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") 2025-04-09 00:26:56.353331: Starting analysis pipeline 2025-04-09 00:26:56.354741: Performing PubMed search 2025-04-09 00:26:57.314839: PubMed search completed. Results: # A tibble: 1 x 4 Gene cancer Total PubMed_Rank 1 MYC 17294 17294 1 2025-04-09 00:26:57.347976: Plotting heatmap of PubMed search results 2025-04-09 00:26:57.356569: 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 2025-04-09 00:28:03.956514: STRING database search completed. Results: data frame with 0 columns and 0 rows 2025-04-09 00:28:03.956978: Plotting STRING network interactions 2025-04-09 00:28:04.644395: Combining summaries 2025-04-09 00:28:04.645094: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 0 obs. of 0 variables NULL 2025-04-09 00:28:04.647448: Inside plot_clustering function 2025-04-09 00:28:04.651753: Categorizing and plotting genes 2025-04-09 00:28:04.655762: FINISHED: Analysis pipeline completed 2025-04-09 00:28:04.696529: Inside plot_clustering function 2025-04-09 00:28:04.718175: Starting analysis pipeline 2025-04-09 00:28:04.718383: Performing PubMed search 2025-04-09 00:28:04.732985: PubMed search completed. Results: # A tibble: 0 x 3 # i 3 variables: Gene , Total , PubMed_Rank 2025-04-09 00:28:04.738807: Plotting heatmap of PubMed search results 2025-04-09 00:28:04.742755: Performing STRING database search 2025-04-09 00:28:04.746668: STRING database search completed. Results: data frame with 0 columns and 0 rows 2025-04-09 00:28:04.746934: Plotting STRING network interactions 2025-04-09 00:28:04.750783: Combining summaries 2025-04-09 00:28:04.751029: Plotting clustering coefficient [1] "Data passed to plot_clustering function" 'data.frame': 0 obs. of 0 variables NULL 2025-04-09 00:28:04.751477: Inside plot_clustering function 2025-04-09 00:28:04.755358: Categorizing and plotting genes 2025-04-09 00:28:04.759223: FINISHED: Analysis pipeline completed 2025-04-09 00:28:04.792689: Inside plot_clustering function 2025-04-09 00:29:04.132064: Starting analysis pipeline 2025-04-09 00:29:04.132322: Performing PubMed search 2025-04-09 00:29:08.906202: 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 2025-04-09 00:29:08.922725: Plotting heatmap of PubMed search results 2025-04-09 00:29:10.587272: Performing STRING database search 2025-04-09 00:29:59.220548: 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 2025-04-09 00:29:59.222242: Plotting STRING network interactions 2025-04-09 00:29:59.86425: Combining summaries 2025-04-09 00:29:59.868329: 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 2025-04-09 00:29:59.872479: Inside plot_clustering function 2025-04-09 00:29:59.872628: 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 2025-04-09 00:29:59.951849: Categorizing and plotting genes 2025-04-09 00:30:00.175322: FINISHED: Analysis pipeline completed 2025-04-09 00:30:00.319451: Inside plot_clustering function 2025-04-09 00:30:00.319639: 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 2025-04-09 00:30:00.517482: Starting analysis pipeline 2025-04-09 00:30:00.517839: Performing PubMed search 2025-04-09 00:30:05.349156: 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 2025-04-09 00:30:05.365412: Plotting heatmap of PubMed search results [1] "Heatmap plot exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file107342c22643e/04.09.2025_PubMed_Heatmap.png" 2025-04-09 00:30:06.016592: Performing STRING database search 2025-04-09 00:31:09.662706: 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 2025-04-09 00:31:09.664431: Plotting STRING network interactions [1] "Network plot exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file107342c22643e/04.09.2025_STRINGdb_Network.pdf" 2025-04-09 00:31:10.357635: Combining summaries [1] "Summary table exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file107342c22643e/04.09.2025_Combined_Summary.csv" 2025-04-09 00:31:10.363875: 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 2025-04-09 00:31:10.369719: Inside plot_clustering function 2025-04-09 00:31:10.369874: 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_09_00_25_17_28233\\RtmpiQYlJ7\\file107342c22643e/04.09.2025_Degree_vs_ClusteringCoefficient.png" 2025-04-09 00:31:10.487721: Scatter plot saved successfully 2025-04-09 00:31:10.487956: Categorizing and plotting genes [1] "Plot exported and device closed." 2025-04-09 00:31:10.646268: FINISHED: Analysis pipeline completed 2025-04-09 00:31:10.670311: Starting analysis pipeline 2025-04-09 00:31:10.670704: Performing PubMed search 2025-04-09 00:31:15.421519: 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 2025-04-09 00:31:15.437973: Plotting heatmap of PubMed search results [1] "Heatmap plot exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file1073419f35573/04.09.2025_PubMed_Heatmap.png" 2025-04-09 00:31:15.637953: Performing STRING database search 2025-04-09 00:32:16.587453: 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 2025-04-09 00:32:16.589137: Plotting STRING network interactions [1] "Network plot exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file1073419f35573/04.09.2025_STRINGdb_Network.pdf" 2025-04-09 00:32:17.265419: Combining summaries [1] "Summary table exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file1073419f35573/04.09.2025_Combined_Summary.tsv" 2025-04-09 00:32:17.271407: 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 2025-04-09 00:32:17.275836: Inside plot_clustering function 2025-04-09 00:32:17.275992: 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_09_00_25_17_28233\\RtmpiQYlJ7\\file1073419f35573/04.09.2025_Degree_vs_ClusteringCoefficient.png" 2025-04-09 00:32:17.386793: Scatter plot saved successfully 2025-04-09 00:32:17.386999: Categorizing and plotting genes [1] "Plot exported and device closed." 2025-04-09 00:32:17.526275: FINISHED: Analysis pipeline completed 2025-04-09 00:32:17.54633: Starting analysis pipeline 2025-04-09 00:32:17.546613: Performing PubMed search 2025-04-09 00:32:22.449359: 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 2025-04-09 00:32:22.466838: Plotting heatmap of PubMed search results [1] "Heatmap plot exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file1073448e276c1/04.09.2025_PubMed_Heatmap.png" 2025-04-09 00:32:22.647925: Performing STRING database search 2025-04-09 00:33:23.567952: 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 2025-04-09 00:33:23.569627: Plotting STRING network interactions [1] "Network plot exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file1073448e276c1/04.09.2025_STRINGdb_Network.pdf" 2025-04-09 00:33:24.225958: Combining summaries [1] "Summary table exported to: D:\\temp\\2025_04_09_00_25_17_28233\\RtmpiQYlJ7\\file1073448e276c1/04.09.2025_Combined_Summary.xlsx" 2025-04-09 00:33:24.303826: 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 2025-04-09 00:33:24.307989: Inside plot_clustering function 2025-04-09 00:33:24.308137: 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_09_00_25_17_28233\\RtmpiQYlJ7\\file1073448e276c1/04.09.2025_Degree_vs_ClusteringCoefficient.png" 2025-04-09 00:33:24.408524: Scatter plot saved successfully 2025-04-09 00:33:24.408698: Categorizing and plotting genes [1] "Plot exported and device closed." 2025-04-09 00:33:24.54: 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 348.25 9.93 391.23