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docs(converters): Add log warning messages indicating that converters…
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… will be deprecated in favor of those in MSstatsConvert (#120)

* docs(converters): Add log warning messages indicating that converters will be deprecated in favor of those in MSstatsConvert

* docs(parallel-processing): Rename MSstatsSummarizeV2.Rd to MSstatsSummarizeWithMultipleCores.Rd

* switched from WARN log to message
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tonywu1999 authored Apr 17, 2024
1 parent 6150270 commit bacd4d5
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Showing 2 changed files with 94 additions and 4 deletions.
92 changes: 91 additions & 1 deletion R/converters.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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),
Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}

Expand Down Expand Up @@ -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.")
message(msg_deprecation)
input
}
6 changes: 3 additions & 3 deletions man/MSstatsSummarizeV2.Rd → man/MSstatsSummarizeWithMultipleCores.Rd
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