lib/optparse/NEWS.md

In arodri7/SAIGE-GPU: Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE)

optparse 1.6.6

• Throws an error for unknown short flags and long flags when positional_arguments=TRUE. Thanks Greg Minshall for bug report (#34).
• If the callback parameter of add_option / make_option is not NULL then the default of action is now "callback". Thanks Greg Minshall for suggestion (#35).
• Better documentation of action=="callback" in the man page for add_option and make_option. Thanks Greg Minshall for bug report (#35).

optparse 1.6.4

• Fixes bug in printing help for action=="callback" when metavar==NULL (#29). Thanks Ni Huang for bug report.
• Throws an error when passed short flags more than one letter long (#32). Thanks Gautier Richard for bug report.

optparse 1.6.2

• Fixs a parsing bug when action=="callback" and positional_argument==TRUE (#28). Thanks Ni Huang for bug report.

optparse 1.6.1

• Improves accuracy of README (#27). Thanks Alex Penson for bug report.

optparse 1.6.0

• Supports callback actions (#26). Thanks Gyu Jin Choi for patch.
• If interactive() == FALSE and print_help_and_exit == TRUE then optparse will now call quit(status=0) instead of quit(status=1) after printing the help message (this matches behaviour of the python package).
• Better error message when forgetting to set add_help_option=FALSE when defining an -h or --help flag. Thanks Jeff P. Bruce for bug report.
• Increment getopt requirement so that empty strings are parsed correctly. Thanks Matthew Flickinger for bug report.

optparse 1.4.4

• Minor documentation fixes. Thanks J. J. Ramsey and Daeyoung Kim for bug reports.
• Fix bug when add_help_option in OptionParser set to FALSE. Thanks to Jeff Bruce for bug report.
• parse_args now supports convert_hyphens_to_underscores argument which converts any hyphens to underscores when returning the list of options
• Now includes the convenience function parse_args2 which wraps parse_args with positional_arguments set to TRUE and convert_hyphens_to_underscores set to TRUE.

optparse 1.3.2

• optparse should no longer give any warnings when options(warnPartialMatchArgs=TRUE). Thanks Rich FitzJohn for patch.
• print_help no longer throws an error if we have a default argument of length zero. Thanks Benjamin Tyner for bug report.

optparse 1.3.0

• OptionParser and OptionParserOption S4 classes are now exported. Thanks Peter Humburg for patch.

optparse 1.2.0

• Parameter positional_arguments of function parse_args now accepts one or two numeric values that denote the minimum and maximum number of supported positional arguments. Thanks Kirill Müller for patch.
• If interactive() == TRUE then parse_args will no longer quit(status=1) after printing a help message but will instead throw an error. optparse will continue to quit(status=1) after printing a help message for non-interactive Rscripts unless print_help_and_exit == FALSE.
• In make_option argument type="numeric" automatically cast to double. Previously users might have received an error passing negative numbers if they accidentally specified "numeric" instead of "double".
• Bug fixed in printing usage message for options with default value of NA and a help string including "%default". Thanks Stefan Seemayer for bug report and patch.

optparse 1.0.2

• Project website moved to https://github.com/trevorld/optparse
• We now replace all occurrences of %prog in usage message (including description and epilogue). Previously we would only replace one occurrence and didn't make replacements in description and epilogue.
• Fix bug in parse_args when we have options with no short flag and positional_arguments=TRUE. Thanks Miroslav Posta for bug report.

optparse 1.0.0

• Added description and epilogue arguments to OptionParser to allow users to add more information to generated help messages
• Slightly alters the generated usage string to match more closely what the Python module does
• No longer exports S4 classes that represent OptionParser and OptionParserOption
• Now requires package getopt (>= 1.19) which has also been moved to Imports field from Depends field in DESCRIPTION
• Now also Suggests stringr package in DESCRIPTION

arodri7/SAIGE-GPU documentation built on Nov. 14, 2020, 5:44 a.m.