[Biopython-dev] [Bug 1733] New: compiler recognition in setup.py

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1733

           Summary: compiler recognition in setup.py
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: MBatLE at gmx.de


in function build_extension (setup.py line 178) the c++ compiler cant get
determined in my installation. 

My os.environ looks the following:

{'SSH_ASKPASS': '/usr/bin/gtk2-ssh-askpass', 'LESS': '-R', 'LESSOPEN':
'|lesspipe.sh %s', 'CVS_RSH': 'ssh', 'LOGNAME': 'root', 'USER': 'root',
'INPUTRC': '/etc/inputrc', 'QTDIR': '/usr/qt/3', 'PATH':
'/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/3.3.5:/opt/ati/bin:/opt/Acrobat5:/usr/X11R6/bin:/opt/blackdown-jdk-1.4.2.01/bin:/opt/blackdown-jdk-1.4.2.01/jre/bin:/usr/qt/3/bin:/usr/kde/3.3/sbin:/usr/kde/3.3/bin',
'PS1': '\\[\\033[01;31m\\]\\h \\[\\033[01;34m\\]\\W \\$ \\[\\033[00m\\]',
'DISPLAY': ':0.0', 'KDEDIR': '/usr/kde/3.3', 'TERM': 'Eterm', 'SHELL':
'/bin/bash', 'JDK_HOME': '/opt/blackdown-jdk-1.4.2.01', 'SHLVL': '1',
'CONFIG_PROTECT_MASK': '/etc/gconf /etc/terminfo', 'G_BROKEN_FILENAMES': '1',
'QMAKESPEC': 'linux-g++', 'EDITOR': '/bin/nano', 'MANPATH':
'/usr/share/man:/usr/local/share/man:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/man:/usr/X11R6/man::/opt/blackdown-jdk-1.4.2.01/man:/usr/qt/3/doc/man',
'JAVA_HOME': '/opt/blackdown-jdk-1.4.2.01', 'HOME': '/root', 'KDE_MALLOC': '1',
'INFODIR': '/usr/share/info', 'INFOPATH':
'/usr/share/info:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/info', 'GCCBITS':
'', 'CLASSPATH': '.', 'PLAT': 'linux-i686', 'XINITRC': '/etc/X11/xinit/xinitrc',
'MOZILLA_FIVE_HOME': '/usr/lib/mozilla', 'XAUTHORITY': '/root/.xauth78ixrX',
'KDEDIRS': '/usr', '_': '/usr/bin/python', 'JAVAC':
'/opt/blackdown-jdk-1.4.2.01/bin/javac', 'ANT_HOME': '/usr/share/ant-core',
'GDK_USE_XFT': '1', 'OLDPWD': '/root', 'HOSTNAME': 'gkws3', 'CONFIG_PROTECT':
'/usr/lib/mozilla/defaults/pref /usr/X11R6/lib/X11/xkb /usr/kde/3.3/share/config
/usr/kde/3.3/env /usr/kde/3.3/shutdown /usr/share/texmf/tex/generic/config/
/usr/share/texmf/tex/platex/config/ /usr/share/texmf/dvips/config/
/usr/share/texmf/dvipdfm/config/ /usr/share/texmf/xdvi/ /usr/share/config',
'PWD': '/tmp/biopython', 'SGML_CATALOG_FILES':
'/etc/sgml/sgml-ent.cat:/etc/sgml/sgml-docbook.cat:/etc/sgml/openjade-1.3.2.cat:/etc/sgml/sgml-docbook-4.1.cat:/etc/sgml/sgml-docbook-4.0.cat:/etc/sgml/dsssl-docbook-stylesheets.cat:/etc/sgml/sgml-docbook-3.0.cat:/etc/sgml/sgml-docbook-3.1.cat:/etc/sgml/sgml-lite.cat',
'MAIL': '/root/', 'PAGER': '/usr/bin/less', 'PYTHONDOCS':
'/usr/share/doc/python-docs-2.3.4/html'}
{'SSH_ASKPASS': '/usr/bin/gtk2-ssh-askpass', 'LESS': '-R', 'LESSOPEN':
'|lesspipe.sh %s', 'CVS_RSH': 'ssh', 'LOGNAME': 'root', 'USER': 'root',
'INPUTRC': '/etc/inputrc', 'QTDIR': '/usr/qt/3', 'PATH':
'/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/3.3.5:/opt/ati/bin:/opt/Acrobat5:/usr/X11R6/bin:/opt/blackdown-jdk-1.4.2.01/bin:/opt/blackdown-jdk-1.4.2.01/jre/bin:/usr/qt/3/bin:/usr/kde/3.3/sbin:/usr/kde/3.3/bin',
'PS1': '\\[\\033[01;31m\\]\\h \\[\\033[01;34m\\]\\W \\$ \\[\\033[00m\\]',
'DISPLAY': ':0.0', 'KDEDIR': '/usr/kde/3.3', 'TERM': 'Eterm', 'SHELL':
'/bin/bash', 'JDK_HOME': '/opt/blackdown-jdk-1.4.2.01', 'SHLVL': '1',
'CONFIG_PROTECT_MASK': '/etc/gconf /etc/terminfo', 'G_BROKEN_FILENAMES': '1',
'QMAKESPEC': 'linux-g++', 'EDITOR': '/bin/nano', 'MANPATH':
'/usr/share/man:/usr/local/share/man:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/man:/usr/X11R6/man::/opt/blackdown-jdk-1.4.2.01/man:/usr/qt/3/doc/man',
'JAVA_HOME': '/opt/blackdown-jdk-1.4.2.01', 'HOME': '/root', 'KDE_MALLOC': '1',
'INFODIR': '/usr/share/info', 'INFOPATH':
'/usr/share/info:/usr/share/gcc-data/i686-pc-linux-gnu/3.3.5/info', 'GCCBITS':
'', 'CLASSPATH': '.', 'PLAT': 'linux-i686', 'XINITRC': '/etc/X11/xinit/xinitrc',
'MOZILLA_FIVE_HOME': '/usr/lib/mozilla', 'XAUTHORITY': '/root/.xauth78ixrX',
'KDEDIRS': '/usr', '_': '/usr/bin/python', 'JAVAC':
'/opt/blackdown-jdk-1.4.2.01/bin/javac', 'ANT_HOME': '/usr/share/ant-core',
'GDK_USE_XFT': '1', 'OLDPWD': '/root', 'HOSTNAME': 'gkws3', 'CONFIG_PROTECT':
'/usr/lib/mozilla/defaults/pref /usr/X11R6/lib/X11/xkb /usr/kde/3.3/share/config
/usr/kde/3.3/env /usr/kde/3.3/shutdown /usr/share/texmf/tex/generic/config/
/usr/share/texmf/tex/platex/config/ /usr/share/texmf/dvips/config/
/usr/share/texmf/dvipdfm/config/ /usr/share/texmf/xdvi/ /usr/share/config',
'PWD': '/tmp/biopython', 'SGML_CATALOG_FILES':
'/etc/sgml/sgml-ent.cat:/etc/sgml/sgml-docbook.cat:/etc/sgml/openjade-1.3.2.cat:/etc/sgml/sgml-docbook-4.1.cat:/etc/sgml/sgml-docbook-4.0.cat:/etc/sgml/dsssl-docbook-stylesheets.cat:/etc/sgml/sgml-docbook-3.0.cat:/etc/sgml/sgml-docbook-3.1.cat:/etc/sgml/sgml-lite.cat',
'MAIL': '/root/', 'PAGER': '/usr/bin/less', 'PYTHONDOCS':
'/usr/share/doc/python-docs-2.3.4/html'}

and (the elif fallback) wont get g++ because :

self.compiler.compiler_cxx = []



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