From a34b008caaceb605581a57a2bd8ede2cce688f6c Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Fri, 12 Apr 2024 16:08:38 -0400 Subject: [PATCH 1/3] docs(converters): Add log warning messages indicating that converters will be deprecated in favor of those in MSstatsConvert --- R/converters.R | 92 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 91 insertions(+), 1 deletion(-) diff --git a/R/converters.R b/R/converters.R index e1386c23..53f6116e 100644 --- a/R/converters.R +++ b/R/converters.R @@ -76,7 +76,7 @@ DIAUmpiretoMSstatsFormat = function( ) { MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, log_file_path) - + input = MSstatsConvert::MSstatsImport(list(Fragments = raw.frag, Peptides = raw.pep, Proteins = raw.pro), @@ -108,6 +108,15 @@ DIAUmpiretoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the DIAUmpiretoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the DIAUmpiretoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::DIAUmpiretoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -194,6 +203,15 @@ MaxQtoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the MaxQtoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the MaxQtoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::MaxQtoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -252,6 +270,15 @@ OpenMStoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the OpenMStoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the OpenMStoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::OpenMStoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -337,6 +364,15 @@ OpenSWATHtoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the OpenSWATHtoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the OpenSWATHtoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::OpenSWATHtoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -460,6 +496,15 @@ DIANNtoMSstatsFormat = function(input, annotation = NULL, getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the DIANNtoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the DIANNtoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::DIANNtoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -537,6 +582,15 @@ ProgenesistoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the ProgenesistoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the ProgenesistoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::ProgenesistoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -621,6 +675,15 @@ PDtoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the PDtoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the PDtoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::PDtoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -724,6 +787,15 @@ SkylinetoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the SkylinetoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the SkylinetoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::SkylinetoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -803,6 +875,15 @@ SpectronauttoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the SpectronauttoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the SpectronauttoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } @@ -858,5 +939,14 @@ FragPipetoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") + msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + "notify you that the FragPipetoMSstatsFormat function", + "currently available in both MSstats and MSstatsConvert,", + "will undergo a transition process. Starting from release 3.21", + "the FragPipetoMSstatsFormat function in MSstats will be deprecated.", + "Please take the necessary steps to update your codebase", + "and migrate to MSstatsConvert::FragPipetoMSstatsFormat before", + "release 3.21 to avoid any disruptions to your workflow.") + getOption("MSstatsMsg")("WARN", msg_deprecation) input } From 1faf04bd5a1645ad43ea82d99518cb8501507bb8 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Fri, 12 Apr 2024 16:32:48 -0400 Subject: [PATCH 2/3] docs(parallel-processing): Rename MSstatsSummarizeV2.Rd to MSstatsSummarizeWithMultipleCores.Rd --- ...sSummarizeV2.Rd => MSstatsSummarizeWithMultipleCores.Rd} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename man/{MSstatsSummarizeV2.Rd => MSstatsSummarizeWithMultipleCores.Rd} (94%) diff --git a/man/MSstatsSummarizeV2.Rd b/man/MSstatsSummarizeWithMultipleCores.Rd similarity index 94% rename from man/MSstatsSummarizeV2.Rd rename to man/MSstatsSummarizeWithMultipleCores.Rd index 6ac84361..60d87efc 100644 --- a/man/MSstatsSummarizeV2.Rd +++ b/man/MSstatsSummarizeWithMultipleCores.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/dataProcess.R -\name{MSstatsSummarizeV2} -\alias{MSstatsSummarizeV2} +\name{MSstatsSummarizeWithMultipleCores} +\alias{MSstatsSummarizeWithMultipleCores} \title{Feature-level data summarization with multiple cores} \usage{ -MSstatsSummarizeV2( +MSstatsSummarizeWithMultipleCores( input, method, impute, From e299377576b61a220a93cdb52c97afaa1f9075ab Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Tue, 16 Apr 2024 11:28:12 -0400 Subject: [PATCH 3/3] switched from WARN log to message --- R/converters.R | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/R/converters.R b/R/converters.R index 53f6116e..2f3ae120 100644 --- a/R/converters.R +++ b/R/converters.R @@ -108,7 +108,7 @@ DIAUmpiretoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the DIAUmpiretoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -116,7 +116,7 @@ DIAUmpiretoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::DIAUmpiretoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -203,7 +203,7 @@ MaxQtoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the MaxQtoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -211,7 +211,7 @@ MaxQtoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::MaxQtoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -270,7 +270,7 @@ OpenMStoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the OpenMStoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -278,7 +278,7 @@ OpenMStoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::OpenMStoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -364,7 +364,7 @@ OpenSWATHtoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the OpenSWATHtoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -372,7 +372,7 @@ OpenSWATHtoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::OpenSWATHtoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -496,7 +496,7 @@ DIANNtoMSstatsFormat = function(input, annotation = NULL, getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the DIANNtoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -504,7 +504,7 @@ DIANNtoMSstatsFormat = function(input, annotation = NULL, "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::DIANNtoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -582,7 +582,7 @@ ProgenesistoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the ProgenesistoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -590,7 +590,7 @@ ProgenesistoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::ProgenesistoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -675,7 +675,7 @@ PDtoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the PDtoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -683,7 +683,7 @@ PDtoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::PDtoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -787,7 +787,7 @@ SkylinetoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the SkylinetoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -795,7 +795,7 @@ SkylinetoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::SkylinetoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -875,7 +875,7 @@ SpectronauttoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the SpectronauttoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -883,7 +883,7 @@ SpectronauttoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input } @@ -939,7 +939,7 @@ FragPipetoMSstatsFormat = function( getOption("MSstatsLog")("INFO", msg_final) getOption("MSstatsMsg")("INFO", msg_final) getOption("MSstatsLog")("INFO", "\n") - msg_deprecation = paste("** FUNCTION DEPRECATION NOTICE: We would like to", + msg_deprecation = paste("FUNCTION DEPRECATION NOTICE: We would like to", "notify you that the FragPipetoMSstatsFormat function", "currently available in both MSstats and MSstatsConvert,", "will undergo a transition process. Starting from release 3.21", @@ -947,6 +947,6 @@ FragPipetoMSstatsFormat = function( "Please take the necessary steps to update your codebase", "and migrate to MSstatsConvert::FragPipetoMSstatsFormat before", "release 3.21 to avoid any disruptions to your workflow.") - getOption("MSstatsMsg")("WARN", msg_deprecation) + message(msg_deprecation) input }