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Old 12-17-2012, 05:49 AM   #1
mattia
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Location: Milano

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Question Cufflinks 2 - install error

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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Old 12-17-2012, 06:37 AM   #2
aafc
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Did you actually compile Eigen with cmake? From your directory structure, it looks likes you just extracted the tarball.
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Old 12-17-2012, 07:06 AM   #3
mattia
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Yes, I compiled eigen in this way:
Code:
mkdir /home/software_analisi/altri_software/Eigen/bin
cd /home/software_analisi/altri_software/Eigen/bin
/home/software_analisi/altri_software/cmake/cmake-2.8.10.2/bin/cmake /home/software_analisi/altri_software/Eigen/eigen-eigen-5097c01bcdc4
make install
However (is not REQUIRED ) to compile eigen.


Code:
./configure --prefix=/home/software_analisi/Cufflinks2/bin --with-boost=/home/software_analisi/boost/librerie --with-bam=/home/software_analisi/SAMTools --with-eigen=/home/software_analisi/altri_software/Eigen/eigen-eigen-5097c01bcdc4/Eigen


the directory /home/software_analisi/altri_software/Eigen/eigen-eigen-5097c01bcdc4/Eigen in --with-eigen option is not the same of /home/software_analisi/altri_software/Eigen/bin/Eigen
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Old 12-17-2012, 07:12 AM   #4
aafc
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Does the Eigen directory that you installed have include as a subdirectory? Does include contain the following files and directories? :

Eigen/ <---- this is /home/software_analisi/altri_software/Eigen/eigen-eigen-5097c01bcdc4/Eigen
--- include/
------ Eigen/{Array,...,Dense,...UmfPackSupport}
------ unsupported/
------ signature_of_eigen3_matrix_library
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Old 12-17-2012, 07:27 AM   #5
mattia
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I have not "include" directory in ../../eigen-eigen-5097c01bcdc4/Eigen

So, do i have to create ../../eigen-eigen-5097c01bcdc4/Eigen/include and put all files in it?????

my directory tree is in attachments.

Thanks a lot.
Attached Images
File Type: jpg dir_tree.jpg (96.6 KB, 20 views)
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Old 12-17-2012, 07:47 AM   #6
aafc
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Yeah, COPY (in case we do something wrong) the library files into Eigen/include. Try that. Otherwise, re-read the Eigen documentation and make sure you've installed it properly.
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Old 12-17-2012, 11:33 PM   #7
mattia
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ok I solve my problem; in particular (for other users):
You have to:
Code:
tar -zxvf eigen-eigen-5097c01bcdc4.tar.gz; (for actual eigen package: version 3.1.2)
cd eigen-eigen-5097c01bcdc4;
mkdir /your/path/include
cp -R eigen-eigen-5097c01bcdc4/Eigen /your/path/include
./configure --prefix=/bin/path --with-boost=/boost/path --with-bam=/sam/path --with-eigen=/your/path
make
make install
.

Thanks a lot aafc.
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