[mlpack] Compilation issue of mlpack on Ubuntu

[Jaskaran Singh]

Hi Ryan

I am done with the cmake step but
During the make step I get a linking error.

jaskaran at ubuntu:~/Desktop/mlpack-1.0.12/build$ cmake ../
-- Armadillo libraries: /usr/lib/libarmadillo.so
CMake Warning at CMakeLists.txt:88 (message):
  This is a 64-bit system, but Armadillo was compiled without 64-bit index
  support.  Consider recompiling Armadillo with ARMA_64BIT_WORD to enable
  64-bit indices (large matrix support).  MLPACK will still work without
  ARMA_64BIT_WORD defined, but will not scale to matrices with more than 4
  billion elements.


-- Could NOT find Doxygen (missing:  DOXYGEN_EXECUTABLE)
CMake Warning at CMakeLists.txt:292 (message):
  txt2man not found; man pages will not be generated.


-- Configuring done
-- Generating done
-- Build files have been written to:
/home/jaskaran/Desktop/mlpack-1.0.12/build
jaskaran at ubuntu:~/Desktop/mlpack-1.0.12/build$ make
Moving header files to include/mlpack/
[  0%] Built target mlpack_headers
[ 30%] Built target mlpack
Linking CXX executable ../../../../bin/cf
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zptgemm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_scopy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_stpsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_saxpy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_srotg'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ztrsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zhpr'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cswap'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_drot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zgeru'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_stbsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dsyr'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zher2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cptgemm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cset'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zdrot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ssyreflect'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_scnrm2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_stbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zpther2k'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cpthemm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cpttrsm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ztbsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sspr'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_csyreflect'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dpttrmm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dscal'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dsyr2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zGetNB'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ddot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zaxpy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cgeru'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ssymv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dzasum'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sptsyrk'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ztbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_snrm2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cptherk'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zhpmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cptsyr2k'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zgbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dptgemm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ccopy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dset'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cptsymm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sger'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cher2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dGetNB'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_crotg'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zswap'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dtbsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zdotc_sub'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zptherk'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ctpmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zpttrsm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ctrsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dptsyrk'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zsyreflect'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dspr'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dtrsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sptgemm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zgemv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cher'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ssbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_caxpy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sptsymm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cgerc'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dnrm2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dsyreflect'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sdsdot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_spttrmm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cscal'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_stpmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sspmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cdotu_sub'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ctbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_icamax'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sscal'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sptsyr2k'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ssyr'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ctbsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_drotmg'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_spttrsm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zhpr2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ctpsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zpthemm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dpttrsm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_strmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zcopy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_idamax'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zscal'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cdotc_sub'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dtbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sspr2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cpther2k'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ztrmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zcopyConj'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zmoveConj'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zptsyrk'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cgemv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zcplxinvert'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cscalConj'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sasum'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zscalConj'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dcopy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zaxpby'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cmoveConj'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_scasum'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_srotmg'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dtpsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sdot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_chpr2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zhemv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zdotu_sub'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zptsyr2k'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_chbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sswap'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ccplxinvert'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zptsymm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_izamax'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_drotg'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dtrmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ztpmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zher'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_srot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dsdot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ztpsv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_srotm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_daxpby'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sset'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zpttrmm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_daxpy'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dgemv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cpttrmm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ctrmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ccopyConj'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zgerc'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dgbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dspr2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sgbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dptsyr2k'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dsymv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sgemv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dsbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dasum'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_saxpby'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dswap'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_chpmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_isamax'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_caxpby'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dtpmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dptsymm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_chpr'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dznrm2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_ssyr2'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_sGetNB'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zset'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zhbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dger'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_chemv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cGetNB'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_csrot'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_dspmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_xerbla'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_drotm'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cptsyrk'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_cgbmv'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_zrotg'
/usr/lib/liblapack.so.3gf: undefined reference to `ATL_strsv'
collect2: ld returned 1 exit status
make[2]: *** [bin/cf] Error 1
make[1]: *** [src/mlpack/methods/cf/CMakeFiles/cf.dir/all] Error 2
make: *** [all] Error 2


On 29 January 2015 at 21:35, Ryan Curtin <ryan at ratml.org> wrote:

> On Thu, Jan 29, 2015 at 08:21:53PM +0530, Jaskaran Singh wrote:
> > Hi
> > I was trying to build mlpack from source according to instructions given
> on
> > the github page.
> > Here is what the compilation log says after I did
> > >>cmake ../
> > CMake Error at
> > /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91
> > (MESSAGE):
> >   Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
> >   (Required is at least version "2.6.0")
> > Call Stack (most recent call first):
> >   /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:252
> > (_FPHSA_FAILURE_MESSAGE)
> >   /usr/share/cmake-2.8/Modules/FindLibXml2.cmake:50
> > (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
> >   CMakeLists.txt:126 (find_package)
> >
> > But I have libxml2 installed with version 2.7.8.
> > jaskaran at ubuntu:~/Desktop/mlpack-1.0.12/build$ dpkg -s libxml2
> > Package: libxml2
> > Status: install ok installed
> > Multi-Arch: same
> > Priority: standard
> > Section: libs
> > Installed-Size: 1750
> > Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
> > Architecture: amd64
> > Version: 2.7.8.dfsg-5.1ubuntu4.11
> > Depends: libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3.dfsg)
> > Pre-Depends: multiarch-support
> > Recommends: xml-core
> >
> > Could somebody please help me out.
>
> Do you have the libxml2-dev package installed?  The headers need to be
> available for compilation.
>
> Hope that helps.
>
> Thanks,
>
> Ryan
>
> --
> Ryan Curtin    | "We need some time for some things to happen!"
> ryan at ratml.org |   - Bells
>



-- 
Cheers
*Jaskaran Singh Virdi*
*Final Year Undergrad Computer Science*
*IIT Ropar*
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