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This page was generated on 2023-11-02 11:40:28 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 218/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioTIP 1.16.0  (landing page)
Yuxi (Jennifer) Sun , Zhezhen Wang , and X Holly Yang
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/BioTIP
git_branch: RELEASE_3_18
git_last_commit: 910489b
git_last_commit_date: 2023-10-24 11:16:46 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for BioTIP on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: BioTIP
Version: 1.16.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BioTIP_1.16.0.tar.gz
StartedAt: 2023-11-02 08:48:29 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:50:43 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 134.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BioTIP.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BioTIP_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BioTIP.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 ‘BioTIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioTIP’ version ‘1.16.0’
* 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 ... OK
* 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
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime_allcells/BioTIP_top0.8FDR0.2_CTS.candidate.RData
  BioTIP/examples/result/hESC_Bargaje2017/C_CollectionTime_allcells/BioTIP_top0.8FDR0.2_IC_Delta_SimresultBoth.pdf
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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 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
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 ... OK
* 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 documentation object 'avg.cor.shrink':
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 documentation object 'cor.shrink':
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 documentation object 'getIc':
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 documentation object 'getIc.new':
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 documentation object 'getMaxMCImember':
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 documentation object 'plotBar_MCI':
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 documentation object 'plotIc':
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 documentation object 'plot_Ic_Simulation':
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 documentation object 'plot_SS_Simulation':
plot_SS_Simulation
  Code: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab =
                 "Density")
  Docs: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab = "1st
                 max - 2nd max")
  Mismatches in argument default values:
    Name: 'ylab' Code: "Density" Docs: "1st max - 2nd max"

Codoc mismatches from documentation object 'simulationMCI':
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 documentation object 'simulation_Ic':
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 documentation object 'simulation_Ic_sample':
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 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: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BioTIP.Rcheck/00check.log’
for details.

Installation output

BioTIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BioTIP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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.shrink3.8990.2354.161
cor.shrink1.0720.1351.224
getBiotypes0.6381.1282.317
getCTS0.0020.0000.001
getCluster_methods0.0900.0130.125
getIc0.010.000.01
getIc.new1.5990.1031.706
getMCI0.0150.0000.015
getMaxMCImember0.0630.0000.063
getMaxStats0.0150.0000.016
getNetwork0.0190.0040.023
getReadthrough3.8800.0393.927
plotBar_MCI0.0350.0000.037
plotIc0.0020.0000.003
plotMaxMCI0.0020.0000.002
plot_Ic_Simulation0.0030.0000.002
plot_MCI_Simulation0.0070.0000.007
plot_SS_Simulation0.0090.0000.009
sd_selection0.0020.0000.002
simulationMCI0.0050.0000.025
simulation_Ic0.0140.0000.044
simulation_Ic_sample0.0070.0000.007