1. mzR
  2. DESCRIPTION
Browse code

Bump version and NEWS. Thanks to Christian Iseli for the PR! Closes #282

Steffen Neumann authored on 28/04/2023 09:13:03
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DESCRIPTION
History View file @ a9788d43f5
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.35.0
5 
+Version: 2.35.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:20:39
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DESCRIPTION
History View file @ e1deaeb8cf
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.34.0
5 
+Version: 2.35.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:20:39
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DESCRIPTION
History View file @ 14ccc37ab3
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.33.1
5 
+Version: 2.34.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

Updating the CV

Steffen Neumann authored on 05/04/2023 12:44:04
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DESCRIPTION
History View file @ 78fc419e8b
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.33.0
5 
+Version: 2.33.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:06:10
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DESCRIPTION
History View file @ f2439b3d94
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.32.0
5 
+Version: 2.33.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:06:10
Showing 1 changed files
DESCRIPTION
History View file @ ef57d59205
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.31.1
5 
+Version: 2.32.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

bump version

Steffen Neumann authored on 24/05/2022 08:45:03
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DESCRIPTION
History View file @ 48029f236c
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.31.0
5 
+Version: 2.31.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:08:40
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DESCRIPTION
History View file @ 0b19fcb4fd
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.30.0
5 
+Version: 2.31.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:08:40
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DESCRIPTION
History View file @ 563ae755cf
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.29.6
5 
+Version: 2.30.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

fix: mzML export

- Don't export/write header variables with missing values (issue #266).

jorainer authored on 22/04/2022 13:50:18
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DESCRIPTION
History View file @ 3b091f3a32
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.29.5
5 
+Version: 2.29.6
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

merge

jorainer authored on 18/03/2022 13:47:56
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Browse code

feat: pwiz returns peak matrices with column names

- `peaks` method for the proteowizard backend also peaks matrices with colnames
set.

jorainer authored on 18/03/2022 10:38:45
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DESCRIPTION
History View file @ c2ab2b8c61
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.27.1
5 
+Version: 2.27.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
             Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

re-apply clang compile fix after pwiz upgrade, closes #263

Steffen Neumann authored on 14/03/2022 10:47:04
Showing 1 changed files
DESCRIPTION
History View file @ 68e17202e1
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.29.3
5 
+Version: 2.29.4
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
... ... 
@@ -12,10 +12,7 @@ Authors@R: c(
12 12 
     )
13 13 
 Description: mzR provides a unified API to the common file formats and
14 14 
         parsers available for mass spectrometry data. It comes with a
15 
-        wrapper for the ISB random access parser for mass spectrometry
16 
-        mzXML, mzData and mzML files. The package contains the
17 
-        original code written by the ISB, and a subset of the
18 
-        proteowizard library for mzML and mzIdentML. The netCDF
15 
+        subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF
19 16 
         reading code has previously been used in XCMS.
20 17 
 License: Artistic-2.0
21 18 
 LazyLoad: yes
Browse code

Add minimum R version: Versioned LinkingTo is only usable in R >= 3.0.2

Steffen Neumann authored on 26/01/2022 20:20:10
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DESCRIPTION
History View file @ 34f92398db
... ... 
@@ -20,6 +20,7 @@ Description: mzR provides a unified API to the common file formats and
20 20 
 License: Artistic-2.0
21 21 
 LazyLoad: yes
22 22 
 Depends:
23 
+    R (>= 4.0.0),
23 24 
     Rcpp (>= 0.10.1),
24 25 
     methods,
25 26 
     utils
Browse code

Cleanup ZLIB from Makevars, enable other arches and disable error on warning in GitHub action, update DESCRIPTION and NEWS

Steffen Neumann authored on 25/01/2022 09:42:19
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DESCRIPTION
History View file @ e43067df3f
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.29.2
5 
+Version: 2.29.3
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Authors@R: c(
8 8 
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
Browse code

Fix compile errors by win_check()

uly55e5 authored on 24/01/2022 17:18:46
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DESCRIPTION
History View file @ 9b60d77203
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@@ -39,7 +39,6 @@ Suggests:
39 39 
 VignetteBuilder: knitr
40 40 
 LinkingTo:
41 41 
     Rcpp,
42 
-    zlibbioc,
43 42 
     Rhdf5lib (>= 1.1.4)
44 43 
 RcppModules:
45 44 
     Pwiz,
Browse code

Change DESCRIPTION to work with devtools::check_win()

uly55e5 authored on 09/12/2021 07:51:46
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DESCRIPTION
History View file @ 87322ebb0c
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@@ -4,9 +4,12 @@ Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 5 
 Version: 2.29.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 
-Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 
-            Laurent Gatto <laurent.gatto@uclouvain.be>,
9 
-            Qiakng Kou <qkou@umail.iu.edu>
7 
+Authors@R: c(
8 
+    person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
9 
+    person("Laurent", "Gatto", email="laurent.gatto@uclouvain.be", role=c("aut")),
10 
+    person("Qiakng", "Kou", email="qkou@umail.iu.edu", role=c("aut")),
11 
+    person("David","Rauh",email="drauh@ipb-halle.de", role=c("ctb"))
12 
+    )
10 13 
 Description: mzR provides a unified API to the common file formats and
11 14 
         parsers available for mass spectrometry data. It comes with a
12 15 
         wrapper for the ISB random access parser for mass spectrometry
Browse code

Add News

Steffen Neumann authored on 20/11/2021 11:19:02
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Browse code

Fix merge conflict on Versions after BioC release

Steffen Neumann authored on 27/10/2021 12:28:00
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bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:59:59
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DESCRIPTION
History View file @ 93b51a7b99
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.28.0
5 
+Version: 2.29.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
             Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:59:59
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DESCRIPTION
History View file @ bee7d6fb5f
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.27.1
5 
+Version: 2.28.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
             Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

refactor: patially rewrite code to exctract header info

- Create index list in R instead of C++.
- Use `size_t` instead of `int` where suitable.
- Ensure that correct data types are passed between R and C++.
- Use new (own) implementation to extract the acquisition number from the
spectrum ID instead of `id::translateNativeIDToScanNumber` from proteowizard
to avoid segfaults on macOS (https://github.com/sneumann/xcms/issues/422).

jorainer authored on 25/10/2021 08:58:52 • Steffen Neumann committed on 25/10/2021 15:08:38
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DESCRIPTION
History View file @ 2aed7135fe
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.27.1
5 
+Version: 2.27.3
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
             Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
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DESCRIPTION
History View file @ e3f79ff5f7
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.27.1
5 
+Version: 2.27.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
             Laurent Gatto <laurent.gatto@uclouvain.be>,
... ... 
@@ -16,12 +16,31 @@ Description: mzR provides a unified API to the common file formats and
16 16 
         reading code has previously been used in XCMS.
17 17 
 License: Artistic-2.0
18 18 
 LazyLoad: yes
19 
-Depends: Rcpp (>= 0.10.1), methods, utils
20 
-Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4
21 
-Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown
19 
+Depends:
20 
+    Rcpp (>= 0.10.1),
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+    methods,
22 
+    utils
23 
+Imports:
24 
+    Biobase,
25 
+    BiocGenerics (>= 0.13.6),
26 
+    ProtGenerics (>= 1.17.3),
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+    ncdf4
28 
+Suggests:
29 
+    msdata (>= 0.15.1),
30 
+    RUnit,
31 
+    mzID,
32 
+    BiocStyle (>= 2.5.19),
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+    knitr,
34 
+    XML,
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+    rmarkdown
22 36 
 VignetteBuilder: knitr
23 
-LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
24 
-RcppModules: Ramp, Pwiz, Ident
37 
+LinkingTo:
38 
+    Rcpp,
39 
+    zlibbioc,
40 
+    Rhdf5lib (>= 1.1.4)
41 
+RcppModules:
42 
+    Pwiz,
43 
+    Ident
25 44 
 SystemRequirements: C++11, GNU make
26 45 
 URL: https://github.com/sneumann/mzR/
27 46 
 BugReports: https://github.com/sneumann/mzR/issues/
Browse code

misc + version update

Laurent Gatto authored on 18/06/2021 16:37:31
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bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:49:34
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DESCRIPTION
History View file @ b1b203ad69
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.26.0
5 
+Version: 2.27.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:49:34
Showing 1 changed files
DESCRIPTION
History View file @ 537e62479e
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@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.25.5
5 
+Version: 2.26.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

Bump version after previous commit & fix, closes #244

Steffen Neumann authored on 08/05/2021 14:06:08
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DESCRIPTION
History View file @ 4c81caf25c
... ... 
@@ -2,11 +2,11 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.25.4
5 
+Version: 2.25.5
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
9 
-	    Qiang Kou <qkou@umail.iu.edu>
9 
+	    Qiakng Kou <qkou@umail.iu.edu>
10 10 
 Description: mzR provides a unified API to the common file formats and
11 11 
 	parsers available for mass spectrometry data. It comes with a
12 12 
 	wrapper for the ISB random access parser for mass spectrometry
Browse code

Add rmarkdown dependency to fix build error

Steffen Neumann authored on 17/04/2021 14:44:00
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DESCRIPTION
History View file @ e294448881
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.25.3
5 
+Version: 2.25.4
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
... ... 
@@ -18,7 +18,7 @@ License: Artistic-2.0
18 18 
 LazyLoad: yes
19 19 
 Depends: Rcpp (>= 0.10.1), methods, utils
20 20 
 Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4
21 
-Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
21 
+Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown
22 22 
 VignetteBuilder: knitr
23 23 
 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
24 24 
 RcppModules: Ramp, Pwiz, Ident
Browse code

fix: ensure columns are returned in correct data type

jorainer authored on 08/02/2021 12:19:25
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DESCRIPTION
History View file @ cc0f816e1a
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.25.2
5 
+Version: 2.25.3
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

fix: ensure header returns the same columns for all backends

- Fix for issue #238: ensure `header` returns the same columns for all backends.

jorainer authored on 02/02/2021 18:46:29
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DESCRIPTION
History View file @ f56e0c92af
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.25.1
5 
+Version: 2.25.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

Bump version to trigger new build and use latest Rcpp

Laurent Gatto authored on 18/11/2020 13:41:52
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DESCRIPTION
History View file @ 09d5907dac
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.25.0
5 
+Version: 2.25.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:42:32
Showing 1 changed files
DESCRIPTION
History View file @ 19d69eb0e1
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.24.0
5 
+Version: 2.25.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:42:32
Showing 1 changed files
DESCRIPTION
History View file @ 4ac45e0e5d
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.23.1
5 
+Version: 2.24.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <laurent.gatto@uclouvain.be>,
Browse code

bump version

Laurent Gatto authored on 09/09/2020 16:05:16
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Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:26:37
Showing 1 changed files
DESCRIPTION
History View file @ b657cceaa1
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.22.0
5 
+Version: 2.23.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:26:37
Showing 1 changed files
DESCRIPTION
History View file @ b432f21559
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.21.1
5 
+Version: 2.22.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

update email

Laurent Gatto authored on 29/03/2020 14:58:52
Showing 1 changed files
DESCRIPTION
History View file @ a6e86e062b
... ... 
@@ -2,10 +2,10 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.21.1
5 
+Version: 2.21.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 
-	    Laurent Gatto <lg390@cam.ac.uk>,
8 
+	    Laurent Gatto <laurent.gatto@uclouvain.be>,
9 9 
 	    Qiang Kou <qkou@umail.iu.edu>
10 10 
 Description: mzR provides a unified API to the common file formats and
11 11 
 	parsers available for mass spectrometry data. It comes with a
Browse code

Fix version and NEWS

Steffen Neumann authored on 14/12/2019 14:37:39
Showing 1 changed files
DESCRIPTION
History View file @ 23b9e52b6f
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.21.0
5 
+Version: 2.21.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:35:48
Showing 1 changed files
DESCRIPTION
History View file @ 627c6a875d
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.20.0
5 
+Version: 2.21.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:08:21
Showing 1 changed files
DESCRIPTION
History View file @ a66df47896
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.7
5 
+Version: 2.20.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Fix issue introduced by changing quotes in Rhdf5lib::pkgconfig()

Mike Smith authored on 15/10/2019 08:12:13
Showing 1 changed files
DESCRIPTION
History View file @ 3c42bd9d61
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.6
5 
+Version: 2.19.7
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

version bump

Laurent Gatto authored on 02/10/2019 19:48:01
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DESCRIPTION
History View file @ dddbebcea9
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.5
5 
+Version: 2.19.6
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump version to force rebuild with Rcpp v1.0.2

Laurent Gatto authored on 23/09/2019 13:15:16
Showing 1 changed files
DESCRIPTION
History View file @ 52a6f7b971
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.4
5 
+Version: 2.19.5
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Add scanWindowLowerLimit and scanWindowUpperLimit to header

- Add scanWindowLowerLimit and scanWindowUpperLimit variables.
- Export scanWindowLowerLimit and scanWindowUpperLimit to mzML (issue #202).
- Update and amend documentation and unit tests accordingly.

jorainer authored on 23/08/2019 14:02:46
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DESCRIPTION
History View file @ 52172a4d17
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.3
5 
+Version: 2.19.4
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump version and update news

Laurent Gatto authored on 16/08/2019 15:56:49
Showing 1 changed files
DESCRIPTION
History View file @ 712c3d620e
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.2
5 
+Version: 2.19.3
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
... ... 
@@ -17,7 +17,7 @@ Description: mzR provides a unified API to the common file formats and
17 17 
 License: Artistic-2.0
18 18 
 LazyLoad: yes
19 19 
 Depends: Rcpp (>= 0.10.1), methods, utils
20 
-Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.2), ncdf4
20 
+Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4
21 21 
 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
22 22 
 VignetteBuilder: knitr
23 23 
 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
Browse code

Bump dependency, version, add NEWS item. Closes #190

Steffen Neumann authored on 17/05/2019 14:29:43
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DESCRIPTION
History View file @ 219af40910
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.1
5 
+Version: 2.19.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
... ... 
@@ -17,7 +17,7 @@ Description: mzR provides a unified API to the common file formats and
17 17 
 License: Artistic-2.0
18 18 
 LazyLoad: yes
19 19 
 Depends: Rcpp (>= 0.10.1), methods, utils
20 
-Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1), ncdf4
20 
+Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.2), ncdf4
21 21 
 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
22 22 
 VignetteBuilder: knitr
23 23 
 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
Browse code

analyzr generic now in ProtGenerics

Laurent Gatto authored on 13/05/2019 20:42:11
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DESCRIPTION
History View file @ 7c0d6bff4f
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.19.0
5 
+Version: 2.19.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:11:05
Showing 1 changed files
DESCRIPTION
History View file @ 6e78d96c2d
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.18.0
5 
+Version: 2.19.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:29
Showing 1 changed files
DESCRIPTION
History View file @ 66b4bdcd9d
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.17.4
5 
+Version: 2.18.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

add not for developers to use OnDiskMSnExp

Laurent Gatto authored on 17/04/2019 15:03:08
Showing 1 changed files
DESCRIPTION
History View file @ 524b2a7d5e
... ... 
@@ -2,18 +2,18 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.17.3
5 
+Version: 2.17.4
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
9 9 
 	    Qiang Kou <qkou@umail.iu.edu>
10 10 
 Description: mzR provides a unified API to the common file formats and
11 
-        parsers available for mass spectrometry data. It comes with a
12 
-        wrapper for the ISB random access parser for mass spectrometry
13 
-        mzXML, mzData and mzML files. The package contains the
14 
-        original code written by the ISB, and a subset of the
15 
-        proteowizard library for mzML and mzIdentML. The netCDF
16 
-        reading code has previously been used in XCMS.
11 
+	parsers available for mass spectrometry data. It comes with a
12 
+	wrapper for the ISB random access parser for mass spectrometry
13 
+	mzXML, mzData and mzML files. The package contains the
14 
+	original code written by the ISB, and a subset of the
15 
+	proteowizard library for mzML and mzIdentML. The netCDF
16 
+	reading code has previously been used in XCMS.
17 17 
 License: Artistic-2.0
18 18 
 LazyLoad: yes
19 19 
 Depends: Rcpp (>= 0.10.1), methods, utils
... ... 
@@ -26,5 +26,5 @@ SystemRequirements: C++11, GNU make
26 26 
 URL: https://github.com/sneumann/mzR/
27 27 
 BugReports: https://github.com/sneumann/mzR/issues/
28 28 
 biocViews: ImmunoOncology, Infrastructure, DataImport, Proteomics, Metabolomics,
29 
-        MassSpectrometry
29 
+	MassSpectrometry
30 30 
 RoxygenNote: 6.0.1
Browse code

Add isolationWindowTargetMZ column to header

- Extract isolation window from mzML files (issue #193): data.frame returned by
jeader gains columns "isolationWindowTargetMZ", "isolationWindowLowerOffset"
and "isolationWindowUpperOffset" enabling SWATH data analysis.
- Adapt documentation and unit tests.

jotsetung authored on 03/04/2019 09:40:16
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DESCRIPTION
History View file @ 2edb9032d0
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.17.2
5 
+Version: 2.17.3
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Bump version after merge which closes #185

Steffen Neumann authored on 05/03/2019 15:26:12
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DESCRIPTION
History View file @ 19812c5c3b
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.17.1
5 
+Version: 2.17.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Add ImmunoOncology biocViews term

Kayla-Morrell authored on 04/01/2019 18:11:07
Showing 1 changed files
DESCRIPTION
History View file @ 06e0c1be31
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.17.0
5 
+Version: 2.17.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
... ... 
@@ -25,6 +25,6 @@ RcppModules: Ramp, Pwiz, Ident
25 25 
 SystemRequirements: C++11, GNU make
26 26 
 URL: https://github.com/sneumann/mzR/
27 27 
 BugReports: https://github.com/sneumann/mzR/issues/
28 
-biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,
28 
+biocViews: ImmunoOncology, Infrastructure, DataImport, Proteomics, Metabolomics,
29 29 
         MassSpectrometry
30 30 
 RoxygenNote: 6.0.1
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:29
Showing 1 changed files
DESCRIPTION
History View file @ 65ead39dc2
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.16.0
5 
+Version: 2.17.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:48
Showing 1 changed files
DESCRIPTION
History View file @ 536d161c7f
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.15.5
5 
+Version: 2.16.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump gh devel version

Laurent authored on 13/09/2018 21:15:13
Showing 1 changed files
DESCRIPTION
History View file @ e7ed4bd57e
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.15.4
5 
+Version: 2.15.5
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Bump version. Merged changes close #178

Steffen Neumann authored on 12/09/2018 06:47:30
Showing 1 changed files
DESCRIPTION
History View file @ 523282dbcc
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.15.3
5 
+Version: 2.15.4
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Removed netCDF.h, can already be used by xcmsRaw

Steffen Neumann authored on 10/09/2018 08:41:50
Showing 1 changed files
DESCRIPTION
History View file @ dfbd825f35
... ... 
@@ -17,12 +17,12 @@ Description: mzR provides a unified API to the common file formats and
17 17 
 License: Artistic-2.0
18 18 
 LazyLoad: yes
19 19 
 Depends: Rcpp (>= 0.10.1), methods, utils
20 
-Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)
20 
+Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1), ncdf4
21 21 
 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
22 22 
 VignetteBuilder: knitr
23 23 
 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
24 24 
 RcppModules: Ramp, Pwiz, Ident
25 
-SystemRequirements: C++11, GNU make, NetCDF
25 
+SystemRequirements: C++11, GNU make
26 26 
 URL: https://github.com/sneumann/mzR/
27 27 
 BugReports: https://github.com/sneumann/mzR/issues/
28 28 
 biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,
Browse code

bump version and update news

Laurent authored on 03/09/2018 12:40:27
Showing 1 changed files
DESCRIPTION
History View file @ 4d6f0569a3
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.15.2
5 
+Version: 2.15.3
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

merge gh version

Laurent authored on 26/05/2018 21:01:44
Showing 1 changed files
DESCRIPTION
History View file @ beb1094765
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.15.1
5 
+Version: 2.15.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump version

Laurent authored on 09/05/2018 02:58:38
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DESCRIPTION
History View file @ d4cada7e56
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.8
5 
+Version: 2.15.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Document missing chrom argument for chromatogram(s)

Sebastian Gibb authored on 29/04/2018 07:53:05
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DESCRIPTION
History View file @ 3c1139ba49
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.7
5 
+Version: 2.13.8
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Bump version after adding a missing header needed on gcc 6.2.0

Steffen Neumann authored on 27/04/2018 20:41:27
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DESCRIPTION
History View file @ 86995a8090
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.6
5 
+Version: 2.13.7
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

new github devel version

Laurent authored on 07/03/2018 19:17:55
Showing 1 changed files
DESCRIPTION
History View file @ fb188884ba
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.5
5 
+Version: 2.13.6
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump version for bioc

Laurent authored on 07/03/2018 19:12:08
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DESCRIPTION
History View file @ 9109625b0c
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.4
5 
+Version: 2.13.5
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

bump version and update news

Laurent authored on 26/02/2018 11:03:13
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DESCRIPTION
History View file @ 94a5fd150a
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.3
5 
+Version: 2.13.4
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

prepare for Rhdf5lib 1.1.4 with c++ headers in /include

Steffen Neumann authored on 09/01/2018 07:55:20
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DESCRIPTION
History View file @ 3333b46b75
... ... 
@@ -20,7 +20,7 @@ Depends: Rcpp (>= 0.10.1), methods, utils
20 20 
 Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)
21 21 
 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
22 22 
 VignetteBuilder: knitr
23 
-LinkingTo: Rcpp, zlibbioc, Rhdf5lib
23 
+LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
24 24 
 RcppModules: Ramp, Pwiz, Ident
25 25 
 SystemRequirements: C++11, GNU make, NetCDF
26 26 
 URL: https://github.com/sneumann/mzR/
Browse code

replace system dependency libhdf5-dev with BioC package Rhdf5lib

Steffen Neumann authored on 03/01/2018 22:22:13
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DESCRIPTION
History View file @ 305e813d01
... ... 
@@ -20,7 +20,7 @@ Depends: Rcpp (>= 0.10.1), methods, utils
20 20 
 Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)
21 21 
 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
22 22 
 VignetteBuilder: knitr
23 
-LinkingTo: Rcpp, zlibbioc
23 
+LinkingTo: Rcpp, zlibbioc, Rhdf5lib
24 24 
 RcppModules: Ramp, Pwiz, Ident
25 25 
 SystemRequirements: C++11, GNU make, NetCDF
26 26 
 URL: https://github.com/sneumann/mzR/
Browse code

bump gh devel version

Laurent authored on 21/12/2017 13:54:49
Showing 1 changed files
DESCRIPTION
History View file @ acb735f25d
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.2
5 
+Version: 2.13.3
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 7 
 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
8 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
Browse code

Add Jo to author list (long overdue)

Laurent Gatto authored on 21/12/2017 13:59:01 • GitHub committed on 21/12/2017 13:59:01
Showing 1 changed files
DESCRIPTION
History View file @ 3d8f858490
... ... 
@@ -3,9 +3,8 @@ Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 5 
 Version: 2.13.2
6 
-Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 
-Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 
-	    Steffen Neumann <sneumann@ipb-halle.de>,
6 
+Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
7 
+Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,
9 8 
 	    Laurent Gatto <lg390@cam.ac.uk>,
10 9 
 	    Qiang Kou <qkou@umail.iu.edu>
11 10 
 Description: mzR provides a unified API to the common file formats and
Browse code

Add chromatogramHeader method

- Add a chromatogramHeader method to extract chromatogram header information
from an mzML file (issue #141).

jotsetung authored on 11/12/2017 09:26:45
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DESCRIPTION
History View file @ 3555a9aa15
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.1
5 
+Version: 2.13.2
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

File extension and content dependent backend selection

- openMsFile selects the backend based on the file extension (and eventually
file content). This is the default behaviour if backend is not manually
specified.
- Add related unit tests and documentation.

jotsetung authored on 23/11/2017 13:19:46
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DESCRIPTION
History View file @ 75d74a65b9
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.13.0
5 
+Version: 2.13.1
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:52:12
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DESCRIPTION
History View file @ f2eaf9cfd1
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.12.0
5 
+Version: 2.13.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:39:35
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DESCRIPTION
History View file @ f05eb27ae3
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.11.11
5 
+Version: 2.12.0
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

Make writeMSData a method

- Import writeMSData generic from ProtGenerics.
- Convert writeMSData from a function to a method.

jotsetung authored on 20/09/2017 10:19:40
Showing 1 changed files
DESCRIPTION
History View file @ 7da97ca984
... ... 
@@ -18,7 +18,7 @@ Description: mzR provides a unified API to the common file formats and
18 18 
 License: Artistic-2.0
19 19 
 LazyLoad: yes
20 20 
 Depends: Rcpp (>= 0.10.1), methods, utils
21 
-Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics
21 
+Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)
22 22 
 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
23 23 
 VignetteBuilder: knitr
24 24 
 LinkingTo: Rcpp, zlibbioc
Browse code

bump gh devel version

Laurent authored on 18/09/2017 14:55:57
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DESCRIPTION
History View file @ f61f6652f9
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.11.10
5 
+Version: 2.11.11
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

bump gh devel version

Laurent authored on 11/09/2017 06:58:30
Showing 1 changed files
DESCRIPTION
History View file @ 74715917ca
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.11.9
5 
+Version: 2.11.10
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

bump version on gh

Laurent authored on 08/09/2017 15:13:11
Showing 1 changed files
DESCRIPTION
History View file @ 2b26189b9d
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.11.8
5 
+Version: 2.11.9
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

moved vignette to Rmd/html using latest BiocStyle style

Laurent authored on 22/08/2017 14:33:49
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DESCRIPTION
History View file @ 7a732e5e35
... ... 
@@ -19,7 +19,7 @@ License: Artistic-2.0
19 19 
 LazyLoad: yes
20 20 
 Depends: Rcpp (>= 0.10.1), methods, utils
21 21 
 Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics
22 
-Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle, knitr, XML
22 
+Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
23 23 
 VignetteBuilder: knitr
24 24 
 LinkingTo: Rcpp, zlibbioc
25 25 
 RcppModules: Ramp, Pwiz, Ident
Browse code

new gh devel version

Laurent authored on 15/08/2017 07:56:49
Showing 1 changed files
DESCRIPTION
History View file @ e15c229b92
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.11.7
5 
+Version: 2.11.8
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

new gh devel version

Laurent authored on 03/08/2017 16:51:45
Showing 1 changed files
DESCRIPTION
History View file @ 36d23910ef
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.11.6
5 
+Version: 2.11.7
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
Browse code

bump gh version

Laurent authored on 28/07/2017 08:19:04
Showing 1 changed files
DESCRIPTION
History View file @ 6640f7f441
... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.11.5
5 
+Version: 2.11.6
6 6