1. mzR
  2. ChangeLog
Raw Blame Patch Log History 
2014-07-12 Qiang Kou  <qkou@umail.iu.edu>

	mzid file reading

2014-05-19 Qiang Kou  <qkou@umail.iu.edu>

	Backend pwiz implemented

2012-08-20  Steffen Neumann  <sneumann@ipb-halle.de>

	* src/boost/thread/xtime.hpp: applied another patch by Alvaro Cuadros Inostroza
	for gcc-4.7.1 compatibility in boost, see e.g. https://bbs.archlinux.org/viewtopic.php?pid=1126282
	and https://svn.boost.org/trac/boost/ticket/6940

2012-05-15  Steffen Neumann  <sneumann@ipb-halle.de>

	* libstdcpp3.hpp: applied patch by Alvaro Cuadros Inostroza
	for gcc-4.7 compatibility in boost

2012-04-04  Steffen Neumann  <sneumann@ipb-halle.de>

	* src/pwiz/data/msdata/RAMPAdapter.cpp (pwiz): Revert hack from 2012-03-26  
	* src/pwiz/data/msdata/MSData.hpp (pwiz): Add Patch suggested by Brian Pratt, 
	for a better fix of problem if first spectrum if it has an index==0
	
2012-04-04  Steffen Neumann  <sneumann@ipb-halle.de>

	* src/ramp.h: enable new I/O on windows

	2012-03-31  Steffen Neumann  <sneumann@ipb-halle.de>

	* src/ramp.h: disable new I/O on windows, should compile, 
	but will fail unit test with *.gz file

2012-03-26  Steffen Neumann  <sneumann@ipb-halle.de>

	* Added unit tests for *.mzdata.gz

2012-03-26  Steffen Neumann  <sneumann@ipb-halle.de>

	* RAMPAdapter.cpp: fix reading the first spectrum 
	if it has an index==0

2012-03-13  Steffen Neumann  <sneumann@ipb-halle.de>

	* R/ramp.R, src/rampR.cpp: back-ported the old XCMS rampR
	interface, which is much faster than cramp

2012-02-28  Steffen Neumann  <sneumann@ipb-halle.de>	

	* src/RcppRamp.cpp: Change the (temporary) Vectors from STL
	to Rcpp::*Vector for reduced memory footprint
	
2011-12-14  Steffen Neumann  <sneumann@ipb-halle.de>

	* Updated to pwiz r3148

2011-11-24  Steffen Neumann  <sneumann@ipb-halle.de>
	* Fixed linking of NetCDF with previous help from 
	  Dan Tenenbaum and Martin Morgan.
	
2011-09-16 Laurent Gatto <lg390@cam.ac.uk>
	* Changed é to \'e in mzR.bib.

2011-09-07 Laurent Gatto <lg390@cam.ac.uk>
	* temporary fixed the 'could not find function "getClass"' warning 
	  adding require("methods", ... ) to .onLoad 
	  (see http://comments.gmane.org/gmane.comp.lang.r.rcpp/2140)
	  but this produces a note about 'Package startup functions should 
	  not change the search path.' But adding methods to the depends 
  	  fiels, as advertised in .onAttach, does not fix the original 
	  warning.
	* Bump version number to 0.99.2 to track changes.

2011-08-10  Steffen Neumann  <sneumann@ipb-halle.de>
	* Temporary Fix for "unable to find ... for function "peaks"
	  by explicitely specifying mzR:: namespace
	* Bump version for resubmission to BioC
	
2011-08-09  Steffen Neumann  <sneumann@ipb-halle.de>
	* Minor fixes in documentation
	* Bump version for resubmission to BioC

2011-08-01  Steffen Neumann  <sneumann@ipb-halle.de>
	* Added header(), peaks(), length()
	and show() for netCDF. This passes all unit tests 
	for a modified version of xcms, closing Issue #15

2011-07-22  Steffen Neumann  <sneumann@ipb-halle.de>
	* Non-functional support for CDF

2011-07-11 Laurent Gatto <lg390@cam.ac.uk>
	* simplified show method
	* rewrote runInfo in R
	* Misc changes in doc and vignette
	* bumped version to 0.5.5
	
2011-07-08 Steffen Neumann <sneumann@ipb-halle.de>
	* fixed Windows, checked for x64
	* bumped version to 0.5.4
	
2011-07-05 Laurent Gatto <lg390@cam.ac.uk>
	* small doc and vignette updates
	* peaks("mzRramp","missing") always returns a list 
	(possibly of length 1) of matrices.
	* bumped version to 0.5.2
	
2011-06-16  Laurent Gatto  <lg390@cam.ac.uk>
	* updated header("mzRamp","numeric") when 
	length(numeric) > 1 to return 'flat' data.frame
	* bumped verison to 0.5.1
	
2011-06-10  Laurent Gatto  <lg390@cam.ac.uk>
	* bumped version to 0.5.0
	* implementing backend design and related changes
	
2011-06-09  Laurent Gatto  <lg390@cam.ac.uk>
	* bumped version to 0.4.4
	* created format specific classes and methods
	* added (optional) format argument to openMSfile
	* updated documentation
	
2011-06-01  Laurent Gatto <lg390@cam.ac.uk>
	* added fileName slot to mzR class (now version 0.1.3)
	* updated openMSfile, fileName and mzR validity to 
	reflect new mzR@fileName slot.
	* update get3Dmap and initializeRamp generics - added 
	explicit non-dispatching elements.
	* added mzR.bib bibtex and Makefile files
	* updated docs and vignette

2011-06-01  Steffen Neumann <sneumann@ipb-halle.de>
	* fix call to fileName() in instrumentInfo()
	* added Makefile for a simple "make" in unitTests
	* added man pages
	
2011-05-31  Laurent Gatto <lg390@cam.ac.uk>
	* file extension is checked to avoid retrieving 
	instrument info for mzdata files (see 
	https://github.com/sneumann/mzR/issues/5)
	* update Rcpp version dependency
	* updated unit test
	
2011-05-27  Laurent Gatto  <lg390@cam.ac.uk>
	* bumped verssion to 0.4.3
	* added further refinements and dummy documenation
	* builds, checks and installs fine 

2011-05-25  Laurent Gatto  <lg390@cam.ac.uk>
	* bumped verion to 0.4.1
	* cleaned up code and file names, to fit with 
	Bioconductor's naming schemes.
	* created S4 classes and methods 
	
2011-05-01  Laurent Gatto  <lg390@cam.ac.uk>
	* added cleanup script to version 0.4

2010-12-16  Steffen Neumann  <sneumann@ipb-halle.de>

	* push 0.3 which adds mzML support, and has (a few) 
	unit tests. R CMD check finishes mostly clean, with 
	some problems with Rcpp/methods