Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1501/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PathNet 1.47.0 (landing page) Ludwig Geistlinger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the PathNet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PathNet.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: PathNet |
Version: 1.47.0 |
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_1.47.0.tar.gz |
StartedAt: 2024-12-23 20:38:40 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:39:03 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 23.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PathNet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PathNet.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PathNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PathNet’ version ‘1.47.0’ * 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 ... NOTE construct.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.table Consider 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 * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/PathNet.Rcheck/00check.log’ for details.
PathNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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’ ... ** 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)
PathNet.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > BiocGenerics:::testPackage("PathNet") Number of genes present in the DirectEvidence File: 100 Starting contextual analysis... Number of significant pathways to use for contextual analysis:130 Performing contextual analysis of ABC transporters pathway Performing contextual analysis of Acute myeloid leukemia pathway Performing contextual analysis of Adherens junction pathway Performing contextual analysis of Adipocytokine signaling pathway pathway Performing contextual analysis of Aldosterone-regulated sodium reabsorption pathway Performing contextual analysis of Allograft rejection pathway Performing contextual analysis of Alzheimers disease pathway Performing contextual analysis of Amoebiasis pathway Performing contextual analysis of Amyotrophic lateral sclerosis (ALS) pathway Performing contextual analysis of Antigen processing and presentation pathway Performing contextual analysis of Apoptosis pathway Performing contextual analysis of Arrhythmogenic right ventricular cardiomyopathy (ARVC) pathway Performing contextual analysis of Asthma pathway Performing contextual analysis of Autoimmune thyroid disease pathway Performing contextual analysis of Axon guidance pathway Performing contextual analysis of B cell receptor signaling pathway pathway Performing contextual analysis of Bacterial invasion of epithelial cells pathway Performing contextual analysis of Basal cell carcinoma pathway Performing contextual analysis of Basal transcription factors pathway Performing contextual analysis of Base excision repair pathway Performing contextual analysis of Bladder cancer pathway Performing contextual analysis of Calcium signaling pathway pathway Performing contextual analysis of Carbohydrate digestion and absorption pathway Performing contextual analysis of Cardiac muscle contraction pathway Performing contextual analysis of Cell adhesion molecules (CAMs) pathway Performing contextual analysis of Cell cycle pathway Performing contextual analysis of Chagas disease pathway Performing contextual analysis of Chemokine signaling pathway pathway Performing contextual analysis of Chronic myeloid leukemia pathway Performing contextual analysis of Circadian rhythm - mammal pathway Performing contextual analysis of Collecting duct acid secretion pathway Performing contextual analysis of Colorectal cancer pathway Performing contextual analysis of Complement and coagulation cascades pathway Performing contextual analysis of Cytokine-cytokine receptor interaction pathway Performing contextual analysis of Cytosolic DNA-sensing pathway pathway Performing contextual analysis of Dilated cardiomyopathy pathway Performing contextual analysis of DNA replication pathway Performing contextual analysis of Dorso-ventral axis formation pathway Performing contextual analysis of ECM-receptor interaction pathway Performing contextual analysis of Endocytosis pathway Performing contextual analysis of Endometrial cancer pathway Performing contextual analysis of Epithelial cell signaling in Helicobacter pylori infection pathway Performing contextual analysis of ErbB signaling pathway pathway Performing contextual analysis of Fc epsilon RI signaling pathway pathway Performing contextual analysis of Fc gamma R-mediated phagocytosis pathway Performing contextual analysis of Focal adhesion pathway Performing contextual analysis of Gap junction pathway Performing contextual analysis of Gastric acid secretion pathway Performing contextual analysis of Glioma pathway Performing contextual analysis of GnRH signaling pathway pathway Performing contextual analysis of Graft-versus-host disease pathway Performing contextual analysis of Hedgehog signaling pathway pathway Performing contextual analysis of Hematopoietic cell lineage pathway Performing contextual analysis of Homologous recombination pathway Performing contextual analysis of Huntingtons disease pathway Performing contextual analysis of Hypertrophic cardiomyopathy (HCM) pathway Performing contextual analysis of Insulin signaling pathway pathway Performing contextual analysis of Intestinal immune network for IgA production pathway Performing contextual analysis of Jak-STAT signaling pathway pathway Performing contextual analysis of Leishmaniasis pathway Performing contextual analysis of Leukocyte transendothelial migration pathway Performing contextual analysis of Long-term depression pathway Performing contextual analysis of Long-term potentiation pathway Performing contextual analysis of Lysosome pathway Performing contextual analysis of Malaria pathway Performing contextual analysis of MAPK signaling pathway pathway Performing contextual analysis of Maturity onset diabetes of the young pathway Performing contextual analysis of Melanogenesis pathway Performing contextual analysis of Melanoma pathway Performing contextual analysis of Mismatch repair pathway Performing contextual analysis of mTOR signaling pathway pathway Performing contextual analysis of Natural killer cell mediated cytotoxicity pathway Performing contextual analysis of Neuroactive ligand-receptor interaction pathway Performing contextual analysis of Neurotrophin signaling pathway pathway Performing contextual analysis of NOD-like receptor signaling pathway pathway Performing contextual analysis of Non-homologous end-joining pathway Performing contextual analysis of Non-small cell lung cancer pathway Performing contextual analysis of Notch signaling pathway pathway Performing contextual analysis of Nucleotide excision repair pathway Performing contextual analysis of Olfactory transduction pathway Performing contextual analysis of Oocyte meiosis pathway Performing contextual analysis of p53 signaling pathway pathway Performing contextual analysis of Pancreatic cancer pathway Performing contextual analysis of Pancreatic secretion pathway Performing contextual analysis of Parkinsons disease pathway Performing contextual analysis of Pathogenic Escherichia coli infection pathway Performing contextual analysis of Pathways in cancer pathway Performing contextual analysis of Peroxisome pathway Performing contextual analysis of Phagosome pathway Performing contextual analysis of Phosphatidylinositol signaling system pathway Performing contextual analysis of Phototransduction pathway Performing contextual analysis of PPAR signaling pathway pathway Performing contextual analysis of Primary immunodeficiency pathway Performing contextual analysis of Prion diseases pathway Performing contextual analysis of Progesterone-mediated oocyte maturation pathway Performing contextual analysis of Prostate cancer pathway Performing contextual analysis of Proteasome pathway Performing contextual analysis of Protein export pathway Performing contextual analysis of Protein processing in endoplasmic reticulum pathway Performing contextual analysis of Proximal tubule bicarbonate reclamation pathway Performing contextual analysis of Regulation of actin cytoskeleton pathway Performing contextual analysis of Regulation of autophagy pathway Performing contextual analysis of Renal cell carcinoma pathway Performing contextual analysis of Renin-angiotensin system pathway Performing contextual analysis of Ribosome pathway Performing contextual analysis of RIG-I-like receptor signaling pathway pathway Performing contextual analysis of RNA degradation pathway Performing contextual analysis of RNA polymerase pathway Performing contextual analysis of Salivary secretion pathway Performing contextual analysis of Shigellosis pathway Performing contextual analysis of Small cell lung cancer pathway Performing contextual analysis of SNARE interactions in vesicular transport pathway Performing contextual analysis of Spliceosome pathway Performing contextual analysis of Systemic lupus erythematosus pathway Performing contextual analysis of T cell receptor signaling pathway pathway Performing contextual analysis of Taste transduction pathway Performing contextual analysis of TGF-beta signaling pathway pathway Performing contextual analysis of Thyroid cancer pathway Performing contextual analysis of Tight junction pathway Performing contextual analysis of Toll-like receptor signaling pathway pathway Performing contextual analysis of Toxoplasmosis pathway Performing contextual analysis of Type I diabetes mellitus pathway Performing contextual analysis of Type II diabetes mellitus pathway Performing contextual analysis of Ubiquitin mediated proteolysis pathway Performing contextual analysis of Vascular smooth muscle contraction pathway Performing contextual analysis of Vasopressin-regulated water reabsorption pathway Performing contextual analysis of VEGF signaling pathway pathway Performing contextual analysis of Vibrio cholerae infection pathway Performing contextual analysis of Viral myocarditis pathway Performing contextual analysis of Wnt signaling pathway pathway Number of genes present in the DirectEvidence File: 20077 Number of genes present in the DirectEvidence File: 401 Number of genes present in the DirectEvidence File: 100 Starting enrichment analysis Processing 130 pathways Completed enrichment analysis of ABC transporters pathway Completed enrichment analysis of Acute myeloid leukemia pathway Completed enrichment analysis of Adherens junction pathway Completed enrichment analysis of Adipocytokine signaling pathway pathway Completed enrichment analysis of Aldosterone-regulated sodium reabsorption pathway Completed enrichment analysis of Allograft rejection pathway Completed enrichment analysis of Alzheimers disease pathway Completed enrichment analysis of Amoebiasis pathway Completed enrichment analysis of Amyotrophic lateral sclerosis (ALS) pathway Completed enrichment analysis of Antigen processing and presentation pathway Completed enrichment analysis of Apoptosis pathway Completed enrichment analysis of Arrhythmogenic right ventricular cardiomyopathy (ARVC) pathway Completed enrichment analysis of Asthma pathway Completed enrichment analysis of Autoimmune thyroid disease pathway Completed enrichment analysis of Axon guidance pathway Completed enrichment analysis of B cell receptor signaling pathway pathway Completed enrichment analysis of Bacterial invasion of epithelial cells pathway Completed enrichment analysis of Basal cell carcinoma pathway Completed enrichment analysis of Basal transcription factors pathway Completed enrichment analysis of Base excision repair pathway Completed enrichment analysis of Bladder cancer pathway Completed enrichment analysis of Calcium signaling pathway pathway Completed enrichment analysis of Carbohydrate digestion and absorption pathway Completed enrichment analysis of Cardiac muscle contraction pathway Completed enrichment analysis of Cell adhesion molecules (CAMs) pathway Completed enrichment analysis of Cell cycle pathway Completed enrichment analysis of Chagas disease pathway Completed enrichment analysis of Chemokine signaling pathway pathway Completed enrichment analysis of Chronic myeloid leukemia pathway Completed enrichment analysis of Circadian rhythm - mammal pathway Completed enrichment analysis of Collecting duct acid secretion pathway Completed enrichment analysis of Colorectal cancer pathway Completed enrichment analysis of Complement and coagulation cascades pathway Completed enrichment analysis of Cytokine-cytokine receptor interaction pathway Completed enrichment analysis of Cytosolic DNA-sensing pathway pathway Completed enrichment analysis of Dilated cardiomyopathy pathway Completed enrichment analysis of DNA replication pathway Completed enrichment analysis of Dorso-ventral axis formation pathway Completed enrichment analysis of ECM-receptor interaction pathway Completed enrichment analysis of Endocytosis pathway Completed enrichment analysis of Endometrial cancer pathway Completed enrichment analysis of Epithelial cell signaling in Helicobacter pylori infection pathway Completed enrichment analysis of ErbB signaling pathway pathway Completed enrichment analysis of Fc epsilon RI signaling pathway pathway Completed enrichment analysis of Fc gamma R-mediated phagocytosis pathway Completed enrichment analysis of Focal adhesion pathway Completed enrichment analysis of Gap junction pathway Completed enrichment analysis of Gastric acid secretion pathway Completed enrichment analysis of Glioma pathway Completed enrichment analysis of GnRH signaling pathway pathway Completed enrichment analysis of Graft-versus-host disease pathway Completed enrichment analysis of Hedgehog signaling pathway pathway Completed enrichment analysis of Hematopoietic cell lineage pathway Completed enrichment analysis of Homologous recombination pathway Completed enrichment analysis of Huntingtons disease pathway Completed enrichment analysis of Hypertrophic cardiomyopathy (HCM) pathway Completed enrichment analysis of Insulin signaling pathway pathway Completed enrichment analysis of Intestinal immune network for IgA production pathway Completed enrichment analysis of Jak-STAT signaling pathway pathway Completed enrichment analysis of Leishmaniasis pathway Completed enrichment analysis of Leukocyte transendothelial migration pathway Completed enrichment analysis of Long-term depression pathway Completed enrichment analysis of Long-term potentiation pathway Completed enrichment analysis of Lysosome pathway Completed enrichment analysis of Malaria pathway Completed enrichment analysis of MAPK signaling pathway pathway Completed enrichment analysis of Maturity onset diabetes of the young pathway Completed enrichment analysis of Melanogenesis pathway Completed enrichment analysis of Melanoma pathway Completed enrichment analysis of Mismatch repair pathway Completed enrichment analysis of mTOR signaling pathway pathway Completed enrichment analysis of Natural killer cell mediated cytotoxicity pathway Completed enrichment analysis of Neuroactive ligand-receptor interaction pathway Completed enrichment analysis of Neurotrophin signaling pathway pathway Completed enrichment analysis of NOD-like receptor signaling pathway pathway Completed enrichment analysis of Non-homologous end-joining pathway Completed enrichment analysis of Non-small cell lung cancer pathway Completed enrichment analysis of Notch signaling pathway pathway Completed enrichment analysis of Nucleotide excision repair pathway Completed enrichment analysis of Olfactory transduction pathway Completed enrichment analysis of Oocyte meiosis pathway Completed enrichment analysis of p53 signaling pathway pathway Completed enrichment analysis of Pancreatic cancer pathway Completed enrichment analysis of Pancreatic secretion pathway Completed enrichment analysis of Parkinsons disease pathway Completed enrichment analysis of Pathogenic Escherichia coli infection pathway Completed enrichment analysis of Pathways in cancer pathway Completed enrichment analysis of Peroxisome pathway Completed enrichment analysis of Phagosome pathway Completed enrichment analysis of Phosphatidylinositol signaling system pathway Completed enrichment analysis of Phototransduction pathway Completed enrichment analysis of PPAR signaling pathway pathway Completed enrichment analysis of Primary immunodeficiency pathway Completed enrichment analysis of Prion diseases pathway Completed enrichment analysis of Progesterone-mediated oocyte maturation pathway Completed enrichment analysis of Prostate cancer pathway Completed enrichment analysis of Proteasome pathway Completed enrichment analysis of Protein export pathway Completed enrichment analysis of Protein processing in endoplasmic reticulum pathway Completed enrichment analysis of Proximal tubule bicarbonate reclamation pathway Completed enrichment analysis of Regulation of actin cytoskeleton pathway Completed enrichment analysis of Regulation of autophagy pathway Completed enrichment analysis of Renal cell carcinoma pathway Completed enrichment analysis of Renin-angiotensin system pathway Completed enrichment analysis of Ribosome pathway Completed enrichment analysis of RIG-I-like receptor signaling pathway pathway Completed enrichment analysis of RNA degradation pathway Completed enrichment analysis of RNA polymerase pathway Completed enrichment analysis of Salivary secretion pathway Completed enrichment analysis of Shigellosis pathway Completed enrichment analysis of Small cell lung cancer pathway Completed enrichment analysis of SNARE interactions in vesicular transport pathway Completed enrichment analysis of Spliceosome pathway Completed enrichment analysis of Systemic lupus erythematosus pathway Completed enrichment analysis of T cell receptor signaling pathway pathway Completed enrichment analysis of Taste transduction pathway Completed enrichment analysis of TGF-beta signaling pathway pathway Completed enrichment analysis of Thyroid cancer pathway Completed enrichment analysis of Tight junction pathway Completed enrichment analysis of Toll-like receptor signaling pathway pathway Completed enrichment analysis of Toxoplasmosis pathway Completed enrichment analysis of Type I diabetes mellitus pathway Completed enrichment analysis of Type II diabetes mellitus pathway Completed enrichment analysis of Ubiquitin mediated proteolysis pathway Completed enrichment analysis of Vascular smooth muscle contraction pathway Completed enrichment analysis of Vasopressin-regulated water reabsorption pathway Completed enrichment analysis of VEGF signaling pathway pathway Completed enrichment analysis of Vibrio cholerae infection pathway Completed enrichment analysis of Viral myocarditis pathway Completed enrichment analysis of Wnt signaling pathway pathway Number of significant genes from direct evidence 14 Number of significant genes from combined evidence 13 Processing 130 pathways Number 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 -- Mon Dec 23 20:39:00 2024 *********************************************** 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 failures Number of test functions: 9 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 10.480 1.839 12.362
PathNet.Rcheck/PathNet-Ex.timings
name | user | system | elapsed | |
PathNet | 0.238 | 0.046 | 0.289 | |