Changes in version 2.45.1 o Load test files from the MsDataHub package and remove dependency on the msdata package. o Catch error in spectrum ID parsing. o Remove support for C++11 and C++14 from R-devel (see issue #315) Changes in version 2.43.3 o Make electronBeamEnergy an optional header field. Changes in version 2.43.2 o More fixes around NaN Changes in version 2.43.1 o Update CV, adds multiple terms Changes in version 2.41.4 o Use "rtime" and "intensity" as column names for the data.frame returned by `chromatogram()`. Fixes #304. Changes in version 2.41.3 o Fixed off-by-one indexing issue with index access for chromatogramHeader vs chromatogram. Fixes #302. Thanks Nils Hoffmann ! Changes in version 2.41.2 o Report also electron beam energy (MS:1003410) for EAD data. Changes in version 2.41.1 o Fix compilation error with stricter compiler checks Changes in version 2.39.2 o Improve openMSfile and openIDfile manual page (contirbuted by rdhale92, PR #299) Changes in version 2.39.1 o Update CV translator, adds support for Astral Changes in version 2.37.3 o Fix compilation on Windows/aarch64 (#290), thanks to Tomas Kalibera for the patch Changes in version 2.37.2 o remove mentions of mzData in the DESCRIPTION, vignette and manual files (support dropped in 2.29.3) Changes in version 2.37.1 o fix compilation on centOS 7 / R-4.3.1 reported in #286 Changes in version 2.35.1 o fix compilation on Fedora 38 / R-4.3.0. Thanks to Christian Iseli! Closes #282 Changes in version 2.33.1 o fix: update to a new PSI-MS OBO for e.g. ZenoTOF CV term Closes #278 Changes in version 2.29.4 o Re-apply fix for compile error on clang by Kurt Hornik, closes #263 o Remove text in DESCRIPTION hinting at the RAMP wrapper for mzData removed in 2.29.3 Changes in version 2.29.3 o Update to Proteowizard 3_0_21263 o Removed RAMP backend, dropping ability to read mzData o header always returns a data.frame even for a single scan. Changes in version 2.29.2 o Cleanup in build files Changes in version 2.29.1 o fix: read full spectra data in get3DMap Closes #269. o Pwiz backend partially re-written to avoid segfault on macOS (https://github.com/sneumann/xcms/issues/422). Changes in version 2.27.6 o Only export certain spectra header parameters if their values are not NA. Closes #266. Changes in version 2.27.5 o `peaks` method for pwiz backend sets colnames on returned matrices. Changes in version 2.27.2 o Remove support for the ramp backend. 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 (see #113). Changes in version 2.11.7 o Nothing yet. o Import fix by Brian Pratt (pwiz r11174) for mzML without 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 o ------------------------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>