NEWS

---

mzR 2.41.1

• Fix compilation error with stricter compiler checks

mzR 2.39.2

• Improve openMSfile and openIDfile manual page (contirbuted by rdhale92, PR #299)

mzR 2.39.1

• Update CV translator, adds support for Astral

mzR 2.37.3

• Fix compilation on Windows/aarch64 (#290), thanks to Tomas Kalibera for the patch

mzR 2.37.2

• remove mentions of mzData in the DESCRIPTION, vignette and manual files (support dropped in 2.29.3)

mzR 2.37.1

• fix compilation on centOS 7 / R-4.3.1 reported in #286

mzR 2.35.1

• fix compilation on Fedora 38 / R-4.3.0. Thanks to Christian Iseli! Closes #282

mzR 2.33.1

• fix: update to a new PSI-MS OBO for e.g. ZenoTOF CV term Closes #278

mzR 2.29.4

• Re-apply fix for compile error on clang by Kurt Hornik, closes #263
• Remove text in DESCRIPTION hinting at the RAMP wrapper for mzData removed in 2.29.3

mzR 2.29.3

• Update to Proteowizard 3_0_21263
• Removed RAMP backend, dropping ability to read mzData
• header always returns a data.frame even for a single scan.

mzR 2.29.2

• Cleanup in build files

mzR 2.29.1

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

mzR 2.27.6

• Only export certain spectra header parameters if their values are not NA. Closes #266.

mzR 2.27.5

• 'peaks' method for pwiz backend sets colnames on returned matrices.

mzR 2.27.2

• Remove support for the ramp backend.

mzR 2.27.1

• Add missing atomic_count_sync.hpp BH file (see PR #248 by vjcitn)

mzR 2.27.0

• New Bioc devel version

mzR 2.25.5

• Fix compile error on clang-11 reported (and fixed!) by Kurt Hornik, closes #244

mzR 2.25.4

• Add dependency "rmarkdown" to "suggests:"

mzR 2.25.3

• Ensure 'header' for CDF returns columns with correct data type.

mzR 2.25.2

• Fix issue #238: ensure 'header' call returns the same columns for all backends.

mzR 2.25.1

• Bump version to trigger new build using latest Rcpp

mzR 2.25.0

• New Bioc devel version

mzR 2.21.2

• Update email address

mzR 2.21.1

• inject a new PSI-MS.obo controlled vocabulary data-version: 4.1.30 date: 30:08:2019 16:10 saved-by: Gerhard Mayer

mzR 2.19.7

• Fix compile error on Windows + Mac (Thanks Mike!)

mzR 2.19.6

• header for the pwiz backend returns NA instead of 0 for not defined or missing information <2019-09-24 Tue>.
• peaks for pwiz backend rewritten (small performance improvement) <2019-09-26 Thu>.

mzR 2.19.5

• version bump to force build with latest Rcpp

mzR 2.19.4

• Add header columns scanWindowLowerLimit and scanWindowUpperLimit

mzR 2.19.3

• use ProtGenerics::tolerance generic <2019-08-16 Fri>

mzR 2.19.2

• Fix issue 190, compiles on clang-8.0

mzR 2.19.1

• Remove analyzer generics, now in ProtGenerics <2019-05-13 Mon>

mzR 2.17.4

• Update documentation, pointing to MSnbase rather than directly use low-level classes. <2019-04-17 Wed>

mzR 2.17.3

• Extract isolation window from mzML files (issue #193): data.frame returned by header gains columns "isolationWindowTargetMZ", "isolationWindowLowerOffset", "isolationWindowUpperOffset".

mzR 2.17.2

• Fix bug #185: Error in R_nc4_open: Too many open files

mzR 2.15.5

• Fix bug #181

mzR 2.15.4

• Use new dependency ncdf4 for netCDF reading, removes a lot of build hassles with old libnetcdf-dev linking.
• specParams returns a numeric scan.number.s.

mzR 2.15.3

• Adds MS-GF+ information such as Scan Time and a more reliable Scan Number, contributed by FarmGeek4Life (see PR #174).

mzR 2.15.2

• Add header column ionMobilityDriftTime to report the corresponding CV parameter (issue https://github.com/sneumann/mzR/issues/44).
• Ensure ion injection time is always reported in milliseconds.
• Replace BiocInstaller::biocLite with BiocManager::install (by Bioc core)

mzR 2.15.1

• Fix typo (see https://github.com/sneumann/mzR/pull/162)
• New .hasSpectra and .hasChromatograms private function (see https://github.com/lgatto/MSnbase/issues/343)
• Fix bug in score when more cvParams than expected are read - see https://github.com/sneumann/mzR/issues/136 <2018-05-26 Sat>

mzR 2.15.0

• New Bioc devel version

mzR 2.13.8

• Document missing chrom argument for chromatogram(s)

mzR 2.13.7

• Add a missing header needed on gcc 6.2.0

mzR 2.13.6

• Add MS CV Term IDs for mzR, MSnbase and CAMERA (issue #151)
• Validate exported mzML files using xsd

mzR 2.13.5

• Fix https://github.com/sneumann/xcms/issues/261
• Fix endian.hpp for new c++ versions (see PR #149)

mzR 2.13.4

• Fix error (see issue #145)

mzR 2.13.3

• Link against Rhdf5lib, allows to read mz5 also on Windows
• Use Rhdf5lib 1.1.4 with c++ headers in /include
• fix BiocStyle related issue in Vignette on Windows

mzR 2.13.2

• Add chromatogramHeader method to read header information for chromatograms from an mzML file.

mzR 2.13.1

• Read filter string from mzML files and add it to the data.frame returned by the header function (see MSnbase issue #278).
• openMsFile automatically determine the backend to use based on file extension and content.

mzR 2.11.11

• Fix problem in writeMSData: ensure precursor data is saved even if precursor scan is not available (see MSnbase issue #245).

mzR 2.11.10

• Fix problem that can cause a SEGFAULT in writeMSData/copyWriteMSData when MS data with spectra linking to missing precursor scans is saved (issue #129).

mzR 2.11.9

• Update peaks man page with details about spectrumId, acquisitionNum and seqNum

mzR 2.11.8

• Add contributions guide with code of conduct.
• Update installation instructions for Mac.
• Report the spectrum ID in the header data.frame (column spectrumId).
• Fix in copyWriteMSData and writeMSData ensuring that MSn data is correctly
• Import pwiz r11174 fix for mzML without componentList (see #113).

mzR 2.11.7

• Nothing yet.
• Import fix by Brian Pratt (pwiz r11174) for mzML without componentList Another way to fix #113
• Removing mz5 support from manual page, as currently unsupported.

mzR 2.11.6

• runInfo returns the run start time stamp from files providing this information (mzML files).

mzR 2.11.5

• writeMSData and copyWriteMSData functions enabling to export MS data to mzML or mzXML files.

mzR 2.11.4

• Use full TMT file pattern to select a single file

mzR 2.11.3

• Read ion injection time from mzML files and add it to the data.frame returned by the header function.

mzR 2.11.2

• New getScanHeaderInfo and getAllScanHeaderInfo implementations for the pwiz backend. Fixes issue #106 and issue #216 in MSnbase.

mzR 2.11.1

• Change default I/O backend from Ramp to pwiz.

mzR 2.11.0

• Bioc devel 3.6

mzR 2.10.0

• Bioc release 3.5

mzR 2.9.11

• Restore -fpermissive flag on windows

mzR 2.9.10

• Remove register keyword causing WARNING.

mzR 2.9.9

• Remove C++ references to cout/cerr/abort in pwiz code (see issue #89)

mzR 2.9.8

• Fix reading spectrum polarity from mzML using pwiz backend, closes #81

mzR 2.9.7

• Fix compilation on macOS

mzR 2.9.6

• Compile on macOS, but hdf5 path hard-coded

mzR 2.9.5

• Add missing boost/config/platform/macos.hpp <2017-01-25 Wed>

mzR 2.9.4

• New chromatogram accessors (for pwiz backend only) - see issue #73 <2017-01-23 Mon>

mzR 2.9.3

• bump to new Rcpp 0.12.8 version <2017-01-05 Thu>

mzR 2.9.2

• cleanup CFLAGS and LIBS for libnetcdf
• add file missing for oaxaca (Apple clang 3.5svn / 600.0.57)

mzR 2.9.1

• Delete RAMPAdapter pointer in pwiz backend (by jotsetung) <2016-11-20 Sun>
• Use spectra in addition to peaks (see issue #15) <2016-12-09 Fri>
• New pwiz (commit 946d23d75dc70a7a4913d8e05e3d59b9255f278e)

mzR 2.9.0

• Bioc devel 3.5

mzR 2.8.0

• Bioc release 3.4

mzR 2.7.13

• Fix waring on OSX (see issue #60)

mzR 2.7.12

• Fixing last warning on MacOS

mzR 2.7.11

• Fix failing example and test due to updated msdata::protemics data

mzR 2.7.10

• compiling and loading on Windows (hopefully)

mzR 2.7.9

• Updating Makevars.win

mzR 2.7.8

• compile pwiz when installing on Windows <2016-09-26 Mon>

mzR 2.7.7

• add netcdf static lib; potential incompatibility <2016-09-22 Thu>

mzR 2.7.6

• new isolationWindow accessor <2016-09-23 Fri>

mzR 2.7.5

• Apply Martin's free/delete patch - see https://github.com/sneumann/mzR/issues/52 <2016-09-22 Thu>

mzR 2.7.4

• upgrade pwiz
• ensure file connections are cleaned and closed for pwiz.

mzR 2.7.1

• revert added compiler switch, and fixed boost code instead to get rid of warnings

mzR 2.5.8

• fix compiler Warning with clang on MacOS

mzR 2.5.7

• fix compilation with clang on MacOS

mzR 2.5.6

• fix compilation on new windows toolchain, thanks to Kasper Daniel Hansen and Dan Tenenbaum

mzR 2.5.3

• new pwiz.version() function returning the pwiz backend version (KK)

mzR 2.5.2

• Provide pre-compiled windows libraries, again thanks to Qiang Kou (KK)

mzR 2.5.1

• Import Boost 1.59, thanks to Qiang Kou (KK)

mzR 2.3.3

• bump to new Rcpp 0.12.1 version <2015-09-29 Tue>

mzR 2.3.2

• Fix typo/bug in peaks,mzRpwiz <2015-07-31 Fri>

mzR 2.3.1

• update Rcpp version message to point to support site <2015-05-08 Fri>

mzR 2.1.12

• Remove superfluous BiocGenerics in Suggests [2015-03-01 Sun]
• Merged KK's Makefile to generate pwiz lib for windows [2015-03-01 Sun]

mzR 2.1.11

• Using generics from BiocGenerics (fileName, score) and ProtGenerics [2015-02-28 Sat]

mzR 2.1.10

• Add instrumentInfo() and runInfo() for CDF backend (closes issue #22)
• Add precompiled libpwiz.a to reduce compile time on Windows (closes issue #21), thanks to KK

mzR 2.1.9

• Fix a compiler warning on OSX in the pep_XML serialiser

mzR 2.1.8

• Fix build on unix with netcdf.h in non-standard location

mzR 2.1.7

• Fix score segfault (see issue #18) and remove usage of ListBuilder.
• Update unit test to reflext new score code.

mzR 2.1.6

• adding an acquisitionNum column to psms (closes issue #17) [2015-02-05 Thu]

mzR 2.1.5

• don't print '1' to the console when calling get3Dmap [2015-01-29 Thu]
• add sequence length in psms output (closes issue #19) [2015-02-04 Wed]

mzR 2.1.4

• documentation and vignette: mzIdentML version 1.1 support only [2015-01-23 Fri]

mzR 2.1.1

• remove dependency on faahKO

mzR 1.99.4

• don't run pwiz example [2014-10-05 Sun]

mzR 1.99.3

• revising unit testing and using suggested convention as described in Bioc unitTesting guidelines [2014-10-02 Thu]

mzR 1.99.2

• bump to new Rcpp 0.11.3 version

mzR 1.99.1

• annoucning pwiz in vignette and that it will become the default backend in Bioc 3.1 [2014-09-25 Thu]
• adding a dummy close for pwiz backend to avoid breaking code that properly closes the previous ramp backend [2014-09-21 Sun]
• Not using ListBuilder to make psms data.frame and fix segfautls, via KK [2014-09-27 Sat]

mzR 1.99.0

• New pwiz backend and support for mzid, contributed by Qiang Kou as part of GSoC 2014.
• Using BiocStyle for vignette [2014-08-26 Tue]

mzR 1.11.11

• Remove superflouus library call in unitTests, should fix R CMD check on windows

mzR 1.11.10

• Remove redundant columns when returning several spectra

mzR 1.11.9

• Fix a bug in header() returning too few columns, introduced during 1.11.7

mzR 1.11.8

• Fix a windows compile problem by early importing Rcpp.h

mzR 1.11.7

• include polarity information into header() output

mzR 1.11.6

• removed one redundant parser which fixes inconsistencies in the scan headers

mzR 1.11.5

• restored the polarity extraction

mzR 1.11.4

• restored the old ramp Interface

mzR 1.11.2

• adding missed src files [2014-05-28 Tue]
• merging master [2014-05-30 Fri]

mzR 1.11.1

• update pwiz/boost to support Maverick [2014-05-26 Mon]

mzR 1.9.8

• Pointing to the relevant wiki page in the Rcpp compiler/linker warning [2014-04-03 Thu]

mzR 1.9.7

• modify to new biocViews to DESCRIPTION file (s.arora)

mzR 1.9.6

• import all of Rcpp to avoid warnings in reverse dependencies <2014-02-14 Fri>

mzR 1.9.3

• fix a string in ramp.cpp to enable compilation on clang-3.4

mzR 1.9.2

• version bump for Rcpp 0.10.6 <2013-10-30 Wed>

mzR 1.9.1

• moved vignettes to /vignettes <2013-10-17 Thu>

mzR 1.7.4

• version bump for Rcpp 0.10.5 <2013-10-02 Wed>

mzR 1.7.3

• Fix a compile error with the clang-3.3 compiler

mzR 1.7.2

• updated Rcpp number mismatch warning to include versions <2013-08-01 Thu>

mzR 1.7.1

• version bump for Rcpp 0.10.4

mzR 1.5.9

• version bump for Rcpp 0.10.3

mzR 1.5.8

• version bump for Rcpp 0.10.2

mzR 1.5.7

• only load Rcpp modules after checking for Rcpp version conflict (DT)

mzR 1.5.6

• Explicitely call utils::packageVersion() to avoid warning (SN) <2012-12-15 Sat>

mzR 1.5.5

• ————————a o Added utils to Depends (SN) <2012-12-14 Fri>

mzR 1.5.4

• requiring Rcpp (>= 0.10.1) LG <2012-12-05 Wed>
• catching Rcpp build-time version (thanks to Dan for help!) LG <2012-12-05 Wed>
• checking Rcpp installed vs building versions and warn if these are different. LG <2012-12-05 Wed>

mzR 1.5.3

• bumping version to force rebuild due to Rcpp change LG <2012-12-05 Wed>
• added NEWS file <2012-12-05 Wed>