ubuntuusers.de

Hallo liebes Forum,

ich habe von Windows auf Lubuntu umgerüstet, weil ich für ein Uni-Projekt mit dem VienneRNA package arbeiten muss. Jetzt versuche ich mich seit längerer Zeit an der Installation, aber ich scheitere jedes Mal an Problemen, die ich (noch) nicht verstehe. Leider ist das kein Programm, was über das Software-Center zu beziehen ist, sondern es muss über einen Source-Code und ein Terminal installiert werden... Bestimmt ist das Ganze für einen erfahrenen Linux-Benutzer recht einfach, daher wollte ich fragen, ob mich vielleicht jemand dabei unterstützen kann.

Der Source-Code stammt von dieser Seite hier: http://www.tbi.univie.ac.at/RNA/ Ich habe ihn bereits heruntergeladen und nun liegt er im Ordner Downloads. Ich habe ebenfalls versucht, die auf dieser Seite: http://www.tbi.univie.ac.at/RNA/documentation.html#install angegebenen Schritte durchzuführen. Das Entpacken

tar -zxvf ViennaRNA-2.2.5.tar.gz

funktioniert! Und

cd ViennaRNA-2.2.5

ebenfalls. Ich glaube,

./configure

funktioniert auch. Jedenfalls sagt mir das Terminal etwas von "Configured successfully" und "files will be installed in the following directories"... Dann habe ich versucht

make

anzuwenden, was aber anscheinend nicht funktioniert. Im nächsten Post werde ich mal versuchen, den Inhalt des Terminals hierher zu kopieren - hoffentlich könnt ihr daraus das Problem auslesen...

Also, das hier ist das Ergebnis meines Versuchs zu konfigurieren:

aileen@aileen-Aspire-7738:~/Schreibtisch/Downloads/ViennaRNA-2.2.5$ ./configure
checking whether make supports nested variables... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking if malloc debugging is wanted... no
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for ar... ar
checking the archiver (ar) interface... ar
checking whether make sets $(MAKE)... (cached) yes
checking for grep that handles long lines and -e... /bin/grep
checking for a sed that does not truncate output... /bin/sed
checking whether ln -s works... yes
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for gcc option to support OpenMP... -fopenmp
checking for exp in -lm... yes
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for unistd.h... (cached) yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for floor... yes
checking for strdup... yes
checking for strstr... yes
checking for strchr... yes
checking for strrchr... yes
checking for strstr... (cached) yes
checking for strtol... yes
checking for strtoul... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for erand48... yes
checking for memset... yes
checking for memmove... yes
checking for erand48... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for pkg-config... no
checking for C compiler vendor... gnu
checking for perl... /usr/bin/perl
checking whether C compiler accepts -flto... yes
configure: WARNING: Trying to re-set ar/ranlib/nm to compiler specific wrappers
checking for gcc-ar... gcc-ar
checking for gcc-ranlib... gcc-ranlib
checking for gcc-nm... gcc-nm
checking for ./src/libsvm-3.20/svm.cpp... yes
checking for ./src/libsvm-3.20/svm.h... yes
checking for ./src/json/json.c... yes
checking for ./src/json/json.h... yes
checking for cblas_dgemm in -lgslcblas... no
checking for gsl_blas_dgemm in -lgsl... no
configure: WARNING: "Can't find libgsl. Falling back to default implementation."
checking for ./src/Kinfold/Makefile.am... yes
checking for ./src/RNAforester/Makefile.am... yes
checking for ./interfaces/Makefile.am... yes
checking for swig... no
checking for swig2.0... no
checking for ./interfaces/Perl/Makefile.am... yes
checking for ./interfaces/Perl/RNA_wrap.cpp... yes
checking for ./interfaces/Perl/RNA.pm... yes
checking for /usr/bin/perl... (cached) /usr/bin/perl
checking for Perl prefix... /usr
checking for Perl siteprefix... /usr/local
checking for Perl vendorprefix... /usr
checking for Perl extension include path... /usr/lib/i386-linux-gnu/perl/5.22/CORE
checking for Perl extension target directory... /usr/local/lib/i386-linux-gnu/perl/5.22.1
checking for architecture dependent Perl extension site target directory... /usr/local/lib/i386-linux-gnu/perl/5.22.1
checking for architecture dependent Perl extension vendor target directory... /usr/lib/i386-linux-gnu/perl5/5.22
checking for architecture independent Perl extension site target directory... /usr/local/share/perl/5.22.1
checking for architecture independent Perl extension vendor target directory... /usr/share/perl5
checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include
checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong
checking for Perl dynamic library extension... .so
checking for perl... /usr/bin/perl
checking for perl module ExtUtils::Embed... yes
checking for perl ccopts embed flags...  -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64  -I/usr/lib/i386-linux-gnu/perl/5.22/CORE 
checking for perl ldopts embed flags... -Wl,-E  -fstack-protector-strong -L/usr/local/lib  -L/usr/lib/i386-linux-gnu/perl/5.22/CORE -lperl -ldl -lm -lpthread -lc -lcrypt
checking for ./interfaces/Python/Makefile.am... yes
checking for ./interfaces/Python/RNA_wrap.cpp... yes
checking for ./interfaces/Python/RNA.py... yes
checking for python2... /usr/bin/python2
checking for python2-config... no
checking for python2.7-config... no
checking for python2.6-config... no
configure: WARNING:
The python2-config program was not found in the search path. Please ensure
that it is installed and its directory is included in the search path.

checking for doxygen... no
checking for pdflatex... no
checking for latex... no
checking for makeindex... no
checking for dot... no
checking for egrep... /bin/egrep
checking for perl... /usr/bin/perl
checking for doc/RNAlib-2.2.5.pdf... yes
checking for doc/html/index.html... yes
checking for CHECK... no
configure: WARNING: check not found -- will not build C-library Unit tests
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating packaging/macosx/Makefile
config.status: creating packaging/macosx/Distribution.xml
config.status: creating packaging/macosx/resources/welcome.txt
config.status: creating interfaces/Perl/Makefile
config.status: creating tests/Makefile
config.status: creating tests/RNApath.py
config.status: creating misc/Makefile
config.status: creating interfaces/Makefile
config.status: creating Makefile
config.status: creating RNAlib2.pc
config.status: creating src/Utils/Makefile
config.status: creating src/bin/Makefile
config.status: creating src/Makefile
config.status: creating man/Makefile
config.status: creating src/ViennaRNA/Makefile
config.status: creating doc/Makefile
config.status: creating man/cmdlopt.sh
config.status: creating packaging/viennarna.spec
config.status: creating packaging/PKGBUILD
config.status: creating packaging/win_installer_archlinux_i686.nsi
config.status: creating packaging/win_installer_archlinux_x86_64.nsi
config.status: creating packaging/win_installer_fedora_i686.nsi
config.status: creating packaging/win_installer_fedora_x86_64.nsi
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in src/Kinfold (/home/aileen/Schreibtisch/Downloads/ViennaRNA-2.2.5/src/Kinfold)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2 -flto' 'CXXFLAGS=-g -O2 -flto' 'LDFLAGS=-flto' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-L$(top_builddir)/../../src/ViennaRNA -lRNA -lgomp -flto' --cache-file=/dev/null --srcdir=.
checking whether make supports nested variables... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking if malloc debugging is wanted... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for strdup... yes
checking for memset... yes
checking for strchr... yes
checking for gcc option to support OpenMP... -fopenmp
checking for ViennaRNA package...  headers in "./../../src" and library... "../../src/ViennaRNA"
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking fold.h usability... no
checking fold.h presence... no
checking for fold.h... no
checking for exp in -lm... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for an ANSI C-conforming const... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Example/Makefile
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
=== configuring in src/RNAforester (/home/aileen/Schreibtisch/Downloads/ViennaRNA-2.2.5/src/RNAforester)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2 -flto' 'CXXFLAGS=-g -O2 -flto' 'LDFLAGS=-flto' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-L$(top_builddir)/../../src/ViennaRNA -lRNA -lgomp -flto' --cache-file=/dev/null --srcdir=.
checking whether make supports nested variables... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking for g++ option to support OpenMP... -fopenmp
using (to be built) libRNA.a in ../ViennaRNA
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking g2.h usability... yes
checking g2.h presence... yes
checking for g2.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating man/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
=== configuring in g2-0.72 (/home/aileen/Schreibtisch/Downloads/ViennaRNA-2.2.5/src/RNAforester/g2-0.72)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  'CC=gcc' 'CXX=g++' 'CFLAGS=-g -O2 -flto' 'CXXFLAGS=-g -O2 -flto' 'LDFLAGS=-flto' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-L$(top_builddir)/../../src/ViennaRNA -lRNA -lgomp -flto' --cache-file=/dev/null --srcdir=.
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for find... find
checking for makedepend... :
checking for dlopen in -ldl... yes
checking for X... no
checking for main in -lm... yes
checking for main in -lX11... no
checking for main in -lXext... no
checking for main in -lgd... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes

configure: creating ./config.status
config.status: creating Makefile
config.status: creating demo/Makefile
config.status: creating g2_perl/Makefile.PL
config.status: creating g2_python/Makefile

Supported devices:
    PostScript
    FIG

Unsupported devices:
    X11
    Xdbe
    Win32
    GD
    GD (GIF)

Run 'make depend' to create dependencies.

configure:

################################################
#         ViennaRNA Package 2.2.5             ##
#                                             ##
# configured successfully with the following  ##
# options:                                    ##
################################################


  * Extra Programs:

    ( Kinfold, RNAforester )

  * Other Options:

    ( SVM, JSON, Boustrophedon, OpenMP, LTO )

  * RNAlib Scripting Language Interfaces:

    ( Perl 5 )

  * RNAlib Documentation:

    ( PDF, HTML )

  * Unit Tests will be performed for:

    ( Perl 5 )


##############################################
# Files will be installed in the following  ##
# directories:                              ##
##############################################

  Executables:        /usr/local/bin
  Libraries:          /usr/local/lib
  Header files:       /usr/local/include
  Extra Data:         /usr/local/share
  Man pages:          /usr/local/share/man
  Documentation:      /usr/local/share/doc/ViennaRNA
    (HTML):           /usr/local/share/doc/ViennaRNA/html
    (PDF):            /usr/local/share/doc/ViennaRNA
  Perl5 Interface:    
    (binaries):       /usr/local/lib/i386-linux-gnu/perl/5.22.1
    (scripts):        /usr/local/share/perl/5.22.1
  Python2 Interface:  Not to be installed
    (binaries):       
    (scripts):        
  Python3 Interface:  Not to be installed
    (binaries):       
    (scripts):        

Ist das soweit in Ordnung? Kann ich von hier weitermachen mit

make

?

Viele liebe Grüße ☺