RELIONトラブルシューティング
提供: Eospedia
Motion Correction
ERROR: TIFF support was not enabled during compilation
症状
2019/5/14, v3.0.5, build from source in Ubuntu 16.04.6 LTS
RELIONチュートリアルでMotion correctionするとき、MoitonCor2のRELION実装使ったら表題のエラーが出た。
対処
- libtiffのdevel入れる必要があったみたいっす。
- https://github.com/3dem/relion/issues/383
- というかrelion.gitのreadmeに書いてあった。 https://github.com/3dem/relion
- sudo apt install ... のところに列挙してなかったから見落としてた。
# relionのルートディレクトリに移動 (cmakeとかsrcとかあるディレクトリ) $ rm -r build/ install/ $ sudo apt install libtiff5-dev $ mkdir build/ install/ $ cd build && cmake -DCMAKE_INSTALL_PREFIX=../install .. $ make -j10 $ make install
cmakeでこけた怒
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): Cannot generate a safe runtime search path for target tiltpair_plot because files in some directories may conflict with libraries in implicit directories: runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib Some of these libraries may not be found correctly.
$ which cmake /home/kttn/miniconda2/bin/cmake
EMAN2インストールするときに入れたminiconda2のbin/に、condaで入れたcmakeが入ってて、それ使ってるのが問題か
cmakeを/usr/bin/cmakeに置き換えて再ビルド
$ /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): Cannot generate a safe runtime search path for target maingui because files in some directories may conflict with libraries in implicit directories: runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib Some of these libraries may not be found correctly.
んぁー cmakeわからん
relion.gitのreadmeに" If you installed libtiff in a non-standard location, specify the location by -DTIFF_INCLUDE_DIR=/path/to/include -DTIFF_LIBRARY=/path/to/libtiff.so.5."なる記述があったので、これを使ってみる
- includeとlibはどこですか
- https://packages.ubuntu.com/xenial/amd64/libtiff5-dev/filelist
- /usr/include/x86_64-linux-gnu と /usr/lib/x86_64-linux-gnu/ でした
$ cmake -DCMAKE_INSTALL_PREFIX=../install -DTIFF_INCLUDE_DIR=/usr/include/x86_64-linux-gnu -DTIFF_LIBRARY=/usr/lib/x86_64-linux-gnu/libtiff.so.5 ..
CMake Error at /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/cmTC_3d3bbTargets.cmake:16 (add_library): Target "MPI::MPI_C" links to item " -Wl,-rpath,/home/kttn/miniconda2/lib -Wl,-rpath -Wl,/home/kttn/miniconda2/lib -Wl,--enable-new-dtags" which has leading or trailing whitespace. This is now an error according to policy CMP0004. Call Stack (most recent call first): /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/CMakeLists.txt:12 (include)
嗚呼...
$ conda remove cmake $ cmake -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): Cannot generate a safe runtime search path for target tiltpair_plot because files in some directories may conflict with libraries in implicit directories: runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib Some of these libraries may not be found correctly.
minicondaの呪縛からどうやって逃れたらいいの?