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branch: master

Sep 24, 2013

  1. Frederic Fournier

    Merge branch 'master' of ssh://gh/Frederic-bioinfo/rTANDEM

    Conflicts:
    	src/Makevars.win
    Frederic-bioinfo authored
  2. Frederic Fournier

    Uniformity added to environment variable use for Windows build.

    Two ways of using environment variable to build on windows were
    proposed (one in dev, one in prod), now either one of them can be used.
    Frederic-bioinfo authored
  3. Frederic Fournier

    Uniformity added to environment variable use for Windows build.

    Two ways of using environment variable to build on windows were
    proposed (one in dev, one in prod), now either one of them can be used.
    Frederic-bioinfo authored
  4. Frederic Fournier

    Solution to bug #4 - memory problem when there is no spectra

    'delete' operators in Cpp were removed to let R do the garbage collection.
    Frederic-bioinfo authored
  5. Frederic Fournier

    Solution to bug #3 - misleading message when using some parameters

    Parameters were added to the rTParam class based on TPP list of
    implemented but undocumented parameters.
    Frederic-bioinfo authored

Jul 31, 2013

  1. Frederic Fournier

    Version bump to 1.1.3

    Corrected some CRLF line endings.

Jul 26, 2013

  1. Frederic Fournier

    Updated the NEWS section.

  2. Frederic Fournier

    Corrected bug #2 - Problem with multithreading.

    It was actually a faulty message that caused R to
    crash, and not multithreading per se.
  3. Frederic Fournier

    Solution to bug #1 - problem using multiple fasta files

    The conversion of the Rdata in deque was using only one out
    of two values (probably on the model of the conversion to map).
    That led X!Tandem to ignore some fasta files.
  4. Frederic Fournier

    Removed source files related to P3 software

    P3 is distributed with X!Tandem. But is a different
    project, its code doesn't belong in rTANDEM.

Jul 22, 2013

  1. Frederic Fournier

    Merge branch 'master' of https://github.com/CharlesJB/rTANDEM

    Conflicts:
    	src/Makevars.win

Jul 19, 2013

  1. Frederic Fournier

    Merge branch 'master' of ssh://gh/Frederic-bioinfo/rTANDEM

  2. Frederic Fournier

    Merge branch 'master' of ssh://gh/Frederic-bioinfo/rTANDEM

  3. Frederic Fournier

    Merge branch 'master' of ssh://gh/Frederic-bioinfo/rTANDEM

  4. Frederic Fournier

    rTANDEM is now based on X!Tandem Jackhammer

    Manually did a three-way merge between X!Tandem-
    Cyclone, X!Tandem-Jackhammer and rTANDEM
  5. Frederic Fournier

    Import the latest from bioconductor's SVN. (rTANDEM version 1.1.1)

  6. Frederic Fournier

    Made the NAMESPACE more exhaustive

    Changes suggested by Martin Morgan following 'codetoolsBioC'.
    Frederic-bioinfo authored
  7. Frederic Fournier

    Version change

    Frederic-bioinfo authored
  8. Frederic Fournier

    Added a setter for rTParam: setParamValue().

    All examples were modified to use the new function.
    Documenation was updated to include the new function.
    Frederic-bioinfo authored
  9. Frederic Fournier

    Corrected the Rprintf commands for better display of output.

    Variables were not correctly interpolated in messages.
    Frederic-bioinfo authored
  10. Frederic Fournier

    Disabled R C-stack checking

    Frederic-bioinfo authored
  11. Frederic Fournier

    revision change

    Frederic-bioinfo authored
  12. Frederic Fournier

    Added examples to the accessors and convertors man pages.

    Frederic-bioinfo authored
  13. Frederic Fournier

    Added xtandem license information

    Frederic-bioinfo authored
  14. Frederic Fournier

    Changed the PKG_LIBS definition

    Change suggesteb by Simon Urbanek:
    change PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`
    to PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` -lpthread -lexpat
    to prevent configure problems.
    Frederic-bioinfo authored
  15. Frederic Fournier

    Added version dependency on data.table.

    Changed procedure for linking against expat during windows build.
    Frederic-bioinfo authored
  16. Frederic Fournier

    Adjusted date, version and 'news' for first submission to bioconductor

    Frederic-bioinfo authored
  17. Frederic Fournier

    Correction of typos and small mistakes in the documentation.

    Frederic-bioinfo authored
  18. Frederic Fournier

    Deleted data and part of fasta file to meet bioconductor 2M limit.

    Frederic-bioinfo authored
  19. Frederic Fournier

    Modifications to Makevar and README for compilation on Windows.

    Frederic-bioinfo authored
  20. Frederic Fournier

    Rene is added as an autor in all documentation

    Removed 'hello world' files.
    Frederic-bioinfo authored
  21. Frederic Fournier

    File renamed to follow bioconductor guidelines

    Frederic-bioinfo authored
  22. Frederic Fournier

    Corrected the function GetDegeneracy

    The function did not work when there was indeed degeneracy
    (accessor problem with array).
    Frederic-bioinfo authored

Jul 02, 2013

  1. Frederic Fournier

    Last file merged (mprocess.cpp) + x!tandem version changed in documen…

    …tation.
  2. Frederic Fournier

    Merged the changes from X!Tandem Cyclone to X!Tandem Jackhammer into …

    …rTANDEM.
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