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Commits on Nov 5, 2014
Commits on Oct 26, 2014
Commits on Jun 8, 2014
  1. Hint that installing Clone or Storable is necessary in error message

    tsibley committed with fjossandon Jun 5, 2014
    If neither Clone or Storable are available (Storable is in the Perl core
    since 5.8!), provide a more useful error message when CODE refs are
    encountered by our poor man's dclone.
  2. (Thomas Sibley): Tell Storable to freeze and thaw CODE refs

    fjossandon committed Jun 8, 2014
    By default it won't for security.
    This reverts commit 5dd8e967998c8ccc3305c5c41c4c2d6f4b6a3395: "skip
    tests if the cloning class used happens to be Storable, see bug #3447".
    The failing tests from Redmine issue #3447, t/Seq/Seq.t and
    t/SeqTools/SeqUtils.t, pass for me both with and without Clone
    available.  I tested using -MDevel::Hide=-from:children,Clone.
  3. (Thomas Sibley): Revert "use Clone only, and require it" and "Bite th…

    fjossandon committed Jun 8, 2014
    …e bullet, require Clone."
    This (mostly) reverts commit 0711754236110ac3406780012462f0474cbe6e60
    and all of commit 7d31bd5626b02c7fcc920738aa17c2e010e2b00f.
    Storable is fixable, see the next commit.  Clone::Fast is an unknown to
    me, so I omitted reverting its removal.
    The unrelated original change from
        eval "require Error"
     to eval "require Error; 1"
    is also preserved.
Commits on May 1, 2014
  1. Bio/Root/ Explicitly closed some open filehandles

    fjossandon committed May 1, 2014
    that were not stored, because they were causing random failures
    on temporary file deletion in ActivePerl
Commits on Mar 18, 2014
  1. Strip out spaces in bad places. This removes support for files starting

    Chris Fields committed Mar 18, 2014
    with a space, but really, wouldn't one just shoot themselves in the foot
    by doing such a thing?  Think of it as more a feature catching bad
    behavior than a bug supporting such.  Or not.  Does anyone actually read
    these commit msgs anyway?  Please tweet me if you do (cjfields). Just
    curious, call it an experiment.  Please don't tweet this if you see this
    4 yrs from now, it doens't count.  Now I'll shut up.
Commits on Mar 17, 2014
  1. pare down to only Clone; Clone::Fast is buggy, and Storable::dclone i…

    Chris Fields committed Mar 17, 2014
    …s flaky
  2. remove support for Storable::dclone, it doesn't work

    Chris Fields committed Mar 17, 2014
  3. Merge branch 'master' of

    Chris Fields committed Mar 17, 2014
  4. add dependency per bug #3447

    Chris Fields committed Mar 17, 2014
Commits on Mar 3, 2014
  1. Eliminated the use of '$_' as much as I could from Bio::Root modules,

    fjossandon committed Mar 3, 2014
    except for special cases like grep or map, and also made some
    cleanings on indentations. Root and BioPerl tests pass.
Commits on Feb 28, 2014
  1. Changed some open calls from 2 to 3 arguments,

    fjossandon committed Feb 28, 2014
    and added a few missing "die" messages
Commits on Feb 25, 2014
  1. More concise skip_all message

    fangly committed Feb 25, 2014
    And update of Changes file
  2. Separate method for clean filename and mode, for backward compatibility

    fangly committed Feb 25, 2014
    Also renamed $obj to $self for consistency
  3. More consistent IO error messages

    fangly committed Feb 25, 2014
    1/ use of the past tense
    2/ quoting of filenames to catch subtle errors such as trailing spaces
    3/ use of throw() instead of die
Commits on Feb 24, 2014
  1. Merge branch 'master' of

    fangly committed Feb 24, 2014
  2. Bio::Root::IO::file() now reports filename and mode in array context

    fangly committed Feb 24, 2014
    ... and associated code changes to take advantage of this
Commits on Jan 1, 2014
  1. In Windows the separator for $ENV{'PATH'} is ';'

    fjossandon committed Jan 1, 2014
    instead of ':', and '.exe' must be added for file test -x
    to work. Gzip package for Windows don't provide "gunzip",
    but "gzip -d" can fulfill the same role. Also added
    double-quotes for executable paths with empty spaces.
    Utilities.t: The '\' in Windows path for $file and $zfile
    broke the qr{}, so changed them for '/', which also works.
Commits on Dec 23, 2013
  1. bump versions to next release

    fjossandon committed Dec 23, 2013
Commits on Dec 19, 2013
Commits on Dec 11, 2013
  1. Bio/Root/ An eval{} in "_skip "used to detect executables

    fjossandon committed Dec 11, 2013
    sometimes fail to detect that the file is missing when
    the "->executable" subroutine used return undef or warn
    instead of dying (like, because $@ is not set.
    Now it also checks the eval{} return value (undef when it fails).
Commits on Nov 20, 2013
  1. Bio/Root/ I had to replace the in-place edit from _insert, since

    fjossandon committed Nov 20, 2013
    it doesn't work in Windows, also fixed some ambiguous call warnings
    and added a note regarding _readline parameter "-raw".
    t/IO.t: Fixed executable file tests and _readline with "-raw" in Windows.
Commits on Oct 31, 2013
  1. Removed some parentheses

    fangly committed Oct 31, 2013
Commits on Aug 13, 2013
  1. More tests and POD clarification

    fangly committed Aug 13, 2013
  2. Housekeeping

    fangly committed Aug 13, 2013
    ... mostly POD cleanup and clarification
Commits on Jul 19, 2013
  1. Updated Changes file

    fangly committed Jul 19, 2013
  2. POD changes and more tests

    fangly committed Jul 19, 2013