Hi,
I am trying to install the bcl2fastq2 soft with no success on linux debian.
I believe I followed the steps given by the Illumina notice.
From the output below, I understand it can't find or use the sys/stat.h.
But the file is definitely there:
hjg@aurigny:/tmp/bcl2fastq2-v2.15.0.4-build$ locate sys/stat.h
/usr/include/x86_64-linux-gnu/sys/stat.h
In anticipation, thanks very much for your help.
Here is the output of the configure command:
hjg@aurigny:/tmp/bcl2fastq2-v2.15.0.4-build$ sudo ${SOURCE}/src/configure --prefix=${INSTALL_DIR}
cmake version "2.8.9" is already installed at /tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake
nothing to be done
Using installed /tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake
-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install prefix: /usr/local/bin/bcl2fastq2-v2.15.0.4
-- install exec prefix: .
-- install bin dir: ./bin
-- install lib dir: ./lib/bcl2fastq-2.15.0.4
-- install libexec dir: ./libexec/bcl2fastq-2.15.0.4
-- install include dir: include/bcl2fastq-2.15.0.4
-- install data dir: share/bcl2fastq-2.15.0.4
-- install doc dir: doc/bcl2fastq-2.15.0.4
-- install man dir: man
-- Could NOT find Boost
-- Boost 1.54.0 not found. Boost will be built from the distribution...
Decompressing /tmp/bcl2fastq/src/../redist/boost_1_54_0.tar.bz2
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... not found.
Backing up existing Boost.Build configuration in project-config.jam.2
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./b2
To adjust configuration, edit 'project-config.jam'.
Further information:
- Command line help:
./b2 --help
- Getting started guide:
- Boost.Build documentation:
Performing configuration checks
- zlib : yes (cached)
- has_icu builds : no (cached)
Component configuration:
- atomic : not building
- chrono : building
- context : not building
- coroutine : not building
- date_time : building
- exception : not building
- filesystem : building
- graph : not building
- graph_parallel : not building
- iostreams : building
- locale : not building
- log : not building
- math : not building
- mpi : not building
- program_options : building
- python : not building
- random : not building
- regex : building
- serialization : building
- signals : not building
- system : building
- test : not building
- thread : building
- timer : building
- wave : not building
...patience...
...patience...
...found 22368 targets...
boost-1_54_0 installed successfully
-- Successfuly built boost 1.54.0 from the distribution package...
-- Verifying target directories access
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- inttypes.h found as /usr/include/inttypes.h
-- malloc.h found as /usr/include/malloc.h
-- mcheck.h found as /usr/include/mcheck.h
-- memory.h found as /usr/include/memory.h
-- signal.h found as /usr/include/signal.h
-- stdint.h found as 1
-- stdlib.h found as /usr/include/stdlib.h
-- string.h found as /usr/include/string.h
-- strings.h found as /usr/include/strings.h
-- time.h found as /usr/include/time.h
-- unistd.h found as /usr/include/unistd.h
CMake Error at cmake/macros.cmake:84 (message):
Required header sys/stat.h not found.
Call Stack (most recent call first):
cmake/cxxConfigure.cmake:44 (bcl2fastq_find_header_or_die)
cxx/CMakeLists.txt:37 (include)
-- Configuring incomplete, errors occurred!
Couldn't configure the project:
/tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake -H'/tmp/bcl2fastq/src' -B'/tmp/bcl2fastq2-v2.15.0.4-build' -G'Unix Makefiles' -DBCL2FASTQ_NAME_SHORT:STRING="bcl2fastq" -DBCL2FASTQ_NAME_LONG:STRING="BCL to FASTQ file converter" -DBCL2FASTQ_COPYRIGHT:STRING="Copyright (c) 2007-2014 Illumina, Inc." -DBCL2FASTQ_VERSION_MAJOR:STRING="2" -DBCL2FASTQ_VERSION_MINOR:STRING="15" -DBCL2FASTQ_VERSION_PATCH:STRING="0" -DBCL2FASTQ_VERSION_BUILD:STRING="4" -DBCL2FASTQ_VERSION:STRING="2.15.0.4" -DBCL2FASTQ_SOURCE_DIR:STRING="/tmp/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/usr/local/bin/bcl2fastq2-v2.15.0.4/" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/usr/local/bin/bcl2fastq2-v2.15.0.4/" -DBCL2FASTQ_BINDIR:PATH="" -DBCL2FASTQ_LIBDIR:PATH="" -DBCL2FASTQ_LIBEXECDIR:PATH="" -DBCL2FASTQ_INCLUDEDIR:PATH="" -DBCL2FASTQ_DATADIR:PATH="" -DBCL2FASTQ_DOCDIR:PATH="" -DBCL2FASTQ_MANDIR:PATH="" -DCMAKE_BUILD_TYPE:STRING="RelWithDebInfo" -DCMAKE_PARALLEL:STRING="1"
Moving CMakeCache.txt to CMakeCache.txt.removed
I am trying to install the bcl2fastq2 soft with no success on linux debian.
I believe I followed the steps given by the Illumina notice.
From the output below, I understand it can't find or use the sys/stat.h.
But the file is definitely there:
hjg@aurigny:/tmp/bcl2fastq2-v2.15.0.4-build$ locate sys/stat.h
/usr/include/x86_64-linux-gnu/sys/stat.h
In anticipation, thanks very much for your help.
Here is the output of the configure command:
hjg@aurigny:/tmp/bcl2fastq2-v2.15.0.4-build$ sudo ${SOURCE}/src/configure --prefix=${INSTALL_DIR}
cmake version "2.8.9" is already installed at /tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake
nothing to be done
Using installed /tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake
-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install prefix: /usr/local/bin/bcl2fastq2-v2.15.0.4
-- install exec prefix: .
-- install bin dir: ./bin
-- install lib dir: ./lib/bcl2fastq-2.15.0.4
-- install libexec dir: ./libexec/bcl2fastq-2.15.0.4
-- install include dir: include/bcl2fastq-2.15.0.4
-- install data dir: share/bcl2fastq-2.15.0.4
-- install doc dir: doc/bcl2fastq-2.15.0.4
-- install man dir: man
-- Could NOT find Boost
-- Boost 1.54.0 not found. Boost will be built from the distribution...
Decompressing /tmp/bcl2fastq/src/../redist/boost_1_54_0.tar.bz2
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... not found.
Backing up existing Boost.Build configuration in project-config.jam.2
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./b2
To adjust configuration, edit 'project-config.jam'.
Further information:
- Command line help:
./b2 --help
- Getting started guide:
- Boost.Build documentation:
Performing configuration checks
- zlib : yes (cached)
- has_icu builds : no (cached)
Component configuration:
- atomic : not building
- chrono : building
- context : not building
- coroutine : not building
- date_time : building
- exception : not building
- filesystem : building
- graph : not building
- graph_parallel : not building
- iostreams : building
- locale : not building
- log : not building
- math : not building
- mpi : not building
- program_options : building
- python : not building
- random : not building
- regex : building
- serialization : building
- signals : not building
- system : building
- test : not building
- thread : building
- timer : building
- wave : not building
...patience...
...patience...
...found 22368 targets...
boost-1_54_0 installed successfully
-- Successfuly built boost 1.54.0 from the distribution package...
-- Verifying target directories access
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- inttypes.h found as /usr/include/inttypes.h
-- malloc.h found as /usr/include/malloc.h
-- mcheck.h found as /usr/include/mcheck.h
-- memory.h found as /usr/include/memory.h
-- signal.h found as /usr/include/signal.h
-- stdint.h found as 1
-- stdlib.h found as /usr/include/stdlib.h
-- string.h found as /usr/include/string.h
-- strings.h found as /usr/include/strings.h
-- time.h found as /usr/include/time.h
-- unistd.h found as /usr/include/unistd.h
CMake Error at cmake/macros.cmake:84 (message):
Required header sys/stat.h not found.
Call Stack (most recent call first):
cmake/cxxConfigure.cmake:44 (bcl2fastq_find_header_or_die)
cxx/CMakeLists.txt:37 (include)
-- Configuring incomplete, errors occurred!
Couldn't configure the project:
/tmp/bcl2fastq2-v2.15.0.4-build/bootstrap_cmake/bin/cmake -H'/tmp/bcl2fastq/src' -B'/tmp/bcl2fastq2-v2.15.0.4-build' -G'Unix Makefiles' -DBCL2FASTQ_NAME_SHORT:STRING="bcl2fastq" -DBCL2FASTQ_NAME_LONG:STRING="BCL to FASTQ file converter" -DBCL2FASTQ_COPYRIGHT:STRING="Copyright (c) 2007-2014 Illumina, Inc." -DBCL2FASTQ_VERSION_MAJOR:STRING="2" -DBCL2FASTQ_VERSION_MINOR:STRING="15" -DBCL2FASTQ_VERSION_PATCH:STRING="0" -DBCL2FASTQ_VERSION_BUILD:STRING="4" -DBCL2FASTQ_VERSION:STRING="2.15.0.4" -DBCL2FASTQ_SOURCE_DIR:STRING="/tmp/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/usr/local/bin/bcl2fastq2-v2.15.0.4/" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/usr/local/bin/bcl2fastq2-v2.15.0.4/" -DBCL2FASTQ_BINDIR:PATH="" -DBCL2FASTQ_LIBDIR:PATH="" -DBCL2FASTQ_LIBEXECDIR:PATH="" -DBCL2FASTQ_INCLUDEDIR:PATH="" -DBCL2FASTQ_DATADIR:PATH="" -DBCL2FASTQ_DOCDIR:PATH="" -DBCL2FASTQ_MANDIR:PATH="" -DCMAKE_BUILD_TYPE:STRING="RelWithDebInfo" -DCMAKE_PARALLEL:STRING="1"
Moving CMakeCache.txt to CMakeCache.txt.removed
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