Re: [scipion-users] Problem compiling Scipion

[Jose M. de la R. T. <del...@gm...>]

Dear Alfonso,

The errors that you are having are very weird, we have never seem before.
Could you provide more information about the installation? What OS and
compiler versions are you using?
What problems did you have when installing external libraries and how did
you solve it?

Best regards,
Jose Miguel.


On Fri, Jul 15, 2016 at 11:53 AM, Alfonso Avino <aa...@ib...> wrote:

> 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
>
>
>
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