1

The full error I get when I type make is

Making install in libraries/utils
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
make  install-am
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
/bin/bash ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../..    -std=c++0x -g -Wall -O0 -fno-omit-frame-pointer -g -O2 -c -o libutils_la-patAbsTime.lo `test -f 'patAbsTime.cc' || echo './'`patAbsTime.cc
rm: cannot remove '.libs/libutils_la-patAbsTime.o': Permission denied
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -std=c++0x -g -Wall -O0 -fno-omit-frame-pointer -g -O2 -c patAbsTime.cc  -fPIC -DPIC -o .libs/libutils_la-patAbsTime.o
Assembler messages:
Fatal error: can't create .libs/libutils_la-patAbsTime.o: Permission denied
Makefile:873: recipe for target 'libutils_la-patAbsTime.lo' failed
make[2]: *** [libutils_la-patAbsTime.lo] Error 1
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
Makefile:1080: recipe for target 'install' failed
make[1]: *** [install] Error 2
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
Makefile:445: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5'
Makefile:377: recipe for target 'all' failed
make: *** [all] Error 2

I am a trying to install a software in Ububtu 16.04 The software is configured fine but when I type make I get the following error

c:19: undefined reference to `patHybridMatrix::cholesky(double, patError*&)'
collect2: error: ld returned 1 exit status
Makefile:460: recipe for target 'biogeme' failed
make[2]: *** [biogeme] Error 1
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/biogeme'
Makefile:445: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5'
Makefile:377: recipe for target 'all' failed
make: *** [all] Error 2

I tried also sudo make install and checkinstal but nothing works. When I use checkinstall I the following error

aking install in libraries/utils
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
make  install-am
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
make[3]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/utils'
Making install in libraries/linearAlgebra
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/linearAlgebra'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/linearAlgebra'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/linearAlgebra'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/linearAlgebra'
Making install in libraries/trustRegion
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/trustRegion'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/trustRegion'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/trustRegion'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/trustRegion'
Making install in libraries/cfsqp
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/cfsqp'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/cfsqp'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/cfsqp'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/cfsqp'
Making install in libraries/solvopt
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/solvopt'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/solvopt'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/solvopt'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/solvopt'
Making install in libraries/randomNumbers
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/randomNumbers'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/randomNumbers'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/randomNumbers'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/randomNumbers'
Making install in libraries/gaussHermite
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/gaussHermite'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/gaussHermite'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/gaussHermite'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/gaussHermite'
Making install in libraries/parameters
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/parameters'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/parameters'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/parameters'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/parameters'
Making install in libraries/bisonbiogeme
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/bisonbiogeme'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/bisonbiogeme'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/bisonbiogeme'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/bisonbiogeme'
Making install in libraries/pythonbiogeme
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/pythonbiogeme'
make  install-am
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/pythonbiogeme'
make[3]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/pythonbiogeme'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/pythonbiogeme'
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/pythonbiogeme'
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/libraries/pythonbiogeme'
Making install in tools/histograms
make[1]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/tools/histograms'
make[2]: Entering directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/tools/histograms'
 /bin/mkdir -p '/usr/local/bin'
 /usr/bin/install -c weightedhistogram histogram '/usr/local/bin'
/usr/bin/install: cannot remove '/usr/local/bin/weightedhistogram': Permission denied
/usr/bin/install: cannot remove '/usr/local/bin/histogram': Permission denied
Makefile:348: recipe for target 'install-binSCRIPTS' failed
make[2]: *** [install-binSCRIPTS] Error 1
make[2]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/tools/histograms'
Makefile:459: recipe for target 'install-am' failed
make[1]: *** [install-am] Error 2
make[1]: Leaving directory '/home/ioanna/Desktop/Biogeme/biogeme-2.5/tools/histograms'
Makefile:445: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

****  Installation failed. Aborting package creation.

    Restoring overwritten files from backup... FAILED!

Cleaning up...OK

Thanks Ioanna

4
  • The relevant part of the error was actually cut out, its the stuff before collect2: error: ld returned 1 exit status. This error (undefined reference) is normally caused by missing library or trying to link to wrong version of library.
    – Daniel
    Commented Jun 30, 2016 at 8:55
  • Which program are you trying to compile? Does it have dependancies? (check its README or INSTALL file). Are those dependancies installed? Does it look for a specific version? Why would adding sudo make any difference in this case? ...
    – Hennes
    Commented Jun 30, 2016 at 8:55
  • Just curious: any particular reason why you didn't install using the .deb provided?
    – edwinksl
    Commented Jun 30, 2016 at 9:17
  • I edited my question with the full error I get. When I try to install with the .deb provied the software runs but it cannot read the libraries. I guess I should install them but I dont know how Commented Jul 4, 2016 at 12:50

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