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This page was generated on 2024-10-14 11:48 -0400 (Mon, 14 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4473
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4728
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4478
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4509
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4457
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4457
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Package 1702/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RegionalST 1.3.0  (landing page)
Ziyi Li
Snapshot Date: 2024-10-13 13:40 -0400 (Sun, 13 Oct 2024)
git_url: https://git.bioconductor.org/packages/RegionalST
git_branch: devel
git_last_commit: 889b990
git_last_commit_date: 2024-04-30 11:50:45 -0400 (Tue, 30 Apr 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for RegionalST on kjohnson3

To the developers/maintainers of the RegionalST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RegionalST.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: RegionalST
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RegionalST_1.3.0.tar.gz
StartedAt: 2024-10-13 23:45:15 -0400 (Sun, 13 Oct 2024)
EndedAt: 2024-10-13 23:46:50 -0400 (Sun, 13 Oct 2024)
EllapsedTime: 95.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RegionalST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RegionalST_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RegionalST.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RegionalST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegionalST’ version ‘1.3.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RegionalST’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK


Installation output

RegionalST.Rcheck/00install.out

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


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

Tests output

RegionalST.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(RegionalST)
> 
> test_check("RegionalST")
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
PC_ 1 
Positive:  PADI2, MIIP, YARS, CLSTN1, VWA1, CITED4, STK40, PSMB2, SDHB, ARHGEF16 
	   MACO1, TMEM54, MRTO4, NOC2L, MTOR, SERINC2, SRRM1, NADK, FBLIM1, TMEM35B 
	   NECAP2, CSF3R, CPTP, TPRG1L, MEAF6, COL9A2, RCC2, HNRNPR, PRXL2B, AKIRIN1 
Negative:  IFI6, MXRA8, RBP7, RAB42, PADI3, FAM131C, C1orf127, C1QC, PDPN, NBL1 
	   C1QB, RSPO1, SAMD11, TRIM63, MMP23B, TAS1R1, LAPTM5, SLC2A5, OXCT2, HPCA 
	   CNR2, TP73, HSPB7, PRAMEF4, ANKRD65, SRARP, A3GALT2, TAS1R3, PERM1, PADI4 
PC_ 2 
Positive:  CNKSR1, CASZ1, CITED4, PADI2, ARHGEF16, SMIM1, EDN2, CD164L2, KDF1, CAMK2N1 
	   NCMAP, GRHL3, IFI6, GRIK3, SMPDL3B, KCNQ4, FOXO6, VPS13D, CTPS1, SH3D21 
	   TRIM62, KAZN, PHF13, TMEM234, EXO5, PADI3, MFSD2A, KIAA1522, RIMS3, PLOD1 
Negative:  CD52, C1QB, LAPTM5, KCNAB2, C1QC, LCK, HSPG2, TNFRSF4, TNFRSF1B, RUNX3 
	   MXRA8, ID3, PIK3CD, TNFRSF18, NBL1, THEMIS2, SH3BGRL3, FGR, ZNF683, H6PD 
	   RSRP1, HEYL, COL8A2, TNFRSF8, WASF2, PSMB2, SDF4, ECE1, SFPQ, PLA2G2D 
PC_ 3 
Positive:  TTLL10, DISP3, SCNN1D, ADGRB2, AUNIP, CROCC, EXTL1, TRNP1, FAM167B, SPOCD1 
	   CDCA8, STMN1, MYOM3, FAM110D, EMC1, TMEM35B, SLC45A1, CRYBG2, TEKT2, ALDH4A1 
	   PEX10, DNAJC11, GJB5, BMP8A, KDF1, ZNF683, STPG1, PINK1, ERRFI1, LYPLA2 
Negative:  FOXO6, PLOD1, C1orf174, SLC30A2, NPHP4, CORT, SLC25A34, FBXO6, DHDDS, CCNL2 
	   HP1BP3, NFYC, KIAA1522, PANK4, KLHL17, COL8A2, MYCBP, TNFRSF14, PLA2G2C, PITHD1 
	   NDUFS5, CITED4, UBIAD1, ADPRHL2, GPN2, PLEKHM2, C1orf109, ZFP69, SF3A3, KPNA6 
PC_ 4 
Positive:  NBL1, MXRA8, ZNF436, ID3, ZCCHC17, NCDN, NOL9, PINK1, COL8A2, HSPG2 
	   PEX14, SLC25A33, CASP9, EPHB2, ASAP3, SYNC, CCNL2, KLHL21, SNIP1, ZBTB8A 
	   ANKRD65, UTP11, FNDC5, MACF1, IGSF21, MECR, COL16A1, TENT5B, MAP3K6, TMEM200B 
Negative:  TNFRSF18, IFI6, FGR, C1QTNF12, ZMYM6, ALDH4A1, RCC1, TNFRSF4, KLHL17, SLC25A34 
	   GNL2, ADGRB2, MAD2L2, PIK3CD, ZNF684, DISP3, UQCRHL, PLA2G2D, SMAP2, SPEN 
	   ZMYM4, MEAF6, TTLL10, PNRC2, CTNNBIP1, ZNF683, THEMIS2, PITHD1, STK40, NADK 
PC_ 5 
Positive:  ADGRB2, SLC25A34, AUNIP, TTLL10, CROCC, DISP3, C1orf216, NMNAT1, ATP13A2, SLC30A2 
	   NCMAP, MFAP2, SLC45A1, CD164L2, KLHL17, RHBDL2, UBE4B, FHAD1, SCMH1, SYNC 
	   GABRD, SCNN1D, TMEM51, PRXL2B, PLA2G2C, ZNF362, SYF2, C1QB, DFFB, PLA2G2F 
Negative:  CLSPN, BMP8A, IFNLR1, CRYBG2, ZNF683, ZBTB8A, KDF1, LDLRAD2, TMEM234, EMC1 
	   INTS11, IFI6, GPR157, MTF1, KIAA0319L, MIB2, ZNF593, C1orf159, SLC35E2A, HEYL 
	   EIF4G3, PLEKHN1, MIIP, CLCN6, IL22RA1, DNAJC16, AHDC1, MYCL, PHACTR4, MORN1 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 246
Number of edges: 9889

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6836
Number of communities: 3
Elapsed time: 0 seconds
Processing to cell type:CAFs
For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
(default method for FindMarkers) please install the presto package
--------------------------------------------
install.packages('devtools')
devtools::install_github('immunogenomics/presto')
--------------------------------------------
After installation of presto, Seurat will automatically use the more 
efficient implementation (no further action necessary).
This message will be shown once per session
Processing to cell type:Myeloid
Processing to cell type:T-cells
Processing to cell type:Cancer Epithelial
Processing to cell type:Normal Epithelial
Processing to cell type:Endothelial
Processing to Radius = 5


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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  8.715   0.427   9.165 

Example timings

RegionalST.Rcheck/RegionalST-Ex.timings

nameusersystemelapsed
DoGSEA1.5690.1361.691
DrawDotplot0.6070.2880.884
DrawRegionProportion0.1200.0260.147
DrawRegionProportion_withProp0.0980.0060.111
FindRegionalCells000
GetCrossRegionalDE_raw2.5040.1872.692
GetCrossRegionalDE_withProp1.1900.1081.298
GetOneRadiusEntropy2.2170.1202.339
GetOneRadiusEntropy_withProp0.8160.0490.866
ManualSelectCenter0.4000.0410.442
PlotOneSelectedCenter0.4720.0380.513
RankCenterByEntropy1.0530.0571.114
RankCenterByEntropy_withProp0.9590.0481.007
exampleRes0.0010.0000.002
example_sce0.0020.0010.003
getProportion000
mySpatialPreprocess0.7290.0470.776
pathways_hallmark0.0050.0000.006
pathways_kegg0.0060.0000.007
pathways_reactome0.0430.0010.045