| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:15 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 1699/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RegionalST 1.5.5 (landing page) Ziyi Li
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
|
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: 1.5.5 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RegionalST_1.5.5.tar.gz |
| StartedAt: 2024-11-28 04:56:38 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 05:05:14 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 515.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RegionalST.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RegionalST_1.5.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RegionalST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegionalST’ version ‘1.5.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘RegionalST-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RankCenterByEntropy
> ### Title: Automatically rank ROI centers based on entropy
> ### Aliases: RankCenterByEntropy
>
> ### ** Examples
>
> data("example_sce")
> example_sce <- mySpatialPreprocess(example_sce, platform="Visium")
> weight <- data.frame(celltype = c("Cancer Epithelial", "CAFs", "T-cells", "Endothelial",
+ "PVL", "Myeloid", "B-cells", "Normal Epithelial", "Plasmablasts"),
+ weight = c(0.25,0.05,
+ 0.25,0.05,
+ 0.025,0.05,
+ 0.25,0.05,0.025))
> example_sce <- RankCenterByEntropy(example_sce, weight, label = "celltype",
+ selectN = round(length(example_sce$spot)/10),
+ topN = 3, min_radius = 10,
+ radius_vec = c(10,15),
+ doPlot = TRUE)
Processing to Radius = 10
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Error in cor(sce$array_col, sce$pxl_col_in_fullres) :
supply both 'x' and 'y' or a matrix-like 'x'
Calls: RankCenterByEntropy ... eval -> <Anonymous> -> .make_vertices -> .flip_axis -> cor
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GetCrossRegionalDE_raw 7.006 0.385 7.391
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck/00check.log’
for details.
RegionalST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL RegionalST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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, CLSTN1, MIIP, YARS, STK40, PSMB2, RAP1GAP, CITED4, MACO1, ZC3H12A
PPT1, SDHB, NOC2L, SERINC2, MTOR, TCEA3, TMEM54, FBLIM1, MRTO4, SRRM1
CSF3R, CPTP, NADK, NECAP2, TMEM35B, TPRG1L, AKIRIN1, ZMPSTE24, RCC2, HNRNPR
Negative: IFI6, MXRA8, RBP7, RAB42, PADI3, FAM131C, C1QC, C1orf127, PDPN, TRIM63
NBL1, SAMD11, LAPTM5, MAN1C1, C1QB, MMP23B, SLC2A5, RSPO1, HPCA, HSPB7
CNR2, PRAMEF4, TP73, SRARP, SH2D5, ANKRD65, EPHA8, PADI6, NT5C1A, RNF186
PC_ 2
Positive: CNKSR1, CITED4, SMIM1, EDN2, CASZ1, KDF1, RAP1GAP, PADI2, CD164L2, GRHL3
SMPDL3B, PPT1, GRIK3, NCMAP, IFI6, VPS13D, FOXO6, KAZN, SH3D21, KCNQ4
KIAA1522, PHF13, ASAP3, RIMS3, PLOD1, TRIM62, PADI3, TMEM234, MFSD2A, GALE
Negative: CD52, C1QB, LAPTM5, C1QC, KCNAB2, TNFRSF1B, LCK, TNFRSF4, HSPG2, RUNX3
ID3, TNFRSF18, PIK3CD, MXRA8, THEMIS2, NBL1, SH3BGRL3, FGR, ZNF683, H6PD
RSRP1, AGO4, COL8A2, HEYL, WASF2, SDF4, ECE1, PLA2G2D, NDUFS5, TNFRSF8
PC_ 3
Positive: ZBTB48, NBL1, NOL9, ID3, ZNF436, EDN2, HSPG2, DDOST, MXRA8, COL16A1
SCNN1D, AUNIP, SLC45A1, SYNC, ATP13A2, ZCCHC17, PAQR7, PDPN, ATP5IF1, EPHB2
RSRP1, TMEM200B, EXTL1, RNF207, ANKRD65, TRNP1, SLC35E2B, C1QC, NCDN, SYF2
Negative: TNFRSF18, IFI6, ZNF683, FGR, SPEN, TRAPPC3, THEMIS2, CTNNBIP1, SLC25A34, IFNLR1
ZNF684, MTF1, EYA3, ZMYM6, C1QTNF12, HES2, CCDC28B, ALDH4A1, PRDM16, PRAMEF4
WDTC1, NADK, PADI2, MEAF6, TNFRSF4, AKIRIN1, CORT, MFSD2A, ZDHHC18, UQCRHL
PC_ 4
Positive: TNFRSF14, C1orf216, FHAD1, SLC25A34, EXO5, MFAP2, UBIAD1, ISG15, LZIC, TNFRSF8
PLA2G2F, SLC30A2, PLA2G5, ZFP69, DFFB, PTPRU, PLA2G2C, CORT, NCMAP, SCMH1
C1orf174, EPB41, RCC2, DNALI1, DDOST, C1orf109, PANK4, CDA, CAPZB, TCEA3
Negative: MYOM3, MYCL, CCDC28B, EMC1, LDLRAD2, RIMS3, PHC2, CRYBG2, PAQR7, GJB5
PNRC2, PLCH2, TMEM222, TEKT2, CPLANE2, PHACTR4, ZFP69B, SLC66A1, TMEM88B, FAM167B
SF3A3, MAD2L2, KDM1A, RHD, SLC35E2A, CDK11B, GMEB1, PIGV, CASZ1, ZMYM4
PC_ 5
Positive: RLF, C1orf216, TMEM35B, SCNN1D, CROCC, TTLL10, AUNIP, ZNF683, TINAGL1, DNAJC11
FAM110D, CRYBG2, MTF1, THEMIS2, SLC45A1, EXTL1, AHDC1, SPOCD1, FGR, SRM
ENO1, HES2, UBXN11, ADGRB2, SMIM1, PRAMEF4, GJB5, FAM167B, SDHB, INPP5B
Negative: IGSF21, TMEM39B, NPHP4, COL16A1, KIAA1522, MAN1C1, RAP1GAP, ZMYM1, PANK4, TP73
COL8A2, SLC25A33, RBP7, PITHD1, B3GALT6, TNFRSF9, PLEKHM2, FOXO6, AGO4, LZIC
PLOD1, CTPS1, CCNL2, PABPC4, ANKRD65, TRIT1, DNAJC16, SDC3, GPN2, EIF4G3
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 248
Number of edges: 10422
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6729
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
23.427 1.009 24.429
RegionalST.Rcheck/RegionalST-Ex.timings
| name | user | system | elapsed | |
| DoGSEA | 3.800 | 0.404 | 4.095 | |
| DrawDotplot | 1.902 | 0.442 | 2.232 | |
| DrawRegionProportion | 0.385 | 0.033 | 0.419 | |
| DrawRegionProportion_withProp | 0.301 | 0.123 | 0.425 | |
| FindRegionalCells | 0.000 | 0.001 | 0.000 | |
| GetCellTypeSpecificDE_withProp | 2.147 | 0.105 | 2.253 | |
| GetCrossRegionalDE_raw | 7.006 | 0.385 | 7.391 | |
| GetCrossRegionalDE_withProp | 3.393 | 0.436 | 3.829 | |
| GetOneRadiusEntropy | 4.172 | 0.081 | 4.253 | |
| GetOneRadiusEntropy_withProp | 3.353 | 0.122 | 3.476 | |
| ManualSelectCenter | 1.764 | 0.003 | 1.767 | |
| PlotOneSelectedCenter | 1.774 | 0.003 | 1.777 | |