ClinSV
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20 hours ago •
KCCG
KCCG
Issue when building the docker image (ERROR [30/39])
Hello
I am a beginner in bioinformatic and the use of command line tools. I am trying to build the image docker using the Dockerfile. The process failed at that step :
RUN cd $clinsv_path &&
git clone --branch latest-stable https://github.com/root-project/root.git root_src &&
mkdir root_build root_install && cd root_build &&
cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src && \
Here is a copy of all the process and the error message that I got. What should I do to solve this problems ? Thank you.
(base) av65@ML22-1060 Downloads % docker build . -f Dockerfile.txt
[+] Building 1868.1s (34/43) docker:desktop-linux
=> [internal] load build definition from Dockerfile.txt 0.0s
=> => transferring dockerfile: 5.89kB 0.0s
=> [internal] load metadata for docker.io/library/ubuntu:20.04 0.9s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [ 1/39] FROM docker.io/library/ubuntu:20.04@sha256:0b897358ff6624825fb50d20ffb605ab0eaea77ced0adb8c6a4b756 0.0s
=> [internal] load build context 0.0s
=> => transferring context: 710B 0.0s
=> CACHED [ 2/39] WORKDIR /app 0.0s
=> CACHED [ 3/39] RUN mkdir clinsv 0.0s
=> CACHED [ 4/39] ADD clinsvScripts.tar.gz /app 0.0s
=> CACHED [ 5/39] ADD installKNITR.r /app 0.0s
=> CACHED [ 6/39] RUN mv clinsvScripts/* clinsv/ 0.0s
=> CACHED [ 7/39] RUN rm -r clinsvScripts 0.0s
=> CACHED [ 8/39] RUN apt-get update 0.0s
=> CACHED [ 9/39] RUN apt-get -y install build-essential 0.0s
=> CACHED [10/39] RUN apt-get -y install wget curl git nano 0.0s
=> CACHED [11/39] RUN apt-get -y install zlib1g-dev 0.0s
=> CACHED [12/39] RUN apt-get -y install libbz2-dev liblzma-dev libcurl4-openssl-dev libncurses5-dev 0.0s
=> CACHED [13/39] RUN apt-get -y install python3.8 python3-pip 0.0s
=> CACHED [14/39] RUN apt-get -y install dpkg-dev cmake g++ gcc binutils libx11-dev libxpm-dev libxft-dev lib 0.0s
=> CACHED [15/39] RUN apt-get -y install dh-autoreconf 0.0s
=> CACHED [16/39] RUN ln -sf ../bin/bash ../bin/sh 0.0s
=> CACHED [17/39] RUN curl -L https://cpanmin.us | perl - App::cpanminus 0.0s
=> CACHED [18/39] RUN mkdir clinsv/perl 0.0s
=> [19/39] RUN cd /app/clinsv/perl && git clone https://github.com/dpryan79/libBigWig && cd libBig 1305.1s
=> [20/39] RUN cd /app/clinsv && mkdir samtools && cd samtools && wget https://github.com/samto 126.0s
=> [21/39] RUN cd /app/clinsv/bin && ln -s ../samtools/bin/bcftools bcftools && ln -s ../samtools/bin 0.1s
=> [22/39] RUN mkdir /app/clinsv/bigWigTools && cd /app/clinsv/bigWigTools && wget http://hgdownloa 131.9s
=> [23/39] RUN cd /app/clinsv/bin && ln -s ../bigWigTools/bigWigToWig bigWigToWig && ln -s ../bigWigT 0.1s
=> [24/39] RUN mkdir /app/clinsv/python 0.1s
=> [25/39] RUN cd /app/clinsv/python && wget https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tgz 60.1s
=> [26/39] RUN cd /app/clinsv/python && rm -r Python-2.7.18* 0.3s
=> [27/39] RUN cd /app/clinsv/bin && ln -s ../python/bin/python python && ln -s ../python/bin/python 0.1s
=> [28/39] RUN pip3 install numpy 2.5s
=> [29/39] RUN pip3 install pysam 149.1s
=> ERROR [30/39] RUN cd /app/clinsv && git clone --branch latest-stable https://github.com/root-project/ 91.6s
------
> [30/39] RUN cd /app/clinsv && git clone --branch latest-stable https://github.com/root-project/root.git root_src && mkdir root_build root_install && cd root_build && cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src && cmake --build . -- install:
0.120 Cloning into 'root_src'...
Updating files: 100% (24200/24200), done.
89.40 -- The C compiler identification is GNU 9.4.0
89.43 -- The CXX compiler identification is GNU 9.4.0
89.44 -- Check for working C compiler: /usr/bin/cc
89.47 -- Check for working C compiler: /usr/bin/cc -- works
89.47 -- Detecting C compiler ABI info
89.49 -- Detecting C compiler ABI info - done
89.50 -- Detecting C compile features
89.50 -- Detecting C compile features - done
89.50 -- Check for working CXX compiler: /usr/bin/c++
89.53 -- Check for working CXX compiler: /usr/bin/c++ -- works
89.53 -- Detecting CXX compiler ABI info
89.57 -- Detecting CXX compiler ABI info - done
89.57 -- Detecting CXX compile features
89.57 -- Detecting CXX compile features - done
89.57 -- Found Git: /usr/bin/git (found version "2.25.1")
89.58 CMake Warning at cmake/modules/SetROOTVersion.cmake:85 (message):
89.58 GIT_DESCRIBE_ALL is `heads/latest-stable`·with a format unexpected for
89.58 tags. Not setting the commit.
89.58 Call Stack (most recent call first):
89.58 cmake/modules/SetROOTVersion.cmake:99 (SET_ROOT_VERSION)
89.58 CMakeLists.txt:75 (include)
89.58
89.58
89.58 -- Building ROOT version 6.32.02
89.58 -- Checking internet connectivity
89.74 -- Checking internet connectivity - found
89.74 -- Looking for a CUDA compiler
89.77 -- Looking for a CUDA compiler - NOTFOUND
89.77 -- Found GCC. Major version 9, minor version 4
89.77 -- The default C++ standard in use by the detected compiler (/usr/bin/c++) is lower than C++17. Setting C++17 as the minimum standard.
89.78 -- Looking for pthread.h
89.81 -- Looking for pthread.h - found
89.81 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
89.84 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
89.84 -- Looking for pthread_create in pthreads
89.86 -- Looking for pthread_create in pthreads - not found
89.86 -- Looking for pthread_create in pthread
89.89 -- Looking for pthread_create in pthread - found
89.89 -- Found Threads: TRUE
89.89 -- Performing Test GLIBCXX_USE_CXX11_ABI
90.00 -- Performing Test GLIBCXX_USE_CXX11_ABI - Success
90.00 -- ROOT default compression algorithm: zlib
90.00 -- Cannot enable cudnn without enabling cuda or tmva-gpu: cudnn is disabled.
90.01 -- Looking for ZLib
90.01 -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11")
90.01 -- Looking for nlohmann/json.hpp
90.02 -- nlohmann/json.hpp not found. Switching on builtin_nlohmannjson option
90.02 -- Looking for Freetype
90.03 -- Found Freetype: /usr/lib/aarch64-linux-gnu/libfreetype.so (found version "2.10.1")
90.03 -- Looking for PCRE
90.04 -- Could NOT find PCRE2 (missing: PCRE2_INCLUDE_DIR PCRE2_PCRE2_LIBRARY)
90.04 -- Could NOT find PCRE (missing: PCRE_INCLUDE_DIR PCRE_PCRE_LIBRARY)
90.04 -- PCRE not found. Switching on builtin_pcre option
90.05 -- Looking for LZMA
90.06 -- Looking for lzma_auto_decoder in /usr/lib/aarch64-linux-gnu/liblzma.so
90.08 -- Looking for lzma_auto_decoder in /usr/lib/aarch64-linux-gnu/liblzma.so - found
90.08 -- Looking for lzma_easy_encoder in /usr/lib/aarch64-linux-gnu/liblzma.so
90.11 -- Looking for lzma_easy_encoder in /usr/lib/aarch64-linux-gnu/liblzma.so - found
90.11 -- Looking for lzma_lzma_preset in /usr/lib/aarch64-linux-gnu/liblzma.so
90.13 -- Looking for lzma_lzma_preset in /usr/lib/aarch64-linux-gnu/liblzma.so - found
90.13 -- Found LibLZMA: /usr/lib/aarch64-linux-gnu/liblzma.so (found version "5.2.4")
90.13 -- Looking for xxHash
90.14 -- Could NOT find xxHash (missing: xxHash_LIBRARY xxHash_INCLUDE_DIR) (Required is at least version "0.8")
90.14 -- xxHash not found. Switching on builtin_xxhash option
90.14 -- Looking for ZSTD
90.14 -- Could NOT find ZSTD (missing: ZSTD_LIBRARIES ZSTD_INCLUDE_DIR ZSTD_VERSION)
90.14 -- ZSTD not found. Switching on builtin_zstd option
90.15 -- Performing Test CXX_FLAG_STD_CPLUSPLUS11
90.18 -- Performing Test CXX_FLAG_STD_CPLUSPLUS11 - Success
90.18 -- Performing Test C_FLAG_STD_C99
90.20 -- Performing Test C_FLAG_STD_C99 - Success
90.20 -- Performing Test C_FLAG_WALL
90.23 -- Performing Test C_FLAG_WALL - Success
90.23 -- Performing Test CXX_FLAG_WALL
90.26 -- Performing Test CXX_FLAG_WALL - Success
90.26 -- Performing Test C_FLAG_WEXTRA
90.29 -- Performing Test C_FLAG_WEXTRA - Success
90.29 -- Performing Test CXX_FLAG_WEXTRA
90.32 -- Performing Test CXX_FLAG_WEXTRA - Success
90.32 -- Performing Test C_FLAG_WUNDEF
90.34 -- Performing Test C_FLAG_WUNDEF - Success
90.34 -- Performing Test CXX_FLAG_WUNDEF
90.37 -- Performing Test CXX_FLAG_WUNDEF - Success
90.37 -- Performing Test C_FLAG_WSHADOW
90.40 -- Performing Test C_FLAG_WSHADOW - Success
90.40 -- Performing Test CXX_FLAG_WSHADOW
90.42 -- Performing Test CXX_FLAG_WSHADOW - Success
90.43 -- Performing Test C_FLAG_WCAST_ALIGN
90.45 -- Performing Test C_FLAG_WCAST_ALIGN - Success
90.45 -- Performing Test CXX_FLAG_WCAST_ALIGN
90.48 -- Performing Test CXX_FLAG_WCAST_ALIGN - Success
90.48 -- Performing Test C_FLAG_WCAST_QUAL
90.51 -- Performing Test C_FLAG_WCAST_QUAL - Success
90.51 -- Performing Test CXX_FLAG_WCAST_QUAL
90.54 -- Performing Test CXX_FLAG_WCAST_QUAL - Success
90.54 -- Performing Test C_FLAG_WSTRICT_PROTOTYPES
90.56 -- Performing Test C_FLAG_WSTRICT_PROTOTYPES - Success
90.56 -- Looking for LZ4
90.57 -- Could NOT find LZ4 (missing: LZ4_LIBRARY LZ4_INCLUDE_DIR)
90.57 -- LZ4 not found. Switching on builtin_lz4 option
90.57 -- Looking for X11
90.60 -- Found X11: /usr/include
90.60 -- Looking for XOpenDisplay in /usr/lib/aarch64-linux-gnu/libX11.so;/usr/lib/aarch64-linux-gnu/libXext.so
90.63 -- Looking for XOpenDisplay in /usr/lib/aarch64-linux-gnu/libX11.so;/usr/lib/aarch64-linux-gnu/libXext.so - found
90.63 -- Looking for gethostbyname
90.66 -- Looking for gethostbyname - found
90.66 -- Looking for connect
90.68 -- Looking for connect - found
90.68 -- Looking for remove
90.71 -- Looking for remove - found
90.71 -- Looking for shmat
90.73 -- Looking for shmat - found
90.73 -- X11_INCLUDE_DIR: /usr/include
90.73 -- X11_LIBRARIES: /usr/lib/aarch64-linux-gnu/libX11.so;/usr/lib/aarch64-linux-gnu/libXext.so
90.73 -- X11_Xpm_INCLUDE_PATH: /usr/include
90.73 -- X11_Xpm_LIB: /usr/lib/aarch64-linux-gnu/libXpm.so
90.73 -- X11_Xft_INCLUDE_PATH: /usr/include
90.73 -- X11_Xft_LIB: /usr/lib/aarch64-linux-gnu/libXft.so
90.73 -- X11_Xext_INCLUDE_PATH: /usr/include
90.73 -- X11_Xext_LIB: /usr/lib/aarch64-linux-gnu/libXext.so
90.74 -- Could NOT find GIF (missing: GIF_LIBRARY GIF_INCLUDE_DIR)
90.74 -- Could NOT find TIFF (missing: TIFF_LIBRARY TIFF_INCLUDE_DIR)
90.75 -- Found PNG: /usr/lib/aarch64-linux-gnu/libpng.so (found version "1.6.37")
90.75 -- Could NOT find JPEG (missing: JPEG_LIBRARY JPEG_INCLUDE_DIR)
90.75 -- Building AfterImage library included in ROOT itself
90.76 -- Looking for Python
90.81 -- Could NOT find Python3 (missing: Python3_EXECUTABLE Interpreter NumPy) (found suitable version "3.8", minimum required is "3.8")
90.81 -- Looking for OpenGL
90.82 -- Could NOT find OpenGL (missing: OPENGL_opengl_LIBRARY OPENGL_glx_LIBRARY OPENGL_INCLUDE_DIR)
90.82 -- OpenGL (with GLU) not found. Switching off opengl option
90.82 -- Looking for LibXml2
90.82 -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARY LIBXML2_INCLUDE_DIR)
90.82 -- LibXml2 not found. Switching off xml option
90.84 -- Found OpenSSL: /usr/lib/aarch64-linux-gnu/libcrypto.so (found version "1.1.1f")
90.84 -- Looking for MySQL
90.84 -- Could NOT find MySQL (missing: MYSQL_INCLUDE_DIR MYSQL_LIBRARIES)
90.84 -- MySQL not found. Switching off mysql option
90.84 -- Looking for PostgreSQL
90.85 -- Could NOT find PostgreSQL (missing: PostgreSQL_LIBRARY PostgreSQL_INCLUDE_DIR)
90.85 -- PostgreSQL not found. Switching off pgsql option
90.85 -- Looking for SQLite
90.85 -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
90.85 -- Could NOT find Sqlite (missing: SQLITE_INCLUDE_DIR SQLITE_LIBRARIES)
90.85 -- SQLite not found. Switching off sqlite option
90.85 -- Looking for CFITSIO
90.86 -- Could NOT find CFITSIO (missing: CFITSIO_LIBRARY CFITSIO_INCLUDE_DIR)
90.86 -- CFITSIO not found. You can enable the option 'builtin_cfitsio' to build the library internally'
90.86 -- For the time being switching off 'fitsio' option
90.86 -- Looking for XROOTD
90.86 CMake Warning at cmake/modules/SearchInstalledSoftware.cmake:18 (_find_package):
90.86 By not providing "FindXRootD.cmake" in CMAKE_MODULE_PATH this project has
90.86 asked CMake to find a package configuration file provided by "XRootD", but
90.86 CMake did not find one.
90.86
90.86 Could not find a package configuration file provided by "XRootD" with any
90.86 of the following names:
90.86
90.86 XRootDConfig.cmake
90.86 xrootd-config.cmake
90.86
90.86 Add the installation prefix of "XRootD" to CMAKE_PREFIX_PATH or set
90.86 "XRootD_DIR" to a directory containing one of the above files. If "XRootD"
90.86 provides a separate development package or SDK, be sure it has been
90.86 installed.
90.86 Call Stack (most recent call first):
90.86 cmake/modules/SearchInstalledSoftware.cmake:922 (find_package)
90.86 CMakeLists.txt:297 (include)
90.86
90.86
90.86 -- XROOTD not found, enabling 'builtin_xrootd' option
90.87 -- Downloading and building XROOTD version 5.5.2
90.88 -- Checking for module 'davix>=0.6.4'
90.88 -- No package 'davix' found
90.88 -- Looking for uuid_generate_random in uuid
90.91 -- Looking for uuid_generate_random in uuid - found
90.91 -- Found libuuid: /usr/include
90.92 -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARY LIBXML2_INCLUDE_DIR)
90.92 -- Davix dependency libxml2 not found, switching OFF 'davix' option.
90.92 -- Looking for TBB
90.92 -- Could NOT find TBB (missing: TBB_ROOT_DIR TBB_INCLUDE_DIR TBB_LIBRARY) (Required is at least version "2020")
90.92 -- TBB not found, enabling 'builtin_tbb' option
90.93 -- Looking for VDT
90.93 -- Could NOT find Vdt (missing: VDT_INCLUDE_DIR VDT_LIBRARY) (Required is at least version "0.4")
90.93 -- VDT not found. Ensure that the installation of VDT is in the CMAKE_PREFIX_PATH
90.93 -- Switching ON 'builtin_vdt' option
90.94 -- Looking for BLAS for optional parts of TMVA
90.94 -- Looking for sgemm_
90.97 -- Looking for sgemm_ - not found
90.98 -- Could NOT find BLAS (missing: BLAS_LIBRARIES)
90.98 -- TMVA: Numpy or Python development package not found for python _Python3_EXECUTABLE-NOTFOUND. Switching off tmva-pymva option
90.98 -- PyROOT: development package found. Building for version 3.8
90.99 -- Performing Test ROOT_HAVE_CXX_ATOMICS_WITHOUT_LIB
91.04 -- Performing Test ROOT_HAVE_CXX_ATOMICS_WITHOUT_LIB - Success
91.14 -- Building LLVM in 'Release' mode.
91.14 -- The ASM compiler identification is GNU
91.14 -- Found assembler: /usr/bin/cc
91.15 -- bolt project is disabled
91.15 -- clang project is enabled
91.15 -- clang-tools-extra project is disabled
91.15 -- compiler-rt project is disabled
91.15 -- cross-project-tests project is disabled
91.15 -- libc project is disabled
91.15 -- libclc project is disabled
91.15 -- lld project is disabled
91.15 -- lldb project is disabled
91.15 -- mlir project is disabled
91.15 -- openmp project is disabled
91.15 -- polly project is disabled
91.15 -- pstl project is disabled
91.15 -- flang project is disabled
91.17 CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
91.17 Could NOT find Python3 (missing: Python3_EXECUTABLE Interpreter) (found
91.17 suitable version "3.8", minimum required is "3.0")
91.17 Call Stack (most recent call first):
91.17 /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
91.17 /usr/share/cmake-3.16/Modules/FindPython/Support.cmake:2214 (find_package_handle_standard_args)
91.17 /usr/share/cmake-3.16/Modules/FindPython3.cmake:300 (include)
91.17 cmake/modules/SearchInstalledSoftware.cmake:18 (_find_package)
91.17 interpreter/llvm-project/llvm/CMakeLists.txt:835 (find_package)
91.17
91.17
91.17 -- Configuring incomplete, errors occurred!
91.17 See also "/app/clinsv/root_build/CMakeFiles/CMakeOutput.log".
91.17 See also "/app/clinsv/root_build/CMakeFiles/CMakeError.log".
------
Dockerfile.txt:126
--------------------
125 | #installing root 6 (root 5 deprecated)
126 | >>> RUN cd $clinsv_path && \
127 | >>> git clone --branch latest-stable https://github.com/root-project/root.git root_src && \
128 | >>> mkdir root_build root_install && cd root_build && \
129 | >>> cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src && \
130 | >>> #add -j4 perhaps, means amount of cores available to build
131 | >>> cmake --build . -- install
132 |
--------------------
ERROR: failed to solve: process "/bin/sh -c cd $clinsv_path && git clone --branch latest-stable https://github.com/root-project/root.git root_src && mkdir root_build root_install && cd root_build && cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src && cmake --build . -- install" did not complete successfully: exit code: 1
