CHANGES IN VERSION 2.27.1 ------------------------- o Add missing atomic_count_sync.hpp BH file (see PR #248 by vjcitn) CHANGES IN VERSION 2.27.0 ------------------------- o New Bioc devel version CHANGES IN VERSION 2.25.5 ------------------------- o Fix compile error on clang-11 reported (and fixed!) by Kurt Hornik, closes #244 CHANGES IN VERSION 2.25.4 ------------------------- o Add dependency "rmarkdown" to "suggests:" CHANGES IN VERSION 2.25.3 ------------------------- o Ensure `header` for CDF returns columns with correct data type. CHANGES IN VERSION 2.25.2 ------------------------- o Fix issue #238: ensure `header` call returns the same columns for all backends. CHANGES IN VERSION 2.25.1 ------------------------- o Bump version to trigger new build using latest Rcpp CHANGES IN VERSION 2.25.0 ------------------------- o New Bioc devel version CHANGES IN VERSION 2.21.2 ------------------------- o Update email address CHANGES IN VERSION 2.21.1 ------------------------- o inject a new PSI-MS.obo controlled vocabulary data-version: 4.1.30 date: 30:08:2019 16:10 saved-by: Gerhard Mayer CHANGES IN VERSION 2.19.7 ------------------------- o Fix compile error on Windows + Mac (Thanks Mike!) CHANGES IN VERSION 2.19.6 ------------------------- o header for the pwiz backend returns NA instead of 0 for not defined or missing information <2019-09-24 Tue>. o peaks for pwiz backend rewritten (small performance improvement) <2019-09-26 Thu>. CHANGES IN VERSION 2.19.5 ------------------------- o version bump to force build with latest Rcpp CHANGES IN VERSION 2.19.4 ------------------------- o Add header columns scanWindowLowerLimit and scanWindowUpperLimit CHANGES IN VERSION 2.19.3 ------------------------- o use ProtGenerics::tolerance generic <2019-08-16 Fri> CHANGES IN VERSION 2.19.2 ------------------------- o Fix issue 190, compiles on clang-8.0 CHANGES IN VERSION 2.19.1 ------------------------- o Remove analyzer generics, now in ProtGenerics <2019-05-13 Mon> CHANGES IN VERSION 2.17.4 ------------------------- o Update documentation, pointing to MSnbase rather than directly use low-level classes. <2019-04-17 Wed> CHANGES IN VERSION 2.17.3 ------------------------- o Extract isolation window from mzML files (issue #193): data.frame returned by header gains columns "isolationWindowTargetMZ", "isolationWindowLowerOffset", "isolationWindowUpperOffset". CHANGES IN VERSION 2.17.2 ------------------------- o Fix bug #185: Error in R_nc4_open: Too many open files CHANGES IN VERSION 2.15.5 ------------------------- o Fix bug #181 CHANGES IN VERSION 2.15.4 ------------------------- o Use new dependency ncdf4 for netCDF reading, removes a lot of build hassles with old libnetcdf-dev linking. o specParams returns a numeric scan.number.s. CHANGES IN VERSION 2.15.3 ------------------------- o Adds MS-GF+ information such as Scan Time and a more reliable Scan Number, contributed by FarmGeek4Life (see PR #174). CHANGES IN VERSION 2.15.2 ------------------------- o Add header column ionMobilityDriftTime to report the corresponding CV parameter (issue https://github.com/sneumann/mzR/issues/44). o Ensure ion injection time is always reported in milliseconds. o Replace BiocInstaller::biocLite with BiocManager::install (by Bioc core) CHANGES IN VERSION 2.15.1 ------------------------- o Fix typo (see https://github.com/sneumann/mzR/pull/162) o New .hasSpectra and .hasChromatograms private function (see https://github.com/lgatto/MSnbase/issues/343) o Fix bug in score when more cvParams than expected are read - see https://github.com/sneumann/mzR/issues/136 <2018-05-26 Sat> CHANGES IN VERSION 2.15.0 ------------------------- o New Bioc devel version CHANGES IN VERSION 2.13.8 ------------------------- o Document missing chrom argument for chromatogram(s) CHANGES IN VERSION 2.13.7 ------------------------- o Add a missing header needed on gcc 6.2.0 CHANGES IN VERSION 2.13.6 ------------------------- o Add MS CV Term IDs for mzR, MSnbase and CAMERA (issue #151) o Validate exported mzML files using xsd CHANGES IN VERSION 2.13.5 ------------------------- o Fix https://github.com/sneumann/xcms/issues/261 o Fix endian.hpp for new c++ versions (see PR #149) CHANGES IN VERSION 2.13.4 ------------------------- o Fix error (see issue #145) CHANGES IN VERSION 2.13.3 ------------------------- o Link against Rhdf5lib, allows to read mz5 also on Windows o Use Rhdf5lib 1.1.4 with c++ headers in /include o fix BiocStyle related issue in Vignette on Windows CHANGES IN VERSION 2.13.2 -------------------------- o Add chromatogramHeader method to read header information for chromatograms from an mzML file. CHANGES IN VERSION 2.13.1 -------------------------- o Read filter string from mzML files and add it to the data.frame returned by the header function (see MSnbase issue #278). o openMsFile automatically determine the backend to use based on file extension and content. CHANGES IN VERSION 2.11.11 -------------------------- o Fix problem in writeMSData: ensure precursor data is saved even if precursor scan is not available (see MSnbase issue #245). CHANGES IN VERSION 2.11.10 -------------------------- o Fix problem that can cause a SEGFAULT in writeMSData/copyWriteMSData when MS data with spectra linking to missing precursor scans is saved (issue #129). CHANGES IN VERSION 2.11.9 ------------------------- o Update peaks man page with details about spectrumId, acquisitionNum and seqNum CHANGES IN VERSION 2.11.8 ------------------------- o Add contributions guide with code of conduct. o Update installation instructions for Mac. o Report the spectrum ID in the header data.frame (column spectrumId). o Fix in copyWriteMSData and writeMSData ensuring that MSn data is correctly o Import pwiz r11174 fix for mzML without <componentList> (see #113). CHANGES IN VERSION 2.11.7 ------------------------- o Nothing yet. o Import fix by Brian Pratt (pwiz r11174) for mzML without <componentList> Another way to fix #113 o Removing mz5 support from manual page, as currently unsupported. CHANGES IN VERSION 2.11.6 ------------------------- o runInfo returns the run start time stamp from files providing this information (mzML files). CHANGES IN VERSION 2.11.5 ------------------------- o writeMSData and copyWriteMSData functions enabling to export MS data to mzML or mzXML files. CHANGES IN VERSION 2.11.4 ------------------------- o Use full TMT file pattern to select a single file CHANGES IN VERSION 2.11.3 ------------------------- o Read ion injection time from mzML files and add it to the data.frame returned by the header function. CHANGES IN VERSION 2.11.2 ------------------------- o New getScanHeaderInfo and getAllScanHeaderInfo implementations for the pwiz backend. Fixes issue #106 and issue #216 in MSnbase. CHANGES IN VERSION 2.11.1 ------------------------- o Change default I/O backend from Ramp to pwiz. CHANGES IN VERSION 2.11.0 ------------------------- o Bioc devel 3.6 CHANGES IN VERSION 2.10.0 ------------------------- o Bioc release 3.5 CHANGES IN VERSION 2.9.11 ------------------------- o Restore -fpermissive flag on windows CHANGES IN VERSION 2.9.10 ------------------------- o Remove register keyword causing WARNING. CHANGES IN VERSION 2.9.9 ------------------------ o Remove C++ references to cout/cerr/abort in pwiz code (see issue #89) CHANGES IN VERSION 2.9.8 ------------------------ o Fix reading spectrum polarity from mzML using pwiz backend, closes #81 CHANGES IN VERSION 2.9.7 ------------------------ o Fix compilation on macOS CHANGES IN VERSION 2.9.6 ------------------------ o Compile on macOS, but hdf5 path hard-coded CHANGES IN VERSION 2.9.5 ------------------------ o Add missing boost/config/platform/macos.hpp <2017-01-25 Wed> CHANGES IN VERSION 2.9.4 ------------------------ o New chromatogram accessors (for pwiz backend only) - see issue #73 <2017-01-23 Mon> CHANGES IN VERSION 2.9.3 ------------------------ o bump to new Rcpp 0.12.8 version <2017-01-05 Thu> CHANGES IN VERSION 2.9.2 ------------------------ o cleanup CFLAGS and LIBS for libnetcdf o add file missing for oaxaca (Apple clang 3.5svn / 600.0.57) CHANGES IN VERSION 2.9.1 ------------------------ o Delete RAMPAdapter pointer in pwiz backend (by jotsetung) <2016-11-20 Sun> o Use spectra in addition to peaks (see issue #15) <2016-12-09 Fri> o New pwiz (commit 946d23d75dc70a7a4913d8e05e3d59b9255f278e) CHANGES IN VERSION 2.9.0 ------------------------ o Bioc devel 3.5 CHANGES IN VERSION 2.8.0 ------------------------ o Bioc release 3.4 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>