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NEWS
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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 2.29.1
-------------------------
o fix: read full spectra data in get3DMap
Closes #269.
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 2.29.4
-------------------------
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 Pwiz backend partially re-written to avoid segfault on macOS
(https://github.com/sneumann/xcms/issues/422).
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 <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>