CODEWITHSUNDEEP
cmakedockerfile
ankit agrawal
ankit agrawal

Reputation: 311

Getting error in Cmake step in Dockerfile installation

I am new to Docker container and kubenetes cluster. I am trying to run following section of command using buildah

  ##install cmake
  USER root 
  RUN apt-get update && apt-get -y install cmake

  USER ${user}
  WORKDIR $HOME 
  ## bustools_dev
  RUN git clone https://github.com/Yenaled/bustools.git && \ 
      cd bustools && \
      mkdir build && \
      cd build 
  RUN cmake ../ 
  RUN make 
  RUN cd src
  RUN mv bustools bustools_dev
  RUN ENV PATH=$HOME/bustools/build/src/:${PATH}

but get the following error. What am I missing here?

  STEP 17: WORKDIR $HOME 
  WARN[0002] SHELL is not supported for OCI image format, [/bin/bash -o pipefail -c] will be ignored. Must use `docker` format 
  --> 770a1b90326
  STEP 18: RUN git clone https://github.com/Yenaled/bustools.git &&     cd bustools &&     mkdir build &&     cd build 
  Cloning into 'bustools'...
  WARN[0005] SHELL is not supported for OCI image format, [/bin/bash -o pipefail -c] will be ignored. Must use `docker` format 
  --> 2b87555e927
  STEP 19: RUN cmake ../ 
  CMake Error: The source directory "/home" does not appear to contain CMakeLists.txt.
  Specify --help for usage, or press the help button on the CMake GUI.
  error building at STEP "RUN cmake ../": error while running runtime: exit status 1
  ERRO[0111] exit status 1

Upvotes: 0

Views: 3725

Answers (1)

Davide Madrisan
Davide Madrisan

Reputation: 2310

I'd simplify the Dockerfile to avoid the issues with the WORKDIR setup that I think are the cause of the problem:

FROM debian:11

RUN apt-get update \
 && apt-get install --assume-yes --no-install-recommends --quiet \
    ca-certificates \
    cmake \
    git \
    g++ \
    make \
    libzip-dev \
 && apt-get clean all

WORKDIR /usr/local/src

RUN git clone https://github.com/Yenaled/bustools.git
RUN mkdir -p /usr/local/src/bustools/build

RUN cd /usr/local/src/bustools/build \
 && cmake .. \
 && make

[...]

Output

[...]
STEP 3/6: WORKDIR /usr/local/src
--> ffb056fd5b3
STEP 4/6: RUN git clone https://github.com/Yenaled/bustools.git
Cloning into 'bustools'...
--> 83afa44c5c8
STEP 5/6: RUN mkdir -p /usr/local/src/bustools/build
--> 2e6ed328088
STEP 6/6: RUN cd /usr/local/src/bustools/build  && cmake ..  && make
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
release mode
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/src/bustools/build
Scanning dependencies of target bustools_core
[  4%] Building CXX object src/CMakeFiles/bustools_core.dir/BUSData.cpp.o
[  8%] Building CXX object src/CMakeFiles/bustools_core.dir/Common.cpp.o
[ 13%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_capture.cpp.o
[ 17%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_clusterhist.cpp.o
[ 21%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_collapse.cpp.o
[ 26%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_correct.cpp.o
[ 30%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_count.cpp.o
[ 34%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_extract.cpp.o
[ 39%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_inspect.cpp.o
[ 43%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_linker.cpp.o
[ 47%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_main.cpp.o
[ 52%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_mash.cpp.o
[ 56%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_merge.cpp.o
[ 60%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_predict.cpp.o
[ 65%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_project.cpp.o
[ 69%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_sort.cpp.o
[ 73%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_text.cpp.o
[ 78%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_umicorrect.cpp.o
[ 82%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_whitelist.cpp.o
[ 86%] Building C object src/CMakeFiles/bustools_core.dir/roaring.c.o
[ 91%] Linking CXX static library libbustools_core.a
[ 91%] Built target bustools_core
Scanning dependencies of target bustools
[ 95%] Building CXX object src/CMakeFiles/bustools.dir/bustools_main.cpp.o
[100%] Linking CXX executable bustools
[100%] Built target bustools
--> b08bc457b5f

Upvotes: 1

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