「RELIONトラブルシューティング」の版間の差分

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(ページの作成:「== Motion Correction == === <u> ERROR: TIFF support was not enabled during compilation</u> === ==== 症状 ==== 2019/5/14, v3.0.5, build from source in Ubuntu 16.04.6 LTS...」)
 
行95: 行95:
 
   files in some directories may conflict with libraries in implicit
 
   files in some directories may conflict with libraries in implicit
 
   directories:
 
   directories:
 
+
 
     runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
 
     runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
 
       /home/kttn/miniconda2/lib
 
       /home/kttn/miniconda2/lib
行102: 行102:
 
     runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
 
     runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
 
       /home/kttn/miniconda2/lib
 
       /home/kttn/miniconda2/lib
 
+
 
   Some of these libraries may not be found correctly.
 
   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?
 
minicondaの呪縛からどうやって逃れたらいいの?

2019年5月14日 (火) 14:08時点における版

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

# 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


$ 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?