run package msbuild

xieguigang · Dec 3, 2024 · 4899c69 · 4899c69
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diff --git a/Rscript/Library/MSI_app b/Rscript/Library/MSI_app
diff --git a/Rscript/Library/mzkit_app/man/.extract_pubmed_evidence.1 b/Rscript/Library/mzkit_app/man/.extract_pubmed_evidence.1
@@ -1,4 +1,4 @@
-.TH .EXTRACT_PUBMED_EVIDENCE 1 2024-Nov "" ".extract_pubmed_evidence"
+.TH .EXTRACT_PUBMED_EVIDENCE 1 2024-Dec "" ".extract_pubmed_evidence"
 .SH NAME
 .extract_pubmed_evidence \- .extract_pubmed_evidence(evidence, u, v,
     <i>type</i> = [<span style='color: brown;'><strong>'disease'</strong></span>,<span style='color: brown;'><strong>'compounds'</strong></span>])

diff --git a/Rscript/Library/mzkit_app/man/.graph_table.1 b/Rscript/Library/mzkit_app/man/.graph_table.1
@@ -1,4 +1,4 @@
-.TH .GRAPH_TABLE 1 2024-Nov "" ".graph_table"
+.TH .GRAPH_TABLE 1 2024-Dec "" ".graph_table"
 .SH NAME
 .graph_table \- .graph_table(nodes,
     <i>type</i> = [<span style='color: brown;'><strong>'disease'</strong></span>,<span style='color: brown;'><strong>'compounds'</strong></span>])

diff --git a/Rscript/Library/mzkit_app/man/.onLoad.1 b/Rscript/Library/mzkit_app/man/.onLoad.1
@@ -1,4 +1,4 @@
-.TH .ONLOAD 1 2024-Nov "" "Hello, world! This is an example function named 'hello' which prints 'Hello, world!'. You can learn more about package authoring with RStudio at: http://r-pkgs.had.co.nz/ Some useful keyboard shortcuts for package authoring: Install Package:           'Ctrl + Shift + B' Check Package:             'Ctrl + Shift + E' Test Package:              'Ctrl + Shift + T'"
+.TH .ONLOAD 1 2024-Dec "" "Hello, world! This is an example function named 'hello' which prints 'Hello, world!'. You can learn more about package authoring with RStudio at: http://r-pkgs.had.co.nz/ Some useful keyboard shortcuts for package authoring: Install Package:           'Ctrl + Shift + B' Check Package:             'Ctrl + Shift + E' Test Package:              'Ctrl + Shift + T'"
 .SH NAME
 .onLoad \- .onLoad()
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/.term_maps.1 b/Rscript/Library/mzkit_app/man/.term_maps.1
@@ -1,4 +1,4 @@
-.TH .TERM_MAPS 1 2024-Nov "" ".term_maps"
+.TH .TERM_MAPS 1 2024-Dec "" ".term_maps"
 .SH NAME
 .term_maps \- .term_maps(x,
     <i>type</i> = [<span style='color: brown;'><strong>'disease'</strong></span>,<span style='color: brown;'><strong>'compounds'</strong></span>])

diff --git a/Rscript/Library/mzkit_app/man/ANOVAGroup.1 b/Rscript/Library/mzkit_app/man/ANOVAGroup.1
@@ -1,4 +1,4 @@
-.TH ANOVAGROUP 1 2024-Nov "" "Create a dataset for evaluate ANOVA p-value"
+.TH ANOVAGROUP 1 2024-Dec "" "Create a dataset for evaluate ANOVA p-value"
 .SH NAME
 ANOVAGroup \- ANOVAGroup(data, sampleinfo)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/GCMS_contentTable.1 b/Rscript/Library/mzkit_app/man/GCMS_contentTable.1
@@ -1,4 +1,4 @@
-.TH GCMS_CONTENTTABLE 1 2024-Nov "" "Create content levels table"
+.TH GCMS_CONTENTTABLE 1 2024-Dec "" "Create content levels table"
 .SH NAME
 GCMS_contentTable \- GCMS_contentTable(mslIons, calfiles)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/GCMS_linearReport.1 b/Rscript/Library/mzkit_app/man/GCMS_linearReport.1
@@ -1,4 +1,4 @@
-.TH GCMS_LINEARREPORT 1 2024-Nov "" "GCMS_linearReport"
+.TH GCMS_LINEARREPORT 1 2024-Dec "" "GCMS_linearReport"
 .SH NAME
 GCMS_linearReport \- GCMS_linearReport(sim, ions, quantify, calfiles,
     <i>output.dir</i> = <span style='color: brown;'><strong>'./'</strong></span>)

diff --git a/Rscript/Library/mzkit_app/man/GCMS_linears.1 b/Rscript/Library/mzkit_app/man/GCMS_linears.1
@@ -1,4 +1,4 @@
-.TH GCMS_LINEARS 1 2024-Nov "" "Create reference linears for GCMS sim data"
+.TH GCMS_LINEARS 1 2024-Dec "" "Create reference linears for GCMS sim data"
 .SH NAME
 GCMS_linears \- GCMS_linears(contentTable, mslIons, calfiles,
     <i>peakwidth</i> = [<span style='color: green;'>13</span>],

diff --git a/Rscript/Library/mzkit_app/man/GCMS_quantify.1 b/Rscript/Library/mzkit_app/man/GCMS_quantify.1
@@ -1,4 +1,4 @@
-.TH GCMS_QUANTIFY 1 2024-Nov "" "GCMS_quantify"
+.TH GCMS_QUANTIFY 1 2024-Dec "" "GCMS_quantify"
 .SH NAME
 GCMS_quantify \- GCMS_quantify(linears, sim, sampleData)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/__deconv_gcms_single.1 b/Rscript/Library/mzkit_app/man/__deconv_gcms_single.1
@@ -1,4 +1,4 @@
-.TH __DECONV_GCMS_SINGLE 1 2024-Nov "" "__deconv_gcms_single"
+.TH __DECONV_GCMS_SINGLE 1 2024-Dec "" "__deconv_gcms_single"
 .SH NAME
 __deconv_gcms_single \- __deconv_gcms_single(file,
     <i>peak.width</i> = [<span style='color: green;'>90</span>])

diff --git a/Rscript/Library/mzkit_app/man/__ms1_xic_bins_single.1 b/Rscript/Library/mzkit_app/man/__ms1_xic_bins_single.1
@@ -1,4 +1,4 @@
-.TH __MS1_XIC_BINS_SINGLE 1 2024-Nov "" "export XIC data for a single rawdata file"
+.TH __MS1_XIC_BINS_SINGLE 1 2024-Dec "" "export XIC data for a single rawdata file"
 .SH NAME
 __ms1_xic_bins_single \- __ms1_xic_bins_single(path, mzdiff, outputdir)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/convertToMzPack.1 b/Rscript/Library/mzkit_app/man/convertToMzPack.1
@@ -1,4 +1,4 @@
-.TH CONVERTTOMZPACK 1 2024-Nov "" "Convert to mzpack data object"
+.TH CONVERTTOMZPACK 1 2024-Dec "" "Convert to mzpack data object"
 .SH NAME
 convertToMzPack \- convertToMzPack(file)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/deconv_gcms.1 b/Rscript/Library/mzkit_app/man/deconv_gcms.1
@@ -1,4 +1,4 @@
-.TH DECONV_GCMS 1 2024-Nov "" "Make expression peak table deconvolution of the GCMS rawdata"
+.TH DECONV_GCMS 1 2024-Dec "" "Make expression peak table deconvolution of the GCMS rawdata"
 .SH NAME
 deconv_gcms \- deconv_gcms(rawdata,
     <i>export.dir</i> = <span style='color: brown;'><strong>'./'</strong></span>,

diff --git a/Rscript/Library/mzkit_app/man/getDataValues.1 b/Rscript/Library/mzkit_app/man/getDataValues.1
@@ -1,4 +1,4 @@
-.TH GETDATAVALUES 1 2024-Nov "" "get values in section$data"
+.TH GETDATAVALUES 1 2024-Dec "" "get values in section$data"
 .SH NAME
 getDataValues \- getDataValues(section)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/getQuery.1 b/Rscript/Library/mzkit_app/man/getQuery.1
@@ -1,4 +1,4 @@
-.TH GETQUERY 1 2024-Nov "" "getQuery"
+.TH GETQUERY 1 2024-Dec "" "getQuery"
 .SH NAME
 getQuery \- getQuery(fileName)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/get_representives.1 b/Rscript/Library/mzkit_app/man/get_representives.1
@@ -1,4 +1,4 @@
-.TH GET_REPRESENTIVES 1 2024-Nov "" "Get n representive spectrums via molecular networking"
+.TH GET_REPRESENTIVES 1 2024-Dec "" "Get n representive spectrums via molecular networking"
 .SH NAME
 get_representives \- get_representives(ions,
     <i>top.n</i> = <span style='color: green;'>5</span>,

diff --git a/Rscript/Library/mzkit_app/man/ionPairsFromMsl.1 b/Rscript/Library/mzkit_app/man/ionPairsFromMsl.1
@@ -1,4 +1,4 @@
-.TH IONPAIRSFROMMSL 1 2024-Nov "" "Read ion pairs data from MSL dataset"
+.TH IONPAIRSFROMMSL 1 2024-Dec "" "Read ion pairs data from MSL dataset"
 .SH NAME
 ionPairsFromMsl \- ionPairsFromMsl(ions,
     <i>unit</i> = <span style='color: brown;'><strong>'Minute'</strong></span>)

diff --git a/Rscript/Library/mzkit_app/man/kegg_compounds.1 b/Rscript/Library/mzkit_app/man/kegg_compounds.1
@@ -1,4 +1,4 @@
-.TH KEGG_COMPOUNDS 1 2024-Nov "" "Load the kegg database for the annotation"
+.TH KEGG_COMPOUNDS 1 2024-Dec "" "Load the kegg database for the annotation"
 .SH NAME
 kegg_compounds \- kegg_compounds(
     <i>precursors</i> = [<span style='color: brown;'><strong>'[M+H]+'</strong></span>,<span style='color: brown;'><strong>'[M+H-H2O]+'</strong></span>],

diff --git a/Rscript/Library/mzkit_app/man/knowledge_graph.1 b/Rscript/Library/mzkit_app/man/knowledge_graph.1
@@ -1,4 +1,4 @@
-.TH KNOWLEDGE_GRAPH 1 2024-Nov "" "Query pubchem for knowledge network"
+.TH KNOWLEDGE_GRAPH 1 2024-Dec "" "Query pubchem for knowledge network"
 .SH NAME
 knowledge_graph \- knowledge_graph(cid,
     <i>cache</i> = <span style='color: brown;'><strong>'./graph_kb'</strong></span>)

diff --git a/Rscript/Library/mzkit_app/man/lipidmaps_repo.1 b/Rscript/Library/mzkit_app/man/lipidmaps_repo.1
@@ -1,4 +1,4 @@
-.TH LIPIDMAPS_REPO 1 2024-Nov "" "Load lipidmaps data repository from internal data pack"
+.TH LIPIDMAPS_REPO 1 2024-Dec "" "Load lipidmaps data repository from internal data pack"
 .SH NAME
 lipidmaps_repo \- lipidmaps_repo(
     <i>repofile</i> = 'system.file'('data/LIPIDMAPS.msgpack', 'package' = 'mzkit'),

diff --git a/Rscript/Library/mzkit_app/man/loadTree.1 b/Rscript/Library/mzkit_app/man/loadTree.1
@@ -1,4 +1,4 @@
-.TH LOADTREE 1 2024-Nov "" "Load spectrum tree from raw data files"
+.TH LOADTREE 1 2024-Dec "" "Load spectrum tree from raw data files"
 .SH NAME
 loadTree \- loadTree(files)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/load_LMSD.1 b/Rscript/Library/mzkit_app/man/load_LMSD.1
@@ -1,4 +1,4 @@
-.TH LOAD_LMSD 1 2024-Nov "" "load the lipidmaps raw database"
+.TH LOAD_LMSD 1 2024-Dec "" "load the lipidmaps raw database"
 .SH NAME
 load_LMSD \- load_LMSD(filepath,
     <i>lazy</i> = <span style='color: blue !important;'>FALSE</span>)

diff --git a/Rscript/Library/mzkit_app/man/mesh_model.1 b/Rscript/Library/mzkit_app/man/mesh_model.1
@@ -1,4 +1,4 @@
-.TH MESH_MODEL 1 2024-Nov "" "Load mesh background model from run enrichment analysis"
+.TH MESH_MODEL 1 2024-Dec "" "Load mesh background model from run enrichment analysis"
 .SH NAME
 mesh_model \- mesh_model(
     <i>topics</i> = <span style='color: blue !important;'>NULL</span>)

diff --git a/Rscript/Library/mzkit_app/man/ms1_mz_bins.1 b/Rscript/Library/mzkit_app/man/ms1_mz_bins.1
@@ -1,4 +1,4 @@
-.TH MS1_MZ_BINS 1 2024-Nov "" "Extract the ion m/z features"
+.TH MS1_MZ_BINS 1 2024-Dec "" "Extract the ion m/z features"
 .SH NAME
 ms1_mz_bins \- ms1_mz_bins(files,
     <i>mzdiff</i> = <span style='color: green;'>0.001</span>)

diff --git a/Rscript/Library/mzkit_app/man/ms1_peaktable.1 b/Rscript/Library/mzkit_app/man/ms1_peaktable.1
@@ -1,4 +1,4 @@
-.TH MS1_PEAKTABLE 1 2024-Nov "" "Export peakstable data from the XIC rawdata files"
+.TH MS1_PEAKTABLE 1 2024-Dec "" "Export peakstable data from the XIC rawdata files"
 .SH NAME
 ms1_peaktable \- ms1_peaktable(files, mzbins,
     <i>mzdiff</i> = <span style='color: green;'>0.005</span>,

diff --git a/Rscript/Library/mzkit_app/man/ms1_xic_bins.1 b/Rscript/Library/mzkit_app/man/ms1_xic_bins.1
@@ -1,4 +1,4 @@
-.TH MS1_XIC_BINS 1 2024-Nov "" "Create XIC rawdata file for run peaktable exports"
+.TH MS1_XIC_BINS 1 2024-Dec "" "Create XIC rawdata file for run peaktable exports"
 .SH NAME
 ms1_xic_bins \- ms1_xic_bins(files,
     <i>mzdiff</i> = <span style='color: green;'>0.005</span>,

diff --git a/Rscript/Library/mzkit_app/man/output_datatables.1 b/Rscript/Library/mzkit_app/man/output_datatables.1
@@ -1,4 +1,4 @@
-.TH OUTPUT_DATATABLES 1 2024-Nov "" "Output result data table"
+.TH OUTPUT_DATATABLES 1 2024-Dec "" "Output result data table"
 .SH NAME
 output_datatables \- output_datatables(quantify, linears,
     <i>output.dir</i> = <span style='color: brown;'><strong>'./'</strong></span>)

diff --git a/Rscript/Library/mzkit_app/man/pack_singleCells.1 b/Rscript/Library/mzkit_app/man/pack_singleCells.1
@@ -1,4 +1,4 @@
-.TH PACK_SINGLECELLS 1 2024-Nov "" "pack the multiple single cells samples into one dataset."
+.TH PACK_SINGLECELLS 1 2024-Dec "" "pack the multiple single cells samples into one dataset."
 .SH NAME
 pack_singleCells \- pack_singleCells(rawdata,
     <i>tag</i> = <span style='color: blue !important;'>NULL</span>)

diff --git a/Rscript/Library/mzkit_app/man/parseDescriptors.1 b/Rscript/Library/mzkit_app/man/parseDescriptors.1
@@ -1,4 +1,4 @@
-.TH PARSEDESCRIPTORS 1 2024-Nov "" "parseDescriptors"
+.TH PARSEDESCRIPTORS 1 2024-Dec "" "parseDescriptors"
 .SH NAME
 parseDescriptors \- parseDescriptors(descriptors)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/parseNames.1 b/Rscript/Library/mzkit_app/man/parseNames.1
@@ -1,4 +1,4 @@
-.TH PARSENAMES 1 2024-Nov "" "parseNames"
+.TH PARSENAMES 1 2024-Dec "" "parseNames"
 .SH NAME
 parseNames \- parseNames(names)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/parsePubchemMeta.1 b/Rscript/Library/mzkit_app/man/parsePubchemMeta.1
@@ -1,4 +1,4 @@
-.TH PARSEPUBCHEMMETA 1 2024-Nov "" "Parse the compound information"
+.TH PARSEPUBCHEMMETA 1 2024-Dec "" "Parse the compound information"
 .SH NAME
 parsePubchemMeta \- parsePubchemMeta(document)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/parseXref.1 b/Rscript/Library/mzkit_app/man/parseXref.1
@@ -1,4 +1,4 @@
-.TH PARSEXREF 1 2024-Nov "" "parseXref"
+.TH PARSEXREF 1 2024-Dec "" "parseXref"
 .SH NAME
 parseXref \- parseXref(refs)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/plotLinears.1 b/Rscript/Library/mzkit_app/man/plotLinears.1
@@ -1,4 +1,4 @@
-.TH PLOTLINEARS 1 2024-Nov "" "plotLinears"
+.TH PLOTLINEARS 1 2024-Dec "" "plotLinears"
 .SH NAME
 plotLinears \- plotLinears(linears,
     <i>mslIons</i> = <span style='color: blue !important;'>NULL</span>,

diff --git a/Rscript/Library/mzkit_app/man/preprocessing_expression.1 b/Rscript/Library/mzkit_app/man/preprocessing_expression.1
@@ -1,4 +1,4 @@
-.TH PREPROCESSING_EXPRESSION 1 2024-Nov "" "Normalize matrix sample data"
+.TH PREPROCESSING_EXPRESSION 1 2024-Dec "" "Normalize matrix sample data"
 .SH NAME
 preprocessing_expression \- preprocessing_expression(x,
     <i>sampleinfo</i> = <span style='color: blue !important;'>NULL</span>,

diff --git a/Rscript/Library/mzkit_app/man/pubchem_graphjson.1 b/Rscript/Library/mzkit_app/man/pubchem_graphjson.1
@@ -1,4 +1,4 @@
-.TH PUBCHEM_GRAPHJSON 1 2024-Nov "" "Parse the pugview xml as the metabolite data object"
+.TH PUBCHEM_GRAPHJSON 1 2024-Dec "" "Parse the pugview xml as the metabolite data object"
 .SH NAME
 pubchem_graphjson \- pubchem_graphjson(dataXml,
     <i>process</i> = <span style='color: blue !important;'>NULL</span>,

diff --git a/Rscript/Library/mzkit_app/man/pubchem_meta.1 b/Rscript/Library/mzkit_app/man/pubchem_meta.1
@@ -1,4 +1,4 @@
-.TH PUBCHEM_META 1 2024-Nov "" "Helper script for run pubchem database query"
+.TH PUBCHEM_META 1 2024-Dec "" "Helper script for run pubchem database query"
 .SH NAME
 pubchem_meta \- pubchem_meta(term)
 .SH SYNOPSIS

diff --git a/Rscript/Library/mzkit_app/man/run.Deconvolution.1 b/Rscript/Library/mzkit_app/man/run.Deconvolution.1
@@ -1,4 +1,4 @@
-.TH RUN.DECONVOLUTION 1 2024-Nov "" "Do ms1 deconvolution of the rawdata"
+.TH RUN.DECONVOLUTION 1 2024-Dec "" "Do ms1 deconvolution of the rawdata"
 .SH NAME
 run.Deconvolution \- run.Deconvolution(rawdata,
     <i>outputdir</i> = <span style='color: brown;'><strong>'./'</strong></span>,

diff --git a/Rscript/Library/mzkit_app/man/tolerance.1 b/Rscript/Library/mzkit_app/man/tolerance.1
@@ -1,4 +1,4 @@
-.TH TOLERANCE 1 2024-Nov "" "Create mzdiff tolerance value"
+.TH TOLERANCE 1 2024-Dec "" "Create mzdiff tolerance value"
 .SH NAME
 tolerance \- tolerance(
     <i>kind</i> = <span style='color: brown;'><strong>'ppm'</strong></span>,

diff --git a/src/mzkit b/src/mzkit