From 9cee1fcbe87959a550b7d45eb7288a6438ef9c41 Mon Sep 17 00:00:00 2001 From: Thomas N Lawson Date: Wed, 30 Aug 2023 10:41:24 +0100 Subject: [PATCH] update news, description and github workflow --- .github/workflows/check-bioc.yml | 8 +- DESCRIPTION | 4 +- NEWS | 220 +++++++++++++------------------ 3 files changed, 100 insertions(+), 132 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 4e2141f..37475e7 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -278,8 +278,14 @@ jobs: BiocCheck::BiocCheck( dir('check', 'tar.gz$', full.names = TRUE), `quit-with-status` = TRUE, + `no-check-namespace` = TRUE, + `no-check-pkg-size` = TRUE, + `no-check-file-size` = TRUE, + `no-check-version-num` = TRUE, `no-check-R-ver` = TRUE, - `no-check-bioc-help` = TRUE + `no-check-bioc-help` = TRUE, + `no-check-dependencies` = TRUE + ) shell: Rscript {0} diff --git a/DESCRIPTION b/DESCRIPTION index 31b08b4..e8541da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: msPurity Type: Package Title: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics -Version: 1.21.2 -Date: 2022-04-12 +Version: 1.27.1 +Date: 2023-08-30 Authors@R: c( person(given = "Thomas N.", family = "Lawson", email = "thomas.nigel.lawson@gmail.com", role = c("aut", "cre"), diff --git a/NEWS b/NEWS index aba3ca7..5394dcd 100644 --- a/NEWS +++ b/NEWS @@ -1,219 +1,181 @@ +CHANGES IN VERSION 1.27.1 ++ createMSP fix - now uses outputs the median precursor MZ and precursor intensity in the MSP file + + CHANGES IN VERSION 1.21.2 -========================= -* Fixes due to mz and intensity being named in columns for mzR and XCMS -* Fixes for connection{base} file() opening changes (no longer accept w+a in function in R v4.2) -* Update tests for the above -* Update a reference of grpid in averageXFragSpectra functions more explicit (no change in functionality) -* Typo fix in vignette ++ Fixes due to mz and intensity being named in columns for mzR and XCMS ++ Fixes for connection{base} file() opening changes (no longer accept w+a in function in R v4.2) ++ Update tests for the above ++ Update a reference of grpid in averageXFragSpectra functions more explicit (no change in functionality) ++ Typo fix in vignette CHANGES IN VERSION 1.21.1 -========================= -* Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93 -* Remove imports that are no longer used ++ Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93 ++ Remove imports that are no longer used CHANGES IN VERSION 1.19.2 -========================= -* XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91 ++ XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91 CHANGES IN VERSION 1.19.1 -========================= -* Bug fix for flagRemove (full width was not calculated as expected) ++ Bug fix for flagRemove (full width was not calculated as expected) CHANGES IN VERSION 1.17.2 -========================= -* Update dev to match bug fixes in master ++ Update dev to match bug fixes in master CHANGES IN VERSION 1.16.2 -========================= -* Author list updated ++ Author list updated CHANGES IN VERSION 1.17.1 -========================= -* Update dev to match bug fixes in master ++ Update dev to match bug fixes in master CHANGES IN VERSION 1.16.1 -========================= -* Update of createDatabase to record all intra average spectra in database -* Add license and copyright info to code -* Add github workflow CI (and subsequent formatting updates to pass tests) ++ Update of createDatabase to record all intra average spectra in database ++ Add license and copyright info to code ++ Add github workflow CI (and subsequent formatting updates to pass tests) CHANGES IN VERSION 1.15.1 -========================= -* Update dev to match bug fixes in master ++ Update dev to match bug fixes in master CHANGES IN VERSION 1.14.1 -========================= -* Update of rdpc algorithm (see https://github.com/computational-metabolomics/msPurity/issues/78) -* Update of align algorithm (see https://github.com/computational-metabolomics/msPurity/issues/79) -* Fix for spectralMatching of type 'scan' previously incorrectly outputing no matches ++ Update of rdpc algorithm (see https://github.com/computational-metabolomics/msPurity/issues/78) ++ Update of align algorithm (see https://github.com/computational-metabolomics/msPurity/issues/79) ++ Fix for spectralMatching of type 'scan' previously incorrectly outputing no matches CHANGES IN VERSION 1.13.2 -========================= -* Update dev to match bug fixes in master ++ Update dev to match bug fixes in master CHANGES IN VERSION 1.12.2 -========================= -* Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded) ++ Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded) CHANGES IN VERSION 1.13.1 -========================= -* Update dev to match bug fixes in master ++ Update dev to match bug fixes in master CHANGES IN VERSION 1.12.1 -========================= -* Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly -* Fillpeaks bug fix see github #68 -* Documentation fixes ++ Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly ++ Fillpeaks bug fix see github #68 ++ Documentation fixes CHANGES IN VERSION 1.13.0 -========================= -* Bioconductor dev (automatic version bump) ++ Bioconductor dev (automatic version bump) CHANGES IN VERSION 1.12.0 -========================= -* Bioconductor release (automatic version bump) ++ Bioconductor release (automatic version bump) CHANGES IN VERSION 1.11.5 -========================= -* frag4feature fileid fix for conversion from factor to character -* Add missing plyr:: reference (thanks jsaintvanne) ++ frag4feature fileid fix for conversion from factor to character ++ Add missing plyr:: reference (thanks jsaintvanne) CHANGES IN VERSION 1.11.3/4 -========================= -* Overhaul of combineAnnotation function. Uses local database now as previously ++ Overhaul of combineAnnotation function. Uses local database now as previously API calls would take too much time to finish and was not usable -* Various updates of createMSP to make compatible with Galaxy workflows -* Parameter added to purityA to allow user to change the PPM tolerance for MZ ++ Various updates of createMSP to make compatible with Galaxy workflows ++ Parameter added to purityA to allow user to change the PPM tolerance for MZ values between scans when calculated the interpolated precursor ion purity -* Update of spectralMatching results columns to include additional details ++ Update of spectralMatching results columns to include additional details (e.g. retention time) -* Update of spectralMatching so that either PostgreSQL or MySQL database can be ++ Update of spectralMatching so that either PostgreSQL or MySQL database can be used as input to either query or library CHANGES IN VERSION 1.11.2 -========================= -* Bug fix for EIC with MSMS data ++ Bug fix for EIC with MSMS data CHANGES IN VERSION 1.11.1 -========================= -* Bug fix for duplicate MSP spectra when not using metadata table -* Added xcms3 to xcmsSet conversion for "create database" code -* Fix for sirius combine annotations (incorrect column format) ++ Bug fix for duplicate MSP spectra when not using metadata table ++ Added xcms3 to xcmsSet conversion for "create database" code ++ Fix for sirius combine annotations (incorrect column format) CHANGES IN VERSION 1.11.0 -========================= -* Bioconductor dev (automatic version bump) ++ Bioconductor dev (automatic version bump) CHANGES IN VERSION 1.10.0 -========================= -* Bioconductor release (automatic version bump) ++ Bioconductor release (automatic version bump) CHANGES IN VERSION 1.9.12 -========================= -* Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error ++ Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error CHANGES IN VERSION 1.9.11 -========================= -* Bug fix for createMSP - now handles metadata with duplicate grpids ++ Bug fix for createMSP - now handles metadata with duplicate grpids CHANGES IN VERSION 1.9.10 -========================= -* Documentation updates ++ Documentation updates CHANGES IN VERSION 1.9.9 -========================= -* NEW FUNCTION: createDatabase - + Updated version of create_database that uses an updated schema -* NEW FUNCTION: spectralMatching - + Updated version spectral_matching that allows for more flexibility -* Vignettes and documentation update ++ NEW FUNCTION: createDatabase + o Updated version of create_database that uses an updated schema ++ NEW FUNCTION: spectralMatching + o Updated version spectral_matching that allows for more flexibility ++ Vignettes and documentation update CHANGES IN VERSION 1.9.8 -========================= -* NEW FUNCTION: filterFragSpectra (for purityA objects) - + LC-MS/MS filtering of spectra (prior to averaging) -* NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects) - + LC-MS/MS averaging and filtering functionality -* NEW FUNCTION: createMSP - + Create msp files from purityA objects where XCMS features have been linked to fragmentation spectra -* Updated create_database and spectral matching to have the option to use averaged fragmentation spectra ++ NEW FUNCTION: filterFragSpectra (for purityA objects) + o LC-MS/MS filtering of spectra (prior to averaging) ++ NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects) + o LC-MS/MS averaging and filtering functionality ++ NEW FUNCTION: createMSP + o Create msp files from purityA objects where XCMS features have been linked to fragmentation spectra ++ Updated create_database and spectral matching to have the option to use averaged fragmentation spectra CHANGES IN VERSION 1.9.2 -========================= -* Bug fix for groupPeaks and groupPeaksEx (the ppm argument was not working and there was inconsistent behaviour with larger datasets). Thanks to Elliot for spotting (https://github.com/litepalmer) -* Updated documentation for spectral matching ++ Bug fix for groupPeaks and groupPeaksEx (the ppm argument was not working and there was inconsistent behaviour with larger datasets). Thanks to Elliot for spotting (https://github.com/litepalmer) ++ Updated documentation for spectral matching CHANGES IN VERSION 1.7.6 -========================= -* create_sql bug fix for msms spectra table. Was crashing due to incorrect ordering. -* Add peak processing (flag remove peaks) for LC-MS XCMS data -* Add option to for frag4feature to just link to the grouped peak rtmin and rtmax (e.g. do not need to link to individual files) ++ create_sql bug fix for msms spectra table. Was crashing due to incorrect ordering. ++ Add peak processing (flag remove peaks) for LC-MS XCMS data ++ Add option to for frag4feature to just link to the grouped peak rtmin and rtmax (e.g. do not need to link to individual files) CHANGES IN VERSION 1.6.1 -========================= -* Bug fix. For pos/neg switching acquisition two files are can be generated when converting from RAW to mzML (1 for pos, 1 for neg). The resulting files retention time scans were not being tracked properly in msPurity in these cases. This is now fixed. Thanks ++ Bug fix. For pos/neg switching acquisition two files are can be generated when converting from RAW to mzML (1 for pos, 1 for neg). The resulting files retention time scans were not being tracked properly in msPurity in these cases. This is now fixed. Thanks to Julien (https://github.com/jsaintvanne) for spotting the bug. CHANGES IN VERSION 1.5.1 -========================= -* Updates for database creation (can use CAMERA objects now) -* averageSpectra parameter 'MSFileReader' deprecated MSFileReader. Should use csvFile instead, MSFileReader option will still work but a warning will be given ++ Updates for database creation (can use CAMERA objects now) ++ averageSpectra parameter 'MSFileReader' deprecated MSFileReader. Should use csvFile instead, MSFileReader option will still work but a warning will be given CHANGES IN VERSION 1.4.1/2/3 -========================= -* Updates for Galaxy for Spectral Matching -* Spectral matching ra_thres_t bugfix -* Separation of sqlite database creation. Now can be called on it's own or with frag4feature ++ Updates for Galaxy for Spectral Matching ++ Spectral matching ra_thres_t bugfix ++ Separation of sqlite database creation. Now can be called on it's own or with frag4feature (allows the Galaxy tool to be simplified) CHANGES IN VERSION 1.3.9 -========================= -* Added very basic SIMS stitch compatibility -* pcalc can handle NAs -* Update of purityX to handle obiwarp RT correction (requires recording the RT RAW at an earlier step) -* bug fix for when library spectra is bigger than target spectra (thanks Martin) ++ Added very basic SIMS stitch compatibility ++ pcalc can handle NAs ++ Update of purityX to handle obiwarp RT correction (requires recording the RT RAW at an earlier step) ++ bug fix for when library spectra is bigger than target spectra (thanks Martin) CHANGES IN VERSION 1.3.1 -========================= -* Add spectral matching functionality for LC-MS/MS ++ Add spectral matching functionality for LC-MS/MS CHANGES IN VERSION 1.1.1 -========================= -* Added pcalc functions to be used by user -* Added option to remove isotopes from calculation ++ Added pcalc functions to be used by user ++ Added option to remove isotopes from calculation CHANGES IN VERSION 0.99.10/11/12 -========================= -* Troubleshooting windows build failure ++ Troubleshooting windows build failure CHANGES IN VERSION 0.99.9 -========================= -* Offset bug fixed (previous only using extracting lower offset from mzML file) -* Updated handling of RT corrected xcmsSet objects for frag4feature function -* Additional column added for tracking ms/ms spectra ++ Offset bug fixed (previous only using extracting lower offset from mzML file) ++ Updated handling of RT corrected xcmsSet objects for frag4feature function ++ Additional column added for tracking ms/ms spectra CHANGES IN VERSION 0.99.8 -========================= -* User option to change the mzR backend library ++ User option to change the mzR backend library CHANGES IN VERSION 0.99.4/5/6/7 -========================= -* Troubleshooting mac build failure ++ Troubleshooting mac build failure CHANGES IN VERSION 0.99.3 -========================= -* Grouping multiple peaklist into one wide dataframe -** Peaklists can now be averaged across each class using the function groupPeaks() for the class purityD -** A list of dataframes can also be grouped together using the function groupPeakEx() ++ Grouping multiple peaklist into one wide dataframe ++ Peaklists can now be averaged across each class using the function groupPeaks() for the class purityD ++ A list of dataframes can also be grouped together using the function groupPeakEx() CHANGES IN VERSION 0.99.2 -========================= -* Updated class names purityPD to purityD -* Updated class names purityLC to purityX -* Updated vignette to reflect slightly different terminology -* Added normalised TIC option for purityD ++ Updated class names purityPD to purityD ++ Updated class names purityLC to purityX ++ Updated vignette to reflect slightly different terminology ++ Added normalised TIC option for purityD msPurity v0.99.0 (Release date: 2016-04-08) -========================= -Initial release! ++ Initial release!