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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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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.35.1
2
+-------------------------
3
+ o fix compilation on Fedora 38 / R-4.3.0. Thanks to Christian Iseli! Closes #282
4
+
1 5
 CHANGES IN VERSION 2.33.1
2 6
 -------------------------
3 7
  o fix: update to a new PSI-MS OBO for e.g. ZenoTOF CV term
Browse code

Updating the CV

Steffen Neumann authored on 05/04/2023 12:44:04
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@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.33.1
2
+-------------------------
3
+ o fix: update to a new PSI-MS OBO for e.g. ZenoTOF CV term
4
+   Closes #278
5
+
1 6
 CHANGES IN VERSION 2.29.1
2 7
 -------------------------
3 8
  o fix: read full spectra data in get3DMap
Browse code

bump version

Steffen Neumann authored on 24/05/2022 08:45:03
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@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.29.1
2
+-------------------------
3
+ o fix: read full spectra data in get3DMap
4
+   Closes #269.
5
+
1 6
 CHANGES IN VERSION 2.27.6
2 7
 -------------------------
3 8
  o Only export certain spectra header parameters if their values are not NA.
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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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@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.27.6
2
+-------------------------
3
+ o Only export certain spectra header parameters if their values are not NA.
4
+   Closes #266.
5
+
1 6
 CHANGES IN VERSION 2.27.5
2 7
 -------------------------
3 8
  o `peaks` method for pwiz backend sets colnames on returned matrices.
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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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.27.2
2
+-------------------------
3
+ o `peaks` method for pwiz backend sets colnames on returned matrices.
4
+
1 5
 CHANGES IN VERSION 2.27.1
2 6
 -------------------------
3 7
  o Add missing atomic_count_sync.hpp BH file (see PR #248 by vjcitn)
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re-apply clang compile fix after pwiz upgrade, closes #263

Steffen Neumann authored on 14/03/2022 10:47:04
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1
+CHANGES IN VERSION 2.29.4
2
+-------------------------
3
+ o Re-apply fix for compile error on clang by Kurt Hornik, closes #263
4
+ o Remove text in DESCRIPTION hinting at the RAMP wrapper for mzData removed in 2.29.3
5
+
1 6
 CHANGES IN VERSION 2.29.3
2 7
 -------------------------
3 8
  o Update to Proteowizard 3_0_21263
... ...
@@ -6,7 +11,7 @@ CHANGES IN VERSION 2.29.3
6 11
 
7 12
 CHANGES IN VERSION 2.29.2
8 13
 -------------------------
9
- o Cleanup in build files 
14
+ o Cleanup in build files
10 15
 
11 16
 CHANGES IN VERSION 2.29.1
12 17
 -------------------------
Browse code

Merge branch 'master' into feature/updatePwiz_3_0_21263

Steffen Neumann authored on 25/01/2022 16:30:31 • GitHub committed on 25/01/2022 16:30:31
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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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1
-CHANGES IN VERSION 2.29.2
1
+CHANGES IN VERSION 2.29.3
2 2
 -------------------------
3 3
  o Update to Proteowizard 3_0_21263
4 4
  o Removed RAMP backend, dropping ability to read mzData
5 5
  o header always returns a data.frame even for a single scan.
6 6
 
7
+ CHANGES IN VERSION 2.29.2
8
+ -------------------------
9
+ o Small fix in build to include fix by UCRT patch from Tomas Kalibera
10
+
7 11
 CHANGES IN VERSION 2.29.1
8 12
 -------------------------
9 13
  o Pwiz backend partially re-written to avoid segfault on macOS
Browse code

Cleanup in build files

Steffen Neumann authored on 13/01/2022 20:21:45
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1
+CHANGES IN VERSION 2.29.2
2
+-------------------------
3
+ o Cleanup in build files 
4
+
1 5
 CHANGES IN VERSION 2.29.1
2 6
 -------------------------
3 7
  o Pwiz backend partially re-written to avoid segfault on macOS
Browse code

refactor: header always returns a `data.frame` (PR #253)

- Fix header for pwiz backend to always return a `data.frame`.
- Update documentation.

jorainer authored on 25/11/2021 08:27:02
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@@ -2,6 +2,7 @@ CHANGES IN VERSION 2.29.2
2 2
 -------------------------
3 3
  o Update to Proteowizard 3_0_21263
4 4
  o Removed RAMP backend, dropping ability to read mzData
5
+ o header always returns a data.frame even for a single scan.
5 6
 
6 7
 CHANGES IN VERSION 2.29.1
7 8
 -------------------------
Browse code

Add News

Steffen Neumann authored on 20/11/2021 11:19:02
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Fix version number after release

Steffen Neumann authored on 27/10/2021 12:39:10
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1
-CHANGES IN VERSION 2.27.3
1
+CHANGES IN VERSION 2.29.1
2 2
 -------------------------
3 3
  o Pwiz backend partially re-written to avoid segfault on macOS
4 4
    (https://github.com/sneumann/xcms/issues/422).
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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1
+CHANGES IN VERSION 2.27.3
2
+-------------------------
3
+ o Pwiz backend partially re-written to avoid segfault on macOS
4
+   (https://github.com/sneumann/xcms/issues/422).
5
+
6
+CHANGES IN VERSION 2.27.2
7
+-------------------------
8
+ o Remove support for the ramp backend.
9
+
1 10
 CHANGES IN VERSION 2.27.1
2 11
 -------------------------
3 12
  o Add missing atomic_count_sync.hpp BH file (see PR #248 by vjcitn)
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
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1
+CHANGES IN VERSION 2.27.2
2
+-------------------------
3
+ o Remove support for the ramp backend.
4
+
1 5
 CHANGES IN VERSION 2.27.1
2 6
 -------------------------
3 7
  o Add missing atomic_count_sync.hpp BH file (see PR #248 by vjcitn)
Browse code

misc + version update

Laurent Gatto authored on 18/06/2021 16:37:31
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Browse code

Bump version after previous commit & fix, closes #244

Steffen Neumann authored on 08/05/2021 14:06:08
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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.25.5
2
+-------------------------
3
+ o Fix compile error on clang-11 reported (and fixed!) by Kurt Hornik, closes #244
4
+
1 5
 CHANGES IN VERSION 2.25.4
2 6
 -------------------------
3 7
  o Add dependency "rmarkdown" to "suggests:"
Browse code

Add rmarkdown dependency to fix build error

Steffen Neumann authored on 17/04/2021 14:44:00
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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.25.4
2
+-------------------------
3
+ o Add dependency "rmarkdown" to "suggests:"
4
+
1 5
 CHANGES IN VERSION 2.25.3
2 6
 -------------------------
3 7
  o Ensure `header` for CDF returns columns with correct data type.
Browse code

fix: ensure columns are returned in correct data type

jorainer authored on 08/02/2021 12:19:25
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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.25.3
2
+-------------------------
3
+ o Ensure `header` for CDF returns columns with correct data type.
4
+
1 5
 CHANGES IN VERSION 2.25.2
2 6
 -------------------------
3 7
  o Fix issue #238: ensure `header` call returns the same columns for all
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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@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.25.2
2
+-------------------------
3
+ o Fix issue #238: ensure `header` call returns the same columns for all
4
+   backends.
5
+
1 6
 CHANGES IN VERSION 2.25.1
2 7
 -------------------------
3 8
  o Bump version to trigger new build using latest Rcpp
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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@@ -1,3 +1,11 @@
1
+CHANGES IN VERSION 2.25.1
2
+-------------------------
3
+ o Bump version to trigger new build using latest Rcpp
4
+
5
+CHANGES IN VERSION 2.25.0
6
+-------------------------
7
+ o New Bioc devel version
8
+ 
1 9
 CHANGES IN VERSION 2.21.2
2 10
 -------------------------
3 11
  o Update email address
Browse code

update email

Laurent Gatto authored on 29/03/2020 14:58:52
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@@ -1,6 +1,10 @@
1
+CHANGES IN VERSION 2.21.2
2
+-------------------------
3
+ o Update email address
4
+
1 5
 CHANGES IN VERSION 2.21.1
2 6
 -------------------------
3
- o inject a new PSI-MS.obo controlled vocabulary 
7
+ o inject a new PSI-MS.obo controlled vocabulary
4 8
    data-version: 4.1.30
5 9
    date: 30:08:2019 16:10
6 10
    saved-by: Gerhard Mayer
... ...
@@ -17,7 +21,7 @@ CHANGES IN VERSION 2.19.6
17 21
    <2019-09-26 Thu>.
18 22
 
19 23
 CHANGES IN VERSION 2.19.5
24
+-------------------------
20 25
  o version bump to force build with latest Rcpp
21 26
 
22 27
 CHANGES IN VERSION 2.19.4
Browse code

Fix version and NEWS

Steffen Neumann authored on 14/12/2019 14:37:39
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@@ -1,4 +1,4 @@
1
-CHANGES IN VERSION 2.19.8
1
+CHANGES IN VERSION 2.21.1
2 2
 -------------------------
3 3
  o inject a new PSI-MS.obo controlled vocabulary 
4 4
    data-version: 4.1.30
Browse code

Update PSI-MS.obo derived cv.cpp and cv.hpp

Steffen Neumann authored on 15/10/2019 08:55:51
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@@ -1,3 +1,14 @@
1
+CHANGES IN VERSION 2.19.8
2
+-------------------------
3
+ o inject a new PSI-MS.obo controlled vocabulary 
4
+   data-version: 4.1.30
5
+   date: 30:08:2019 16:10
6
+   saved-by: Gerhard Mayer
7
+
8
+CHANGES IN VERSION 2.19.7
9
+-------------------------
10
+ o Fix compile error on Windows + Mac (Thanks Mike!)
11
+
1 12
 CHANGES IN VERSION 2.19.6
2 13
 -------------------------
3 14
  o header for the pwiz backend returns NA instead of 0 for not defined or
Browse code

version bump

Laurent Gatto authored on 02/10/2019 19:48:01
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@@ -1,10 +1,14 @@
1
-CHANGES IN VERSION 2.19.5
1
+CHANGES IN VERSION 2.19.6
2 2
 -------------------------
3 3
  o header for the pwiz backend returns NA instead of 0 for not defined or
4 4
    missing information <2019-09-24 Tue>.
5 5
  o peaks for pwiz backend rewritten (small performance improvement)
6 6
    <2019-09-26 Thu>.
7 7
 
8
+CHANGES IN VERSION 2.19.5
9
+-------------------------   
10
+ o version bump to force build with latest Rcpp
11
+
8 12
 CHANGES IN VERSION 2.19.4
9 13
 -------------------------
10 14
  o Add header columns scanWindowLowerLimit and scanWindowUpperLimit
Browse code

refactor: rewrite the peak extraction function for pwiz

- Rewrite the C++ code for peak data extraction with the pwiz backend.
- Fix unit tests.

jorainer authored on 26/09/2019 10:09:04
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@@ -2,6 +2,8 @@ CHANGES IN VERSION 2.19.5
2 2
 -------------------------
3 3
  o header for the pwiz backend returns NA instead of 0 for not defined or
4 4
    missing information <2019-09-24 Tue>.
5
+ o peaks for pwiz backend rewritten (small performance improvement)
6
+   <2019-09-26 Thu>.
5 7
 
6 8
 CHANGES IN VERSION 2.19.4
7 9
 -------------------------
Browse code

refactor: avoid usage of RAMPAdapter in pwiz header function

- RcppPwiz::getScanHeaderInfo does no longer use the pwiz RAMPadaptor to get
some spectra header information but extracts all information directly within
the function (making it also considerably faster). Comparison is provided in
issue #205.

jorainer authored on 24/09/2019 12:49:46
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@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.19.5
2
+-------------------------
3
+ o header for the pwiz backend returns NA instead of 0 for not defined or
4
+   missing information <2019-09-24 Tue>.
5
+
1 6
 CHANGES IN VERSION 2.19.4
2 7
 -------------------------
3 8
  o Add header columns scanWindowLowerLimit and scanWindowUpperLimit
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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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.19.4
2
+-------------------------
3
+ o Add header columns scanWindowLowerLimit and scanWindowUpperLimit
4
+
1 5
 CHANGES IN VERSION 2.19.3
2 6
 -------------------------
3 7
  o use ProtGenerics::tolerance generic <2019-08-16 Fri>
Browse code

bump version and update news

Laurent Gatto authored on 16/08/2019 15:56:49
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@@ -1,6 +1,10 @@
1
+CHANGES IN VERSION 2.19.3
2
+-------------------------
3
+ o use ProtGenerics::tolerance generic <2019-08-16 Fri>
4
+
1 5
 CHANGES IN VERSION 2.19.2
2 6
 -------------------------
3
- o Fix issue 190, compiles on clang-8.0 
7
+ o Fix issue 190, compiles on clang-8.0
4 8
 
5 9
 CHANGES IN VERSION 2.19.1
6 10
 -------------------------
Browse code

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

Steffen Neumann authored on 17/05/2019 14:29:43
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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.19.2
2
+-------------------------
3
+ o Fix issue 190, compiles on clang-8.0 
4
+
1 5
 CHANGES IN VERSION 2.19.1
2 6
 -------------------------
3 7
  o Remove analyzer generics, now in ProtGenerics <2019-05-13 Mon>
Browse code

analyzr generic now in ProtGenerics

Laurent Gatto authored on 13/05/2019 20:42:11
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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.19.1
2
+-------------------------
3
+ o Remove analyzer generics, now in ProtGenerics <2019-05-13 Mon>
4
+
1 5
 CHANGES IN VERSION 2.17.4
2 6
 -------------------------
3 7
  o Update documentation, pointing to MSnbase rather than directly use
Browse code

add not for developers to use OnDiskMSnExp

Laurent Gatto authored on 17/04/2019 15:03:08
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@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.17.4
2
+-------------------------
3
+ o Update documentation, pointing to MSnbase rather than directly use
4
+   low-level classes. <2019-04-17 Wed>
5
+
1 6
 CHANGES IN VERSION 2.17.3
2 7
 -------------------------
3 8
  o Extract isolation window from mzML files (issue #193): data.frame returned
... ...
@@ -14,9 +19,9 @@ CHANGES IN VERSION 2.15.5
14 19
 
15 20
 CHANGES IN VERSION 2.15.4
16 21
 -------------------------
17
- o Use new dependency ncdf4 for netCDF reading, 
22
+ o Use new dependency ncdf4 for netCDF reading,
18 23
    removes a lot of build hassles with old libnetcdf-dev linking.
19
- o specParams returns a numeric scan.number.s. 
24
+ o specParams returns a numeric scan.number.s.
20 25
 
21 26
 CHANGES IN VERSION 2.15.3
22 27
 -------------------------
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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@@ -1,3 +1,9 @@
1
+CHANGES IN VERSION 2.17.3
2
+-------------------------
3
+ o Extract isolation window from mzML files (issue #193): data.frame returned
4
+   by header gains columns "isolationWindowTargetMZ",
5
+   "isolationWindowLowerOffset", "isolationWindowUpperOffset".
6
+
1 7
 CHANGES IN VERSION 2.17.2
2 8
 -------------------------
3 9
  o Fix bug #185: Error in R_nc4_open: Too many open files
Browse code

Bump version after merge which closes #185

Steffen Neumann authored on 05/03/2019 15:26:12
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@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.17.2
2
+-------------------------
3
+ o Fix bug #185: Error in R_nc4_open: Too many open files
4
+
1 5
 CHANGES IN VERSION 2.15.5
2 6
 -------------------------
3 7
  o Fix bug #181
Browse code

reference correct issue number

Laurent authored on 15/09/2018 21:11:27
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... ...
@@ -1,6 +1,6 @@
1 1
 CHANGES IN VERSION 2.15.5
2 2
 -------------------------
3
- o Fix bug #188
3
+ o Fix bug #181
4 4
 
5 5
 CHANGES IN VERSION 2.15.4
6 6
 -------------------------
Browse code

Closing #181

Steffen Neumann authored on 15/09/2018 20:11:56
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@@ -1,6 +1,6 @@
1 1
 CHANGES IN VERSION 2.15.5
2 2
 -------------------------
3
- o nothing yet
3
+ o Fix bug #188
4 4
 
5 5
 CHANGES IN VERSION 2.15.4
6 6
 -------------------------
Browse code

bump gh devel version

Laurent authored on 13/09/2018 21:15:13
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... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.15.5
2
+-------------------------
3
+ o nothing yet
4
+
1 5
 CHANGES IN VERSION 2.15.4
2 6
 -------------------------
3 7
  o Use new dependency ncdf4 for netCDF reading, 
Browse code

update news

Laurent authored on 13/09/2018 21:14:04
Showing 1 changed files
... ...
@@ -2,6 +2,7 @@ CHANGES IN VERSION 2.15.4
2 2
 -------------------------
3 3
  o Use new dependency ncdf4 for netCDF reading, 
4 4
    removes a lot of build hassles with old libnetcdf-dev linking.
5
+ o specParams returns a numeric scan.number.s. 
5 6
 
6 7
 CHANGES IN VERSION 2.15.3
7 8
 -------------------------
Browse code

Bump version. Merged changes close #178

Steffen Neumann authored on 12/09/2018 06:47:30
Showing 1 changed files
... ...
@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.15.4
2
+-------------------------
3
+ o Use new dependency ncdf4 for netCDF reading, 
4
+   removes a lot of build hassles with old libnetcdf-dev linking.
5
+
1 6
 CHANGES IN VERSION 2.15.3
2 7
 -------------------------
3 8
  o Adds MS-GF+ information such as Scan Time and a more reliable Scan
Browse code

update news with BiocManager fix

Laurent authored on 03/09/2018 13:10:17
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... ...
@@ -1,13 +1,15 @@
1 1
 CHANGES IN VERSION 2.15.3
2 2
 -------------------------
3
-o Adds MS-GF+ information such as Scan Time and a more reliable Scan
4
-  Number, contributed by FarmGeek4Life (see PR #174).
3
+ o Adds MS-GF+ information such as Scan Time and a more reliable Scan
4
+   Number, contributed by FarmGeek4Life (see PR #174).
5 5
 
6 6
 CHANGES IN VERSION 2.15.2
7 7
 -------------------------
8 8
  o Add header column ionMobilityDriftTime to report the corresponding CV
9 9
    parameter (issue https://github.com/sneumann/mzR/issues/44).
10 10
  o Ensure ion injection time is always reported in milliseconds.
11
+ o Replace BiocInstaller::biocLite with BiocManager::install (by Bioc
12
+   core)
11 13
 
12 14
 CHANGES IN VERSION 2.15.1
13 15
 -------------------------
Browse code

bump version and update news

Laurent authored on 03/09/2018 12:40:27
Showing 1 changed files
... ...
@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.15.3
2
+-------------------------
3
+o Adds MS-GF+ information such as Scan Time and a more reliable Scan
4
+  Number, contributed by FarmGeek4Life (see PR #174).
5
+
1 6
 CHANGES IN VERSION 2.15.2
2 7
 -------------------------
3 8
  o Add header column ionMobilityDriftTime to report the corresponding CV
Browse code

Add ionMobilityDriftTime to header (issue #44)

- Extract the ion mobility drift time from mzML files (if available).
- Ensure that ion injection time is always reported in milliseconds.
- Update unit tests and documentation.

jotsetung authored on 30/08/2018 09:25:03
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... ...
@@ -1,6 +1,8 @@
1
-CHANGES IN VERSION 2.15.1
1
+CHANGES IN VERSION 2.15.2
2 2
 -------------------------
3
- o Nothing yet
3
+ o Add header column ionMobilityDriftTime to report the corresponding CV
4
+   parameter (issue https://github.com/sneumann/mzR/issues/44).
5
+ o Ensure ion injection time is always reported in milliseconds.
4 6
 
5 7
 CHANGES IN VERSION 2.15.1
6 8
 -------------------------
Browse code

merge gh version

Laurent authored on 26/05/2018 21:01:44
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.15.1
2
+-------------------------
3
+ o Nothing yet
4
+
1 5
 CHANGES IN VERSION 2.15.1
2 6
 -------------------------
3 7
  o Fix typo (see https://github.com/sneumann/mzR/pull/162)
Browse code

Fix bug in score when more cvParams than expected are read - close #136

Laurent authored on 26/05/2018 20:44:04
Showing 1 changed files
... ...
@@ -3,6 +3,8 @@ CHANGES IN VERSION 2.15.1
3 3
  o Fix typo (see https://github.com/sneumann/mzR/pull/162)
4 4
  o New .hasSpectra and .hasChromatograms private function (see
5 5
    https://github.com/lgatto/MSnbase/issues/343)
6
+ o Fix bug in score when more cvParams than expected are read - see
7
+   https://github.com/sneumann/mzR/issues/136 <2018-05-26 Sat>
6 8
 
7 9
 CHANGES IN VERSION 2.15.0
8 10
 -------------------------
... ...
@@ -35,7 +37,7 @@ CHANGES IN VERSION 2.13.3
35 37
  o Link against Rhdf5lib, allows to read mz5 also on Windows
36 38
  o Use Rhdf5lib 1.1.4 with c++ headers in /include
37 39
  o fix BiocStyle related issue in Vignette on Windows
38
- 
40
+
39 41
 CHANGES IN VERSION 2.13.2
40 42
 --------------------------
41 43
  o Add chromatogramHeader method to read header information for chromatograms
... ...
@@ -47,12 +49,12 @@ CHANGES IN VERSION 2.13.1
47 49
    the header function (see MSnbase issue #278).
48 50
  o openMsFile automatically determine the backend to use based on file extension
49 51
    and content.
50
- 
52
+
51 53
 CHANGES IN VERSION 2.11.11
52 54
 --------------------------
53 55
  o Fix problem in writeMSData: ensure precursor data is saved even if precursor
54 56
    scan is not available (see MSnbase issue #245).
55
- 
57
+
56 58
 CHANGES IN VERSION 2.11.10
57 59
 --------------------------
58 60
  o Fix problem that can cause a SEGFAULT in writeMSData/copyWriteMSData when MS
... ...
@@ -70,33 +72,33 @@ CHANGES IN VERSION 2.11.8
70 72
  o Report the spectrum ID in the header data.frame (column spectrumId).
71 73
  o Fix in copyWriteMSData and writeMSData ensuring that MSn data is correctly
72 74
  o Import pwiz r11174 fix for mzML without <componentList> (see #113).
73
- 
75
+
74 76
 CHANGES IN VERSION 2.11.7
75 77
 -------------------------
76 78
  o Nothing yet.
77 79
  o Import fix by Brian Pratt (pwiz r11174) for mzML without <componentList>
78
-   Another way to fix #113 
80
+   Another way to fix #113
79 81
  o Removing mz5 support from manual page, as currently unsupported.
80
- 
82
+
81 83
 CHANGES IN VERSION 2.11.6
82 84
 -------------------------
83 85
  o runInfo returns the run start time stamp from files providing this
84 86
    information (mzML files).
85
- 
87
+
86 88
 CHANGES IN VERSION 2.11.5
87 89
 -------------------------
88 90
  o writeMSData and copyWriteMSData functions enabling to export MS data to
89 91
    mzML or mzXML files.
90
- 
92
+
91 93
 CHANGES IN VERSION 2.11.4
92 94
 -------------------------
93 95
  o Use full TMT file pattern to select a single file
94
- 
96
+
95 97
 CHANGES IN VERSION 2.11.3
96 98
 -------------------------
97 99
  o Read ion injection time from mzML files and add it to the data.frame returned
98 100
    by the header function.
99
- 
101
+
100 102
 CHANGES IN VERSION 2.11.2
101 103
 -------------------------
102 104
  o New getScanHeaderInfo and getAllScanHeaderInfo implementations for the pwiz
... ...
@@ -109,7 +111,7 @@ CHANGES IN VERSION 2.11.1
109 111
 CHANGES IN VERSION 2.11.0
110 112
 -------------------------
111 113
  o Bioc devel 3.6
112
- 
114
+
113 115
 CHANGES IN VERSION 2.10.0
114 116
 -------------------------
115 117
  o Bioc release 3.5
... ...
@@ -120,7 +122,7 @@ CHANGES IN VERSION 2.9.11
120 122
 
121 123
 CHANGES IN VERSION 2.9.10
122 124
 -------------------------
123
- o Remove register keyword causing WARNING. 
125
+ o Remove register keyword causing WARNING.
124 126
 
125 127
 CHANGES IN VERSION 2.9.9
126 128
 ------------------------
... ...
@@ -137,25 +139,25 @@ CHANGES IN VERSION 2.9.7
137 139
 CHANGES IN VERSION 2.9.6
138 140
 ------------------------
139 141
  o Compile on macOS, but hdf5 path hard-coded
140
- 
142
+
141 143
 CHANGES IN VERSION 2.9.5
142 144
 ------------------------
143 145
  o Add missing boost/config/platform/macos.hpp <2017-01-25 Wed>
144
- 
146
+
145 147
 CHANGES IN VERSION 2.9.4
146 148
 ------------------------
147 149
  o New chromatogram accessors (for pwiz backend only) - see issue #73
148 150
    <2017-01-23 Mon>
149
- 
151
+
150 152
 CHANGES IN VERSION 2.9.3
151 153
 ------------------------
152 154
  o bump to new Rcpp 0.12.8 version <2017-01-05 Thu>
153
- 
155
+
154 156
 CHANGES IN VERSION 2.9.2
155 157
 ------------------------
156 158
  o cleanup CFLAGS and LIBS for libnetcdf
157 159
  o add file missing for oaxaca (Apple clang 3.5svn / 600.0.57)
158
- 
160
+
159 161
 CHANGES IN VERSION 2.9.1
160 162
 ------------------------
161 163
  o Delete RAMPAdapter pointer in pwiz backend (by jotsetung)
... ...
@@ -167,7 +169,7 @@ CHANGES IN VERSION 2.9.1
167 169
 CHANGES IN VERSION 2.9.0
168 170
 ------------------------
169 171
  o Bioc devel 3.5
170
- 
172
+
171 173
 CHANGES IN VERSION 2.8.0
172 174
 ------------------------
173 175
  o Bioc release 3.4
... ...
@@ -175,40 +177,40 @@ CHANGES IN VERSION 2.8.0
175 177
 CHANGES IN VERSION 2.7.13
176 178
 -------------------------
177 179
  o Fix waring on OSX (see issue #60)
178
- 
180
+
179 181
 CHANGES IN VERSION 2.7.12
180 182
 -------------------------
181 183
  o Fixing last warning on MacOS
182
- 
184
+
183 185
 CHANGES IN VERSION 2.7.11
184 186
 -------------------------
185 187
  o Fix failing example and test due to updated msdata::protemics data
186
- 
188
+
187 189
 CHANGES IN VERSION 2.7.10
188 190
 -------------------------
189 191
  o compiling and loading on Windows (hopefully)
190
- 
192
+
191 193
 CHANGES IN VERSION 2.7.9
192 194
 ------------------------
193
- o Updating Makevars.win 
194
- 
195
+ o Updating Makevars.win
196
+
195 197
 CHANGES IN VERSION 2.7.8
196 198
 ------------------------
197 199
  o compile pwiz when installing on Windows <2016-09-26 Mon>
198
- 
200
+
199 201
 CHANGES IN VERSION 2.7.7
200 202
 ------------------------
201 203
  o add netcdf static lib; potential incompatibility <2016-09-22 Thu>
202
- 
204
+
203 205
 CHANGES IN VERSION 2.7.6
204 206
 ------------------------
205 207
  o new isolationWindow accessor <2016-09-23 Fri>
206
- 
208
+
207 209
 CHANGES IN VERSION 2.7.5
208 210
 ------------------------
209 211
  o Apply Martin's free/delete patch - see
210 212
    https://github.com/sneumann/mzR/issues/52 <2016-09-22 Thu>
211
- 
213
+
212 214
 CHANGES IN VERSION 2.7.4
213 215
 ------------------------
214 216
  o upgrade pwiz
Browse code

update news

Laurent authored on 16/05/2018 13:39:38
Showing 1 changed files
... ...
@@ -1,7 +1,7 @@
1 1
 CHANGES IN VERSION 2.15.1
2 2
 -------------------------
3 3
  o Fix typo (see https://github.com/sneumann/mzR/pull/162)
4
- o New .hasSpectra private function (see
4
+ o New .hasSpectra and .hasChromatograms private function (see
5 5
    https://github.com/lgatto/MSnbase/issues/343)
6 6
 
7 7
 CHANGES IN VERSION 2.15.0
Browse code

new .hasSpectra function

Laurent authored on 16/05/2018 07:30:42
Showing 1 changed files
... ...
@@ -1,6 +1,8 @@
1 1
 CHANGES IN VERSION 2.15.1
2 2
 -------------------------
3
- o Fix type (see https://github.com/sneumann/mzR/pull/162)
3
+ o Fix typo (see https://github.com/sneumann/mzR/pull/162)
4
+ o New .hasSpectra private function (see
5
+   https://github.com/lgatto/MSnbase/issues/343)
4 6
 
5 7
 CHANGES IN VERSION 2.15.0
6 8
 -------------------------
Browse code

bump version

Laurent authored on 09/05/2018 02:58:38
Showing 1 changed files
... ...
@@ -1,3 +1,11 @@
1
+CHANGES IN VERSION 2.15.1
2
+-------------------------
3
+ o Fix type (see https://github.com/sneumann/mzR/pull/162)
4
+
5
+CHANGES IN VERSION 2.15.0
6
+-------------------------
7
+ o New Bioc devel version
8
+
1 9
 CHANGES IN VERSION 2.13.8
2 10
 -------------------------
3 11
  o Document missing chrom argument for chromatogram(s)
Browse code

Document missing chrom argument for chromatogram(s)

Sebastian Gibb authored on 29/04/2018 07:53:05
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.13.8
2
+-------------------------
3
+ o Document missing chrom argument for chromatogram(s)
4
+
1 5
 CHANGES IN VERSION 2.13.7
2 6
 -------------------------
3 7
  o Add a missing header needed on gcc 6.2.0
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
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.13.7
2
+-------------------------
3
+ o Add a missing header needed on gcc 6.2.0
4
+
1 5
 CHANGES IN VERSION 2.13.6
2 6
 -------------------------
3 7
  o Add MS CV Term IDs for mzR, MSnbase and CAMERA (issue #151)
Browse code

update news

Laurent authored on 29/03/2018 09:15:30
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES IN VERSION 2.13.6
2 2
 -------------------------
3
- o Nothing yet
3
+ o Add MS CV Term IDs for mzR, MSnbase and CAMERA (issue #151)
4
+ o Validate exported mzML files using xsd
4 5
 
5 6
 CHANGES IN VERSION 2.13.5
6 7
 -------------------------
Browse code

new github devel version

Laurent authored on 07/03/2018 19:17:55
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.13.6
2
+-------------------------
3
+ o Nothing yet
4
+
1 5
 CHANGES IN VERSION 2.13.5
2 6
 -------------------------
3 7
  o Fix https://github.com/sneumann/xcms/issues/261
Browse code

udpate news for PR #149

Laurent authored on 07/03/2018 19:16:57
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES IN VERSION 2.13.5
2 2
 -------------------------
3 3
  o Fix https://github.com/sneumann/xcms/issues/261
4
+ o Fix endian.hpp for new c++ versions (see PR #149)
4 5
 
5 6
 CHANGES IN VERSION 2.13.4
6 7
 -------------------------
Browse code

update news

Laurent authored on 07/03/2018 19:11:36
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.13.5
2
+-------------------------
3
+ o Fix https://github.com/sneumann/xcms/issues/261
4
+
1 5
 CHANGES IN VERSION 2.13.4
2 6
 -------------------------
3 7
  o Fix error (see issue #145)
Browse code

bump version and update news

Laurent authored on 26/02/2018 11:03:13
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.13.4
2
+-------------------------
3
+ o Fix error (see issue #145)
4
+
1 5
 CHANGES IN VERSION 2.13.3
2 6
 -------------------------
3 7
  o Link against Rhdf5lib, allows to read mz5 also on Windows
Browse code

Update NEWS

sneumann authored on 10/01/2018 07:52:57 • GitHub committed on 10/01/2018 07:52:57
Showing 1 changed files
... ...
@@ -1,6 +1,8 @@
1 1
 CHANGES IN VERSION 2.13.3
2 2
 -------------------------
3
+ o Link against Rhdf5lib, allows to read mz5 also on Windows
3 4
  o Use Rhdf5lib 1.1.4 with c++ headers in /include
5
+ o fix BiocStyle related issue in Vignette on Windows
4 6
  
5 7
 CHANGES IN VERSION 2.13.2
6 8
 --------------------------
Browse code

update NEWS file

Laurent authored on 09/01/2018 20:59:38
Showing 1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 CHANGES IN VERSION 2.13.3
2 2
 -------------------------
3
- o Nothing yet
3
+ o Use Rhdf5lib 1.1.4 with c++ headers in /include
4 4
  
5 5
 CHANGES IN VERSION 2.13.2
6 6
 --------------------------
Browse code

Add NEWS. Now Closes #146, Closes #122 and Closes #123

Steffen Neumann authored on 09/01/2018 18:41:38
Showing 1 changed files
... ...
@@ -1,7 +1,6 @@
1 1
 CHANGES IN VERSION 2.13.3
2 2
 -------------------------
3
- o Link against Rhdf5lib, allows to read mz5 also on Windows
4
- o fix Vignette on Windows
3
+ o Nothing yet
5 4
  
6 5
 CHANGES IN VERSION 2.13.2
7 6
 --------------------------
Browse code

Add NEWS. Now Closes #146, Closes #122 and Closes #123

Steffen Neumann authored on 09/01/2018 18:40:10
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES IN VERSION 2.13.3
2 2
 -------------------------
3
- o Nothing yet
3
+ o Link against Rhdf5lib, allows to read mz5 also on Windows
4
+ o fix Vignette on Windows
4 5
  
5 6
 CHANGES IN VERSION 2.13.2
6 7
 --------------------------
Browse code

bump gh devel version

Laurent authored on 21/12/2017 13:54:49
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.13.3
2
+-------------------------
3
+ o Nothing yet
4
+ 
1 5
 CHANGES IN VERSION 2.13.2
2 6
 --------------------------
3 7
  o Add chromatogramHeader method to read header information for chromatograms
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
Showing 1 changed files
... ...
@@ -1,3 +1,8 @@
1
+CHANGES IN VERSION 2.13.2
2
+--------------------------
3
+ o Add chromatogramHeader method to read header information for chromatograms
4
+   from an mzML file.
5
+
1 6
 CHANGES IN VERSION 2.13.1
2 7
 --------------------------
3 8
  o Read filter string from mzML files and add it to the data.frame returned by
Browse code

Merge branch 'master' into filterString

Laurent Gatto authored on 24/11/2017 14:12:57 • GitHub committed on 24/11/2017 14:12:57
Showing 0 changed files
Browse code

Add NEWS entry

Sebastian Gibb authored on 24/11/2017 11:39:48
Showing 1 changed files
... ...
@@ -1,7 +1,8 @@
1 1
 CHANGES IN VERSION 2.11.12
2 2
 --------------------------
3
- o Nothing yet
4
- 
3
+ o Read filter string from mzML files and add it to the data.frame returned by
4
+   the header function (see MSnbase issue #278).
5
+
5 6
 CHANGES IN VERSION 2.11.11
6 7
 --------------------------
7 8
  o Fix problem in writeMSData: ensure precursor data is saved even if precursor
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
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1
-CHANGES IN VERSION 2.11.12
1
+CHANGES IN VERSION 2.13.1
2 2
 --------------------------
3
- o Nothing yet
3
+ o openMsFile automatically determine the backend to use based on file extension
4
+   and content.
4 5
  
5 6
 CHANGES IN VERSION 2.11.11
6 7
 --------------------------
Browse code

bump gh devel version

Laurent authored on 22/09/2017 22:01:32
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.11.12
2
+--------------------------
3
+ o Nothing yet
4
+ 
1 5
 CHANGES IN VERSION 2.11.11
2 6
 --------------------------
3 7
  o Fix problem in writeMSData: ensure precursor data is saved even if precursor
Browse code

Update NEWS

jotsetung authored on 19/09/2017 06:18:45
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1
-CHANGES IN VERSION 2.11.10
1
+CHANGES IN VERSION 2.11.11
2 2
 --------------------------
3
- o Nothing yet
3
+ o Fix problem in writeMSData: ensure precursor data is saved even if precursor
4
+   scan is not available (see MSnbase issue #245).
4 5
  
5 6
 CHANGES IN VERSION 2.11.10
6 7
 --------------------------
Browse code

bump gh devel version

Laurent authored on 18/09/2017 14:55:57
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.11.10
2
+--------------------------
3
+ o Nothing yet
4
+ 
1 5
 CHANGES IN VERSION 2.11.10
2 6
 --------------------------
3 7
  o Fix problem that can cause a SEGFAULT in writeMSData/copyWriteMSData when MS
Browse code

Fix potential SEGFAULT in writeMSData/copyWriteMSData

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

jotsetung authored on 14/09/2017 06:24:41
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES IN VERSION 2.11.10
2 2
 --------------------------
3
- o Nothing yet
3
+ o Fix problem that can cause a SEGFAULT in writeMSData/copyWriteMSData when MS
4
+   data with spectra linking to missing precursor scans is saved (issue #129).
4 5
 
5 6
 CHANGES IN VERSION 2.11.9
6 7
 -------------------------
Browse code

bump gh devel version

Laurent authored on 11/09/2017 06:58:30
Showing 1 changed files
... ...
@@ -1,7 +1,11 @@
1
+CHANGES IN VERSION 2.11.10
2
+--------------------------
3
+ o Nothing yet
4
+
1 5
 CHANGES IN VERSION 2.11.9
2 6
 -------------------------
3
-o Update peaks man page with details about spectrumId, acquisitionNum
4
-  and seqNum
7
+ o Update peaks man page with details about spectrumId, acquisitionNum
8
+   and seqNum
5 9
 
6 10
 CHANGES IN VERSION 2.11.8
7 11
 -------------------------
Browse code

update news

Laurent authored on 11/09/2017 06:31:58
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES IN VERSION 2.11.9
2 2
 -------------------------
3
-o Nothing yet <2017-09-08 Fri>
3
+o Update peaks man page with details about spectrumId, acquisitionNum
4
+  and seqNum
4 5
 
5 6
 CHANGES IN VERSION 2.11.8
6 7
 -------------------------
Browse code

update news

Laurent authored on 10/09/2017 21:10:04
Showing 1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 2.11.9
2
+-------------------------
3
+o Nothing yet <2017-09-08 Fri>
4
+
1 5
 CHANGES IN VERSION 2.11.8
2 6
 -------------------------
3 7
  o Add contributions guide with code of conduct.
Browse code

Merge branch 'master' into spectrumId

Laurent Gatto authored on 08/09/2017 14:24:55 • GitHub committed on 08/09/2017 14:24:55
Showing 0 changed files
Browse code

update news

Laurent authored on 08/09/2017 13:31:24
Showing 1 changed files
... ...
@@ -2,6 +2,7 @@ CHANGES IN VERSION 2.11.8
2 2
 -------------------------
3 3
  o Add contributions guide with code of conduct.
4 4
  o Update installation instructions for Mac.
5
+ o Import pwiz r11174 fix for mzML without <componentList> (see #113).
5 6
  
6 7
 CHANGES IN VERSION 2.11.7
7 8
 -------------------------
Browse code

Merge branch 'master' into featureUpdateLegacyAdapter

Laurent Gatto authored on 08/09/2017 12:31:30 • GitHub committed on 08/09/2017 12:31:30
Showing 0 changed files
Browse code

Merge NEWS file

jotsetung authored on 08/09/2017 12:07:56
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES IN VERSION 2.11.8
2 2
 -------------------------
3 3
  o Add contributions guide with code of conduct.
4
+ o Update installation instructions for Mac.
4 5
  o Report the spectrum ID in the header data.frame (column spectrumId).
5 6
  o Fix in copyWriteMSData and writeMSData ensuring that MSn data is correctly
6 7
    saved.
Browse code

update NEWS

Laurent authored on 08/09/2017 11:43:21
Showing 1 changed files
... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES IN VERSION 2.11.8
2 2
 -------------------------
3 3
  o Add contributions guide with code of conduct.
4
+ o Update installation instructions for Mac.
4 5
  
5 6
 CHANGES IN VERSION 2.11.7
6 7
 -------------------------
Browse code

Read spectrumId using pwiz backend

- Read the spectrum ID with the pwiz backend and report the ID in the header
column spectrumId (issue #124).
- Update related documentation and unit tests.
- Fix assignment between spectra and precursor spectra based on the spectrum ID.

jotsetung authored on 07/09/2017 16:09:12
Showing 1 changed files
... ...
@@ -1,7 +1,10 @@
1 1
 CHANGES IN VERSION 2.11.8
2 2
 -------------------------
3