Steffen Neumann authored on 24/05/2022 08:45:03
- Don't export/write header variables with missing values (issue #266).
jorainer authored on 22/04/2022 13:50:18
| ... | ... |
@@ -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
- `peaks` method for the proteowizard backend also peaks matrices with colnames
set.
jorainer authored on 18/03/2022 10:38:45
Steffen Neumann authored on 14/03/2022 10:47:04
| ... | ... |
@@ -1,3 +1,8 @@ |
| 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 |
------------------------- |
Steffen Neumann authored on 25/01/2022 16:30:31
• GitHub committed on 25/01/2022 16:30:31
Steffen Neumann authored on 25/01/2022 09:42:19
| ... | ... |
@@ -1,9 +1,13 @@ |
| 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 |
Steffen Neumann authored on 13/01/2022 20:21:45
- Fix header for pwiz backend to always return a `data.frame`.
- Update documentation.
jorainer authored on 25/11/2021 08:27:02
| ... | ... |
@@ -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 |
------------------------- |
Steffen Neumann authored on 20/11/2021 11:19:02
Steffen Neumann authored on 27/10/2021 12:39:10
- 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
| ... | ... |
@@ -1,3 +1,12 @@ |
| 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) |
jorainer authored on 20/09/2021 12:19:56
Laurent Gatto authored on 18/06/2021 16:37:31
Steffen Neumann authored on 08/05/2021 14:06:08
Steffen Neumann authored on 17/04/2021 14:44:00
jorainer authored on 08/02/2021 12:19:25
- Fix for issue #238: ensure `header` returns the same columns for all backends.
jorainer authored on 02/02/2021 18:46:29
Laurent Gatto authored on 18/11/2020 13:41:52
| ... | ... |
@@ -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 |
Laurent Gatto authored on 29/03/2020 14:58:52
| ... | ... |
@@ -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 |
Steffen Neumann authored on 14/12/2019 14:37:39
Steffen Neumann authored on 15/10/2019 08:55:51
| ... | ... |
@@ -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 |
Laurent Gatto authored on 02/10/2019 19:48:01
| ... | ... |
@@ -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 |
- Rewrite the C++ code for peak data extraction with the pwiz backend.
- Fix unit tests.
jorainer authored on 26/09/2019 10:09:04
| ... | ... |
@@ -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 |
------------------------- |
- 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
| ... | ... |
@@ -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 |
- 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
Laurent Gatto authored on 16/08/2019 15:56:49
| ... | ... |
@@ -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 |
------------------------- |
Steffen Neumann authored on 17/05/2019 14:29:43
Laurent Gatto authored on 13/05/2019 20:42:11
Laurent Gatto authored on 17/04/2019 15:03:08
| ... | ... |
@@ -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 |
------------------------- |
- 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
| ... | ... |
@@ -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 |
Steffen Neumann authored on 05/03/2019 15:26:12
Laurent authored on 15/09/2018 21:11:27
Steffen Neumann authored on 15/09/2018 20:11:56
Laurent authored on 13/09/2018 21:15:13
Laurent authored on 13/09/2018 21:14:04
| ... | ... |
@@ -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 |
------------------------- |
Steffen Neumann authored on 12/09/2018 06:47:30
| ... | ... |
@@ -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 |
Laurent authored on 03/09/2018 13:10:17
| ... | ... |
@@ -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 |
------------------------- |
Laurent authored on 03/09/2018 12:40:27
| ... | ... |
@@ -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 |
- 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
| ... | ... |
@@ -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 |
------------------------- |
Laurent authored on 26/05/2018 21:01:44
Laurent authored on 26/05/2018 20:44:04
| ... | ... |
@@ -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 |
Laurent authored on 16/05/2018 13:39:38
| ... | ... |
@@ -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 |
Laurent authored on 16/05/2018 07:30:42
| ... | ... |
@@ -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 |
------------------------- |
Laurent authored on 09/05/2018 02:58:38
| ... | ... |
@@ -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) |
Sebastian Gibb authored on 29/04/2018 07:53:05
Steffen Neumann authored on 27/04/2018 20:41:27
Laurent authored on 29/03/2018 09:15:30
Laurent authored on 07/03/2018 19:17:55
Laurent authored on 07/03/2018 19:16:57
Laurent authored on 07/03/2018 19:11:36
Laurent authored on 26/02/2018 11:03:13
| ... | ... |
@@ -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 |
-------------------------- |
Laurent authored on 09/01/2018 20:59:38
Steffen Neumann authored on 09/01/2018 18:41:38
Steffen Neumann authored on 09/01/2018 18:40:10
Laurent authored on 21/12/2017 13:54:49
- Add a chromatogramHeader method to extract chromatogram header information
from an mzML file (issue #141).
jotsetung authored on 11/12/2017 09:26:45
| ... | ... |
@@ -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 |
Laurent Gatto authored on 24/11/2017 14:12:57
• GitHub committed on 24/11/2017 14:12:57
Sebastian Gibb authored on 24/11/2017 11:39:48
| ... | ... |
@@ -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 |
- 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
Laurent authored on 22/09/2017 22:01:32
jotsetung authored on 19/09/2017 06:18:45
| ... | ... |
@@ -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 |
-------------------------- |
Laurent authored on 18/09/2017 14:55:57
- 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
| ... | ... |
@@ -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 |
------------------------- |
Laurent authored on 11/09/2017 06:58:30
| ... | ... |
@@ -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 |
------------------------- |
Laurent authored on 11/09/2017 06:31:58
Laurent authored on 10/09/2017 21:10:04
Laurent Gatto authored on 08/09/2017 14:24:55
• GitHub committed on 08/09/2017 14:24:55
Laurent authored on 08/09/2017 13:31:24
| ... | ... |
@@ -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 |
------------------------- |
Laurent Gatto authored on 08/09/2017 12:31:30
• GitHub committed on 08/09/2017 12:31:30
jotsetung authored on 08/09/2017 12:07:56
| ... | ... |
@@ -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. |
Laurent authored on 08/09/2017 11:43:21
- 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
| ... | ... |
@@ -1,7 +1,10 @@ |
| 1 | 1 |
CHANGES IN VERSION 2.11.8 |
| 2 | 2 |
------------------------- |
| 3 | 3 |
o Add contributions guide with code of conduct. |
| 4 |
- |
|
| 4 |
+ o Report the spectrum ID in the header data.frame (column spectrumId). |
|
| 5 |
+ o Fix in copyWriteMSData and writeMSData ensuring that MSn data is correctly |
|
| 6 |
+ saved. |
|
| 7 |
+ |
|
| 5 | 8 |
CHANGES IN VERSION 2.11.7 |
| 6 | 9 |
------------------------- |
| 7 | 10 |
o Removing mz5 support from manual page, as currently unsupported. |
Laurent authored on 22/08/2017 13:32:37
Laurent authored on 15/08/2017 07:56:49