Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PathNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PathNet_1.50.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PathNet.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by    Apple clang version 16.0.0 (clang-1600.0.26.6)    GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘PathNet/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘PathNet’ version ‘1.50.0’* 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 ‘PathNet’ 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 code 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 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 ... NOTEconstruct.DirectEvidence: no visible global function definition for  ‘write.table’do.contextual.analysis: no visible global function definition for  ‘phyper’do.enrichment.analysis: no visible global function definition for  ‘phyper’do.enrichment.analysis: no visible global function definition for  ‘p.adjust’Undefined global functions or variables:  p.adjust phyper write.tableConsider adding  importFrom("stats", "p.adjust", "phyper")  importFrom("utils", "write.table")to your NAMESPACE file.* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... OK* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking sizes of PDF files under ‘inst/doc’ ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OK* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘runTests.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 1 NOTESee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/PathNet.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PathNet###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘PathNet’ ...** this is package ‘PathNet’ version ‘1.50.0’** using staged installation** R** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (PathNet)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R 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.> BiocGenerics:::testPackage("PathNet")Number of genes present in the DirectEvidence File:100Starting contextual analysis...Number of significant pathways to use for contextual analysis:130Performing contextual analysis of ABC transporters pathwayPerforming contextual analysis of Acute myeloid leukemia pathwayPerforming contextual analysis of Adherens junction pathwayPerforming contextual analysis of Adipocytokine signaling pathway pathwayPerforming contextual analysis of Aldosterone-regulated sodium reabsorption pathwayPerforming contextual analysis of Allograft rejection pathwayPerforming contextual analysis of Alzheimers disease pathwayPerforming contextual analysis of Amoebiasis pathwayPerforming contextual analysis of Amyotrophic lateral sclerosis (ALS) pathwayPerforming contextual analysis of Antigen processing and presentation pathwayPerforming contextual analysis of Apoptosis pathwayPerforming contextual analysis of Arrhythmogenic right ventricular cardiomyopathy (ARVC) pathwayPerforming contextual analysis of Asthma pathwayPerforming contextual analysis of Autoimmune thyroid disease pathwayPerforming contextual analysis of Axon guidance pathwayPerforming contextual analysis of B cell receptor signaling pathway pathwayPerforming contextual analysis of Bacterial invasion of epithelial cells pathwayPerforming contextual analysis of Basal cell carcinoma pathwayPerforming contextual analysis of Basal transcription factors pathwayPerforming contextual analysis of Base excision repair pathwayPerforming contextual analysis of Bladder cancer pathwayPerforming contextual analysis of Calcium signaling pathway pathwayPerforming contextual analysis of Carbohydrate digestion and absorption pathwayPerforming contextual analysis of Cardiac muscle contraction pathwayPerforming contextual analysis of Cell adhesion molecules (CAMs) pathwayPerforming contextual analysis of Cell cycle pathwayPerforming contextual analysis of Chagas disease pathwayPerforming contextual analysis of Chemokine signaling pathway pathwayPerforming contextual analysis of Chronic myeloid leukemia pathwayPerforming contextual analysis of Circadian rhythm - mammal pathwayPerforming contextual analysis of Collecting duct acid secretion pathwayPerforming contextual analysis of Colorectal cancer pathwayPerforming contextual analysis of Complement and coagulation cascades pathwayPerforming contextual analysis of Cytokine-cytokine receptor interaction pathwayPerforming contextual analysis of Cytosolic DNA-sensing pathway pathwayPerforming contextual analysis of Dilated cardiomyopathy pathwayPerforming contextual analysis of DNA replication pathwayPerforming contextual analysis of Dorso-ventral axis formation pathwayPerforming contextual analysis of ECM-receptor interaction pathwayPerforming contextual analysis of Endocytosis pathwayPerforming contextual analysis of Endometrial cancer pathwayPerforming contextual analysis of Epithelial cell signaling in Helicobacter pylori infection pathwayPerforming contextual analysis of ErbB signaling pathway pathwayPerforming contextual analysis of Fc epsilon RI signaling pathway pathwayPerforming contextual analysis of Fc gamma R-mediated phagocytosis pathwayPerforming contextual analysis of Focal adhesion pathwayPerforming contextual analysis of Gap junction pathwayPerforming contextual analysis of Gastric acid secretion pathwayPerforming contextual analysis of Glioma pathwayPerforming contextual analysis of GnRH signaling pathway pathwayPerforming contextual analysis of Graft-versus-host disease pathwayPerforming contextual analysis of Hedgehog signaling pathway pathwayPerforming contextual analysis of Hematopoietic cell lineage pathwayPerforming contextual analysis of Homologous recombination pathwayPerforming contextual analysis of Huntingtons disease pathwayPerforming contextual analysis of Hypertrophic cardiomyopathy (HCM) pathwayPerforming contextual analysis of Insulin signaling pathway pathwayPerforming contextual analysis of Intestinal immune network for IgA production pathwayPerforming contextual analysis of Jak-STAT signaling pathway pathwayPerforming contextual analysis of Leishmaniasis pathwayPerforming contextual analysis of Leukocyte transendothelial migration pathwayPerforming contextual analysis of Long-term depression pathwayPerforming contextual analysis of Long-term potentiation pathwayPerforming contextual analysis of Lysosome pathwayPerforming contextual analysis of Malaria pathwayPerforming contextual analysis of MAPK signaling pathway pathwayPerforming contextual analysis of Maturity onset diabetes of the young pathwayPerforming contextual analysis of Melanogenesis pathwayPerforming contextual analysis of Melanoma pathwayPerforming contextual analysis of Mismatch repair pathwayPerforming contextual analysis of mTOR signaling pathway pathwayPerforming contextual analysis of Natural killer cell mediated cytotoxicity pathwayPerforming contextual analysis of Neuroactive ligand-receptor interaction pathwayPerforming contextual analysis of Neurotrophin signaling pathway pathwayPerforming contextual analysis of NOD-like receptor signaling pathway pathwayPerforming contextual analysis of Non-homologous end-joining pathwayPerforming contextual analysis of Non-small cell lung cancer pathwayPerforming contextual analysis of Notch signaling pathway pathwayPerforming contextual analysis of Nucleotide excision repair pathwayPerforming contextual analysis of Olfactory transduction pathwayPerforming contextual analysis of Oocyte meiosis pathwayPerforming contextual analysis of p53 signaling pathway pathwayPerforming contextual analysis of Pancreatic cancer pathwayPerforming contextual analysis of Pancreatic secretion pathwayPerforming contextual analysis of Parkinsons disease pathwayPerforming contextual analysis of Pathogenic Escherichia coli infection pathwayPerforming contextual analysis of Pathways in cancer pathwayPerforming contextual analysis of Peroxisome pathwayPerforming contextual analysis of Phagosome pathwayPerforming contextual analysis of Phosphatidylinositol signaling system pathwayPerforming contextual analysis of Phototransduction pathwayPerforming contextual analysis of PPAR signaling pathway pathwayPerforming contextual analysis of Primary immunodeficiency pathwayPerforming contextual analysis of Prion diseases pathwayPerforming contextual analysis of Progesterone-mediated oocyte maturation pathwayPerforming contextual analysis of Prostate cancer pathwayPerforming contextual analysis of Proteasome pathwayPerforming contextual analysis of Protein export pathwayPerforming contextual analysis of Protein processing in endoplasmic reticulum pathwayPerforming contextual analysis of Proximal tubule bicarbonate reclamation pathwayPerforming contextual analysis of Regulation of actin cytoskeleton pathwayPerforming contextual analysis of Regulation of autophagy pathwayPerforming contextual analysis of Renal cell carcinoma pathwayPerforming contextual analysis of Renin-angiotensin system pathwayPerforming contextual analysis of Ribosome pathwayPerforming contextual analysis of RIG-I-like receptor signaling pathway pathwayPerforming contextual analysis of RNA degradation pathwayPerforming contextual analysis of RNA polymerase pathwayPerforming contextual analysis of Salivary secretion pathwayPerforming contextual analysis of Shigellosis pathwayPerforming contextual analysis of Small cell lung cancer pathwayPerforming contextual analysis of SNARE interactions in vesicular transport pathwayPerforming contextual analysis of Spliceosome pathwayPerforming contextual analysis of Systemic lupus erythematosus pathwayPerforming contextual analysis of T cell receptor signaling pathway pathwayPerforming contextual analysis of Taste transduction pathwayPerforming contextual analysis of TGF-beta signaling pathway pathwayPerforming contextual analysis of Thyroid cancer pathwayPerforming contextual analysis of Tight junction pathwayPerforming contextual analysis of Toll-like receptor signaling pathway pathwayPerforming contextual analysis of Toxoplasmosis pathwayPerforming contextual analysis of Type I diabetes mellitus pathwayPerforming contextual analysis of Type II diabetes mellitus pathwayPerforming contextual analysis of Ubiquitin mediated proteolysis pathwayPerforming contextual analysis of Vascular smooth muscle contraction pathwayPerforming contextual analysis of Vasopressin-regulated water reabsorption pathwayPerforming contextual analysis of VEGF signaling pathway pathwayPerforming contextual analysis of Vibrio cholerae infection pathwayPerforming contextual analysis of Viral myocarditis pathwayPerforming contextual analysis of Wnt signaling pathway pathwayNumber of genes present in the DirectEvidence File:20077Number of genes present in the DirectEvidence File:401Number of genes present in the DirectEvidence File:100Starting enrichment analysisProcessing  130 pathwaysCompleted enrichment analysis of ABC transporters pathwayCompleted enrichment analysis of Acute myeloid leukemia pathwayCompleted enrichment analysis of Adherens junction pathwayCompleted enrichment analysis of Adipocytokine signaling pathway pathwayCompleted enrichment analysis of Aldosterone-regulated sodium reabsorption pathwayCompleted enrichment analysis of Allograft rejection pathwayCompleted enrichment analysis of Alzheimers disease pathwayCompleted enrichment analysis of Amoebiasis pathwayCompleted enrichment analysis of Amyotrophic lateral sclerosis (ALS) pathwayCompleted enrichment analysis of Antigen processing and presentation pathwayCompleted enrichment analysis of Apoptosis pathwayCompleted enrichment analysis of Arrhythmogenic right ventricular cardiomyopathy (ARVC) pathwayCompleted enrichment analysis of Asthma pathwayCompleted enrichment analysis of Autoimmune thyroid disease pathwayCompleted enrichment analysis of Axon guidance pathwayCompleted enrichment analysis of B cell receptor signaling pathway pathwayCompleted enrichment analysis of Bacterial invasion of epithelial cells pathwayCompleted enrichment analysis of Basal cell carcinoma pathwayCompleted enrichment analysis of Basal transcription factors pathwayCompleted enrichment analysis of Base excision repair pathwayCompleted enrichment analysis of Bladder cancer pathwayCompleted enrichment analysis of Calcium signaling pathway pathwayCompleted enrichment analysis of Carbohydrate digestion and absorption pathwayCompleted enrichment analysis of Cardiac muscle contraction pathwayCompleted enrichment analysis of Cell adhesion molecules (CAMs) pathwayCompleted enrichment analysis of Cell cycle pathwayCompleted enrichment analysis of Chagas disease pathwayCompleted enrichment analysis of Chemokine signaling pathway pathwayCompleted enrichment analysis of Chronic myeloid leukemia pathwayCompleted enrichment analysis of Circadian rhythm - mammal pathwayCompleted enrichment analysis of Collecting duct acid secretion pathwayCompleted enrichment analysis of Colorectal cancer pathwayCompleted enrichment analysis of Complement and coagulation cascades pathwayCompleted enrichment analysis of Cytokine-cytokine receptor interaction pathwayCompleted enrichment analysis of Cytosolic DNA-sensing pathway pathwayCompleted enrichment analysis of Dilated cardiomyopathy pathwayCompleted enrichment analysis of DNA replication pathwayCompleted enrichment analysis of Dorso-ventral axis formation pathwayCompleted enrichment analysis of ECM-receptor interaction pathwayCompleted enrichment analysis of Endocytosis pathwayCompleted enrichment analysis of Endometrial cancer pathwayCompleted enrichment analysis of Epithelial cell signaling in Helicobacter pylori infection pathwayCompleted enrichment analysis of ErbB signaling pathway pathwayCompleted enrichment analysis of Fc epsilon RI signaling pathway pathwayCompleted enrichment analysis of Fc gamma R-mediated phagocytosis pathwayCompleted enrichment analysis of Focal adhesion pathwayCompleted enrichment analysis of Gap junction pathwayCompleted enrichment analysis of Gastric acid secretion pathwayCompleted enrichment analysis of Glioma pathwayCompleted enrichment analysis of GnRH signaling pathway pathwayCompleted enrichment analysis of Graft-versus-host disease pathwayCompleted enrichment analysis of Hedgehog signaling pathway pathwayCompleted enrichment analysis of Hematopoietic cell lineage pathwayCompleted enrichment analysis of Homologous recombination pathwayCompleted enrichment analysis of Huntingtons disease pathwayCompleted enrichment analysis of Hypertrophic cardiomyopathy (HCM) pathwayCompleted enrichment analysis of Insulin signaling pathway pathwayCompleted enrichment analysis of Intestinal immune network for IgA production pathwayCompleted enrichment analysis of Jak-STAT signaling pathway pathwayCompleted enrichment analysis of Leishmaniasis pathwayCompleted enrichment analysis of Leukocyte transendothelial migration pathwayCompleted enrichment analysis of Long-term depression pathwayCompleted enrichment analysis of Long-term potentiation pathwayCompleted enrichment analysis of Lysosome pathwayCompleted enrichment analysis of Malaria pathwayCompleted enrichment analysis of MAPK signaling pathway pathwayCompleted enrichment analysis of Maturity onset diabetes of the young pathwayCompleted enrichment analysis of Melanogenesis pathwayCompleted enrichment analysis of Melanoma pathwayCompleted enrichment analysis of Mismatch repair pathwayCompleted enrichment analysis of mTOR signaling pathway pathwayCompleted enrichment analysis of Natural killer cell mediated cytotoxicity pathwayCompleted enrichment analysis of Neuroactive ligand-receptor interaction pathwayCompleted enrichment analysis of Neurotrophin signaling pathway pathwayCompleted enrichment analysis of NOD-like receptor signaling pathway pathwayCompleted enrichment analysis of Non-homologous end-joining pathwayCompleted enrichment analysis of Non-small cell lung cancer pathwayCompleted enrichment analysis of Notch signaling pathway pathwayCompleted enrichment analysis of Nucleotide excision repair pathwayCompleted enrichment analysis of Olfactory transduction pathwayCompleted enrichment analysis of Oocyte meiosis pathwayCompleted enrichment analysis of p53 signaling pathway pathwayCompleted enrichment analysis of Pancreatic cancer pathwayCompleted enrichment analysis of Pancreatic secretion pathwayCompleted enrichment analysis of Parkinsons disease pathwayCompleted enrichment analysis of Pathogenic Escherichia coli infection pathwayCompleted enrichment analysis of Pathways in cancer pathwayCompleted enrichment analysis of Peroxisome pathwayCompleted enrichment analysis of Phagosome pathwayCompleted enrichment analysis of Phosphatidylinositol signaling system pathwayCompleted enrichment analysis of Phototransduction pathwayCompleted enrichment analysis of PPAR signaling pathway pathwayCompleted enrichment analysis of Primary immunodeficiency pathwayCompleted enrichment analysis of Prion diseases pathwayCompleted enrichment analysis of Progesterone-mediated oocyte maturation pathwayCompleted enrichment analysis of Prostate cancer pathwayCompleted enrichment analysis of Proteasome pathwayCompleted enrichment analysis of Protein export pathwayCompleted enrichment analysis of Protein processing in endoplasmic reticulum pathwayCompleted enrichment analysis of Proximal tubule bicarbonate reclamation pathwayCompleted enrichment analysis of Regulation of actin cytoskeleton pathwayCompleted enrichment analysis of Regulation of autophagy pathwayCompleted enrichment analysis of Renal cell carcinoma pathwayCompleted enrichment analysis of Renin-angiotensin system pathwayCompleted enrichment analysis of Ribosome pathwayCompleted enrichment analysis of RIG-I-like receptor signaling pathway pathwayCompleted enrichment analysis of RNA degradation pathwayCompleted enrichment analysis of RNA polymerase pathwayCompleted enrichment analysis of Salivary secretion pathwayCompleted enrichment analysis of Shigellosis pathwayCompleted enrichment analysis of Small cell lung cancer pathwayCompleted enrichment analysis of SNARE interactions in vesicular transport pathwayCompleted enrichment analysis of Spliceosome pathwayCompleted enrichment analysis of Systemic lupus erythematosus pathwayCompleted enrichment analysis of T cell receptor signaling pathway pathwayCompleted enrichment analysis of Taste transduction pathwayCompleted enrichment analysis of TGF-beta signaling pathway pathwayCompleted enrichment analysis of Thyroid cancer pathwayCompleted enrichment analysis of Tight junction pathwayCompleted enrichment analysis of Toll-like receptor signaling pathway pathwayCompleted enrichment analysis of Toxoplasmosis pathwayCompleted enrichment analysis of Type I diabetes mellitus pathwayCompleted enrichment analysis of Type II diabetes mellitus pathwayCompleted enrichment analysis of Ubiquitin mediated proteolysis pathwayCompleted enrichment analysis of Vascular smooth muscle contraction pathwayCompleted enrichment analysis of Vasopressin-regulated water reabsorption pathwayCompleted enrichment analysis of VEGF signaling pathway pathwayCompleted enrichment analysis of Vibrio cholerae infection pathwayCompleted enrichment analysis of Viral myocarditis pathwayCompleted enrichment analysis of Wnt signaling pathway pathwayNumber of significant genes from direct evidence14Number of significant genes from combined evidence13Processing  130 pathwaysNumber of genes present in the DirectEvidence File:20077[1] "Using significant pathways requires enrichment analysis to be performed, run PathNet with Enrichment_Analysis=TRUE"[1] "Using significant pathways requires enrichment analysis to be performed, run PathNet with Enrichment_Analysis=TRUE"RUNIT TEST PROTOCOL -- Sat Dec 13 17:28:35 2025 *********************************************** Number of test functions: 9 Number of errors: 0 Number of failures: 0  1 Test Suite : PathNet RUnit Tests - 9 test functions, 0 errors, 0 failuresNumber of test functions: 9 Number of errors: 0 Number of failures: 0 > > proc.time()   user  system elapsed  34.552   5.692  56.684