CHANGES IN VERSION 2.7.13 ------------------------- o Fix waring on OSX (see issue #60) CHANGES IN VERSION 2.7.12 ------------------------- o Fixing last warning on MacOS CHANGES IN VERSION 2.7.11 ------------------------- o Fix failing example and test due to updated msdata::protemics data CHANGES IN VERSION 2.7.10 ------------------------- o compiling and loading on Windows (hopefully) CHANGES IN VERSION 2.7.9 ------------------------ o Updating Makevars.win CHANGES IN VERSION 2.7.8 ------------------------ o compile pwiz when installing on Windows <2016-09-26 Mon> CHANGES IN VERSION 2.7.7 ------------------------ o add netcdf static lib; potential incompatibility <2016-09-22 Thu> CHANGES IN VERSION 2.7.6 ------------------------ o new isolationWindow accessor <2016-09-23 Fri> CHANGES IN VERSION 2.7.5 ------------------------ o Apply Martin's free/delete patch - see https://github.com/sneumann/mzR/issues/52 <2016-09-22 Thu> CHANGES IN VERSION 2.7.4 ------------------------ o upgrade pwiz o ensure file connections are cleaned and closed for pwiz. CHANGES IN VERSION 2.7.1 ------------------------ o revert added compiler switch, and fixed boost code instead to get rid of warnings CHANGES IN VERSION 2.5.8 ------------------------ o fix compiler Warning with clang on MacOS CHANGES IN VERSION 2.5.7 ------------------------ o fix compilation with clang on MacOS CHANGES IN VERSION 2.5.6 ------------------------ o fix compilation on new windows toolchain, thanks to Kasper Daniel Hansen and Dan Tenenbaum CHANGES IN VERSION 2.5.3 ------------------------ o new pwiz.version() function returning the pwiz backend version (KK) CHANGES IN VERSION 2.5.2 ------------------------ o Provide pre-compiled windows libraries, again thanks to Qiang Kou (KK) CHANGES IN VERSION 2.5.1 ------------------------ o Import Boost 1.59, thanks to Qiang Kou (KK) CHANGES IN VERSION 2.3.3 ------------------------ o bump to new Rcpp 0.12.1 version <2015-09-29 Tue> CHANGES IN VERSION 2.3.2 ------------------------ o Fix typo/bug in peaks,mzRpwiz <2015-07-31 Fri> CHANGES IN VERSION 2.3.1 ------------------------ o update Rcpp version message to point to support site <2015-05-08 Fri> CHANGES IN VERSION 2.1.12 ------------------------- o Remove superfluous BiocGenerics in Suggests [2015-03-01 Sun] o Merged KK's Makefile to generate pwiz lib for windows [2015-03-01 Sun] CHANGES IN VERSION 2.1.11 ------------------------- o Using generics from BiocGenerics (fileName, score) and ProtGenerics [2015-02-28 Sat] CHANGES IN VERSION 2.1.10 ------------------------- o Add instrumentInfo() and runInfo() for CDF backend (closes issue #22) o Add precompiled libpwiz.a to reduce compile time on Windows (closes issue #21), thanks to KK CHANGES IN VERSION 2.1.9 ------------------------ o Fix a compiler warning on OSX in the pep_XML serialiser CHANGES IN VERSION 2.1.8 ------------------------ o Fix build on unix with netcdf.h in non-standard location CHANGES IN VERSION 2.1.7 ------------------------ o Fix score segfault (see issue #18) and remove usage of ListBuilder. o Update unit test to reflext new score code. CHANGES IN VERSION 2.1.6 ------------------------ o adding an acquisitionNum column to psms (closes issue #17) [2015-02-05 Thu] CHANGES IN VERSION 2.1.5 ------------------------ o don't print '1' to the console when calling get3Dmap [2015-01-29 Thu] o add sequence length in psms output (closes issue #19) [2015-02-04 Wed] CHANGES IN VERSION 2.1.4 ------------------------ o documentation and vignette: mzIdentML version 1.1 support only [2015-01-23 Fri] CHANGES IN VERSION 2.1.1 ------------------------ o remove dependency on faahKO CHANGES IN VERSION 1.99.4 ------------------------- o don't run pwiz example [2014-10-05 Sun] CHANGES IN VERSION 1.99.3 ------------------------- o revising unit testing and using suggested convention as described in Bioc unitTesting guidelines [2014-10-02 Thu] CHANGES IN VERSION 1.99.2 ------------------------- o bump to new Rcpp 0.11.3 version CHANGES IN VERSION 1.99.1 ------------------------- o annoucning pwiz in vignette and that it will become the default backend in Bioc 3.1 [2014-09-25 Thu] o adding a dummy close for pwiz backend to avoid breaking code that properly closes the previous ramp backend [2014-09-21 Sun] o Not using ListBuilder to make psms data.frame and fix segfautls, via KK [2014-09-27 Sat] CHANGES IN VERSION 1.99.0 ------------------------- o New pwiz backend and support for mzid, contributed by Qiang Kou as part of GSoC 2014. o Using BiocStyle for vignette [2014-08-26 Tue] CHANGES IN VERSION 1.11.11 ------------------------- o Remove superflouus library call in unitTests, should fix R CMD check on windows CHANGES IN VERSION 1.11.10 ------------------------- o Remove redundant columns when returning several spectra CHANGES IN VERSION 1.11.9 ------------------------- o Fix a bug in header() returning too few columns, introduced during 1.11.7 CHANGES IN VERSION 1.11.8 ------------------------- o Fix a windows compile problem by early importing Rcpp.h CHANGES IN VERSION 1.11.7 ------------------------- o include polarity information into header() output CHANGES IN VERSION 1.11.6 ------------------------- o removed one redundant parser which fixes inconsistencies in the scan headers CHANGES IN VERSION 1.11.5 ------------------------- o restored the polarity extraction CHANGES IN VERSION 1.11.4 ------------------------- o restored the old ramp Interface CHANGES IN VERSION 1.11.2 ------------------------- o adding missed src files [2014-05-28 Tue] o merging master [2014-05-30 Fri] CHANGES IN VERSION 1.11.1 ------------------------- o update pwiz/boost to support Maverick [2014-05-26 Mon] CHANGES IN VERSION 1.9.8 ------------------------ o Pointing to the relevant wiki page in the Rcpp compiler/linker warning [2014-04-03 Thu] CHANGES IN VERSION 1.9.7 ------------------------ o modify to new biocViews to DESCRIPTION file (s.arora) CHANGES IN VERSION 1.9.6 ------------------------ o import all of Rcpp to avoid warnings in reverse dependencies <2014-02-14 Fri> CHANGES IN VERSION 1.9.3 ------------------------ o fix a string in ramp.cpp to enable compilation on clang-3.4 CHANGES IN VERSION 1.9.2 ------------------------ o version bump for Rcpp 0.10.6 <2013-10-30 Wed> CHANGES IN VERSION 1.9.1 ------------------------ o moved vignettes to /vignettes <2013-10-17 Thu> CHANGES IN VERSION 1.7.4 ------------------------ o version bump for Rcpp 0.10.5 <2013-10-02 Wed> CHANGES IN VERSION 1.7.3 ------------------------ o Fix a compile error with the clang-3.3 compiler CHANGES IN VERSION 1.7.2 ------------------------ o updated Rcpp number mismatch warning to include versions <2013-08-01 Thu> CHANGES IN VERSION 1.7.1 ------------------------ o version bump for Rcpp 0.10.4 CHANGES IN VERSION 1.5.9 ------------------------ o version bump for Rcpp 0.10.3 CHANGES IN VERSION 1.5.8 ------------------------ o version bump for Rcpp 0.10.2 CHANGES IN VERSION 1.5.7 ------------------------ o only load Rcpp modules after checking for Rcpp version conflict (DT) CHANGES IN VERSION 1.5.6 ------------------------ o Explicitely call utils::packageVersion() to avoid warning (SN) <2012-12-15 Sat> CHANGES IN VERSION 1.5.5 ------------------------a o Added utils to Depends (SN) <2012-12-14 Fri> CHANGES IN VERSION 1.5.4 ------------------------ o requiring Rcpp (>= 0.10.1) LG <2012-12-05 Wed> o catching Rcpp build-time version (thanks to Dan for help!) LG <2012-12-05 Wed> o checking Rcpp installed vs building versions and warn if these are different. LG <2012-12-05 Wed> CHANGES IN VERSION 1.5.3 ------------------------ o bumping version to force rebuild due to Rcpp change LG <2012-12-05 Wed> o added NEWS file <2012-12-05 Wed>