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Old 12-17-2012, 06:51 AM   #1
mattia
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Location: Milano

Join Date: Aug 2011
Posts: 30
Question Cufflinks 2 - error message

Hi,
I'm trying to install Cufflink2.0.2 in order to compare new version and "old" version (1.3.0) and to upgrade my pipeline. I type:

Code:
./configure --prefix=$HOME/path/to/my/Cufflinks2/dir --with-boost=/path/to/boost/library --with-bam=path/to/Samtools/dir --with-eigen=/path/to/Eigen/eigen-eigen-5097c01bcdc4/Eigen
up to here, so good (I used the same command without --with-eigen option to install old version); however when i type "make" command, I see this error message:

Code:
[user@server]$ make
make  all-recursive
make[1]: Entering directory `/home/software_analisi/Cufflinks2/cufflinks-2.0.2'
Making all in src
make[2]: Entering directory `/home/software_analisi/Cufflinks2/cufflinks-2.0.2/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/home/software_analisi/boost/librerie/include -I/home/software_analisi/SAMTools/include -I/home/software_analisi/altri_software/Eigen/eigen-eigen-5097c01bcdc4/Eigen/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
        then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
In file included from clustering.h:38,
                 from clustering.cpp:10:
abundances.h:21:23: error: Eigen/Dense: No such file or directory
progressbar.h: In constructor ‚ProgressBar::ProgressBar(std::string, double)‚:
progressbar.h:28: warning: converting to ‚int‚ from ‚double‚
progressbar.h: In member function ‚void ProgressBar::update(const char*, double)‚:
progressbar.h:61: warning: converting to ‚int‚ from ‚long double‚
progressbar.h: In member function ‚void ProgressBar::remaining(int)‚:
progressbar.h:81: warning: converting to ‚int‚ from ‚long double‚
abundances.h: At global scope:
abundances.h:379: error: ‚Eigen‚ was not declared in this scope
abundances.h:379: error: template argument 1 is invalid
abundances.h:379: error: template argument 2 is invalid
abundances.h:465: error: ‚Eigen‚ was not declared in this scope
abundances.h:465: error: template argument 1 is invalid
abundances.h:465: error: template argument 2 is invalid
abundances.h:558: error: ‚Eigen‚ was not declared in this scope
abundances.h:558: error: template argument 1 is invalid
abundances.h:558: error: template argument 2 is invalid
abundances.h:641: error: ‚Eigen‚ was not declared in this scope
abundances.h:641: error: template argument 1 is invalid
abundances.h:641: error: template argument 2 is invalid
abundances.h:645: error: expected ‚,‚ or ‚...‚ before ‚::‚ token
abundances.h:648: error: ISO C++ forbids declaration of ‚Eigen‚ with no type
abundances.h:650: error: expected ‚,‚ or ‚...‚ before ‚::‚ token
abundances.h:653: error: ISO C++ forbids declaration of ‚Eigen‚ with no type
clustering.h:85: error: ‚Eigen‚ was not declared in this scope
clustering.h:85: error: template argument 1 is invalid
clustering.h:85: error: template argument 2 is invalid
clustering.h: In function ‚void cluster_transcripts(const AbundanceGroup&, std::vector<AbundanceGroup, std::allocator<AbundanceGroup> >&, boost::numeric::ublas::matrix<double, boost::numeric::ublas::basic_row_major<long unsigned int, long int>, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >*, boost::numeric::ublas::matrix<double, boost::numeric::ublas::basic_row_major<long unsigned int, long int>, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >*, boost::numeric::ublas::matrix<double, boost::numeric::ublas::basic_row_major<long unsigned int, long int>, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >*, boost::numeric::ublas::matrix<double, boost::numeric::ublas::basic_row_major<long unsigned int, long int>, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >*, int*)‚:
clustering.h:129: error: ‚Eigen‚ was not declared in this scope
clustering.h:129: error: template argument 1 is invalid
clustering.h:129: error: template argument 2 is invalid
clustering.h:129: error: invalid type in declaration before ‚=‚ token
clustering.h:135: error: ‚Eigen‚ cannot appear in a constant-expression
clustering.h:135: error: template argument 1 is invalid
clustering.h:135: error: template argument 2 is invalid
clustering.h:135: error: invalid type in declaration before ‚=‚ token
clustering.h:144: error: ‚Eigen‚ cannot appear in a constant-expression
clustering.h:144: error: template argument 1 is invalid
clustering.h:144: error: template argument 2 is invalid
clustering.h:144: error: request for member ‚size‚ in ‚trans_assigned_counts‚, which is of non-class type ‚const int‚
clustering.h:144: error: request for member ‚size‚ in ‚trans_assigned_counts‚, which is of non-class type ‚const int‚
clustering.h:144: error: ‚Eigen‚ is not a class or namespace
clustering.h:170: error: request for member ‚size‚ in ‚assigned_counts‚, which is of non-class type ‚int‚
clustering.h:175: error: invalid types ‚const int[size_t]‚ for array subscript
clustering.h:177: error: invalid types ‚int[size_t]‚ for array subscript
make[2]: *** [clustering.o] Error 1
make[2]: Leaving directory `/home/software_analisi/Cufflinks2/cufflinks-2.0.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/software_analisi/Cufflinks2/cufflinks-2.0.2'
make: *** [all] Error 2
Do you have any suggestions to solve my issue?

Thanks.
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