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iontorrent / TS

Torrent Suite
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Unable to compile using docker image #51

Open dguettler opened 5 years ago

dguettler commented 5 years ago

I'm following instructions provided here: https://hub.docker.com/r/iontorrent/tsbuild/

docker pull iontorrent/tsbuild

# build all modules:
docker run -v /home/ionadmin/codes/TS:/src iontorrent/tsbuild

However the build is failing for all modules.

$ docker run -v /workspace/TS:/src iontorrent/tsbuild
Building TSS packages: (all)
==================================================
 Building module gpu
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
-- Searching for an ION_UPDATE_SERVER...
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
CMake Warning at CMakeLists.txt:33 (message):
  Could not find a valid ION_UPDATE_SERVER.

-- BUILD with CUDA 
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:95 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/gpu/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/gpu/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/gpu
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
Running CMake to regenerate build system...
[  2%] [  8%] Performing patch step for 'armadillo_proj'
Performing patch step for 'bamtools'
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- CMakeLists.txt 2015-10-01 22:44:31.000000000 -0400
|+++ CMakeLists.txt 2015-10-13 10:44:27.273499054 -0400
--------------------------
No file to patch.  Skipping patch.
[ 14%] 3 out of 3 hunks ignored
Built target eigen_proj
make[2]: *** [../armadillo-6.100.0+ion0-prefix/src/armadillo_proj-stamp/armadillo_proj-patch] Error 1
make[1]: *** [CMakeFiles/armadillo_proj.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- src/api/internal/bam/BamWriter_p.cpp   2016-04-26 11:05:21.846478000 -0700
|+++ src/api/internal/bam/BamWriter_p.cpp   2016-04-26 11:06:15.838242000 -0700
--------------------------
No file to patch.  Skipping patch.
1 out of 1 hunk ignored
make[2]: *** [../bamtools-2.4.0.20150702+git15eadb925f-prefix/src/bamtools-stamp/bamtools-patch] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 22%] No update step for 'bamtools'
[ 28%] Built target cuda_toolkit
make[1]: *** [CMakeFiles/bamtools.dir/all] Error 2
Scanning dependencies of target gpu_devdriver
[ 29%] Creating directories for 'gpu_devdriver'
[ 31%] Performing download step (download, verify and extract) for 'gpu_devdriver'
-- downloading...
     src='http:///updates/software/external/devdriver_NVIDIA-Linux-x86_64-375.26.run.tar.gz'
     dst='/src/build/gpu/../gpu_devdriver-375.26-prefix/src/devdriver_NVIDIA-Linux-x86_64-375.26.run.tar.gz'
     timeout='3600 seconds'
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
-- Searching for an ION_UPDATE_SERVER...
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
CMake Warning at CMakeLists.txt:33 (message):
  Could not find a valid ION_UPDATE_SERVER.

-- BUILD with CUDA 
-- Searching for an ION_UPDATE_SERVER...
-- [download 0% complete]
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:95 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- downloading... done
-- verifying file...
     file='/src/build/gpu/../gpu_devdriver-375.26-prefix/src/devdriver_NVIDIA-Linux-x86_64-375.26.run.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
     src='/src/build/gpu_devdriver-375.26-prefix/src/devdriver_NVIDIA-Linux-x86_64-375.26.run.tar.gz'
     dst='/src/build/gpu_devdriver-375.26'
-- extracting... [tar xfz]
-- CUDA_LIBRARIES: /src/build/gpu/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/gpu/../cuda_toolkit-8.0.44-21122537/include
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 34%] [ 34%] No update step for 'gpu_devdriver'
No patch step for 'gpu_devdriver'
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
[ 35%] No configure step for 'gpu_devdriver'
[ 37%] No build step for 'gpu_devdriver'
[ 38%] No install step for 'gpu_devdriver'
[ 40%] Completed 'gpu_devdriver'
[ 40%] Built target gpu_devdriver
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/gpu
[ 40%] Built target IONVERSION
make: *** [all] Error 2
Running tests...
Test project /src/build/gpu
No tests were found!!!
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
-- Searching for an ION_UPDATE_SERVER...
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
CMake Warning at CMakeLists.txt:33 (message):
  Could not find a valid ION_UPDATE_SERVER.

-- BUILD with CUDA 
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:95 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/gpu/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/gpu/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/gpu
[  0%] Built target IONVERSION
[  1%] Performing patch step for 'armadillo_proj'
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- CMakeLists.txt 2015-10-01 22:44:31.000000000 -0400
|+++ CMakeLists.txt 2015-10-13 10:44:27.273499054 -0400
--------------------------
No file to patch.  Skipping patch.
3 out of 3 hunks ignored
make[2]: *** [../armadillo-6.100.0+ion0-prefix/src/armadillo_proj-stamp/armadillo_proj-patch] Error 1
make[1]: *** [CMakeFiles/armadillo_proj.dir/all] Error 2
make: *** [all] Error 2
==================================================

==================================================
 Building module Analysis
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:54 (include)

-- LSB release codename: trusty
Not setting mkl root 
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/Analysis/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/Analysis/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- BUILD with ION_USE_CUDA ON
-- BUILD with ION_USE_SYSTEM_CUDA OFF
-- BUILD with CUDA 8.0
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/Analysis
[  0%] make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
[  0%] Built target hdf5_proj
Performing patch step for 'armadillo_proj'
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- CMakeLists.txt 2015-10-01 22:44:31.000000000 -0400
|+++ CMakeLists.txt 2015-10-13 10:44:27.273499054 -0400
--------------------------
No file to patch.  Skipping patch.
3 out of 3 hunks ignored
[  1%] make[2]: *** [../armadillo-6.100.0+ion0-prefix/src/armadillo_proj-stamp/armadillo_proj-patch] Error 1
make[1]: *** [CMakeFiles/armadillo_proj.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Built target cuda_toolkit
Running CMake to regenerate build system...
[  1%] Built target boost_proj
[  4%] Built target file-io
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:54 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/Analysis/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/Analysis/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- BUILD with ION_USE_CUDA ON
-- BUILD with ION_USE_SYSTEM_CUDA OFF
-- BUILD with CUDA 8.0
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/Analysis
[  4%] Built target IONVERSION
make: *** [all] Error 2
Running tests...
Test project /src/build/Analysis
    Start 1: trimfastq.pl
1/1 Test #1: trimfastq.pl .....................   Passed    0.06 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =   0.14 sec
[  3%] Built target file-io
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:54 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/Analysis/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/Analysis/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- BUILD with ION_USE_CUDA ON
-- BUILD with ION_USE_SYSTEM_CUDA OFF
-- BUILD with CUDA 8.0
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/Analysis
[  3%] Built target IONVERSION
[  3%] Built target boost_proj
[  3%] Built target hdf5_proj
[  4%] Built target cuda_toolkit
Scanning dependencies of target htslib_proj
[  4%] Creating directories for 'htslib_proj'
[  4%] Performing download step (download, verify and extract) for 'htslib_proj'
-- downloading...
     src='http:///updates/software/external/htslib-1.2.1.tar.gz'
     dst='/src/build/Analysis/../htslib-1.2.1+ion0-prefix/src/htslib-1.2.1.tar.gz'
     timeout='none'
-- [download 0% complete]
-- downloading... done
-- verifying file...
     file='/src/build/Analysis/../htslib-1.2.1+ion0-prefix/src/htslib-1.2.1.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
     src='/src/build/htslib-1.2.1+ion0-prefix/src/htslib-1.2.1.tar.gz'
     dst='/src/build/htslib-1.2.1+ion0'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[  4%] Performing patch step for 'htslib_proj'
[  4%] No update step for 'htslib_proj'
[  4%] No configure step for 'htslib_proj'
[  5%] Performing build step for 'htslib_proj'
make[3]: *** No targets specified and no makefile found.  Stop.
make[2]: *** [../htslib-1.2.1+ion0-prefix/src/htslib_proj-stamp/htslib_proj-build] Error 2
make[1]: *** [CMakeFiles/htslib_proj.dir/all] Error 2
make: *** [all] Error 2
==================================================

==================================================
 Building module torrentR
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:9 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/torrentR/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/torrentR/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/torrentR
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
clean torrentR objects in: /src/torrentR/src
Running CMake to regenerate build system...
[  1%] [  1%] Performing patch step for 'armadillo_proj'
Built target LIBTORRENTRCLEAN
[ 10%] can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- CMakeLists.txt 2015-10-01 22:44:31.000000000 -0400
|+++ CMakeLists.txt 2015-10-13 10:44:27.273499054 -0400
--------------------------
No file to patch.  Skipping patch.
3 out of 3 hunks ignored
make[2]: *** [../armadillo-6.100.0+ion0-prefix/src/armadillo_proj-stamp/armadillo_proj-patch] Error 1
make[1]: *** [CMakeFiles/armadillo_proj.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Performing patch step for 'bamtools'
[ 17%] Built target cuda_toolkit
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- src/api/internal/bam/BamWriter_p.cpp   2016-04-26 11:05:21.846478000 -0700
|+++ src/api/internal/bam/BamWriter_p.cpp   2016-04-26 11:06:15.838242000 -0700
--------------------------
No file to patch.  Skipping patch.
1 out of 1 hunk ignored
make[2]: *** [../bamtools-2.4.0.20150702+git15eadb925f-prefix/src/bamtools-stamp/bamtools-patch] Error 1
make[1]: *** [CMakeFiles/bamtools.dir/all] Error 2
[ 32%] Built target eigen_proj
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:9 (include)

-- LSB release codename: trusty
Not setting mkl root 
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/torrentR/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/torrentR/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/torrentR
[ 32%] Built target IONVERSION
make: *** [all] Error 2
Running tests...
Test project /src/build/torrentR
No tests were found!!!
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:9 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/torrentR/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/torrentR/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/torrentR
[  0%] Built target IONVERSION
clean torrentR objects in: /src/torrentR/src
[  0%] Built target LIBTORRENTRCLEAN
* installing *source* package 'torrentR' ...
** libs
In file included from BamHelper.cpp:5:0:
BamHelper.h:7:27: fatal error: api/BamReader.h: No such file or directory
 #include "api/BamReader.h"
                           ^
compilation terminated.
In file included from ExtendedReadData.cpp:5:0:
ExtendedReadData.h:7:27: fatal error: api/BamReader.h: No such file or directory
 #include "api/BamReader.h"
                           ^
compilation terminated.
In file included from StackEngine.cpp:3:0:
StackEngine.h:7:27: fatal error: api/BamReader.h: No such file or directory
 #include "api/BamReader.h"
                           ^
compilation terminated.
make[3]: *** [ExtendedReadData.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [BamHelper.o] Error 1
make[3]: *** [StackEngine.o] Error 1
mixedReads.cpp:5:21: fatal error: armadillo: No such file or directory
 #include <armadillo>
                     ^
compilation terminated.
make[3]: *** [mixedReads.o] Error 1
g++: internal compiler error: Killed (program cc1plus)
g++: internal compiler error: Killed (program cc1plus)
g++: internal compiler error: Killed (program cc1plus)
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
g++: internal compiler error: Killed (program cc1plus)
make[3]: *** [SimulateCAFIE.o] Error 4
make[3]: *** [GenerateHydrogen.o] Error 4
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [PurpleTrace.o] Error 4
make[3]: *** [fitBkgTrace.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
make[3]: *** [readBeadParamV2.o] Error 4
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [multreePhaser.o] Error 4
make[3]: *** [treePhaser.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [readStack.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [findBestCafie.o] Error 4
In file included from flowAlignment.cpp:4:0:
/src/torrentR/../Analysis/Calibration/FlowAlignment.h:8:30: fatal error: api/BamAlignment.h: No such file or directory
 #include "api/BamAlignment.h"
                              ^
compilation terminated.
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [FlowErr.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [calcHypothesesDistances.o] Error 4
readIonBam.cpp:3:27: fatal error: api/BamReader.h: No such file or directory
 #include "api/BamReader.h"
                           ^
compilation terminated.
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [normalizeRead.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [DPTreephaserM.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [calcHypothesesDistancesEngine.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [findAdapter.o] Error 4
In file included from PhaseFit.h:6:0,
                 from PhaseFitCfIe.h:5,
                 from PhaseFitCfIe.cpp:3:
/src/torrentR/../Analysis/LevMarFitter.h:5:21: fatal error: armadillo: No such file or directory
 #include <armadillo>
                     ^
compilation terminated.
In file included from PhaseFit.h:6:0,
                 from PhaseFit.cpp:5:
/src/torrentR/../Analysis/LevMarFitter.h:5:21: fatal error: armadillo: No such file or directory
 #include <armadillo>
                     ^
compilation terminated.
In file included from DroopFit.h:5:0,
                 from CafieSolver.cpp:19:
/src/torrentR/../Analysis/LevMarFitter.h:5:21: fatal error: armadillo: No such file or directory
 #include <armadillo>
                     ^
compilation terminated.
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [keyStats.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [emphasisVector.o] Error 4
In file included from PhaseFit.h:6:0,
                 from PhaseFitCfIe.h:5,
                 from phaseFit_R.cpp:4:
/src/torrentR/../Analysis/LevMarFitter.h:5:21: fatal error: armadillo: No such file or directory
 #include <armadillo>
                     ^
compilation terminated.
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [phaseSimulator.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [normalizeIonogram.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [readBeadFindMask.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [OneFlowFit.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [readBeadParam.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [readWells.o] Error 4
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [phaseSolve_R.o] Error 4
make[3]: *** [flowAlignment.o] Error 1
make[3]: *** [readIonBam.o] Error 1
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[3]: *** [correctCafie.o] Error 4
make[3]: *** [PhaseFit.o] Error 1
make[3]: *** [PhaseFitCfIe.o] Error 1
make[3]: *** [CafieSolver.o] Error 1
make[3]: *** [phaseFit_R.o] Error 1
ERROR: compilation failed for package 'torrentR'
* removing '/src/build/torrentR/rlib/torrentR'
make[2]: *** [CMakeFiles/LIBTORRENTR] Error 1
make[1]: *** [CMakeFiles/LIBTORRENTR.dir/all] Error 2
make: *** [all] Error 2
==================================================

==================================================
 Building module torrentPy
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:18 (include)

Not setting mkl root 
-- LSB release codename: trusty
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/torrentPy/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/torrentPy/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   python
-- ION_LIBS: /src/build/torrentPy/../Analysis/libion-analysis.a;/src/build/torrentPy/../Analysis/libfile-io.a;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/src/build/torrentPy/../bamtools-2.4.0.20150702+git15eadb925f-install/lib/bamtools/libbamtools.a;/usr/lib/x86_64-linux-gnu/libboost_python.so
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/torrentPy
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
Running CMake to regenerate build system...
[  1%] [  3%] Performing patch step for 'bamtools'
Performing patch step for 'armadillo_proj'
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- src/api/internal/bam/BamWriter_p.cpp   2016-04-26 11:05:21.846478000 -0700
|+++ src/api/internal/bam/BamWriter_p.cpp   2016-04-26 11:06:15.838242000 -0700
--------------------------
No file to patch.  Skipping patch.
1 out of 1 hunk ignored
make[2]: *** [../bamtools-2.4.0.20150702+git15eadb925f-prefix/src/bamtools-stamp/bamtools-patch] Error 1
make[1]: *** [CMakeFiles/bamtools.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- CMakeLists.txt 2015-10-01 22:44:31.000000000 -0400
|+++ CMakeLists.txt 2015-10-13 10:44:27.273499054 -0400
--------------------------
No file to patch.  Skipping patch.
3 out of 3 hunks ignored
make[2]: *** [../armadillo-6.100.0+ion0-prefix/src/armadillo_proj-stamp/armadillo_proj-patch] Error 1
make[1]: *** [CMakeFiles/armadillo_proj.dir/all] Error 2
[ 22%] Built target eigen_proj
[ 31%] Built target cuda_toolkit
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:18 (include)

-- LSB release codename: trusty
Not setting mkl root 
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/torrentPy/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/torrentPy/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   python
-- ION_LIBS: /src/build/torrentPy/../Analysis/libion-analysis.a;/src/build/torrentPy/../Analysis/libfile-io.a;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/src/build/torrentPy/../bamtools-2.4.0.20150702+git15eadb925f-install/lib/bamtools/libbamtools.a;/usr/lib/x86_64-linux-gnu/libboost_python.so
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/torrentPy
[ 31%] Built target IONVERSION
make: *** [all] Error 2
Running tests...
Test project /src/build/torrentPy
    Start 1: 00_Install
1/2 Test #1: 00_Install .......................***Failed    2.18 sec
    Start 2: Test_torrentPy
2/2 Test #2: Test_torrentPy ...................***Failed    0.07 sec

0% tests passed, 2 tests failed out of 2

Total Test time (real) =   2.30 sec

The following tests FAILED:
      1 - 00_Install (Failed)
      2 - Test_torrentPy (Failed)
Errors while running CTest
make: *** [test] Error 8
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Searching for an ION_UPDATE_SERVER...
CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.
Call Stack (most recent call first):
  CMakeLists.txt:18 (include)

-- LSB release codename: trusty
Not setting mkl root 
-- BUILD with CUDA 8.0
-- CUDA_LIBRARIES: /src/build/torrentPy/../cuda_toolkit-8.0.44-21122537/lib64/libcudart.so
-- CUDA_INCLUDE_DIRS: /src/build/torrentPy/../cuda_toolkit-8.0.44-21122537/include
-- ION_HDF5_LIBS: hdf5;hdf5_hl;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_INCLUDE_DIRS: /usr/include
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   serialization
-- ION_BOOST_LIBS: /usr/lib/x86_64-linux-gnu/libboost_serialization.a
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   python
-- ION_LIBS: /src/build/torrentPy/../Analysis/libion-analysis.a;/src/build/torrentPy/../Analysis/libfile-io.a;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/src/build/torrentPy/../bamtools-2.4.0.20150702+git15eadb925f-install/lib/bamtools/libbamtools.a;/usr/lib/x86_64-linux-gnu/libboost_python.so
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/torrentPy
[  0%] Built target IONVERSION
[  1%] Performing patch step for 'armadillo_proj'
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- CMakeLists.txt 2015-10-01 22:44:31.000000000 -0400
|+++ CMakeLists.txt 2015-10-13 10:44:27.273499054 -0400
--------------------------
No file to patch.  Skipping patch.
3 out of 3 hunks ignored
make[2]: *** [../armadillo-6.100.0+ion0-prefix/src/armadillo_proj-stamp/armadillo_proj-patch] Error 1
make[1]: *** [CMakeFiles/armadillo_proj.dir/all] Error 2
make: *** [all] Error 2
==================================================

==================================================
 Building module dbReports
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/dbReports
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/dbReports
Built target IONVERSION
Built target compileall
Running tests...
Test project /src/build/dbReports
No tests were found!!!
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/dbReports
Built target IONVERSION
Built target compileall
Run CPack packaging tool...
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: ion-dbreports
CPack: - Install project: ion-dbreports
CPack: Create package
CPack: - package: /src/build/dbReports/ion-dbreports_5.10.27-1_Linux_amd64.deb generated.
==================================================

==================================================
 Building module pipeline
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/pipeline
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/pipeline
Built target IONVERSION
Built target compileall
Running tests...
Test project /src/build/pipeline
No tests were found!!!
Running CMake to regenerate build system...
-- LSB release codename: trusty
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/pipeline
Built target IONVERSION
Built target compileall
Run CPack packaging tool...
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: ion-pipeline
CPack: - Install project: ion-pipeline
CPack: Create package
CPack: - package: /src/build/pipeline/ion-pipeline_5.10.10-1_Linux_amd64.deb generated.
==================================================

==================================================
 Building module publishers
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/publishers
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/publishers
Built target IONVERSION
Running tests...
Test project /src/build/publishers
No tests were found!!!
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/publishers
Built target IONVERSION
Run CPack packaging tool...
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: ion-publishers
CPack: - Install project: ion-publishers
CPack: Create package
CPack: - package: /src/build/publishers/ion-publishers_5.10.2-1_Linux_amd64.deb generated.
==================================================

==================================================
 Building module tsconfig
==================================================
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/tsconfig
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/tsconfig
Built target IONVERSION
Running tests...
Test project /src/build/tsconfig
No tests were found!!!
Running CMake to regenerate build system...
-- LSB release codename: trusty
-- common compiler flags:  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3
DEBUG CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O0 -g -DION_DEBUG  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
RELEASE CXXFLAGS  -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter
-- Configuring done
-- Generating done
-- Build files have been written to: /src/build/tsconfig
Built target IONVERSION
Run CPack packaging tool...
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: ion-tsconfig
CPack: - Install project: ion-tsconfig
CPack: Create package
CPack: - package: /src/build/tsconfig/ion-tsconfig_5.10.5-1_Linux_amd64.deb generated.
==================================================

Build of module gpu failed.
Build of module Analysis failed.
Build of module torrentR failed.
Build of module torrentPy failed.

FAILURES: 4 modules failed to build.
$

I tried with master branch and with the latest tagged version. Same outcome for both.

Thanks.

sgsfak commented 4 years ago

It seems the host command used in the CMake files for determining the 'best' update server is not quite right. See the changes at my forked repo at https://github.com/sgsfak/TS/commit/7136beb65885b7db32a1e5f9a134d28c063e98ab

morrychan commented 4 years ago

Have you solved it yet? I met with the same error,how can I work around this?

morrychan commented 4 years ago

It seems the host command used in the CMake files for determining the 'best' update server is not quite right. See the changes at my forked repo at sgsfak@7136beb

does not work

sgsfak commented 4 years ago

The change I proposed addressed (at least for me) the following error:

CMake Warning at /src/buildTools/cmake/CMakeLists.dependencies.txt:26 (message):
  Could not find a valid ION_UPDATE_SERVER.

But since then, in release 5.12 the change has been incorporated in the official trunk: https://github.com/iontorrent/TS/blame/108989c200fb896c1366786a70f4a5e166dc733c/buildTools/cmake/CMakeLists.dependencies.txt#L12

So maybe you have a different error...

kevin3 commented 4 years ago

Can you test if you can ping updates.iontorrent.com ? that seems to be the public facing server, maybe you have a connection issue versus a code issue?