Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 221/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioTIP 1.20.0  (landing page)
Yuxi (Jennifer) Sun , Zhezhen Wang , and X Holly Yang
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/BioTIP
git_branch: RELEASE_3_20
git_last_commit: fb1b632
git_last_commit_date: 2024-10-29 10:40:29 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for BioTIP on kjohnson1

To the developers/maintainers of the BioTIP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioTIP.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.

raw results


Summary

Package: BioTIP
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioTIP_1.20.0.tar.gz
StartedAt: 2024-12-20 12:48:06 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 12:49:55 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 109.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BioTIP.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioTIP_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BioTIP.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘BioTIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioTIP’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  examples/code/gastrulationE8.25_Pijuan-Sala2019/.RData
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  BioTIP/examples/code/gastrulationE8.25_Pijuan-Sala2019/2.2_E8.25_mesoderm_runBioTP_different.clustering.R
  BioTIP/examples/code/gastrulationE8.25_Pijuan-Sala2019/3_E8.25_mesoderm_runBioTIP_stability_1360cell.R
  BioTIP/examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/EB_Zhao2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/EB_Zhao2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/EB_Zhao2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/EB_Zhao2019/C_SNNGraph_k10/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks17/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/EB_Zhao2019/C_consensus_ks19/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/BioTIP_res_10runs_MCIbottom2_Modulesize20.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/BioTIP_res_10runs_MCIbottom2_Modulesize30.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/BioTIP_res_10runs_MCIbottom2_Modulesize40.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.detection_variable.Modulesize.Rdata
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CT.detection_variable.Modulesize_MCIbottom2.pdf
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/CTS.F1_variable.ModuleSize_GS_2CTs.pdf
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/F1.CTS.eCardiac.a_MCIbottom2.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/stability/F1.CTS.endothelial.b_MCIbottom2.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_CTS.candidate.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_IC_sim.Permutation.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_MCIBar_0.1_fdr0.05_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_SimuMCI_100_0.1_fdr0.05_minsize30.RData
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Ibarra-Soria2018/subcelltype/BioTIP_top0.1FDR0.05_optimized_local.HVG_selection.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_0.8/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Leiden_1.2/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_CTS.candidate.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_IC_sim.Permutation.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_SNNGraph_allcells/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4.wo.TC/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4.wo.TC/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4.wo.TC/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6.wo.TC/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6.wo.TC/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6.wo.TC/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_Soft_k6/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks4/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks4/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks4/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks5/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks5/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks5/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks6/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks6/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks6/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks7/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks7/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks7/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks8/BioTIP_top0.1FDR0.2_IC_Delta_SimresultGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks8/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/C_consensus_ks8/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/GS.CTS.EP_at.least.4identificaitons_fr.7predicitons.txt
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/GS.CTS.HP_at.least.5identificaitons_fr.9predicitons.txt
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/GS.CTS.eHEP_at.least.3identificaitons_fr.8predicitons.txt
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/GS.CTS.lHEP_at.least.4identificaitons_fr.8predicitons.txt
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/original_run/optimized_test_sd_selection_E8.25.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom2_Modulesize10.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom2_Modulesize20.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom2_Modulesize30.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom2_Modulesize40.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom3_Modulesize10.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom3_Modulesize20.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom3_Modulesize30.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom3_Modulesize40.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom4_Modulesize10.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom4_Modulesize20.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom4_Modulesize30.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/BioTIP_res_20runs_MCIbottom4_Modulesize40.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/CT.detection_variable.MCIbottom2_Modulesize.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/CT.detection_variable.MCIbottom_Modulesize.Rdata
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/CTS.F1_variable.ModuleSize_GS.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/CTS.F1_variable.ModuleSize_GS_4CTs.pdf
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/F1.CTS_MCIbottom2_GS.C13.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/F1.CTS_MCIbottom2_GS.C15.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/F1.CTS_MCIbottom2_GS.C6.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/stability_1360cell/F1.CTS_MCIbottom2_GS.C7.RData
  BioTIP/examples/result/gastrulationE8.25_Pijuan-Sala2019/umap.E8.25_mesoderm_robustness_clustering_methods.pdf
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_IC_sim.PermutateBoth.RData
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_MCIBar_0.8_fdr0.2_minsize10.pdf
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_SimuMCI_100_0.8_fdr0.2_minsize10.RData
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime/BioTIP_top0.8FDR0.2_optimized_local.HVG_selection.RData
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  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks3/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks3/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks3/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_IC_sim.PermutateBoth.RData
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks5/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_IC_Delta_SimresultBoth.pdf
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_IC_sim.PermutateBoth.RData
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_MCIBar_0.1_fdr0.2_minsize30.pdf
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_SimuMCI_100_0.1_fdr0.2_minsize30.RData
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/lung_Treutlein2014/C_consensus_ks7/BioTIP_top0.1FDR0.2_optimized_local.HVG_selection.RData
  BioTIP/examples/result/simulated_EMT/C_Leiden_0.4/BioTIP_top1FDR0.05_SimuMCI_100_1_fdr0.05_minsize6.RData
  BioTIP/examples/result/simulated_EMT/C_Leiden_0.4/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
  BioTIP/examples/result/simulated_EMT/C_Leiden_0.8/BioTIP_top1FDR0.05_SimuMCI_100_1_fdr0.05_minsize6.RData
  BioTIP/examples/result/simulated_EMT/C_Leiden_0.8/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
  BioTIP/examples/result/simulated_EMT/C_Leiden_1.2/BioTIP_top1FDR0.05_SimuMCI_100_1_fdr0.05_minsize6.RData
  BioTIP/examples/result/simulated_EMT/C_Leiden_1.2/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_SimuMCI_100_1_fdr0.05_minsize6.RData
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k100/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_SimuMCI_100_1_fdr0.05_minsize6.RData
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k20/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_MCIBar_1_fdr0.05_minsize6.pdf
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_SimuMCI_100_1_fdr0.05_minsize6.RData
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_barplot_MCI_Sim_RandomGene.pdf
  BioTIP/examples/result/simulated_EMT/C_SNNGraph.k200/BioTIP_top1FDR0.05_optimized_local.HVG_selection.RData

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BioTIP’ 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
BioTIP.wrap: warning in getMaxMCImember(membersL[["members"]],
  membersL[["MCI"]], min = getTopMCI.gene.minsize, n =
  n.getMaxMCImember): partial argument match of 'min' to 'minsize'
getCluster: warning in cluster_walktrap(igraphL[[i]], weight =
  abs(E(igraphL[[i]])$weight), steps = steps[i]): partial argument
  match of 'weight' to 'weights'
BioTIP.wrap: no visible global function definition for ‘assayNames’
BioTIP.wrap : myplotIc: no visible global function definition for ‘pdf’
BioTIP.wrap : myplotIc: no visible global function definition for ‘par’
BioTIP.wrap : myplotIc: no visible global function definition for
  ‘text’
BioTIP.wrap : myplotIc: no visible global function definition for
  ‘dev.off’
BioTIP.wrap: no visible global function definition for ‘getTopHVGs’
BioTIP.wrap: no visible global function definition for
  ‘normalized_counts’
BioTIP.wrap: no visible global function definition for ‘logcounts’
BioTIP.wrap: no visible global function definition for ‘pdf’
BioTIP.wrap: no visible global function definition for ‘abline’
BioTIP.wrap: no visible global function definition for ‘dev.off’
BioTIP.wrap: no visible global function definition for ‘par’
BioTIP.wrap: no visible binding for global variable
  ‘getTopMCI.gene.maxsiz’
cor.shrink: no visible binding for global variable ‘sd’
getBiotypes: no visible global function definition for ‘is’
getBiotypes: no visible global function definition for ‘queryHits’
getBiotypes: no visible global function definition for ‘subjectHits’
getBiotypes: no visible global function definition for ‘aggregate’
getCluster_methods : <anonymous>: no visible global function definition
  for ‘hclust’
getCluster_methods : <anonymous>: no visible global function definition
  for ‘dist’
getCluster_methods: no visible global function definition for ‘par’
getCluster_methods : <anonymous>: no visible global function definition
  for ‘cutree’
getIc : <anonymous>: no visible global function definition for ‘cor’
getMCI : <anonymous>: no visible global function definition for ‘cor’
getMCI : <anonymous>: no visible binding for global variable ‘sd’
getMCI_inner : <anonymous>: no visible global function definition for
  ‘cor’
getMCI_inner : <anonymous>: no visible binding for global variable ‘sd’
getNextMaxStats: no visible binding for global variable ‘maxMCIms’
getReadthrough: no visible global function definition for ‘subjectHits’
getReadthrough: no visible binding for global variable ‘readthrough’
getReadthrough : <anonymous>: no visible global function definition for
  ‘queryHits’
getReadthrough : <anonymous>: no visible global function definition for
  ‘subjectHits’
optimize.sd_selection: no visible binding for global variable ‘pb’
optimize.sd_selection : <anonymous>: no visible binding for global
  variable ‘sd’
optimize.sd_selection : <anonymous> : <anonymous>: no visible global
  function definition for ‘sd’
plotBar_MCI: no visible global function definition for ‘par’
plotBar_MCI: no visible global function definition for ‘barplot’
plotBar_MCI: no visible global function definition for ‘rainbow’
plotBar_MCI: no visible global function definition for ‘title’
plotBar_MCI: no visible global function definition for ‘text’
plotIc: no visible global function definition for ‘matplot’
plotIc: no visible global function definition for ‘axis’
plotMaxMCI: no visible global function definition for ‘is’
plotMaxMCI: no visible global function definition for ‘matplot’
plotMaxMCI: no visible global function definition for ‘text’
plotMaxMCI: no visible global function definition for ‘axis’
plot_Ic_Simulation: no visible global function definition for ‘matplot’
plot_Ic_Simulation: no visible global function definition for ‘boxplot’
plot_Ic_Simulation: no visible global function definition for ‘points’
plot_Ic_Simulation: no visible global function definition for ‘mtext’
plot_Ic_Simulation: no visible global function definition for ‘axis’
plot_Ic_Simulation: no visible global function definition for ‘abline’
plot_MCI_Simulation: no visible global function definition for
  ‘boxplot’
plot_MCI_Simulation: no visible global function definition for ‘axis’
plot_MCI_Simulation: no visible global function definition for ‘points’
plot_MCI_Simulation: no visible global function definition for ‘abline’
plot_SS_Simulation: no visible global function definition for ‘density’
plot_SS_Simulation: no visible global function definition for ‘abline’
plot_SS_Simulation: no visible global function definition for ‘legend’
sd_selection : <anonymous>: no visible binding for global variable ‘sd’
sd_selection: no visible binding for global variable ‘sd’
sd_selection: no visible binding for global variable ‘i’
simulation_Ic_sample: no visible global function definition for
  ‘density’
simulation_Ic_sample: no visible global function definition for
  ‘abline’
simulation_Ic_sample: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline aggregate assayNames axis barplot boxplot cor cutree density
  dev.off dist getTopHVGs getTopMCI.gene.maxsiz hclust i is legend
  logcounts matplot maxMCIms mtext normalized_counts par pb pdf points
  queryHits rainbow readthrough sd subjectHits text title
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot",
             "legend", "matplot", "mtext", "par", "points", "text",
             "title")
  importFrom("methods", "is")
  importFrom("stats", "aggregate", "cor", "cutree", "density", "dist",
             "hclust", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) cod.Rd:11: Lost braces
    11 | \item{ranges}{ranges}{chromosome ranges on the genome (10906201-11029719)}
       |                      ^
checkRd: (-1) plotIc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels.
       |                       ^
checkRd: (-1) plotMaxMCI.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. Default is 0, meaning labels are parallel.
       |                       ^
checkRd: (-1) plot_Ic_Simulation.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels.
       |                       ^
checkRd: (-1) plot_MCI_Simulation.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. Default is 0, meaning labels are parallel.
       |                       ^
checkRd: (-1) plot_SS_Simulation.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels.
       |                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘TSdist’
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getNextMaxStats’ ‘getTopMCI’ ‘membersL’ ‘subcounts’
Undocumented data sets:
  ‘membersL’ ‘subcounts’
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 ... WARNING
Codoc mismatches from Rd file 'avg.cor.shrink.Rd':
avg.cor.shrink
  Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs =
                 FALSE, target = 0)
  Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs =
                 FALSE, target = c("zero", "average", "half"))
  Mismatches in argument default values:
    Name: 'target' Code: 0 Docs: c("zero", "average", "half")

Codoc mismatches from Rd file 'cor.shrink.Rd':
cor.shrink
  Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target =
                 0)
  Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target =
                 c("zero", "average", "half"))
  Mismatches in argument default values:
    Name: 'target' Code: 0 Docs: c("zero", "average", "half")

Codoc mismatches from Rd file 'getIc.Rd':
getIc
  Code: function(counts, sampleL, genes, output = c("Ic", "PCCg",
                 "PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use
                 = c("everything", "all.obs", "complete.obs",
                 "na.or.complete", "pairwise.complete.obs"),
                 PCC_sample.target = 1)
  Docs: function(counts, sampleL, genes, output = c("Ic", "PCCg",
                 "PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use
                 = c("everything", "all.obs", "complete.obs",
                 "na.or.complete", "pairwise.complete.obs"))
  Argument names in code not in docs:
    PCC_sample.target

Codoc mismatches from Rd file 'getIc.new.Rd':
getIc.new
  Code: function(X, method = c("BioTIP", "Ic"), PCC_sample.target = 1,
                 output = c("Ic", "PCCg", "PCCs"))
  Docs: function(X, method = c("BioTIP", "Ic"), PCC_sample.target =
                 c("average", "zero", "half"), output = c("IndexScore",
                 "PCCg", "PCCs"))
  Mismatches in argument default values:
    Name: 'PCC_sample.target' Code: 1 Docs: c("average", "zero", "half")
    Name: 'output' Code: c("Ic", "PCCg", "PCCs") Docs: c("IndexScore", "PCCg", "PCCs")

Codoc mismatches from Rd file 'getMaxMCImember.Rd':
getMaxMCImember
  Code: function(membersL, MCIl, minsize = 1, n = 1)
  Docs: function(membersL, MCIl, minsize = 1)
  Argument names in code not in docs:
    n

Codoc mismatches from Rd file 'plotBar_MCI.Rd':
plotBar_MCI
  Code: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL,
                 minsize = 3, states = NULL, title.size = 30)
  Docs: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL,
                 minsize = 3, states = NULL)
  Argument names in code not in docs:
    title.size

Codoc mismatches from Rd file 'plotIc.Rd':
plotIc
  Code: function(Ic, las = 0, order = NULL, ylab = "Ic.shrink", col =
                 "black", main = NULL, add = FALSE, ylim = NULL, lty =
                 1:5, lwd = 1)
  Docs: function(Ic, las = 0, order = NULL, ylab = "Ic", col = "black",
                 main = NULL, add = FALSE, ylim = NULL, lty = 1:5, lwd
                 = 1)
  Mismatches in argument default values:
    Name: 'ylab' Code: "Ic.shrink" Docs: "Ic"

Codoc mismatches from Rd file 'plot_Ic_Simulation.Rd':
plot_Ic_Simulation
  Code: function(Ic, simulation, las = 0, ylim = NULL, order = NULL,
                 main = NULL, ylab = "Ic.shrink", fun = c("matplot",
                 "boxplot"), which2point = NULL)
  Docs: function(Ic, simulation, las = 0, ylim = NULL, order = NULL,
                 main = NULL, ylab = "Ic", fun = c("matplot",
                 "boxplot"), which2point = NULL)
  Mismatches in argument default values:
    Name: 'ylab' Code: "Ic.shrink" Docs: "Ic"

Codoc mismatches from Rd file 'plot_SS_Simulation.Rd':
plot_SS_Simulation
  Code: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab =
                 "Density", na.rm = TRUE)
  Docs: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab = "1st
                 max - 2nd max")
  Argument names in code not in docs:
    na.rm
  Mismatches in argument default values:
    Name: 'ylab' Code: "Density" Docs: "1st max - 2nd max"

Codoc mismatches from Rd file 'simulationMCI.Rd':
simulationMCI
  Code: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun
                 = c("cor", "BioTIP"), M = NULL)
  Docs: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun
                 = c("cor", "BioTIP"))
  Argument names in code not in docs:
    M

Codoc mismatches from Rd file 'simulation_Ic.Rd':
simulation_Ic
  Code: function(obs.x, sampleL, counts, B = 1000, fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"), PCC_sample.target = 1)
  Docs: function(obs.x, sampleL, counts, B = 1000, fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"))
  Argument names in code not in docs:
    PCC_sample.target

Codoc mismatches from Rd file 'simulation_Ic_sample.Rd':
simulation_Ic_sample
  Code: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim =
                 NULL, main = "simulation of samples", fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"), plot = FALSE, PCC_sample.target = 1)
  Docs: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim =
                 NULL, main = "simulation of samples", fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"), plot = FALSE)
  Argument names in code not in docs:
    PCC_sample.target

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 15 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/BioTIP.Rcheck/00check.log’
for details.

Installation output

BioTIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioTIP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘BioTIP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (BioTIP)

Tests output


Example timings

BioTIP.Rcheck/BioTIP-Ex.timings

nameusersystemelapsed
avg.cor.shrink2.5660.2292.796
cor.shrink0.5470.0840.632
getBiotypes0.4820.0660.548
getCTS0.0010.0000.001
getCluster_methods0.080.010.09
getIc0.0060.0010.007
getIc.new0.4680.2220.692
getMCI0.0110.0010.012
getMaxMCImember0.0460.0030.049
getMaxStats0.0100.0010.010
getNetwork0.0150.0020.015
getReadthrough2.5810.0542.635
plotBar_MCI0.0340.0010.035
plotIc0.0030.0010.003
plotMaxMCI0.0020.0000.002
plot_Ic_Simulation0.0020.0010.002
plot_MCI_Simulation0.0060.0010.007
plot_SS_Simulation0.0090.0010.010
sd_selection0.0020.0000.003
simulationMCI0.0040.0010.185
simulation_Ic0.0090.0010.280
simulation_Ic_sample0.0060.0000.006