Ziyi Li
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/RegionalST |
| git_branch: RELEASE_3_20 |
| git_last_commit: e896620 |
| git_last_commit_date: 2024-12-05 12:58:48 -0500 (Thu, 05 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 1714/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RegionalST 1.4.2 (landing page) Ziyi Li
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: RegionalST |
| Version: 1.4.2 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RegionalST.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RegionalST_1.4.2.tar.gz |
| StartedAt: 2024-12-20 05:08:21 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 05:14:00 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 339.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RegionalST.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RegionalST.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RegionalST_1.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RegionalST.Rcheck'
* using R version 4.4.2 (2024-10-31 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 '1.4.2'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GetCrossRegionalDE_raw 8.81 0.45 9.28
RankCenterByEntropy 6.37 0.10 6.49
DoGSEA 5.72 0.20 18.78
GetCrossRegionalDE_withProp 5.25 0.36 5.61
GetOneRadiusEntropy 5.02 0.25 5.27
DrawDotplot 4.14 0.16 16.97
* 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
'F:/biocbuild/bbs-3.20-bioc/meat/RegionalST.Rcheck/00check.log'
for details.
RegionalST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RegionalST ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)
RegionalST.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 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
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|======================================================================| 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, YARS, VWA1, STK40, ZC3H12A, ARHGEF16, SDHB, NOC2L, MRTO4, TMEM54
CITED4, TCEA3, MACO1, TMEM35B, SRRM1, NADK, SERINC2, MFN2, MTOR, CPTP
FBLIM1, NECAP2, YTHDF2, TPRG1L, KHDRBS1, ZMPSTE24, BSDC1, CSF3R, STMN1, COL9A2
Negative: IFI6, RBP7, MXRA8, RAB42, C1orf127, FAM131C, PDPN, PADI3, C1QC, C1QB
RSPO1, NBL1, TRIM63, MMP23B, OXCT2, SAMD11, MAN1C1, TAS1R1, SLC2A5, LAPTM5
CNR2, HSPB7, TP73, HPCA, PRAMEF4, ANKRD65, SRARP, RUNX3, SH2D5, UTS2
PC_ 2
Positive: CNKSR1, CASZ1, CITED4, KDF1, SMIM1, EDN2, ARHGEF16, CD164L2, PADI2, NCMAP
SMPDL3B, IFI6, GRHL3, GRIK3, TRIM62, KCNQ4, FOXO6, RCC1, SH3D21, MFSD2A
PADI3, CTPS1, KIAA1522, UBXN11, RIMS3, PLOD1, EXO5, PHF13, COL9A2, ASAP3
Negative: CD52, C1QB, LAPTM5, C1QC, KCNAB2, HSPG2, LCK, MXRA8, ID3, TNFRSF1B
NBL1, TNFRSF4, RUNX3, THEMIS2, SH3BGRL3, TNFRSF18, ZNF683, HEYL, COL8A2, RSRP1
PIK3CD, WASF2, H6PD, PTAFR, NDUFS5, TNFRSF8, AGO4, PLEKHM2, LZIC, TNFRSF9
PC_ 3
Positive: ZNF683, TNFRSF18, CLSPN, BMP8A, IFNLR1, SPEN, CTRC, CRYBG2, FAM110D, EMC1
ALDH4A1, TRAPPC3, IL22RA1, STMN1, TMEM35B, SPOCD1, MTF1, GJB5, AHDC1, C1orf159
MYOM3, IFI6, GPR157, DNAJC11, KIF1B, CPLANE2, THEMIS2, ZNF593, KDF1, ZBTB40
Negative: SYNC, NBL1, PLOD1, SLC30A2, FOXO6, ZFP69, ANKRD65, DHDDS, HSPG2, CCNL2
KLHL17, DFFB, SLC25A34, LDLRAP1, ATP13A2, COL16A1, MFAP2, PLA2G2C, C1orf174, C1QB
BSDC1, EXOSC10, NFYC, PRXL2B, GNB1, CORT, UBE4B, NCDN, PLA2G5, CITED4
PC_ 4
Positive: ZBTB48, ID3, CRYBG2, MYOM3, NOL9, EDN2, MYCL, SCNN1D, PAQR7, PDPN
SRM, GJB4, OPRD1, ZNF436, AUNIP, KDF1, PEX14, BMP8A, EMC1, ZNF593
TRNP1, NBL1, EPHB2, MXRA8, COL16A1, PEX10, ZBTB8A, GJB5, HSPG2, TMEM200B
Negative: SLC25A34, CORT, KLHL17, IFI6, TNFRSF14, PANK4, TNFRSF18, SLC30A2, PITHD1, FBXO6
WDTC1, FHAD1, PLA2G2C, WNT4, ZNF684, NADK, ZMYM6, CTNNBIP1, UQCRHL, FOXO6
EXO5, LAPTM5, MUL1, TRAPPC3, KPNA6, C1orf174, RSPO1, PLA2G2D, EYA3, PRDM16
PC_ 5
Positive: TTLL10, TNFRSF4, AUNIP, PNRC2, LYPLA2, ATAD3C, PIK3CD, ADGRB2, RHD, ZFP69B
PIGV, CROCC, TMEM88B, CD164L2, ZNF362, SLC25A34, TNFRSF1B, THEMIS2, RLF, PRXL2B
SLC45A1, NFYC, SCMH1, KLHL17, PPIE, THRAP3, RHBDL2, SZRD1, FAM167B, RCC1
Negative: IGSF21, USP48, EPHA10, GPN2, PLOD1, MORN1, TNFRSF14, E2F2, CDA, CASP9
FAM229A, LZIC, PANK4, ASAP3, HES4, MXRA8, NCDN, TP73, MUL1, WDTC1
LUZP1, HEYL, DNAJC16, PUSL1, NOL9, SRRM1, PRKCZ, HP1BP3, FNDC5, HMGCL
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 247
Number of edges: 10029
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6720
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
29.67 1.57 31.40
RegionalST.Rcheck/RegionalST-Ex.timings
| name | user | system | elapsed | |
| DoGSEA | 5.72 | 0.20 | 18.78 | |
| DrawDotplot | 4.14 | 0.16 | 16.97 | |
| DrawRegionProportion | 0.59 | 0.06 | 0.66 | |
| DrawRegionProportion_withProp | 0.41 | 0.03 | 0.43 | |
| FindRegionalCells | 0 | 0 | 0 | |
| GetCellTypeSpecificDE_withProp | 2.72 | 0.18 | 2.92 | |
| GetCrossRegionalDE_raw | 8.81 | 0.45 | 9.28 | |
| GetCrossRegionalDE_withProp | 5.25 | 0.36 | 5.61 | |
| GetOneRadiusEntropy | 5.02 | 0.25 | 5.27 | |
| GetOneRadiusEntropy_withProp | 4.73 | 0.23 | 4.98 | |
| ManualSelectCenter | 2.24 | 0.08 | 2.31 | |
| PlotOneSelectedCenter | 2.19 | 0.03 | 2.22 | |
| RankCenterByEntropy | 6.37 | 0.10 | 6.49 | |
| RankCenterByEntropy_withProp | 4.31 | 0.11 | 4.42 | |
| exampleRes | 0 | 0 | 0 | |
| example_sce | 0.02 | 0.00 | 0.01 | |
| getProportion | 0 | 0 | 0 | |
| mySpatialPreprocess | 1.98 | 0.07 | 2.07 | |
| pathways_hallmark | 0.04 | 0.04 | 0.06 | |
| pathways_kegg | 0.06 | 0.07 | 0.14 | |
| pathways_reactome | 0.20 | 0.19 | 0.39 | |