Ziyi Li
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/RegionalST |
| git_branch: RELEASE_3_18 |
| git_last_commit: 2544b3c |
| git_last_commit_date: 2023-12-01 13:10:48 -0400 (Fri, 01 Dec 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:29 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 1710/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RegionalST 1.0.1 (landing page) Ziyi Li
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the RegionalST package: - 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: 1.0.1 |
| 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_1.0.1.tar.gz |
| StartedAt: 2024-03-28 00:00:11 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 00:05:11 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 299.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RegionalST.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/RegionalST.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RegionalST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegionalST’ version ‘1.0.1’
* 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 ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 4.8Mb
* 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 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 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 7.756 0.467 8.324
GetOneRadiusEntropy 6.784 0.239 7.049
DoGSEA 4.946 0.544 5.423
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/RegionalST.Rcheck/00check.log’
for details.
RegionalST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RegionalST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)
RegionalST.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
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|======================================================================| 100%
Finding variable features for layer counts
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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, TAS1R3, A3GALT2, 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: 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
Negative: 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
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...
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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
27.344 1.071 28.620
RegionalST.Rcheck/RegionalST-Ex.timings
| name | user | system | elapsed | |
| DoGSEA | 4.946 | 0.544 | 5.423 | |
| DrawDotplot | 2.001 | 0.608 | 2.581 | |
| DrawRegionProportion | 0.496 | 0.045 | 0.543 | |
| DrawRegionProportion_withProp | 0.309 | 0.006 | 0.317 | |
| FindRegionalCells | 0 | 0 | 0 | |
| GetCrossRegionalDE_raw | 7.756 | 0.467 | 8.324 | |
| GetCrossRegionalDE_withProp | 3.630 | 0.332 | 3.975 | |
| GetOneRadiusEntropy | 6.784 | 0.239 | 7.049 | |
| GetOneRadiusEntropy_withProp | 1.809 | 0.055 | 1.868 | |
| ManualSelectCenter | 0.458 | 0.042 | 0.500 | |
| PlotOneSelectedCenter | 0.593 | 0.041 | 0.634 | |
| RankCenterByEntropy | 2.998 | 0.056 | 3.064 | |
| RankCenterByEntropy_withProp | 2.624 | 0.052 | 2.677 | |
| exampleRes | 0.004 | 0.002 | 0.006 | |
| example_sce | 0.010 | 0.002 | 0.012 | |
| getProportion | 0 | 0 | 0 | |
| mySpatialPreprocess | 0.476 | 0.023 | 0.498 | |
| pathways_hallmark | 0.017 | 0.003 | 0.019 | |
| pathways_kegg | 0.026 | 0.003 | 0.027 | |
| pathways_reactome | 0.183 | 0.004 | 0.187 | |