Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-19 11:43 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1727/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RegionalST 1.5.8  (landing page)
Ziyi Li
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/RegionalST
git_branch: devel
git_last_commit: 0ddee1b
git_last_commit_date: 2024-12-05 13:00:47 -0400 (Thu, 05 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BayesSpace' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RegionalST on palomino7

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: 1.5.8
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RegionalST.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings RegionalST_1.5.8.tar.gz
StartedAt: 2025-03-19 05:13:08 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 05:18:58 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 350.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RegionalST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RegionalST.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings RegionalST_1.5.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RegionalST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RegionalST' version '1.5.8'
* 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 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 ... NOTE
Namespace in Imports field not imported from: 'BiocStyle'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  'OneRegOut1'
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  'twoCenter'
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  'OneRegOut2'
Undefined global functions or variables:
  OneRegOut1 OneRegOut2 twoCenter
* 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
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
GetCrossRegionalDE_raw       8.87   0.42   13.55
RankCenterByEntropy          6.14   0.07    6.20
GetOneRadiusEntropy          5.77   0.24    6.00
RankCenterByEntropy_withProp 5.59   0.18    5.78
DoGSEA                       5.47   0.21   17.67
GetCrossRegionalDE_withProp  5.03   0.37    5.40
GetOneRadiusEntropy_withProp 4.30   0.41    6.96
DrawDotplot                  4.56   0.11   16.10
* 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: 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck/00check.log'
for details.


Installation output

RegionalST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL RegionalST
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'RegionalST' ...
** this is package 'RegionalST' version '1.5.8'
** 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 Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, VWA1, STK40, ARHGEF16, ZC3H12A, PSMB2, SDHB, PPT1, CITED4, TMEM54 
	   TCEA3, MFN2, SERINC2, NOC2L, MRTO4, MTOR, SRRM1, TMEM35B, NADK, FBLIM1 
	   CPTP, CSF3R, NECAP2, TPRG1L, ZMPSTE24, KHDRBS1, AKIRIN1, AGTRAP, RCC2, RSRP1 
Negative:  IFI6, RBP7, MXRA8, RAB42, C1orf127, PADI3, FAM131C, PDPN, C1QC, C1QB 
	   SAMD11, TRIM63, NBL1, RSPO1, OXCT2, SLC2A5, MMP23B, LAPTM5, CNR2, HPCA 
	   TP73, HSPB7, PRAMEF4, SRARP, SH2D5, RUNX3, ANKRD65, TAS1R3, PERM1, A3GALT2 
PC_ 2 
Positive:  CNKSR1, CASZ1, EDN2, CAMK2N1, CITED4, SMIM1, KDF1, PADI2, ARHGEF16, CD164L2 
	   GRHL3, SMPDL3B, IFI6, GRIK3, KCNQ4, NCMAP, FOXO6, VPS13D, PADI3, PPT1 
	   MFSD2A, TRIM62, KIAA1522, SH3D21, PHF13, CTPS1, ASAP3, PDIK1L, KAZN, RCC1 
Negative:  CD52, C1QB, LAPTM5, KCNAB2, C1QC, LCK, TNFRSF1B, HSPG2, TNFRSF4, MXRA8 
	   TNFRSF18, ID3, THEMIS2, RUNX3, NBL1, PIK3CD, SH3BGRL3, ZNF683, COL8A2, HEYL 
	   RSRP1, WASF2, TNFRSF9, LZIC, PLA2G2D, ECE1, TNFRSF8, SDF4, PSMB2, MFAP2 
PC_ 3 
Positive:  NBL1, HSPG2, ZBTB48, ZNF436, DDOST, ZCCHC17, EDN2, MEGF6, TMEM200B, MXRA8 
	   SRM, PLA2G5, ID3, C1orf216, C1QB, PEX14, SYNC, EPHB2, PINK1, TMEM51 
	   SLC45A1, PDPN, ASAP3, FAM229A, C1QC, UTP11, ATP13A2, EXOSC10, ANKRD65, GNB1 
Negative:  TNFRSF18, IFI6, ZMYM6, C1QTNF12, ZNF684, ALDH4A1, PLA2G2D, RBP7, PADI2, TNFRSF4 
	   ZDHHC18, IFNLR1, TMEM39B, PRDM16, MEAF6, GPR157, TMEM222, EYA3, CTNNBIP1, SLC25A34 
	   WDTC1, ZNF683, SMAP2, FBXO6, EIF4G3, CPLANE2, UQCRHL, DNAJC16, PANK4, KPNA6 
PC_ 4 
Positive:  TNFRSF14, SLC25A34, SLC30A2, CORT, FOXO6, FHAD1, PLA2G2C, PANK4, LZIC, IQCC 
	   C1orf174, PLOD1, UBIAD1, EXO5, MFAP2, CDA, NPHP4, PTPRU, TNFRSF8, PITHD1 
	   ZFP69, ISG15, TMEM39B, WDTC1, EPHA10, ADPRHL2, SRSF10, LRRC47, KIAA1522, DFFB 
Negative:  MYOM3, EMC1, MYCL, CRYBG2, ZNF593, GJB5, TTLL10, LDLRAD2, TEKT2, KDF1 
	   AUNIP, FAM167B, PAQR7, CEP85, PLCH2, BMP8A, PIGV, ID3, CPLANE2, TRNP1 
	   SPOCD1, SCNN1D, PNRC2, EXTL1, ERRFI1, SLC66A1, CLCN6, TNFRSF4, AGO3, PLEKHG5 
PC_ 5 
Positive:  NFYC, ZFP69B, PIK3CD, PIGV, SYF2, LAPTM5, PADI3, PNRC2, OXCT2, RHD 
	   TMEM88B, IQCC, SZRD1, PGD, DHRS3, FAM76A, C1QC, PSMB2, TNFRSF4, C1QB 
	   GNB1, ATAD3C, SLC25A34, SLC30A2, ENO1, RCC1, ELOA, C1orf127, SF3A3, RER1 
Negative:  IGSF21, SCNN1D, CASP9, LUZP1, PINK1, NCDN, EPHA10, EYA3, ZNF436, TMCO4 
	   USP48, GJB4, OPRD1, MORN1, STMN1, HMGCL, FNDC5, HES4, TRIT1, LRRC47 
	   VWA1, TMEM234, TNFRSF25, MXRA8, BMP8A, EPB41, TNFRSF14, HDAC1, RERE, MECR 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 249
Number of edges: 10482

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6846
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 
  30.15    1.64   31.81 

Example timings

RegionalST.Rcheck/RegionalST-Ex.timings

nameusersystemelapsed
DoGSEA 5.47 0.2117.67
DrawDotplot 4.56 0.1116.10
DrawRegionProportion0.550.050.59
DrawRegionProportion_withProp0.450.000.45
FindRegionalCells000
GetCellTypeSpecificDE_withProp2.720.193.39
GetCrossRegionalDE_raw 8.87 0.4213.55
GetCrossRegionalDE_withProp5.030.375.40
GetOneRadiusEntropy5.770.246.00
GetOneRadiusEntropy_withProp4.300.416.96
ManualSelectCenter2.430.072.51
PlotOneSelectedCenter1.990.032.02
RankCenterByEntropy6.140.076.20
RankCenterByEntropy_withProp5.590.185.78
exampleRes000
example_sce0.010.000.01
getProportion000
mySpatialPreprocess2.160.002.16
pathways_hallmark0.050.040.08
pathways_kegg0.080.010.09
pathways_reactome0.120.110.24