############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:EGSEA.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings EGSEA_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/EGSEA.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EGSEA/DESCRIPTION’ ... OK * this is package ‘EGSEA’ version ‘1.30.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘EGSEA’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE buildGeneSetDBIdx: no visible binding for global variable ‘GOTERM’ buildMSigDBIdx: no visible binding for global variable ‘msigdb’ generateSummaryPlots: no visible binding for global variable ‘x.data’ generateSummaryPlots: no visible binding for global variable ‘y.data’ generateSummaryPlots: no visible binding for global variable ‘gsSize’ generateSummaryPlots: no visible binding for global variable ‘id’ generateSummaryPlots: no visible binding for global variable ‘sig’ loadKeggData: no visible binding for global variable ‘kegg.pathways’ Undefined global functions or variables: GOTERM gsSize id kegg.pathways msigdb sig x.data y.data * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘arraydata’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING 'library' or 'require' call not declared from: ‘Glimma’ * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘EGSEA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: EGSEAResults > ### Title: The EGSEAResults class > ### Aliases: EGSEAResults EGSEAResults-class $,EGSEAResults-method topSets > ### topSets,EGSEAResults-method show,EGSEAResults-method > ### summary,EGSEAResults-method limmaTopTable > ### limmaTopTable,EGSEAResults-method generateReport > ### generateReport,EGSEAResults-method getlimmaResults > ### getlimmaResults,EGSEAResults-method plotHeatmap > ### plotHeatmap,EGSEAResults-method plotSummaryHeatmap > ### plotSummaryHeatmap,EGSEAResults-method plotPathway > ### plotPathway,EGSEAResults-method plotMethods > ### plotMethods,EGSEAResults-method plotSummary > ### plotSummary,EGSEAResults-method plotGOGraph > ### plotGOGraph,EGSEAResults-method plotBars plotBars,EGSEAResults-method > ### showSetByName showSetByName,EGSEAResults-method showSetByID > ### showSetByID,EGSEAResults-method getSetScores > ### getSetScores,EGSEAResults-method > > ### ** Examples > > # Exampple of EGSEAResults > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > print(gsa$baseMethods) [1] "camera" "safe" "gage" "padog" "plage" [6] "zscore" "gsva" "ssgsea" "globaltest" "ora" > > # Example of topSets > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > topSets(gsa, gs.label="kegg",contrast=1, number = 10) Extracting the top gene sets of the collection KEGG Pathways for the contrast X24IL13-X24 Sorted by avg.rank [1] "Amoebiasis" [2] "Asthma" [3] "Intestinal immune network for IgA production" [4] "Endocrine and other factor-regulated calcium reabsorption" [5] "Viral myocarditis" [6] "HTLV-I infection" [7] "Prion diseases" [8] "Proteoglycans in cancer" [9] "Hematopoietic cell lineage" [10] "Legionellosis" > topSets(gsa, gs.label=1, contrast=1, sort.by="ora", number = 10, + names.only=FALSE) Extracting the top gene sets of the collection c2 Curated Gene Sets for the contrast X24IL13-X24 Sorted by ora Rank p.value p.adj TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN 1 2.084798e-49 3.901699e-46 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP 2 5.752312e-28 1.957355e-25 NABA_MATRISOME 3 2.503133e-24 4.461536e-22 RUTELLA_RESPONSE_TO_HGF_UP 4 7.905113e-33 4.931473e-30 NABA_MATRISOME_ASSOCIATED 5 2.007033e-61 7.512324e-58 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN 6 6.058174e-37 5.668936e-34 MCLACHLAN_DENTAL_CARIES_UP 7 4.443436e-34 3.326356e-31 LENAOUR_DENDRITIC_CELL_MATURATION_UP 8 2.413176e-43 3.010840e-40 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 9 1.818059e-29 7.561105e-27 ONDER_CDH1_TARGETS_2_DN 10 7.407783e-31 3.961047e-28 vote.rank avg.rank med.rank TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN 5 1573.9 1061.5 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP 355 815.8 403.5 NABA_MATRISOME 5 1666.3 1495.0 RUTELLA_RESPONSE_TO_HGF_UP 3210 1519.6 1242.5 NABA_MATRISOME_ASSOCIATED 5 1292.7 1117.5 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN 10 1414.5 1343.5 MCLACHLAN_DENTAL_CARIES_UP 10 1509.0 1626.0 LENAOUR_DENDRITIC_CELL_MATURATION_UP 20 224.8 69.5 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 10 817.3 695.5 ONDER_CDH1_TARGETS_2_DN 10 1420.6 1561.0 min.pvalue min.rank avg.logfc TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN 6.105360e-32 1 2.479176 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP 6.316000e-28 2 1.733495 NABA_MATRISOME 1.924738e-27 3 2.367135 RUTELLA_RESPONSE_TO_HGF_UP 4.873555e-27 4 1.743617 NABA_MATRISOME_ASSOCIATED 1.486914e-42 1 2.425162 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN 8.472735e-26 4 1.894696 MCLACHLAN_DENTAL_CARIES_UP 4.952318e-25 7 1.517220 LENAOUR_DENDRITIC_CELL_MATURATION_UP 2.474903e-21 8 2.483170 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 1.277895e-20 9 1.535780 ONDER_CDH1_TARGETS_2_DN 2.310221e-19 6 1.578958 avg.logfc.dir direction TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN 2.832590 Up FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP 1.924505 Up NABA_MATRISOME 2.669640 Up RUTELLA_RESPONSE_TO_HGF_UP -1.687618 Down NABA_MATRISOME_ASSOCIATED 2.816744 Up TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN 1.881403 Up MCLACHLAN_DENTAL_CARIES_UP -1.380719 Down LENAOUR_DENDRITIC_CELL_MATURATION_UP 2.518874 Up RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP -1.639309 Down ONDER_CDH1_TARGETS_2_DN -1.465519 Down significance camera safe gage TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN 81.26167 2822 891 2 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP 30.91754 353 702 3389 NABA_MATRISOME 36.48130 1131 704 3743 RUTELLA_RESPONSE_TO_HGF_UP 36.88600 3206 731 21 NABA_MATRISOME_ASSOCIATED 100.00000 1508 727 1 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN 45.46993 1856 831 7 MCLACHLAN_DENTAL_CARIES_UP 33.37908 1157 797 9 LENAOUR_DENDRITIC_CELL_MATURATION_UP 70.83970 17 917 18 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 28.95774 263 732 33 ONDER_CDH1_TARGETS_2_DN 31.23164 1671 1451 6 padog plage zscore gsva ssgsea TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN 2 3310 3676 3536 1232 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP 192 1161 441 1435 366 NABA_MATRISOME 3 3161 1859 2109 3426 RUTELLA_RESPONSE_TO_HGF_UP 195 1754 2679 3227 3035 NABA_MATRISOME_ASSOCIATED 1 2680 2220 2350 3007 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN 4 2970 2005 2494 3497 MCLACHLAN_DENTAL_CARIES_UP 200 3031 2777 2796 2095 LENAOUR_DENDRITIC_CELL_MATURATION_UP 193 756 17 183 28 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 10 1811 1769 1598 1289 ONDER_CDH1_TARGETS_2_DN 8 2245 2448 2736 2931 globaltest ora TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN 267 1 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP 117 2 NABA_MATRISOME 524 3 RUTELLA_RESPONSE_TO_HGF_UP 344 4 NABA_MATRISOME_ASSOCIATED 428 5 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN 475 6 MCLACHLAN_DENTAL_CARIES_UP 2221 7 LENAOUR_DENDRITIC_CELL_MATURATION_UP 111 8 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 659 9 ONDER_CDH1_TARGETS_2_DN 700 10 > topSets(gsa, gs.label="kegg",contrast=0, number = 10) Extracting the top gene sets of the collection KEGG Pathways for the contrast comparison Sorted by avg.rank [1] "Asthma" [2] "Viral myocarditis" [3] "Intestinal immune network for IgA production" [4] "Amoebiasis" [5] "HTLV-I infection" [6] "NOD-like receptor signaling pathway" [7] "Hematopoietic cell lineage" [8] "Malaria" [9] "Legionellosis" [10] "Toll-like receptor signaling pathway" > > # Example of show > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > show(gsa) An object of class "EGSEAResults" Total number of genes: 17343 Total number of samples: 8 Contrasts: X24IL13-X24, X24IL13Ant-X24IL13 Base GSE methods: camera (limma:3.31.10), safe (safe:3.15.0), gage (gage:2.25.0), padog (PADOG:1.17.0), plage (GSVA:1.23.3), zscore (GSVA:1.23.3), gsva (GSVA:1.23.3), ssgsea (GSVA:1.23.3), globaltest (globaltest:5.29.1), ora (stats:3.4.0) P-values combining method: fisher Sorting statistic: avg.rank Organism: Homo sapiens HTML report generated: Yes HTML report directory: ./il13-egsea-report Tested gene set collections: c2 Curated Gene Sets (c2): 3747 gene sets - Version: 5.2, Update date: 07 March 2017 c5 GO Gene Sets (c5): 6166 gene sets - Version: 5.2, Update date: 07 March 2017 KEGG Pathways (kegg): 203 gene sets - Version: NA, Update date: 07 March 2017 EGSEA version: 1.3.1 EGSEAdata version: 1.3.1 Use summary(object) and topSets(object, ...) to explore this object. > > # Example of summary > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > summary(gsa) **** Top 10 gene sets in the c2 Curated Gene Sets collection **** ** Contrast X24IL13-X24 ** LU_IL4_SIGNALING | LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP LINDSTEDT_DENDRITIC_CELL_MATURATION_D | LENAOUR_DENDRITIC_CELL_MATURATION_UP REACTOME_PD1_SIGNALING | SCHOEN_NFKB_SIGNALING PID_NOTCH_PATHWAY | PID_INTEGRIN_A9B1_PATHWAY MAHADEVAN_IMATINIB_RESISTANCE_UP | LUI_THYROID_CANCER_CLUSTER_4 ** Contrast X24IL13Ant-X24IL13 ** SCHOEN_NFKB_SIGNALING | GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_UP MAHADEVAN_IMATINIB_RESISTANCE_UP | DAZARD_UV_RESPONSE_CLUSTER_G28 HAHTOLA_MYCOSIS_FUNGOIDES_CD4_UP | LU_IL4_SIGNALING TIAN_TNF_SIGNALING_VIA_NFKB | ZHAN_MULTIPLE_MYELOMA_DN LIANG_SILENCED_BY_METHYLATION_2 | REACTOME_PD1_SIGNALING ** Comparison analysis ** SCHOEN_NFKB_SIGNALING | LU_IL4_SIGNALING MAHADEVAN_IMATINIB_RESISTANCE_UP | REACTOME_PD1_SIGNALING LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP | LENAOUR_DENDRITIC_CELL_MATURATION_UP LUI_THYROID_CANCER_CLUSTER_4 | LINDSTEDT_DENDRITIC_CELL_MATURATION_D IIZUKA_LIVER_CANCER_EARLY_RECURRENCE | WU_HBX_TARGETS_3_DN **** Top 10 gene sets in the c5 GO Gene Sets collection **** ** Contrast X24IL13-X24 ** GO_CLATHRIN_COATED_ENDOCYTIC_VESICLE_MEMBRANE | GO_CLATHRIN_COATED_VESICLE_MEMBRANE GO_CLATHRIN_COATED_ENDOCYTIC_VESICLE | GO_ICOSANOID_BIOSYNTHETIC_PROCESS GO_FATTY_ACID_DERIVATIVE_BIOSYNTHETIC_PROCESS | GO_UNSATURATED_FATTY_ACID_BIOSYNTHETIC_PROCESS GO_POSITIVE_REGULATION_OF_CYTOKINE_SECRETION | GO_MHC_CLASS_II_PROTEIN_COMPLEX GO_MHC_CLASS_II_RECEPTOR_ACTIVITY | GO_LEUKOTRIENE_METABOLIC_PROCESS ** Contrast X24IL13Ant-X24IL13 ** GO_CLATHRIN_COATED_ENDOCYTIC_VESICLE_MEMBRANE | GO_POSITIVE_REGULATION_OF_NF_KAPPAB_IMPORT_INTO_NUCLEUS GO_MHC_CLASS_II_PROTEIN_COMPLEX | GO_CLATHRIN_COATED_VESICLE_MEMBRANE GO_IGG_BINDING | GO_POSITIVE_REGULATION_OF_ACUTE_INFLAMMATORY_RESPONSE GO_CXCR_CHEMOKINE_RECEPTOR_BINDING | GO_CLATHRIN_COATED_ENDOCYTIC_VESICLE GO_POSITIVE_REGULATION_OF_INTERLEUKIN_1_SECRETION | GO_MHC_CLASS_II_RECEPTOR_ACTIVITY ** Comparison analysis ** GO_CLATHRIN_COATED_ENDOCYTIC_VESICLE_MEMBRANE | GO_CLATHRIN_COATED_VESICLE_MEMBRANE GO_CLATHRIN_COATED_ENDOCYTIC_VESICLE | GO_MHC_CLASS_II_PROTEIN_COMPLEX GO_POSITIVE_REGULATION_OF_NF_KAPPAB_IMPORT_INTO_NUCLEUS | GO_MHC_CLASS_II_RECEPTOR_ACTIVITY GO_POSITIVE_REGULATION_OF_CYTOKINE_SECRETION | GO_POSITIVE_REGULATION_OF_ACUTE_INFLAMMATORY_RESPONSE GO_IGG_BINDING | GO_ANTIGEN_BINDING **** Top 10 gene sets in the KEGG Pathways collection **** ** Contrast X24IL13-X24 ** Amoebiasis | Asthma Intestinal immune network for IgA production | Endocrine and other factor-regulated calcium reabsorption Viral myocarditis | HTLV-I infection Prion diseases | Proteoglycans in cancer Hematopoietic cell lineage | Legionellosis ** Contrast X24IL13Ant-X24IL13 ** Malaria | Viral myocarditis NOD-like receptor signaling pathway | Toll-like receptor signaling pathway Asthma | Legionellosis Hematopoietic cell lineage | Rheumatoid arthritis HTLV-I infection | Melanoma ** Comparison analysis ** Asthma | Viral myocarditis Intestinal immune network for IgA production | Amoebiasis HTLV-I infection | NOD-like receptor signaling pathway Hematopoietic cell lineage | Malaria Legionellosis | Toll-like receptor signaling pathway > > # Example of limmaTopTable > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > colnames(limmaTopTable(gsa)) [1] "FeatureID" "Symbols" "logFC" "AveExpr" "t" "P.Value" [7] "adj.P.Val" "B" > head(limmaTopTable(gsa)) FeatureID Symbols logFC AveExpr t P.Value adj.P.Val 2208 2208 FCER2 5.818129 3.356316 24.97210 2.328014e-10 2.018738e-06 30835 30835 CD209 3.882492 4.818066 25.93935 1.598970e-10 2.018738e-06 2675 2675 GFRA2 3.277526 3.319754 22.93290 5.395423e-10 2.339320e-06 3554 3554 IL1R1 2.303161 5.728493 22.98881 5.267500e-10 2.339320e-06 55022 55022 PID1 -3.454681 4.012016 -21.56122 9.900617e-10 3.434128e-06 7850 7850 IL1R2 3.336171 4.158437 20.19777 1.880207e-09 5.434739e-06 B 2208 13.25669 30835 14.52844 2675 13.13380 3554 13.62705 55022 12.71054 7850 12.26003 > > # Example of generateReport > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > # generateReport(gsa) > > # Example of getlimmaResults > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > fit = getlimmaResults(gsa) > class(fit) [1] "MArrayLM" attr(,"package") [1] "limma" > names(fit) [1] "coefficients" "stdev.unscaled" "sigma" "df.residual" [5] "cov.coefficients" "rank" "genes" "Amean" [9] "method" "design" "contrasts" "df.prior" [13] "s2.prior" "var.prior" "proportion" "s2.post" [17] "t" "df.total" "p.value" "lods" [21] "F" "F.p.value" > > # Example of plotHeatmap > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > plotHeatmap(gsa, "Asthma", gs.label="kegg") Generating heatmap for Asthma from the collection KEGG Pathways and for the contrast X24IL13-X24 > plotHeatmap(gsa, "Asthma", gs.label="kegg", contrast = "comparison", + file.name = "asthma.hm.cmp") Generating heatmap for Asthma from the collection KEGG Pathways and for the contrast comparison > > # Example of plotSummaryHeatmap > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > plotSummaryHeatmap(gsa, gs.label="kegg") Generating summary heatmap for the collection KEGG Pathways sort.by: avg.rank, hm.vals: avg.rank, show.vals: > > # Example of plotPathway > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > plotPathway(gsa, gs.label="kegg", "Asthma") Generating pathway map for Asthma from the collection KEGG Pathways and for the contrast X24IL13-X24 [1] TRUE > plotPathway(gsa, gs.label="kegg", "Asthma", contrast="comparison", + file.name = "asthma.map.cmp") Generating pathway map for Asthma from the collection KEGG Pathways and for the contrast comparison [1] TRUE > > # Example of plotMethods > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > plotMethods(gsa) Generating methods plot for the collection c2 Curated Gene Sets and for the contrast X24IL13-X24 character(0) > > # Example of plotSummary > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > plotSummary(gsa) Generating Summary plots for the collection c2 Curated Gene Sets and for the contrast X24IL13-X24 > plotSummary(gsa, contrast=c(1,2), file.name = "summary.cmp") Generating Summary plots for the collection c2 Curated Gene Sets and for the comparison X24IL13-X24 vs X24IL13Ant-X24IL13 > > # Example of plotGOGraph > library(EGSEAdata) > data(il13.gsa) > gsa = il13.gsa > class(gsa) [1] "EGSEAResults" attr(,"package") [1] "EGSEA" > plotGOGraph(gsa, sort.by="avg.rank") Generating GO Graphs for the collection c5 GO Gene Sets and for the contrast X24IL13-X24 based on the avg.rank Building most specific GOs ..... Loading required package: org.Hs.eg.db ( 11140 GO terms found. ) Build GO DAG topology .......... ( 14547 GO terms and 32701 relations. ) Annotating nodes ............... * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/EGSEA.Rcheck/00check.log’ for details.