Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[package] itk/5.1.2: undefined reference in shared configuration #10392

Closed
Nekto89 opened this issue Apr 20, 2022 · 1 comment
Closed

[package] itk/5.1.2: undefined reference in shared configuration #10392

Nekto89 opened this issue Apr 20, 2022 · 1 comment
Labels
bug Something isn't working

Comments

@Nekto89
Copy link
Contributor

Nekto89 commented Apr 20, 2022

Package and Environment Details (include every applicable attribute)

  • Package Name/Version: itk/5.1.2
  • Operating System+version: Linux Ubuntu 20.04.4 LTS (inside WSL2)
  • Compiler+version: GCC 9 (Ubuntu 9.4.0-1ubuntu1~20.04.1)
  • Docker image: -
  • Conan version: conan 1.47.0
  • Python version: Python 3.8.10

Conan profile (output of conan profile show default or conan profile show <profile> if custom profile is in use)

Configuration for profile default:

[settings]
os=Linux
os_build=Linux
arch=x86_64
arch_build=x86_64
build_type=Release
compiler=gcc
compiler.cppstd=17
compiler.libcxx=libstdc++11
compiler.version=9
[options]
[conf]
[build_requires]
[env]

Steps to reproduce (Include if Applicable)

conan install itk/5.1.2@ -o itk:shared=True -o hdf5:shared=True --build=missing

Logs (Include/Attach if Applicable)

Click to expand log 
Configuration:
[settings]
arch=x86_64
arch_build=x86_64
build_type=Release
compiler=gcc
compiler.cppstd=17
compiler.libcxx=libstdc++11
compiler.version=9
os=Linux
os_build=Linux
[options]
hdf5:shared=True
itk:shared=True
[build_requires]
[env]

WARN: hdf5/1.12.0: requirement zlib/1.2.11 overridden by itk/5.1.2 to zlib/1.2.12
itk/5.1.2: WARN: Package binary is corrupted, removing: 3c110c6771514c5d7ce190c98818580b391dafa4
Installing package: itk/5.1.2
Requirements
    dcmtk/3.6.6 from 'conancenter' - Cache
    double-conversion/3.2.0 from 'conancenter' - Cache
    eigen/3.4.0 from 'conancenter' - Cache
    expat/2.4.8 from 'conancenter' - Cache
    fftw/3.3.9 from 'conancenter' - Cache
    gdcm/3.0.9 from 'conancenter' - Cache
    hdf5/1.12.0 from 'conancenter' - Cache
    icu/71.1 from 'conancenter' - Cache
    itk/5.1.2 from 'conancenter' - Cache
    jbig/20160605 from 'conancenter' - Cache
    libdeflate/1.10 from 'conancenter' - Cache
    libiconv/1.16 from 'conancenter' - Cache
    libjpeg/9d from 'conancenter' - Cache
    libpng/1.6.37 from 'conancenter' - Cache
    libtiff/4.3.0 from 'conancenter' - Cache
    libwebp/1.2.2 from 'conancenter' - Cache
    libxml2/2.9.13 from 'conancenter' - Cache
    onetbb/2020.3 from 'conancenter' - Cache
    openjpeg/2.4.0 from 'conancenter' - Cache
    openssl/1.1.1n from 'conancenter' - Cache
    xz_utils/5.2.5 from 'conancenter' - Cache
    zlib/1.2.12 from 'conancenter' - Cache
    zstd/1.5.2 from 'conancenter' - Cache
Packages
    dcmtk/3.6.6:3f40acffa6836c4f777e98501ce1543ecc2e9a61 - Cache
    double-conversion/3.2.0:8646734ee3e7fd5a9de3513cba5a40bc700a885d - Cache
    eigen/3.4.0:5ab84d6acfe1f23c4fae0ab88f26e3a396351ac9 - Cache
    expat/2.4.8:c215f67ac7fc6a34d9d0fb90b0450016be569d86 - Cache
    fftw/3.3.9:72302bb1b3da57e232c2fc5c2e7f81bdc3405ccf - Cache
    gdcm/3.0.9:1ebbf499737f6ea30c4662898fb0545f6c7a7a6b - Cache
    hdf5/1.12.0:9508bd2ac8dbe47e41ef7c3d6fc74477c91bd819 - Cache
    icu/71.1:1a05e7f2a60c9e5796561e31eb7aeeadc12d7b98 - Cache
    itk/5.1.2:3c110c6771514c5d7ce190c98818580b391dafa4 - Build
    jbig/20160605:f2711434c4877d0e0aa8cdcc4da2a295d5d80304 - Cache
    libdeflate/1.10:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache
    libiconv/1.16:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache
    libjpeg/9d:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache
    libpng/1.6.37:7929d8ecf29c60d74fd3c1f6cb78bbb3cb49c0c7 - Cache
    libtiff/4.3.0:06e23eb234c79e8935f7b1a90d37d134ae33fdcd - Cache
    libwebp/1.2.2:034afc24309e6fc60dbccb1dab5b0f9cad6ec656 - Cache
    libxml2/2.9.13:e9a3e7dd6ab9bf161be4ac8c0925d9a6ba8f2645 - Cache
    onetbb/2020.3:9559105bf27da09bb163021398de2f5474adca73 - Cache
    openjpeg/2.4.0:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache
    openssl/1.1.1n:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache
    xz_utils/5.2.5:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache
    zlib/1.2.12:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache
    zstd/1.5.2:a1fcff3227a663d62f35b4eedde78f4ce0fcd438 - Cache

Installing (downloading, building) binaries...
double-conversion/3.2.0: Already installed!
eigen/3.4.0: Already installed!
expat/2.4.8: Already installed!
fftw/3.3.9: Already installed!
icu/71.1: Already installed!
icu/71.1: Prepending to ICU_DATA runtime environment variable: /home/mklymov/.conan/data/icu/71.1/_/_/package/1a05e7f2a60c9e5796561e31eb7aeeadc12d7b98/res/icudt71l.dat
icu/71.1: Appending PATH environment variable: /home/mklymov/.conan/data/icu/71.1/_/_/package/1a05e7f2a60c9e5796561e31eb7aeeadc12d7b98/bin
jbig/20160605: Already installed!
jbig/20160605: Appending PATH environment variable: /home/mklymov/.conan/data/jbig/20160605/_/_/package/f2711434c4877d0e0aa8cdcc4da2a295d5d80304/bin
libdeflate/1.10: Already installed!
libiconv/1.16: Already installed!
libiconv/1.16: Appending PATH environment var: /home/mklymov/.conan/data/libiconv/1.16/_/_/package/6af9cc7cb931c5ad942174fd7838eb655717c709/bin
libjpeg/9d: Already installed!
libwebp/1.2.2: Already installed!
onetbb/2020.3: Already installed!
openjpeg/2.4.0: Already installed!
openssl/1.1.1n: Already installed!
xz_utils/5.2.5: Already installed!
zlib/1.2.12: Already installed!
zstd/1.5.2: Already installed!
gdcm/3.0.9: Already installed!
hdf5/1.12.0: Already installed!
libpng/1.6.37: Already installed!
libtiff/4.3.0: Already installed!
libxml2/2.9.13: Already installed!
libxml2/2.9.13: Appending PATH environment variable: /home/mklymov/.conan/data/libxml2/2.9.13/_/_/package/e9a3e7dd6ab9bf161be4ac8c0925d9a6ba8f2645/bin
dcmtk/3.6.6: Already installed!
dcmtk/3.6.6: Settings DCMDICTPATH environment variable: /home/mklymov/.conan/data/dcmtk/3.6.6/_/_/package/3f40acffa6836c4f777e98501ce1543ecc2e9a61/bin/share/dcmtk/dicom.dic
itk/5.1.2: WARN: Build folder is dirty, removing it: /home/mklymov/.conan/data/itk/5.1.2/_/_/build/3c110c6771514c5d7ce190c98818580b391dafa4
itk/5.1.2: Copying sources to build folder
itk/5.1.2: Building your package in /home/mklymov/.conan/data/itk/5.1.2/_/_/build/3c110c6771514c5d7ce190c98818580b391dafa4
itk/5.1.2: Generator cmake_find_package created FindDCMTK.cmake
itk/5.1.2: Generator cmake_find_package created Finddouble-conversion.cmake
itk/5.1.2: Generator cmake_find_package created FindEigen3.cmake
itk/5.1.2: Generator cmake_find_package created FindFFTW3.cmake
itk/5.1.2: Generator cmake_find_package created FindGDCM.cmake
itk/5.1.2: Generator cmake_find_package created FindHDF5.cmake
itk/5.1.2: Generator cmake_find_package created FindICU.cmake
itk/5.1.2: Generator cmake_find_package created FindTBB.cmake
itk/5.1.2: Generator cmake_find_package created FindLibXml2.cmake
itk/5.1.2: Generator cmake_find_package created FindOpenSSL.cmake
itk/5.1.2: Generator cmake_find_package created FindPNG.cmake
itk/5.1.2: Generator cmake_find_package created FindTIFF.cmake
itk/5.1.2: Generator cmake_find_package created FindEXPAT.cmake
itk/5.1.2: Generator cmake_find_package created FindOpenJPEG.cmake
itk/5.1.2: Generator cmake_find_package created FindIconv.cmake
itk/5.1.2: Generator cmake_find_package created FindZLIB.cmake
itk/5.1.2: Generator cmake_find_package created Findlibdeflate.cmake
itk/5.1.2: Generator cmake_find_package created FindLibLZMA.cmake
itk/5.1.2: Generator cmake_find_package created FindJPEG.cmake
itk/5.1.2: Generator cmake_find_package created Findjbig.cmake
itk/5.1.2: Generator cmake_find_package created Findzstd.cmake
itk/5.1.2: Generator cmake_find_package created FindWebP.cmake
itk/5.1.2: Generator cmake created conanbuildinfo.cmake
itk/5.1.2: Aggregating env generators
itk/5.1.2: Calling build()
-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Conan: called by CMake conan helper
-- Conan: called inside local cache
-- Conan: Adjusting output directories
-- Conan: Using cmake global configuration
-- Conan: Adjusting language standard
-- Conan setting CPP STANDARD: 17 WITH EXTENSIONS OFF
-- Conan: Compiler GCC>=5, checking major version 9
-- Conan: Checking correct version: 9
-- Conan: C++ stdlib: libstdc++11
...
Comment is too long
...
[100%] Building CXX object source_subfolder/Modules/Nonunit/Review/src/CMakeFiles/ITKReview.dir/itkVoxBoCUBImageIO.cxx.o
[100%] Linking CXX shared library ../../../../../lib/libITKReview-5.1.so
[100%] Built target ITKReview
Scanning dependencies of target ITKReview-all
[100%] Built target ITKReview-all
[100%] Linking CXX shared library ../../../../../lib/libITKTestKernel-5.1.so
[100%] Built target ITKTestKernel
Scanning dependencies of target itkTestDriver
[100%] Building CXX object source_subfolder/Modules/Core/TestKernel/src/CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o
[100%] Linking CXX executable ../../../../../bin/itkTestDriver
../../../../../lib/libITKIOGDCM-5.1.so.1: error: undefined reference to '__exp2_finite'
../../../../../lib/libITKIOGDCM-5.1.so.1: error: undefined reference to '__exp_finite'
collect2: error: ld returned 1 exit status
make[2]: *** [source_subfolder/Modules/Core/TestKernel/src/CMakeFiles/itkTestDriver.dir/build.make:116: bin/itkTestDriver] Error 1
make[1]: *** [CMakeFiles/Makefile2:11748: source_subfolder/Modules/Core/TestKernel/src/CMakeFiles/itkTestDriver.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
itk/5.1.2:
itk/5.1.2: ERROR: Package '3c110c6771514c5d7ce190c98818580b391dafa4' build failed
itk/5.1.2: WARN: Build folder /home/mklymov/.conan/data/itk/5.1.2/_/_/build/3c110c6771514c5d7ce190c98818580b391dafa4
ERROR: itk/5.1.2: Error in build() method, line 249
        cmake.build()
        ConanException: Error 2 while executing cmake --build '/home/mklymov/.conan/data/itk/5.1.2/_/_/build/3c110c6771514c5d7ce190c98818580b391dafa4/build_subfolder' '--' '-j20'
@Nekto89 Nekto89 added the bug Something isn't working label Apr 20, 2022
@valgur valgur mentioned this issue Jul 31, 2023
Open
@perseoGI
Copy link
Contributor

Hi there,
I was reviewing old issues and I have come across this one.

This issue is already resolved!
Also, a newer version has just been released and added to CCI:
#25246

Happy coding 🐸

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@Nekto89 @perseoGI