[scipion-users] Problem compiling Scipion

[Alfonso A. <aa...@ib...>]

Hi there.
I'm writing because I had several problem compiling your software.
After fixing some problem had during the installation of the external
softwares, now I'm having this error.

Any idea to fix it it and go ahead with the installation?
Thanks in advance for your help.



g++ -o
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.o
-c -Isoftware/em/xmipp/external -Isoftware/em/xmipp/libraries
-Isoftware/em/xmipp/libraries -Isoftware/include
-Isoftware/include/python2.7
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:31:
error: expected constructor, destructor, or type conversion before string
constant
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:48:
error: expected class-name before '{' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:51:
error: 'FileName' does not name a type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:52:
error: 'FileName' does not name a type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:53:
error: ISO C++ forbids declaration of 'MultidimArray' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:53:
error: expected ';' before '<' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: 'Matrix1D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: template argument 1 is invalid
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: template argument 2 is invalid
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:54:
error: expected unqualified-id before '>' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:55:
error: 'MetaData' does not name a type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:116:
error: ISO C++ forbids declaration of 'string' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:116:
error: expected ',' or '...' before '&' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:151:
error: ISO C++ forbids declaration of 'string' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:151:
error: expected ',' or '...' before '&' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:202:
error: ISO C++ forbids declaration of 'MultidimArray' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:202:
error: expected ',' or '...' before '<' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:212:
error: ISO C++ forbids declaration of 'cv' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:212:
error: expected ',' or '...' before '::' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:222:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:222:
error: expected ',' or '...' before 'opencvDoubleMat'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:230:
error: ISO C++ forbids declaration of 'FileName' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:230:
error: expected ',' or '...' before '&' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:261:
error: ISO C++ forbids declaration of 'cv' with no type
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:261:
error: expected ',' or '...' before '::' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::defineParams()':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:63:
error: 'addUsageLine' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:64:
error: 'addParamsLine' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::readParams()':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:83:
error: 'fname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:83:
error: 'getParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:84:
error: 'foname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:85:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:87:
error: 'gianRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:89:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:91:
error: 'darkRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:93:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:95:
error: 'globalShiftFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:97:
error: 'getIntParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:101:
error: 'checkParam' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'int ProgOpticalAligment::saveMat(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:118:
error: 'M' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:122:
error: 'ofstream' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:122:
error: expected ';' before 'out'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:123:
error: 'out' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:126:
error: 'M' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:132:
error: 'out' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'int ProgOpticalAligment::readMat(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:153:
error: 'ifstream' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:153:
error: expected ';' before 'in'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:154:
error: 'in' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:165:
error: 'in' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:175:
error: 'CV_8UC' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:178:
error: 'CV_32FC' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:181:
error: 'CV_64FC' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
error: 'M' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:186:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::xmipp2Opencv(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:204:
error: 'xmippArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:204:
error: 'YSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:205:
error: 'XSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
error: 'opencvMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:206:
error: 'CV_32FC1' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:207:
error: 'FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:208:
error: expected ';' before 'opencvMat'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::opencv2Xmipp(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:214:
error: 'opencvMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:216:
error: 'xmippArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:217:
error: 'FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:218:
error: expected ';' before 'DIRECT_A2D_ELEM'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::convert2Uint8(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:225:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:225:
error: 'opencvDoubleMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:226:
error: 'opencvUintMat' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:226:
error: 'CV_8U' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::computeAvg(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:232:
error: 'ImageGeneric' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:232:
error: expected ';' before 'movieStack'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
error: 'MultidimArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:233:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
error: 'Matrix1D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:234:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:235:
error: 'end' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:235:
error: 'begin' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:239:
error: 'movieStack' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:239:
error: 'movieFile' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:240:
error: 'frameImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
error: 'YSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:242:
error: 'XSIZE' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:244:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:246:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
error: 'shiftMatrix' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
error: 'XX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:249:
error: 'shiftVector' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:250:
error: 'YY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'LINEAR' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'shiftedFrame' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'WRAP' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:251:
error: 'translate' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:252:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:255:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:257:
error: 'avgImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:258:
error: 'frameImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:259:
error: 'movieStack' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'void ProgOpticalAligment::std_dev2(int)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:267:
error: 'flowx' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
error: 'planes' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:273:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:275:
error: 'abs' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:277:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:277:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:284:
error: 'meanStdDev' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:285:
error: 'sqrt' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In member function 'int ProgOpticalAligment::main2()':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
error: 'MultidimArray' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:293:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:294:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:294:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
error: 'Matrix1D' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:295:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:296:
error: 'ImageGeneric' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:296:
error: expected ';' before 'movieStack'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
error: 'Image' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:297:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:298:
error: 'MetaData' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:298:
error: expected ';' before 'MD'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:299:
error: 'FileName' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:299:
error: expected ';' before 'motionInfFile'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:300:
error: 'ArrayDim' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:300:
error: expected ';' before 'aDim'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:312:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:312:
error: expected ';' before 'flow'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:313:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:313:
error: expected ';' before 'flowxPre'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:314:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:314:
error: expected ';' before 'avgcurr'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:315:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:315:
error: expected ';' before 'planes'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:320:
error: 'motionInfFile' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:320:
error: 'foname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:321:
error: 'fname' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:324:
error: 'movieStack' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:324:
error: 'HEADER' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:325:
error: 'aDim' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:331:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:331:
error: 'darkRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:332:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:336:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:336:
error: 'gianRefFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:337:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:339:
error: 'meanStdev' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:341:
error: 'avgCurr' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
error: 'flowxPre' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:342:
error: 'CV_32FC1' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:343:
error: 'flowyPre' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:343:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:362:
error: 'outputMovie' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:366:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:366:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:367:
error: 'shiftVector' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:368:
error: 'shiftMD' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:368:
error: 'globalShiftFilename' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:369:
error: 'FOR_ALL_OBJECTS_IN_METADATA' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:370:
error: expected ';' before '{' token
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:383:
error: 'sqrt' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:388:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:392:
error: 'avgcurr' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:393:
error: 'cout' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:398:
error: 'avgstep' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:398:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:415:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:415:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:416:
error: expected primary-expression before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:416:
error: expected ';' before 'double'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:418:
error: 'frameImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:420:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:422:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
error: 'shiftMatrix' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
error: 'XX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:423:
error: 'shiftVector' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:424:
error: 'YY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'BSPLINE3' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'WRAP' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:425:
error: 'translate' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:430:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:432:
error: 'darkImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:434:
error: 'gainImage' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:436:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:436:
error: 'preimg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:441:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:443:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:445:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:445:
error: 'preimg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:447:
error: 'avgcurr8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:448:
error: 'preimg8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:475:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:475:
error: 'calcOpticalFlowFarneback' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:478:
error: 'flowFileName' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:478:
error: 'formatString' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:479:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:480:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:480:
error: 'calcOpticalFlowFarneback' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
error: 'planes' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:482:
error: 'split' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:491:
error: 'MD' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:492:
error: 'MDL_OPTICALFLOW_MEANX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:493:
error: 'MDL_OPTICALFLOW_MEANY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:494:
error: 'MDL_OPTICALFLOW_STDX' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:495:
error: 'MDL_OPTICALFLOW_STDY' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:496:
error: 'MD_APPEND' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:510:
error: 'flowFileName' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:510:
error: 'formatString' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:520:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:520:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:521:
error: expected primary-expression before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:521:
error: expected ';' before 'float'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
error: 'dest' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:523:
error: 'cv' has not been declared
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:526:
error: 'mappedImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:526:
error: 'outputMovie' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:538:
error: 'II' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:543:
error: 'outputMovie' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:548:
error: 'avgstep' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:549:
error: 'preimg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:550:
error: 'avgcurr8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:551:
error: 'preimg8' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:552:
error: 'flow' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:553:
error: 'planes' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:558:
error: 'preImg' was not declared in this scope
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:
In function 'int main(int, char**)':
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:568:
error: 'class ProgOpticalAligment' has no member named 'read'
software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp:569:
error: 'class ProgOpticalAligment' has no member named 'tryRun'
scons: ***
[software/em/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.o]
Error 1
scons: building terminated because of errors.

-- 
Alfonso Avino
Informatica
IBMB-CSIC
C/ Baldiri Reixac 15, 3 A17
08028, Barcelona, España
Tel. (+34)934020194