R version 4.5.0 RC (2025-04-04 r88118 ucrt) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(DeSciDe) > > test_check("DeSciDe") 2025-04-08 20:16:15.843269: Starting analysis pipeline 2025-04-08 20:16:15.845333: Performing PubMed search 2025-04-08 20:16:16.72497: PubMed search completed. Results: # A tibble: 1 x 4 Gene cancer Total PubMed_Rank 1 MYC 17294 17294 1 2025-04-08 20:16:16.770076: Plotting heatmap of PubMed search results 2025-04-08 20:16:16.784266: Performing STRING database search trying URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz' Content type 'application/octet-stream' length 19777800 bytes (18.9 MB) ================================================== downloaded 18.9 MB trying URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz' Content type 'application/octet-stream' length 1970090 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz' Content type 'application/octet-stream' length 83164437 bytes (79.3 MB) ================================================== downloaded 79.3 MB 2025-04-08 20:18:15.912785: STRING database search completed. Results: data frame with 0 columns and 0 rows 2025-04-08 20:18:15.913326: Plotting STRING network interactions 2025-04-08 20:18:21.617917: Combining summaries 2025-04-08 20:18:21.618737: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 0 obs. of 0 variables NULL 2025-04-08 20:18:21.621311: Inside plot_clustering function 2025-04-08 20:18:21.62586: Categorizing and plotting genes 2025-04-08 20:18:21.632528: FINISHED: Analysis pipeline completed 2025-04-08 20:18:21.700675: Inside plot_clustering function 2025-04-08 20:18:21.73851: Starting analysis pipeline 2025-04-08 20:18:21.738942: Performing PubMed search 2025-04-08 20:18:21.759986: PubMed search completed. Results: # A tibble: 0 x 3 # i 3 variables: Gene , Total , PubMed_Rank 2025-04-08 20:18:21.77003: Plotting heatmap of PubMed search results 2025-04-08 20:18:21.778: Performing STRING database search 2025-04-08 20:18:21.78473: STRING database search completed. Results: data frame with 0 columns and 0 rows 2025-04-08 20:18:21.785107: Plotting STRING network interactions 2025-04-08 20:18:21.790273: Combining summaries 2025-04-08 20:18:21.790638: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 0 obs. of 0 variables NULL 2025-04-08 20:18:21.791304: Inside plot_clustering function 2025-04-08 20:18:21.798046: Categorizing and plotting genes 2025-04-08 20:18:21.805681: FINISHED: Analysis pipeline completed 2025-04-08 20:18:21.867377: Inside plot_clustering function 2025-04-08 20:20:09.020717: Starting analysis pipeline 2025-04-08 20:20:09.021075: Performing PubMed search 2025-04-08 20:20:13.827654: PubMed search completed. Results: # A tibble: 4 x 5 Gene cancer romidepsin Total PubMed_Rank 1 MYC 17294 21 17315 1 2 JUN 6509 3 6512 2 3 HDAC1 1549 55 1604 3 4 TRIM33 41 0 41 4 2025-04-08 20:20:13.861193: Plotting heatmap of PubMed search results 2025-04-08 20:20:17.016219: Performing STRING database search 2025-04-08 20:21:55.510226: STRING database search completed. Results: Gene_Symbol Degree Clustering_Coefficient_Percent 9606.ENSP00000360266 JUN 3 33.33333 9606.ENSP00000362649 HDAC1 2 100.00000 9606.ENSP00000478887 MYC 2 100.00000 9606.ENSP00000351250 TRIM33 1 0.00000 Clustering_Coefficient_Fraction Connected_Component_id 9606.ENSP00000360266 1/3 1 9606.ENSP00000362649 1/1 1 9606.ENSP00000478887 1/1 1 9606.ENSP00000351250 0 / 0 1 Nodes_in_Connected_Component 9606.ENSP00000360266 4 9606.ENSP00000362649 4 9606.ENSP00000478887 4 9606.ENSP00000351250 4 total_number_of_connected_components Connectivity_Rank 9606.ENSP00000360266 1 1 9606.ENSP00000362649 1 2 9606.ENSP00000478887 1 3 9606.ENSP00000351250 1 4 2025-04-08 20:21:55.512555: Plotting STRING network interactions 2025-04-08 20:21:56.182032: Combining summaries 2025-04-08 20:21:56.188026: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL 2025-04-08 20:21:56.193898: Inside plot_clustering function 2025-04-08 20:21:56.194115: After conversion - Data types of columns: 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL 2025-04-08 20:21:56.328678: Categorizing and plotting genes 2025-04-08 20:21:56.671431: FINISHED: Analysis pipeline completed 2025-04-08 20:21:56.9201: Inside plot_clustering function 2025-04-08 20:21:56.920323: After conversion - Data types of columns: 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL 2025-04-08 20:21:57.222236: Starting analysis pipeline 2025-04-08 20:21:57.222682: Performing PubMed search 2025-04-08 20:22:03.022594: PubMed search completed. Results: # A tibble: 4 x 5 Gene cancer romidepsin Total PubMed_Rank 1 MYC 17294 21 17315 1 2 JUN 6509 3 6512 2 3 HDAC1 1549 55 1604 3 4 TRIM33 41 0 41 4 2025-04-08 20:22:03.048907: Plotting heatmap of PubMed search results [1] "Heatmap plot exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887cb20b5/04.08.2025_PubMed_Heatmap.png" 2025-04-08 20:22:03.341419: Performing STRING database search 2025-04-08 20:23:40.768528: STRING database search completed. Results: Gene_Symbol Degree Clustering_Coefficient_Percent 9606.ENSP00000360266 JUN 3 33.33333 9606.ENSP00000362649 HDAC1 2 100.00000 9606.ENSP00000478887 MYC 2 100.00000 9606.ENSP00000351250 TRIM33 1 0.00000 Clustering_Coefficient_Fraction Connected_Component_id 9606.ENSP00000360266 1/3 1 9606.ENSP00000362649 1/1 1 9606.ENSP00000478887 1/1 1 9606.ENSP00000351250 0 / 0 1 Nodes_in_Connected_Component 9606.ENSP00000360266 4 9606.ENSP00000362649 4 9606.ENSP00000478887 4 9606.ENSP00000351250 4 total_number_of_connected_components Connectivity_Rank 9606.ENSP00000360266 1 1 9606.ENSP00000362649 1 2 9606.ENSP00000478887 1 3 9606.ENSP00000351250 1 4 2025-04-08 20:23:40.770677: Plotting STRING network interactions [1] "Network plot exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887cb20b5/04.08.2025_STRINGdb_Network.pdf" 2025-04-08 20:23:41.485969: Combining summaries [1] "Summary table exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887cb20b5/04.08.2025_Combined_Summary.csv" 2025-04-08 20:23:41.495329: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL 2025-04-08 20:23:41.503269: Inside plot_clustering function 2025-04-08 20:23:41.503555: After conversion - Data types of columns: 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL [1] "Full scatter plot file path: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887cb20b5/04.08.2025_Degree_vs_ClusteringCoefficient.png" 2025-04-08 20:23:41.701356: Scatter plot saved successfully 2025-04-08 20:23:41.701679: Categorizing and plotting genes [1] "Plot exported and device closed." 2025-04-08 20:23:41.895749: FINISHED: Analysis pipeline completed 2025-04-08 20:23:41.926772: Starting analysis pipeline 2025-04-08 20:23:41.927174: Performing PubMed search 2025-04-08 20:23:46.729381: PubMed search completed. Results: # A tibble: 4 x 5 Gene cancer romidepsin Total PubMed_Rank 1 MYC 17294 21 17315 1 2 JUN 6509 3 6512 2 3 HDAC1 1549 55 1604 3 4 TRIM33 41 0 41 4 2025-04-08 20:23:46.75077: Plotting heatmap of PubMed search results [1] "Heatmap plot exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887366809/04.08.2025_PubMed_Heatmap.png" 2025-04-08 20:23:47.071704: Performing STRING database search 2025-04-08 20:25:23.766616: STRING database search completed. Results: Gene_Symbol Degree Clustering_Coefficient_Percent 9606.ENSP00000360266 JUN 3 33.33333 9606.ENSP00000362649 HDAC1 2 100.00000 9606.ENSP00000478887 MYC 2 100.00000 9606.ENSP00000351250 TRIM33 1 0.00000 Clustering_Coefficient_Fraction Connected_Component_id 9606.ENSP00000360266 1/3 1 9606.ENSP00000362649 1/1 1 9606.ENSP00000478887 1/1 1 9606.ENSP00000351250 0 / 0 1 Nodes_in_Connected_Component 9606.ENSP00000360266 4 9606.ENSP00000362649 4 9606.ENSP00000478887 4 9606.ENSP00000351250 4 total_number_of_connected_components Connectivity_Rank 9606.ENSP00000360266 1 1 9606.ENSP00000362649 1 2 9606.ENSP00000478887 1 3 9606.ENSP00000351250 1 4 2025-04-08 20:25:23.768876: Plotting STRING network interactions [1] "Network plot exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887366809/04.08.2025_STRINGdb_Network.pdf" 2025-04-08 20:25:24.498036: Combining summaries [1] "Summary table exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887366809/04.08.2025_Combined_Summary.tsv" 2025-04-08 20:25:24.506455: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL 2025-04-08 20:25:24.513531: Inside plot_clustering function 2025-04-08 20:25:24.513831: After conversion - Data types of columns: 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL [1] "Full scatter plot file path: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file127887366809/04.08.2025_Degree_vs_ClusteringCoefficient.png" 2025-04-08 20:25:24.652006: Scatter plot saved successfully 2025-04-08 20:25:24.652265: Categorizing and plotting genes [1] "Plot exported and device closed." 2025-04-08 20:25:24.850322: FINISHED: Analysis pipeline completed 2025-04-08 20:25:24.877946: Starting analysis pipeline 2025-04-08 20:25:24.878315: Performing PubMed search 2025-04-08 20:25:29.708686: PubMed search completed. Results: # A tibble: 4 x 5 Gene cancer romidepsin Total PubMed_Rank 1 MYC 17294 21 17315 1 2 JUN 6509 3 6512 2 3 HDAC1 1549 55 1604 3 4 TRIM33 41 0 41 4 2025-04-08 20:25:29.73266: Plotting heatmap of PubMed search results [1] "Heatmap plot exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file12788123ccb3/04.08.2025_PubMed_Heatmap.png" 2025-04-08 20:25:30.024588: Performing STRING database search 2025-04-08 20:27:15.46276: STRING database search completed. Results: Gene_Symbol Degree Clustering_Coefficient_Percent 9606.ENSP00000360266 JUN 3 33.33333 9606.ENSP00000362649 HDAC1 2 100.00000 9606.ENSP00000478887 MYC 2 100.00000 9606.ENSP00000351250 TRIM33 1 0.00000 Clustering_Coefficient_Fraction Connected_Component_id 9606.ENSP00000360266 1/3 1 9606.ENSP00000362649 1/1 1 9606.ENSP00000478887 1/1 1 9606.ENSP00000351250 0 / 0 1 Nodes_in_Connected_Component 9606.ENSP00000360266 4 9606.ENSP00000362649 4 9606.ENSP00000478887 4 9606.ENSP00000351250 4 total_number_of_connected_components Connectivity_Rank 9606.ENSP00000360266 1 1 9606.ENSP00000362649 1 2 9606.ENSP00000478887 1 3 9606.ENSP00000351250 1 4 2025-04-08 20:27:15.465441: Plotting STRING network interactions [1] "Network plot exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file12788123ccb3/04.08.2025_STRINGdb_Network.pdf" 2025-04-08 20:27:16.204199: Combining summaries [1] "Summary table exported to: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file12788123ccb3/04.08.2025_Combined_Summary.xlsx" 2025-04-08 20:27:16.288084: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL 2025-04-08 20:27:16.294175: Inside plot_clustering function 2025-04-08 20:27:16.294405: After conversion - Data types of columns: 'data.frame': 4 obs. of 8 variables: $ Gene_Symbol : chr "JUN" "HDAC1" "MYC" "TRIM33" $ Degree : num 3 2 2 1 $ Clustering_Coefficient_Percent : num 33.3 100 100 0 $ Clustering_Coefficient_Fraction : chr "1/3" "1/1" "1/1" "0 / 0" $ Connected_Component_id : num 1 1 1 1 $ Nodes_in_Connected_Component : num 4 4 4 4 $ total_number_of_connected_components: num 1 1 1 1 $ Connectivity_Rank : int 1 2 3 4 NULL [1] "Full scatter plot file path: D:\\temp\\2025_04_08_19_05_17_31070\\RtmpG8IV9c\\file12788123ccb3/04.08.2025_Degree_vs_ClusteringCoefficient.png" 2025-04-08 20:27:16.467656: Scatter plot saved successfully 2025-04-08 20:27:16.467914: Categorizing and plotting genes [1] "Plot exported and device closed." 2025-04-08 20:27:16.702355: FINISHED: Analysis pipeline completed [ FAIL 0 | WARN 9 | SKIP 0 | PASS 61 ] [ FAIL 0 | WARN 9 | SKIP 0 | PASS 61 ] > > proc.time() user system elapsed 599.84 26.54 666.03