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NEWS
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RELEASE HISTORY OF THE "cleaver" PACKAGE
========================================
Version 1.35.1 [2022-08-31]:
- Fix: adapt vignette code to new UniProt.ws.
Version 1.27.1 [2020-06-05]:
- Fix cleavage rule for glutamyl endopeptidase in documentation
Thanks to Mariia Chernigovskaya <[email protected]> for
reporting this error.
Version 1.25.1 [2019-12-30]:
- Add missing space in vignette.
Version 1.21.4 [2018-12-26]:
- Use "https" in hyperlinks (where possible).
Version 1.21.3 [2018-12-26]:
- Correct cleavage rules for "pepsin" and "pepsin1.3". According to the
peptidecutter documentation "pepsin1.3" is more specific (cleaves at [FL])
than "pepsin" (cleaves [FLWY]); see https://github.com/sgibb/cleaver/issues/6
for details.
Thanks to Jean Manguy <[email protected]> for reporting this error.
Version 1.21.2 [2018-11-03]:
- Convert vignette from Sweave to rmarkdown.
- Another try to fix links in manual pages to avoid WARNING on Windows.
Version 1.21.1 [2018-11-01]:
- Add my ORCID to the Author field in DESCRIPTION.
- Fix links in manual pages to avoid WARNING on Windows.
Version 1.15.1 [2017-06-08]:
- Don't consider the last aminoacid as cleavage site.
`cleavageSites("ACK", custom="K")` results in `integer()` instead of `3` now.
Thanks Apurva Hegde <[email protected]> for reporting this issue.
- Remove superfluous "missedCleavages" argument in `cleavageSites`.
Version 1.13.2 [2017-02-14]:
- Use `expect_equal` instead of `expect_identical` to avoid failing of the
`.revsequence` unit test on "toluca2" (Mac OS X Mavericks (10.9.5) / x86_64).
- Add "importFrom(stats, setNames)" to NAMESPACE.
Version 1.13.1 [2017-01-04]:
- Remove GPL headers from *.R files.
- Remove useless return calls.
Version 1.5.3 [2015-02-02]:
- Set taxId=9606 for UniProt.ws in vignette.
Version 1.5.1 [2015-01-24]:
- Add test case if number of cleavage sites is smaller than the number of
allowed missed cleavages.
Version 1.3.8 [2014-09-28]:
- Use title case in the "Title:" field of the DESCRIPTION file.
Version 1.3.7 [2014-05-08]:
- Create an IRangesList using `split` instead of `lapply` in the
cleavageRanges,AAStringSet-method is more than two times faster.
Version 1.3.6 [2014-05-03]:
- Add cleavageRanges method for character, AAString and AAStringSet.
- cleave,AAString returns an AAStringSet instead of an AAStringSetList object.
- Fix return value of cleavageSites,AAStringSet.
Version 1.3.5 [2014-04-30]:
- Fix defintion of cleavageSites,AAStringSet.
Version 1.3.4 [2014-04-30]:
- Add cleavageSites method for character, AAString and AAStringSet.
Version 1.3.3 [2014-04-28]:
- Avoid duplicated digest of peptides results in a hugh speed improvement and a
hugh memory reduction (removes fix from 1.1.8 and partly reintroduces original
algorithm).
- Remove memory test and "memoryThreshold" argument (fails on different
platforms and is not important anymore using the "new" cleavage algorithm).
- Change default of "unique" argument to "unique=TRUE".
Version 1.3.2 [2014-04-25]:
- Introduce simple memory test and "memoryThreshold" argument to avoid the
calculation of ridiculous high numbers of "missedCleavages" and peptide
combinations.
Version 1.3.1 [2014-04-25]:
- Add "custom" argument to allow the user defining own cleavage rules.
Version 1.1.8 [2014-03-26]:
- Fix missedCleavages>1.
- Add argument "unique".
- Add methods, Biostrings, IRanges to NAMESPACE.
Version 1.1.7 [2014-03-25]:
- Typo in the manual page.
Version 1.1.5 [2014-02-25]:
- Using AAStringSetList constructor for list of characters instead of
creating a lot of AAStringSets dramatically decreases running time for
cleave,AAStringSet-method.
Version 1.1.4 [2013-12-20]:
- tests:
- move tests into tests/testthat to adapt to testthat 0.8 and new
CRAN policy.
Version 0.99.5 [2013-07-24]:
- vignette:
- remove duplicated sessionInfo entries.
Version 0.99.4 [2013-07-23]:
- vignette:
- use BiocStyle.
- add sessionInfo() and TOC.
Version 0.99.3 [2013-07-08]:
- vignette: add second BRAIN reference.
Version 0.99.2 [2013-06-17]:
- Replace own AAStringSetList constructor by Biostrings::AAStringSetList.
- man/cleaver-package.Rd: remove static date.
- vignette: add dynamic date and don't load Biostrings manually anymore.
- NAMESPACE: don't import from Biostrings and IRanges.
Version 0.99.1 [2013-05-30]:
- Add S4-methods for character, AAString, AAStringSet.
- man/cleave-methods.Rd: split table of cleavage rules to reduce table width.
- Extend vignette (add BRAIN and UniProt.ws based examples).
Version 0.99.0 [2013-04-27]:
- Initial release.