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Commits on Sep 24, 2013
  1. @Frederic-bioinfo

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

    Conflicts:
    	src/Makevars.win
    Frederic-bioinfo committed Sep 24, 2013
  2. @Frederic-bioinfo

    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 committed Sep 24, 2013
  3. @Frederic-bioinfo

    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 committed Sep 24, 2013
  4. @Frederic-bioinfo

    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 committed Sep 24, 2013
  5. @Frederic-bioinfo

    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 committed Sep 24, 2013
Commits on Jul 31, 2013
  1. @Frederic-bioinfo

    Version bump to 1.1.3

    Corrected some CRLF line endings.
    Frederic-bioinfo committed Jul 31, 2013
Commits on Jul 26, 2013
  1. @Frederic-bioinfo
  2. @Frederic-bioinfo

    Corrected bug #2 - Problem with multithreading.

    It was actually a faulty message that caused R to
    crash, and not multithreading per se.
    Frederic-bioinfo committed Jul 25, 2013
  3. @Frederic-bioinfo

    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.
    Frederic-bioinfo committed Jul 24, 2013
  4. @Frederic-bioinfo

    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.
    Frederic-bioinfo committed Jul 24, 2013
Commits on Jul 22, 2013
  1. @Frederic-bioinfo

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

    Conflicts:
    	src/Makevars.win
    Frederic-bioinfo committed Jul 22, 2013
Commits on Jul 19, 2013
  1. @Frederic-bioinfo
  2. @Frederic-bioinfo
  3. @Frederic-bioinfo
  4. @Frederic-bioinfo

    rTANDEM is now based on X!Tandem Jackhammer

    Manually did a three-way merge between X!Tandem-
    Cyclone, X!Tandem-Jackhammer and rTANDEM
    Frederic-bioinfo committed Jul 2, 2013
  5. @Frederic-bioinfo
  6. @Frederic-bioinfo

    Made the NAMESPACE more exhaustive

    Changes suggested by Martin Morgan following 'codetoolsBioC'.
    Frederic-bioinfo committed Dec 20, 2012
  7. @Frederic-bioinfo

    Version change

    Frederic-bioinfo committed Dec 14, 2012
  8. @Frederic-bioinfo

    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 committed Dec 14, 2012
  9. @Frederic-bioinfo

    Corrected the Rprintf commands for better display of output.

    Variables were not correctly interpolated in messages.
    Frederic-bioinfo committed Dec 14, 2012
  10. @Frederic-bioinfo
  11. @Frederic-bioinfo

    revision change

    Frederic-bioinfo committed Dec 13, 2012
  12. @Frederic-bioinfo
  13. @Frederic-bioinfo
  14. @Frederic-bioinfo

    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 committed Dec 11, 2012
  15. @Frederic-bioinfo

    Added version dependency on data.table.

    Changed procedure for linking against expat during windows build.
    Frederic-bioinfo committed Nov 27, 2012
  16. @Frederic-bioinfo
  17. @Frederic-bioinfo
  18. @Frederic-bioinfo
  19. @Frederic-bioinfo
  20. @Frederic-bioinfo

    Rene is added as an autor in all documentation

    Removed 'hello world' files.
    Frederic-bioinfo committed Nov 20, 2012
  21. @Frederic-bioinfo
  22. @Frederic-bioinfo

    Corrected the function GetDegeneracy

    The function did not work when there was indeed degeneracy
    (accessor problem with array).
    Frederic-bioinfo committed Nov 19, 2012
Commits on Jul 2, 2013
  1. @Frederic-bioinfo
  2. @Frederic-bioinfo
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