o [ 29%] Building CXX object common/CMakeFiles/hts_common_test.dir/src/read.cpp.o [ 31%] Building CXX object common/CMakeFiles/hts_common_test.dir/src/utils.cpp.o [ 33%] Linking CXX executable hts_common_test CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::internal::PrintTo(std::string const&, std::ostream)': testIO.cpp:(.text._ZN7testing8internal7PrintToERKSsPSo[_ZN7testing8internal7PrintToERKSsPSo]+0x1f): undefined reference to testing::internal::PrintStringTo(std::string const&, std::ostream)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function boost::system::generic_category()': testIO.cpp:(.text._ZN5boost6system16generic_categoryEv[_ZN5boost6system16generic_categoryEv]+0x5): undefined reference to boost::system::detail::generic_category_ncx()' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::AssertionResult testing::internal::CmpHelperEQ<char [26], std::string>(char const, char const, char const (&) [26], std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0[_ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0]+0x94): undefined reference to testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::AssertionResult testing::internal::CmpHelperEQ<char [10], std::string>(char const, char const, char const (&) [10], std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQIA10_cSsEENS_15AssertionResultEPKcS5_RKTRKT0[_ZN7testing8internal11CmpHelperEQIA10_cSsEENS_15AssertionResultEPKcS5_RKTRKT0]+0x94): undefined reference to testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::AssertionResult testing::internal::CmpHelperEQ<unsigned long, int>(char const, char const, unsigned long const&, int const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQImiEENS_15AssertionResultEPKcS4_RKTRKT0[_ZN7testing8internal11CmpHelperEQImiEENS_15AssertionResultEPKcS4_RKTRKT0]+0x91): undefined reference to testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::AssertionResult testing::internal::CmpHelperEQ<std::string, std::string>(char const, char const, std::string const&, std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQISsSsEENS_15AssertionResultEPKcS4_RKTRKT0[_ZN7testing8internal11CmpHelperEQISsSsEENS_15AssertionResultEPKcS4_RKTRKT0]+0x94): undefined reference to testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testRead.cpp.o: In function testing::AssertionResult testing::internal::CmpHelperEQ<int, double>(char const, char const, int const&, double const&)': testRead.cpp:(.text._ZN7testing8internal11CmpHelperEQIidEENS_15AssertionResultEPKcS4_RKTRKT0[_ZN7testing8internal11CmpHelperEQIidEENS_15AssertionResultEPKcS4_RKTRKT0]+0x9b): undefined reference to testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' CMakeFiles/hts_common_test.dir/test/testRead.cpp.o:testRead.cpp:(.text. ZN7testing8internal11CmpHelperEQIN5boost8optionalINS2_14dynamic_bitsetImSaImEEEEES7_EENS_15AssertionResultEPKcSA_RKT_RKT0 [ ZN7testing8internal11CmpHelperEQIN5boost8optionalINS2_14dynamic_bitsetImSaImEEEEES7_EENS_15AssertionResultEPKcSA_RKT_RKT0]+0x94): more undefined references to `testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)' follow /home/alu/ekushele/HTStream/build/src/googletest-buil

Than it keeps going, and write many errors, and then: tail: /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function gnu_cxx::__enable_if<std::is_char::value, bool>::type std::operator==(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)': gtest-all.cc:(.text._ZSteqIcEN9gnu_cxx11__enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE[_ZSteqIcEN9__gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE]+0x1b): undefined reference to std::cxx11::basic_string<char, std::char_traits, std::allocator >::size() const' gtest-all.cc:(.text. *ZSteqIcEN9gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE [ ZSteqIcEN9gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE*]+0x2a): undefined reference to std::cxx11::basic_string<char, std::char_traits, std::allocator >::size() const' gtest-all.cc:(.text._ZSteqIcEN9gnu_cxx11__enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE[_ZSteqIcEN9__gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE]+0x3b): undefined reference to std::cxx11::basic_string<char, std::char_traits, std::allocator >::size() const' gtest-all.cc:(.text. *ZSteqIcEN9gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE [ ZSteqIcEN9gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE*]+0x4a): undefined reference to std::cxx11::basic_string<char, std::char_traits, std::allocator >::data() const' gtest-all.cc:(.text._ZSteqIcEN9gnu_cxx11__enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE[_ZSteqIcEN9__gnu_cxx11enable_ifIXsrSt9is_charIT_E7valueEbE6typeERKNSt7cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3EEESE]+0x59): undefined reference to std::cxx11::basic_string<char, std::char_traits, std::allocator >::data() const' /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function std::cxx11::basic_string<char, std::char_traits, std::allocator > std::__copy_move_backward<false, false, std::random_access_iterator_tag>::copy_move_b<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >*>(std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >*)': gtest-all.cc:(.text._ZNSt20__copy_move_backwardILb0ELb0ESt26random_access_iterator_tagE13copy_move_bIPNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EET0_T_SBSA[_ZNSt20copy_move_backwardILb0ELb0ESt26random_access_iterator_tagE13copy_move_bIPNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EET0_T_SBSA]+0x4a): undefined reference to std::cxx11::basic_string<char, std::char_traits, std::allocator >::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function void std::_Construct<std::cxx11::basic_string<char, std::char_traits, std::allocator >, char const*>(std::cxx11::basic_string<char, std::char_traits, std::allocator >, char const const&)': gtest-all.cc:(.text._ZSt10_ConstructINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKcEvPTRKT0[_ZSt10_ConstructINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKcEvPTRKT0]+0x4f): undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::basic_string(char const*, std::allocator const&)' /home/alu/ekushele/HTStream/build/src/googletest-build/libgtest.a(gtest-all.cc.o): In function testing::internal::XmlUnitTestResultPrinter::~XmlUnitTestResultPrinter()': gtest-all.cc:(.text._ZN7testing8internal24XmlUnitTestResultPrinterD2Ev[_ZN7testing8internal24XmlUnitTestResultPrinterD5Ev]+0x25): undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::~basic_string()' collect2: error: ld returned 1 exit status make[2]: [common/hts_common_test] Error 1 make[1]: [common/CMakeFiles/hts_common_test.dir/all] Error 2 make: *** [all] Error 2

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-451760038, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyc6xH3ZMQTpS47qE0vuk3987zGL_ks5vAjW8gaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

The error starts here:

[ 33%] Linking CXX executable hts_common_test cd /home/alu/ekushele/HTStream/build/common && /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/hts_common_test.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall CMakeFiles/hts_common_test.dir/test/testIO.cpp.o CMakeFiles/hts_common_test.dir/test/testRead.cpp.o CMakeFiles/hts_common_test.dir/src/ioHandler.cpp.o CMakeFiles/hts_common_test.dir/src/read.cpp.o CMakeFiles/hts_common_test.dir/src/utils.cpp.o -o hts_common_test -L/home/alu/ekushele/HTStream/build/src/googletest-build -rdynamic -lgtest -lgtest_main -lpthread -Wl,-Bstatic -lboost_system -lboost_program_options -lboost_filesystem -lboost_iostreams -Wl,-Bdynamic -Wl,-rpath,/home/alu/ekushele/HTStream/build/src/googletest-build CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::internal::PrintTo(std::string const&, std::ostream*)': testIO.cpp:(.text._ZN7testing8internal7PrintToERKSsPSo[_ZN7testing8internal7PrintToERKSsPSo]+0x1f): undefined reference totesting::internal::PrintStringTo(std::string const&, std::ostream)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function boost::system::generic_category()': testIO.cpp:(.text._ZN5boost6system16generic_categoryEv[_ZN5boost6system16generic_categoryEv]+0x5): undefined reference toboost::system::detail::generic_category_ncx()' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function `testing::AssertionResult testing::internal::CmpHelperEQ<char [26], std::string>(char const, char const, char const (&) [26], std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0[_ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0]+0x94): undefined reference to `testing::internal::EqFailure(char const, char const*, std::string const&, std::string const&, bool)'

joe-angell commented 5 years ago

hmm it's not adding the boost lib path it seems like, double check to make sure the boost directories are accurate on the command to cmake. Maybe create a new build dir and try running cmake again on a clean build directory. If you still can't get it maybe I can build a static version that will work on kernel 3.10.

joe

On Sun, Jan 6, 2019 at 10:02 AM efratushava notifications@github.com wrote:

The error starts here:

[ 33%] Linking CXX executable hts_common_test cd /home/alu/ekushele/HTStream/build/common && /private/common/Software/Cmake/cmake-3.3.0-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/hts_common_test.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall CMakeFiles/hts_common_test.dir/test/testIO.cpp.o CMakeFiles/hts_common_test.dir/test/testRead.cpp.o CMakeFiles/hts_common_test.dir/src/ioHandler.cpp.o CMakeFiles/hts_common_test.dir/src/read.cpp.o CMakeFiles/hts_common_test.dir/src/utils.cpp.o -o hts_common_test -L/home/alu/ekushele/HTStream/build/src/googletest-build -rdynamic -lgtest -lgtest_main -lpthread -Wl,-Bstatic -lboost_system -lboost_program_options -lboost_filesystem -lboost_iostreams -Wl,-Bdynamic -Wl,-rpath,/home/alu/ekushele/HTStream/build/src/googletest-build CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::internal::PrintTo(std::string const&, std::ostream)': testIO.cpp:(.text._ZN7testing8internal7PrintToERKSsPSo[_ZN7testing8internal7PrintToERKSsPSo]+0x1f): undefined reference to testing::internal::PrintStringTo(std::string const&, std::ostream)' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function boost::system::generic_category()': testIO.cpp:(.text._ZN5boost6system16generic_categoryEv[_ZN5boost6system16generic_categoryEv]+0x5): undefined reference to boost::system::detail::generic_category_ncx()' CMakeFiles/hts_common_test.dir/test/testIO.cpp.o: In function testing::AssertionResult testing::internal::CmpHelperEQ<char [26], std::string>(char const, char const, char const (&) [26], std::string const&)': testIO.cpp:(.text._ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0[_ZN7testing8internal11CmpHelperEQIA26_cSsEENS_15AssertionResultEPKcS5_RKTRKT0]+0x94): undefined reference to testing::internal::EqFailure(char const, char const, std::string const&, std::string const&, bool)'

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-451761396, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveySoVbgKY_5YUJJvDaHOiiTWMdqDLks5vAjokgaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

Unfortunately I steill can't get it.

The thing is, in hts_Super_deduper, all reads that has "N" in them are ignored. The only thing I wanted, is to change the source code, so it won't ignore such reads, because I need them. And that's why I tried to build the directory myself, and didn't use the executable files @samhunter gave my above

joe-angell commented 5 years ago

For development I highly recommend ubuntu, you can install boost from packages and it's a much better environment.

On Sun, Jan 6, 2019 at 9:19 PM efratushava notifications@github.com wrote:

Unfortunately I steill can't get it.

The thing is, in hts_Super_deduper, all reads that has "N" in them are ignored. The only thing I wanted, is to change the source code, so it won't ignore such reads, because I need them. And that's why I tried to build the directory myself, and didn't use the executable files @samhunter https://github.com/samhunter gave my above

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-451824825, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyecpuSG6nUVnMPSF2Rv5PUZ9N4rEks5vAtjugaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

Sorry, but I don't really understand. Should I install ubuntu? I'm running in shell, without GUI. How can I do that?

joe-angell commented 5 years ago

I'll look into adding the option you want for hts_Super_deduper, :P.

joe

On Mon, Jan 7, 2019 at 10:27 AM efratushava notifications@github.com wrote:

Sorry, but I don't really understand. Should I install ubuntu? I'm running in shell, without GUI. How can I do that?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-452032984, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyd_TMTYjnHQMwTgFwIz9-Nf1PU3Pks5vA5GXgaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

Thank you!

efratushava commented 5 years ago

Another thing: In "common/src/read.cpp", inside: double PairedEndRead::avg_q_score() { double sum = std::accumulate(one.get_qual().begin(), one.get_qual().end(), double(0), qual_sum); sum += std::accumulate(one.get_qual().begin(), one.get_qual().end(), double(0), qual_sum); return sum/double(one.get_qual().length() + two.get_qual().length()); }

In the seconed line, doesn't it have to be: sum += std::accumulate(two.get_qual().begin(), two.get_qual().end(), double(0), qual_sum);

efratushava commented 5 years ago

any news?

joe-angell commented 5 years ago

Yeah appears to be a bug, good find thanks.

On Thu, Jan 10, 2019 at 11:18 AM efratushava notifications@github.com wrote:

any news?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ibest/HTStream/issues/148#issuecomment-453219178, or mute the thread https://github.com/notifications/unsubscribe-auth/AHveyQYc9Hafa8x3non7hugdX12dcayFks5vB5HugaJpZM4ZlCQv .

--

Joe Angell cell: (720) 260-2190

efratushava commented 5 years ago

And what about the N option?

samhunter commented 5 years ago

Hi @efratushava, the HTS team had a discussion regarding whether SuperDeduper should discard reads containing "N" in the key region. In the end we decided that it was probably the best behavior, but we are interested in learning which behavior you would prefer.

If your run had a bad flow (so one of the bases is consistently N) you can change the starting position of SuperDeduper using the -s switch. For example if base 12 is N is most/all of your reads, you could use -s 13 so that the window starts at the 13th base.

Alternatively, you could use CutTrim to trim a fixed number of bases from read1 (e.g. -a 12) before sending the reads through SuperDeduper, so that the portion of the read with an N was removed.

msettles commented 5 years ago

Seems like the issue is resolved and an be close, any objects @efratushava ?

efratushava commented 5 years ago

Yes, I solved this problem for myself. Thank you!