2014-07-12 Qiang Kou mzid file reading 2014-05-19 Qiang Kou Backend pwiz implemented 2012-08-20 Steffen Neumann * 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 * libstdcpp3.hpp: applied patch by Alvaro Cuadros Inostroza for gcc-4.7 compatibility in boost 2012-04-04 Steffen Neumann * 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 * src/ramp.h: enable new I/O on windows 2012-03-31 Steffen Neumann * src/ramp.h: disable new I/O on windows, should compile, but will fail unit test with *.gz file 2012-03-26 Steffen Neumann * Added unit tests for *.mzdata.gz 2012-03-26 Steffen Neumann * RAMPAdapter.cpp: fix reading the first spectrum if it has an index==0 2012-03-13 Steffen Neumann * R/ramp.R, src/rampR.cpp: back-ported the old XCMS rampR interface, which is much faster than cramp 2012-02-28 Steffen Neumann * src/RcppRamp.cpp: Change the (temporary) Vectors from STL to Rcpp::*Vector for reduced memory footprint 2011-12-14 Steffen Neumann * Updated to pwiz r3148 2011-11-24 Steffen Neumann * Fixed linking of NetCDF with previous help from Dan Tenenbaum and Martin Morgan. 2011-09-16 Laurent Gatto * Changed é to \'e in mzR.bib. 2011-09-07 Laurent Gatto * 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 * 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 * Minor fixes in documentation * Bump version for resubmission to BioC 2011-08-01 Steffen Neumann * 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 * Non-functional support for CDF 2011-07-11 Laurent Gatto * simplified show method * rewrote runInfo in R * Misc changes in doc and vignette * bumped version to 0.5.5 2011-07-08 Steffen Neumann * fixed Windows, checked for x64 * bumped version to 0.5.4 2011-07-05 Laurent Gatto * 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 * updated header("mzRamp","numeric") when length(numeric) > 1 to return 'flat' data.frame * bumped verison to 0.5.1 2011-06-10 Laurent Gatto * bumped version to 0.5.0 * implementing backend design and related changes 2011-06-09 Laurent Gatto * 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 * 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 * fix call to fileName() in instrumentInfo() * added Makefile for a simple "make" in unitTests * added man pages 2011-05-31 Laurent Gatto * 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 * bumped verssion to 0.4.3 * added further refinements and dummy documenation * builds, checks and installs fine 2011-05-25 Laurent Gatto * 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 * added cleanup script to version 0.4 2010-12-16 Steffen Neumann * 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