# $Id: PLATFORMS,v 1.13.2.5 2002-07-15 19:39:30 jason Exp $ Perl general comments: o Perl 5.00404 and lower often have problems with GDB.t o Perl on Digital Unix, WindowsNT, and MacOS has been reported to have problems with the Bio::DB::GDB on module (and consequently the test GDB.t). This is due to different versions of HTML::Parser. o DB.t has intermittent time-out failures (which will most likely cause tests 3 and/or 27 to fail). o Index.t will fail if you have an out-of-date DBM file installation. o On some machines (IRIX, OSF) there can be a shell buffer overrun which will not allow the makefile to work. This is due to a limitation in the makefile generated by the ExtUtils::MakeMaker module. The best course of action is to installed the latest ExtUtils::MakeMaker. You will likely still see a problem with make test, but you should still be able to issue a make install. UPDATE (1.0.2): ExtUtils::MakeMaker 6.00 and should work for most IRIX installs. Try installing this module first before doing the Bioperl installation procedure. You can also always still use Bioperl by setting your PERL5LIB directory to the downloaded distribution directory. Tested systems & OS Specific Comments or Warnings ================================================== Machine : RedHat Linux 7.2 i686 Compiler: cc Perl : 5.004-5.6.1 Comments: XML::Writer tests fails (segfault), but do an install/force anyways and all will work. Machine : Linux i386 Compiler: cc Perl : 5.004-5.6.1 Comments: none Machine : Digital Unix Compiler: cc Perl : 5.004 Comments: Failure on GDB.t, possibly due to LWP issues Machine : OpenBSD 2.8 i386 Compiler: cc Perl : 5.6.0 Comments: none Machine : Solaris 2.8 UltraSparc Compiler: gcc Perl : 5.6.0 Comments: The t/flat.t test may report errors being unable to remove a temp directory, these can be safely ignored although an uncessary directory t/tmp may get created as result of this test. This has since been fixed (Bioperl 1.0.2+). Machine : FreeBSD 4.2 i386 Compiler: gcc Perl : 5.005_03 Comments: none Machine : IRIX64 6.5 SGI Compiler: cc Perl : 5.004_04 Comments: Some warnings about which can be safely ignored. Bio::DB::GenBank/GenPept cannot be used because IO::String cannot be installed on 5.004. Bio::DB::GDB will not work on pre 5.005 versions of perl. See notes at the top about problem with makefiles generated and limited buffer size on typical IRIX boxes. Upgrading ExtUtils::MakeMaker should work on most systems. Machine : Win32, WinNT i386 Compiler: -- Perl : ActiveState Perl 5.6, 5.5.1 Comments: Be sure that the module DB_File is installed and up-to-date to allow Bio::Index modules to work properly. File::Temp potentially broken (causing at least BPpsilite to fail) Installing ppm's IO-stringy and IO-String and File-Temp are necessary as well. See http://bioperl.org/Core/windows-bioperl.html for more info on installing on Windows. Machine : MacOS Compiler: -- Perl : MacPerl Comments: Issues and possible ways to fix them summarized by Todd Richmond on the bioperl.org Wiki. Machine : MacOS X Compiler: gcc Perl : 5.6.0 Comments: Steve Cannon has made available Bioperl OS X installation directions and notes online at the following URL: http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html Machine : HP-UX / PA-RISC 11.0 Compiler: gcc Perl : 5.6.1 Comments: Tested by (dag@sonsorol.org) on a barebones 8-cpu system without the various dependencies installed. All tests pass except those skipped by the test harness due to missing external packages. Thanks due to HP for providing the OBF with an Itanium workstation plus internet access to other HP test platforms. Feedback from HP-UX users is appreciated. Machine : HP-UX / Itanium ('ia64') 11.0 Compiler: gcc Perl : 5.6.1 Comments: Tested by (dag@sonsorol.org) on a barebones 4-cpu system without the various dependencies installed. 96% of the tests pass; OBF is working on getting 100% pass rate. Thanks due to HP for providing the OBF with an Itanium workstation plus internet access to other HP test platforms. Feedback from HP-UX users is appreciated.