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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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")),
jorainer authored on 18/03/2022 13:47:56
Showing0 changed files
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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing0 changed files
Browse code

Fix merge conflict on Versions after BioC release

Steffen Neumann authored on 27/10/2021 12:28:00
Showing0 changed files
Browse code

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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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),
21
+    methods,
22
+    utils
23
+Imports:
24
+    Biobase,
25
+    BiocGenerics (>= 0.13.6),
26
+    ProtGenerics (>= 1.17.3),
27
+    ncdf4
28
+Suggests:
29
+    msdata (>= 0.15.1),
30
+    RUnit,
31
+    mzID,
32
+    BiocStyle (>= 2.5.19),
33
+    knitr,
34
+    XML,
35
+    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
Showing0 changed files
Browse code

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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing0 changed files
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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
 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

Merge branch 'master' into write_support

jotsetung authored on 10/07/2017 11:29:35
Showing0 changed files
Browse code

new gh devel version

Laurent authored on 23/06/2017 16:24:49
Showing1 changed files
... ...
@@ -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: 2.11.4
5
+Version: 2.11.5
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

Enable MS data write support

- export writeMSData and copyWriteMSData functions.
- Add related unit tests and documentation.

jotsetung authored on 23/06/2017 14:15:37
Showing1 changed files
... ...
@@ -28,3 +28,4 @@ URL: https://github.com/sneumann/mzR/
28 28
 BugReports: https://github.com/sneumann/mzR/issues/
29 29
 biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,
30 30
         MassSpectrometry
31
+RoxygenNote: 6.0.1
Browse code

bump gh devel version

Laurent authored on 13/06/2017 12:09:44
Showing1 changed files
... ...
@@ -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: 2.11.3
5
+Version: 2.11.4
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 06/06/2017 18:12:03
Showing1 changed files
... ...
@@ -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: 2.11.2
5
+Version: 2.11.3
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 and add description

jotsetung authored on 31/05/2017 06:19:08
Showing1 changed files
... ...
@@ -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: 2.11.1
5
+Version: 2.11.2
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

fix version

Laurent authored on 26/05/2017 07:46:48
Showing1 changed files
... ...
@@ -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: 2.9.12
5
+Version: 2.11.1
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

Make pwiz default backend (issue #84)

- Change default backend to pwiz.
- Update documentation.
- Passes R CMD check.

jotsetung authored on 23/05/2017 09:10:08
Showing1 changed files
... ...
@@ -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: 2.9.11
5
+Version: 2.9.12
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 verison

Laurent authored on 21/04/2017 09:14:14
Showing1 changed files
... ...
@@ -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: 2.9.10
5
+Version: 2.9.11
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

remove digitalmars line - see issue #90

Laurent authored on 30/03/2017 13:33:56
Showing1 changed files
... ...
@@ -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: 2.9.9
5
+Version: 2.9.10
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 and upate news files

Laurent authored on 25/03/2017 18:33:22
Showing1 changed files
... ...
@@ -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: 2.9.8
5
+Version: 2.9.9
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

Bump version, closes #81

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@127280 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 09/03/2017 21:38:00
Showing1 changed files
... ...
@@ -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: 2.9.7
5
+Version: 2.9.8
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

github devel version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@127261 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 08/03/2017 21:23:36
Showing1 changed files
... ...
@@ -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: 2.9.6
5
+Version: 2.9.7
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

new gh devel version

Laurent authored on 25/01/2017 09:51:58
Showing1 changed files
... ...
@@ -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: 2.9.5
5
+Version: 2.9.6
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 github devel version

Laurent authored on 24/01/2017 21:23:22
Showing1 changed files
... ...
@@ -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: 2.9.4
5
+Version: 2.9.5
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 chromatogram[s] and tic methods

Laurent authored on 24/01/2017 10:03:19
Showing1 changed files
... ...
@@ -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 (>= 0.3.5), RUnit, mzID, BiocStyle, knitr, XML
22
+Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle, 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 05/01/2017 18:15:37
Showing1 changed files
... ...
@@ -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: 2.9.3
5
+Version: 2.9.4
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 github devel version

Laurent authored on 03/01/2017 21:08:22
Showing1 changed files
... ...
@@ -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: 2.9.2
5
+Version: 2.9.3
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 github devel version

Laurent authored on 15/12/2016 15:00:06
Showing1 changed files
... ...
@@ -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: 2.9.1
5
+Version: 2.9.2
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

bump version

Laurent authored on 20/11/2016 12:03:00
Showing1 changed files
... ...
@@ -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: 2.9.0
5
+Version: 2.9.1
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 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 17/10/2016 19:10:43
Showing1 changed files
... ...
@@ -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: 2.8.0
5
+Version: 2.9.0
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 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 17/10/2016 18:45:06
Showing1 changed files
... ...
@@ -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: 2.7.13
5
+Version: 2.8.0
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 version

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@122219 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 11/10/2016 21:42:47
Showing1 changed files
... ...
@@ -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: 2.7.12
5
+Version: 2.7.13
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

Laurent authored on 09/10/2016 10:20:56
Showing1 changed files
... ...
@@ -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: 2.7.11
5
+Version: 2.7.12
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

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

Laurent authored on 06/10/2016 21:44:57
Showing1 changed files
... ...
@@ -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: 2.7.10
5
+Version: 2.7.11
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 version

Laurent authored on 05/10/2016 12:13:29
Showing1 changed files
... ...
@@ -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: 2.7.9
5
+Version: 2.7.10
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

Laurent authored on 29/09/2016 09:01:59
Showing1 changed files
... ...
@@ -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: 2.7.8
5
+Version: 2.7.9
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

bump version and update readme

Laurent authored on 27/09/2016 08:52:31
Showing1 changed files
... ...
@@ -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: 2.7.7
5
+Version: 2.7.8
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

bump version

Laurent authored on 26/09/2016 08:00:57
Showing1 changed files
... ...
@@ -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: 2.7.6
5
+Version: 2.7.7
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

suggest xml

Laurent authored on 23/09/2016 21:22:08
Showing1 changed files
... ...
@@ -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 (>= 0.3.5), RUnit, mzID, BiocStyle, knitr
22
+Suggests: msdata (>= 0.3.5), RUnit, mzID, BiocStyle, knitr, XML
23 23
 VignetteBuilder: knitr
24 24
 LinkingTo: Rcpp, zlibbioc
25 25
 RcppModules: Ramp, Pwiz, Ident
Browse code

new isolationWindow accessor

Laurent authored on 23/09/2016 20:45:16
Showing1 changed files
... ...
@@ -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: 2.7.5
5
+Version: 2.7.6
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

replace free by delete - see issue #52

Laurent authored on 22/09/2016 15:52:12
Showing1 changed files
... ...
@@ -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: 2.7.4
5
+Version: 2.7.5
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

update version number

Laurent authored on 01/06/2016 13:55:04
Showing1 changed files
... ...
@@ -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: 2.7.1
5
+Version: 2.7.4
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

update description

Qiang Kou authored on 28/05/2016 16:57:21
Showing1 changed files
... ...
@@ -2,19 +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
-<<<<<<< HEAD
6
-Version: 2.5.3
7
-Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
8
-Maintainer: Bernd Fischer <b.fischer@dkfz.de>, 
9
-	    Steffen Neumann <sneumann@ipb-halle.de>, 
10
-	    Laurent Gatto <lg390@cam.ac.uk>, 
11
-=======
12 5
 Version: 2.7.1
13 6
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
14 7
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
15 8
 	    Steffen Neumann <sneumann@ipb-halle.de>,
16 9
 	    Laurent Gatto <lg390@cam.ac.uk>,
17
->>>>>>> devel
18 10
 	    Qiang Kou <qkou@umail.iu.edu>
19 11
 Description: mzR provides a unified API to the common file formats and
20 12
         parsers available for mass spectrometry data. It comes with a
... ...
@@ -31,14 +23,8 @@ Suggests: msdata (>= 0.3.5), RUnit, mzID, BiocStyle, knitr
31 23
 VignetteBuilder: knitr
32 24
 LinkingTo: Rcpp, zlibbioc
33 25
 RcppModules: Ramp, Pwiz, Ident
34
-<<<<<<< HEAD
35
-SystemRequirements: GNU make, NetCDF
36
-URL: https://github.com/sneumann/mzR/
37
-BugReports: https://github.com/sneumann/mzR/issues/new
38
-=======
39 26
 SystemRequirements: C++11, GNU make, NetCDF
40 27
 URL: https://github.com/sneumann/mzR/
41 28
 BugReports: https://github.com/sneumann/mzR/issues/
42
->>>>>>> devel
43 29
 biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,
44 30
         MassSpectrometry
Browse code

Merge branch 'devel'

Qiang Kou authored on 28/05/2016 16:55:25
Showing0 changed files
Browse code

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

Steffen Neumann authored on 05/05/2016 16:50:08
Showing1 changed files
... ...
@@ -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: 2.7.0
5
+Version: 2.7.1
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 version after creating 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 03/05/2016 21:30:44
Showing1 changed files
... ...
@@ -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: 2.6.0
5
+Version: 2.7.0
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 versions prior to creation of 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 03/05/2016 21:20:18
Showing1 changed files
... ...
@@ -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: 2.5.8
5
+Version: 2.6.0
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

fix compiler Warning with clang on MacOS

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@116967 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 02/05/2016 07:38:33
Showing1 changed files
... ...
@@ -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: 2.5.7
5
+Version: 2.5.8
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

Some C pointer casting to fix clang compilation, closes #38

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@116538 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 19/04/2016 09:10:04
Showing1 changed files
... ...
@@ -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: 2.5.6
5
+Version: 2.5.7
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

Shorten the BugReports URL to point at bug tracker, rather than only at New reports

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@116410 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 17/04/2016 11:41:55
Showing1 changed files
... ...
@@ -25,6 +25,6 @@ LinkingTo: Rcpp, zlibbioc
25 25
 RcppModules: Ramp, Pwiz, Ident
26 26
 SystemRequirements: C++11, GNU make, NetCDF
27 27
 URL: https://github.com/sneumann/mzR/
28
-BugReports: https://github.com/sneumann/mzR/issues/new
28
+BugReports: https://github.com/sneumann/mzR/issues/
29 29
 biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,
30 30
         MassSpectrometry
Browse code

works with Rcpp from github

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@116300 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 14/04/2016 22:16:29
Showing1 changed files
... ...
@@ -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: 2.5.5
5
+Version: 2.5.6
6 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>, 
9
-	    Laurent Gatto <lg390@cam.ac.uk>, 
7
+Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8
+	    Steffen Neumann <sneumann@ipb-halle.de>,
9
+	    Laurent Gatto <lg390@cam.ac.uk>,
10 10
 	    Qiang Kou <qkou@umail.iu.edu>
11 11
 Description: mzR provides a unified API to the common file formats and
12 12
         parsers available for mass spectrometry data. It comes with a
... ...
@@ -23,7 +23,7 @@ Suggests: msdata (>= 0.3.5), RUnit, mzID, BiocStyle, knitr
23 23
 VignetteBuilder: knitr
24 24
 LinkingTo: Rcpp, zlibbioc
25 25
 RcppModules: Ramp, Pwiz, Ident
26
-SystemRequirements: GNU make, NetCDF
26
+SystemRequirements: C++11, GNU make, NetCDF
27 27
 URL: https://github.com/sneumann/mzR/
28 28
 BugReports: https://github.com/sneumann/mzR/issues/new
29 29
 biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,
Browse code

revert to libnetcdf from previous commit, update libpwiz for new toolchain

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@115473 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 31/03/2016 02:06:20
Showing1 changed files
... ...
@@ -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: 2.5.4
5
+Version: 2.5.5
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

partial changes for new toolchain

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@115391 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 29/03/2016 23:41:28
Showing1 changed files
... ...
@@ -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: 2.5.3
5
+Version: 2.5.4
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

merge master

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@113918 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 23/02/2016 00:45:13
Showing1 changed files
... ...
@@ -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: 2.5.2
5
+Version: 2.5.3
6 6
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,