| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-15 11:34 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 1188/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mastR 1.11.0 (landing page) Jinjin Chen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the mastR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mastR.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: mastR |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:mastR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings mastR_1.11.0.tar.gz |
| StartedAt: 2025-12-15 01:28:56 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 01:38:18 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 562.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: mastR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:mastR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings mastR_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/mastR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘mastR/DESCRIPTION’ ... OK
* this is package ‘mastR’ version ‘1.11.0’
* 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 ‘mastR’ 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 ... 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'DEGs_Group.Rd':
‘[limma:ebayes]{limma::treat()}’
Non-topic package-anchored link(s) in Rd file 'DEGs_RP.Rd':
‘[limma:ebayes]{limma::treat()}’
Non-topic package-anchored link(s) in Rd file 'de_analysis.Rd':
‘[limma:ebayes]{limma::treat()}’
Non-topic package-anchored link(s) in Rd file 'process_data.Rd':
‘[limma:ebayes]{limma::treat()}’
Non-topic package-anchored link(s) in Rd file 'select_sig.Rd':
‘[limma:ebayes]{limma::treat()}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ‘mastR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pseudo_samples
> ### Title: Aggregate single cells to pseudo-samples according to specific
> ### factors
> ### Aliases: pseudo_samples pseudo_samples,matrix,data.frame-method
> ### pseudo_samples,matrix,vector-method
> ### pseudo_samples,Seurat,character-method
> ### pseudo_samples,SummarizedExperiment,character-method
>
> ### ** Examples
>
> counts <- matrix(abs(rnorm(10000, 10, 10)), 100)
> rownames(counts) <- 1:100
> colnames(counts) <- 1:100
> meta <- data.frame(
+ subset = rep(c("A", "B"), 50),
+ level = rep(1:4, each = 25)
+ )
> rownames(meta) <- 1:100
> scRNA <- SeuratObject::CreateSeuratObject(counts = counts, meta.data = meta)
Warning: Data is of class matrix. Coercing to dgCMatrix.
> pseudo_samples(scRNA,
+ by = c("subset", "level"),
+ min.cells = 10, max.cells = 20
+ )
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::pseudo_samples(...)
2. └─mastR::pseudo_samples(...)
3. ├─base::as.matrix(SeuratObject::GetAssayData(data, slot = slot))
4. ├─SeuratObject::GetAssayData(data, slot = slot)
5. └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
6. └─SeuratObject::.Deprecate(...)
7. └─lifecycle::deprecate_stop(...)
8. └─lifecycle:::deprecate_stop0(msg)
9. └─rlang::cnd_signal(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_diagnostics 9.895 0.214 10.110
get_panglao_sig 5.255 0.246 10.729
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
3. │ ├─mastR::sig_scatter_plot(...)
4. │ ├─SeuratObject::GetAssayData(data, slot = slot)
5. │ └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
6. │ └─SeuratObject::.Deprecate(...)
7. │ └─lifecycle::deprecate_stop(...)
8. │ └─lifecycle:::deprecate_stop0(msg)
9. │ └─rlang::cnd_signal(...)
10. │ └─rlang:::signal_abort(cnd)
11. │ └─base::signalCondition(cnd)
12. └─base (local) `<fn>`(`<lfcycl__>`)
[ FAIL 11 | WARN 41 | SKIP 0 | PASS 91 ]
Error:
! Test failures.
Execution halted
* 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: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/mastR.Rcheck/00check.log’
for details.
mastR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL mastR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘mastR’ ... ** this is package ‘mastR’ version ‘1.11.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (mastR)
mastR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(mastR)
>
> test_check("mastR")
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 2794 3366 3888 2947 1955
NotSig 2465 5052 10779 43514 45073
Up 44786 41627 35378 3584 3017
NK-Others
Down 107
NotSig 48972
Up 966
NK-Others
Down 29581
NotSig 17543
Up 2921
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 2794 3366 3888 2947 1955
NotSig 2465 5052 10779 43514 45073
Up 44786 41627 35378 3584 3017
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 2794 3366 3888 2947 1955
NotSig 2465 5052 10779 43514 45073
Up 44786 41627 35378 3584 3017
'select()' returned 1:many mapping between keys and columns
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4013 3946 3149 2701 2154
NotSig 1482 2687 4412 4986 6192
Up 4940 3802 2874 2748 2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4013 3946 3149 2701 2154
NotSig 1482 2687 4412 4986 6192
Up 4940 3802 2874 2748 2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4013 3946 3149 2701 2154
NotSig 1482 2687 4412 4986 6192
Up 4940 3802 2874 2748 2089
'select()' returned 1:many mapping between keys and columns
Saving _problems/test-filter_subset_sig-45.R
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 3056 2843 2174 1824 1444
NotSig 1246 2669 4189 4576 5527
Up 3926 2716 1865 1828 1257
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
Saving _problems/test-get_de_table-45.R
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 3629 3510 2668 2189 1728
NotSig 1957 3500 5403 5947 7039
Up 4714 3290 2229 2164 1533
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
Saving _problems/test-get_degs-38.R
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Saving _problems/test-pca_matrix_plot-53.R
'select()' returned 1:many mapping between keys and columns
Saving _problems/test-pseudo_samples-25.R
All samples in sig_data are used!
All samples in bg_data are used!
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Saving _problems/test-remove_bg_exp-78.R
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Saving _problems/test-sig_boxplot-47.R
'select()' returned 1:many mapping between keys and columns
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4012 3944 3148 2697 2153
NotSig 1472 2679 4402 4978 6179
Up 4931 3792 2865 2740 2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4012 3944 3148 2697 2153
NotSig 1472 2679 4402 4978 6179
Up 4931 3792 2865 2740 2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4012 3944 3148 2697 2153
NotSig 1472 2679 4402 4978 6179
Up 4931 3792 2865 2740 2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Saving _problems/test-sig_gseaplot-54.R
'select()' returned 1:many mapping between keys and columns
Gene KIR2DL2 is not in data.
Gene KIR2DL5A is not in data.
Gene KIR2DS2 is not in data.
Gene KIR2DS5 is not in data.
Gene KLRA1P is not in data.
Gene LOC653757 is not in data.
Gene MGC24103 is not in data.
Gene TRDC is not in data.
Gene CCL4 is not in data.
Gene CCL5 is not in data.
The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.
Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.
The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.
Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.
The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.
Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.
The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.
Use `suppressMessages()` to turn off this message.
Saving _problems/test-sig_heatmap-46.R
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Saving _problems/test-sig_rankdensity_plot-65.R
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Saving _problems/test-sig_scatter_plot-35.R
NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down 4011 3943 3147 2697 2154
NotSig 1471 2680 4400 4980 6178
Up 4929 3788 2864 2734 2079
[ FAIL 11 | WARN 41 | SKIP 0 | PASS 91 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-filter_subset_sig.R:40:3'): filter_subset_sig works ────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::filter_subset_sig(...) at test-filter_subset_sig.R:40:3
2. └─mastR::filter_subset_sig(...)
3. ├─mastR::get_degs(...)
4. └─mastR::get_degs(...)
5. ├─SeuratObject::GetAssayData(data, slot = slot)
6. └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
── Error ('test-get_de_table.R:42:3'): get_de_table works ──────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::get_de_table(...) at test-get_de_table.R:42:3
2. └─mastR::get_de_table(...)
3. ├─SeuratObject::GetAssayData(data, slot = slot)
4. └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
── Error ('test-get_degs.R:35:3'): get_degs works ──────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::get_degs(data_seurat, group_col = "celltype.ch1", target_group = "NK") at test-get_degs.R:35:3
2. └─mastR::get_degs(data_seurat, group_col = "celltype.ch1", target_group = "NK")
3. ├─SeuratObject::GetAssayData(data, slot = slot)
4. └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
── Error ('test-pca_matrix_plot.R:48:3'): pca_matrix_plot works ────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::pca_matrix_plot(...) at test-pca_matrix_plot.R:48:3
2. └─mastR::pca_matrix_plot(...)
3. ├─SeuratObject::GetAssayData(data, slot = slot)
4. └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
── Error ('test-pseudo_samples.R:21:3'): pseudo_samples works ──────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::pseudo_samples(...) at test-pseudo_samples.R:21:3
2. └─mastR::pseudo_samples(...)
3. ├─base::as.matrix(SeuratObject::GetAssayData(data, slot = slot))
4. ├─SeuratObject::GetAssayData(data, slot = slot)
5. └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
6. └─SeuratObject::.Deprecate(...)
7. └─lifecycle::deprecate_stop(...)
8. └─lifecycle:::deprecate_stop0(msg)
9. └─rlang::cnd_signal(...)
── Error ('test-remove_bg_exp.R:69:3'): remove_bg_exp works ────────────────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c("The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.", i = "Please use the `layer` argument instead."), trace = structure(list(call = list(remove_bg_exp(bg_data = data_seurat, sig_data = Biobase::exprs(im_data_6), b_group_col = "cancer", b_target_group = "CRC", s_group_col = im_data_6$`celltype:ch1`, s_target_group = "NK", markers = nk_markers$HGNC_Symbol[40:50], gene_id = c("ENSEMBL", "SYMBOL")), remove_bg_exp(bg_data = data_seurat, sig_data = Biobase::exprs(im_data_6), b_group_col = "cancer", b_target_group = "CRC", s_group_col = im_data_6$`celltype:ch1`, s_target_group = "NK", markers = nk_markers$HGNC_Symbol[40:50], gene_id = c("ENSEMBL", "SYMBOL")), remove_bg_exp(bg_data = SeuratObject::GetAssayData(bg_data, slot = b_slot), sig_data = sig_data, b_group_col = b_group_col, b_target_group = b_target_group, s_group_col = s_group_col, s_target_group = s_target_group, markers = markers, snr = snr, ..., filter = filter, gene_id = gene_id, s_slot = s_slot), SeuratObject::GetAssayData(bg_data, slot = b_slot), GetAssayData.Seurat(bg_data, slot = b_slot), .Deprecate(when = "5.0.0", what = "GetAssayData(slot = )", with = "GetAssayData(layer = )"), deprecate_stop(when = wv, what = what, with = with, env = caller, ...), deprecate_stop0(msg), cnd_signal(error_cnd(c("lifecycle_error_deprecated", "defunctError"), old = NULL, new = NULL, package = NULL, message = msg))), parent = c(0L, 0L, 2L, 2L, 2L, 5L, 6L, 7L, 8L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE), namespace = c("mastR", "mastR", "mastR", "SeuratObject", "SeuratObject", "SeuratObject", "lifecycle", "lifecycle", "rlang"), scope = c("::", "::", "::", "::", ":::", "::", "::", ":::", "::")), row.names = c(NA, -9L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, old = NULL, new = NULL, package = NULL, call = NULL, use_cli_format = TRUE), class = c("lifecycle_error_deprecated", "defunctError", "rlang_error", "error", "condition")))`: error in evaluating the argument 'bg_data' in selecting a method for function 'remove_bg_exp': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::remove_bg_exp(...) at test-remove_bg_exp.R:69:3
2. ├─mastR::remove_bg_exp(...)
3. │ ├─mastR::remove_bg_exp(...)
4. │ ├─SeuratObject::GetAssayData(bg_data, slot = b_slot)
5. │ └─SeuratObject:::GetAssayData.Seurat(bg_data, slot = b_slot)
6. │ └─SeuratObject::.Deprecate(...)
7. │ └─lifecycle::deprecate_stop(...)
8. │ └─lifecycle:::deprecate_stop0(msg)
9. │ └─rlang::cnd_signal(...)
10. │ └─rlang:::signal_abort(cnd)
11. │ └─base::signalCondition(cnd)
12. └─base (local) `<fn>`(`<lfcycl__>`)
── Error ('test-sig_boxplot.R:42:3'): sig_boxplot works ────────────────────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c("The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.", i = "Please use the `layer` argument instead."), trace = structure(list(call = list(sig_boxplot(data_seurat, sigs = nk_markers$HGNC_Symbol[10:30], group_col = "group", target_group = "NK", gene_id = "ENSEMBL"), sig_boxplot(data_seurat, sigs = nk_markers$HGNC_Symbol[10:30], group_col = "group", target_group = "NK", gene_id = "ENSEMBL"), sig_boxplot(data = SeuratObject::GetAssayData(data, slot = slot), sigs = sigs, group_col = slot(data, "meta.data")[[group_col]], target_group = target_group, type = type, method = method, gene_id = gene_id), SeuratObject::GetAssayData(data, slot = slot), GetAssayData.Seurat(data, slot = slot), .Deprecate(when = "5.0.0", what = "GetAssayData(slot = )", with = "GetAssayData(layer = )"), deprecate_stop(when = wv, what = what, with = with, env = caller, ...), deprecate_stop0(msg), cnd_signal(error_cnd(c("lifecycle_error_deprecated", "defunctError"), old = NULL, new = NULL, package = NULL, message = msg))), parent = c(0L, 0L, 2L, 2L, 2L, 5L, 6L, 7L, 8L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE), namespace = c("mastR", "mastR", "mastR", "SeuratObject", "SeuratObject", "SeuratObject", "lifecycle", "lifecycle", "rlang"), scope = c("::", "::", "::", "::", ":::", "::", "::", ":::", "::")), row.names = c(NA, -9L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, old = NULL, new = NULL, package = NULL, call = NULL, use_cli_format = TRUE), class = c("lifecycle_error_deprecated", "defunctError", "rlang_error", "error", "condition")))`: error in evaluating the argument 'data' in selecting a method for function 'sig_boxplot': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::sig_boxplot(...) at test-sig_boxplot.R:42:3
2. ├─mastR::sig_boxplot(...)
3. │ ├─mastR::sig_boxplot(...)
4. │ ├─SeuratObject::GetAssayData(data, slot = slot)
5. │ └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
6. │ └─SeuratObject::.Deprecate(...)
7. │ └─lifecycle::deprecate_stop(...)
8. │ └─lifecycle:::deprecate_stop0(msg)
9. │ └─rlang::cnd_signal(...)
10. │ └─rlang:::signal_abort(cnd)
11. │ └─base::signalCondition(cnd)
12. └─base (local) `<fn>`(`<lfcycl__>`)
── Error ('test-sig_gseaplot.R:47:3'): sig_gseaplot works ──────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-sig_gseaplot.R:47:3
2. │ └─base::withCallingHandlers(...)
3. ├─mastR::sig_gseaplot(...)
4. └─mastR::sig_gseaplot(...)
5. ├─mastR::process_data(...)
6. └─mastR::process_data(...)
7. └─mastR (local) .local(...)
8. ├─edgeR::DGEList(...)
9. ├─SeuratObject::GetAssayData(data, slot = slot)
10. └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
11. └─SeuratObject::.Deprecate(...)
12. └─lifecycle::deprecate_stop(...)
13. └─lifecycle:::deprecate_stop0(msg)
14. └─rlang::cnd_signal(...)
── Error ('test-sig_heatmap.R:41:3'): sig_heatmap works ────────────────────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c("The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.", i = "Please use the `layer` argument instead."), trace = structure(list(call = list(sig_heatmap(data_seurat, sigs = nk_markers$HGNC_Symbol[1:20], group_col = "group", gene_id = "ENSEMBL"), sig_heatmap(data_seurat, sigs = nk_markers$HGNC_Symbol[1:20], group_col = "group", gene_id = "ENSEMBL"), sig_heatmap(data = SeuratObject::GetAssayData(data, slot = slot), sigs = sigs, group_col = slot(data, "meta.data")[[group_col]], scale = scale, gene_id = gene_id, ranks_plot = ranks_plot, ...), SeuratObject::GetAssayData(data, slot = slot), GetAssayData.Seurat(data, slot = slot), .Deprecate(when = "5.0.0", what = "GetAssayData(slot = )", with = "GetAssayData(layer = )"), deprecate_stop(when = wv, what = what, with = with, env = caller, ...), deprecate_stop0(msg), cnd_signal(error_cnd(c("lifecycle_error_deprecated", "defunctError"), old = NULL, new = NULL, package = NULL, message = msg))), parent = c(0L, 0L, 2L, 2L, 2L, 5L, 6L, 7L, 8L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE), namespace = c("mastR", "mastR", "mastR", "SeuratObject", "SeuratObject", "SeuratObject", "lifecycle", "lifecycle", "rlang"), scope = c("::", "::", "::", "::", ":::", "::", "::", ":::", "::")), row.names = c(NA, -9L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, old = NULL, new = NULL, package = NULL, call = NULL, use_cli_format = TRUE), class = c("lifecycle_error_deprecated", "defunctError", "rlang_error", "error", "condition")))`: error in evaluating the argument 'data' in selecting a method for function 'sig_heatmap': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::sig_heatmap(...) at test-sig_heatmap.R:41:3
2. ├─mastR::sig_heatmap(...)
3. │ ├─mastR::sig_heatmap(...)
4. │ ├─SeuratObject::GetAssayData(data, slot = slot)
5. │ └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
6. │ └─SeuratObject::.Deprecate(...)
7. │ └─lifecycle::deprecate_stop(...)
8. │ └─lifecycle:::deprecate_stop0(msg)
9. │ └─rlang::cnd_signal(...)
10. │ └─rlang:::signal_abort(cnd)
11. │ └─base::signalCondition(cnd)
12. └─base (local) `<fn>`(`<lfcycl__>`)
── Error ('test-sig_rankdensity_plot.R:60:3'): sig_rankdensity_plot works ──────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c("The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.", i = "Please use the `layer` argument instead."), trace = structure(list(call = list(sig_rankdensity_plot(data_seurat, sigs = nk_markers$HGNC_Symbol[1:20], group_col = "group", gene_id = "ENSEMBL"), sig_rankdensity_plot(data_seurat, sigs = nk_markers$HGNC_Symbol[1:20], group_col = "group", gene_id = "ENSEMBL"), sig_rankdensity_plot(data = SeuratObject::GetAssayData(data, slot = slot), sigs = sigs, group_col = slot(data, "meta.data")[[group_col]], aggregate = aggregate, gene_id = gene_id), SeuratObject::GetAssayData(data, slot = slot), GetAssayData.Seurat(data, slot = slot), .Deprecate(when = "5.0.0", what = "GetAssayData(slot = )", with = "GetAssayData(layer = )"), deprecate_stop(when = wv, what = what, with = with, env = caller, ...), deprecate_stop0(msg), cnd_signal(error_cnd(c("lifecycle_error_deprecated", "defunctError"), old = NULL, new = NULL, package = NULL, message = msg))), parent = c(0L, 0L, 2L, 2L, 2L, 5L, 6L, 7L, 8L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE), namespace = c("mastR", "mastR", "mastR", "SeuratObject", "SeuratObject", "SeuratObject", "lifecycle", "lifecycle", "rlang"), scope = c("::", "::", "::", "::", ":::", "::", "::", ":::", "::")), row.names = c(NA, -9L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, old = NULL, new = NULL, package = NULL, call = NULL, use_cli_format = TRUE), class = c("lifecycle_error_deprecated", "defunctError", "rlang_error", "error", "condition")))`: error in evaluating the argument 'data' in selecting a method for function 'sig_rankdensity_plot': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::sig_rankdensity_plot(...) at test-sig_rankdensity_plot.R:60:3
2. ├─mastR::sig_rankdensity_plot(...)
3. │ ├─mastR::sig_rankdensity_plot(...)
4. │ ├─SeuratObject::GetAssayData(data, slot = slot)
5. │ └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
6. │ └─SeuratObject::.Deprecate(...)
7. │ └─lifecycle::deprecate_stop(...)
8. │ └─lifecycle:::deprecate_stop0(msg)
9. │ └─rlang::cnd_signal(...)
10. │ └─rlang:::signal_abort(cnd)
11. │ └─base::signalCondition(cnd)
12. └─base (local) `<fn>`(`<lfcycl__>`)
── Error ('test-sig_scatter_plot.R:30:3'): multiplication works ────────────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c("The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.", i = "Please use the `layer` argument instead."), trace = structure(list(call = list(sig_scatter_plot(data_seurat, sigs = nk_markers$HGNC_Symbol, group_col = "group", target_group = "NK", gene_id = "ENSEMBL"), sig_scatter_plot(data_seurat, sigs = nk_markers$HGNC_Symbol, group_col = "group", target_group = "NK", gene_id = "ENSEMBL"), sig_scatter_plot(data = SeuratObject::GetAssayData(data, slot = slot), sigs = sigs, group_col = slot(data, "meta.data")[[group_col]], target_group = target_group, xint = xint, yint = yint, gene_id = gene_id), SeuratObject::GetAssayData(data, slot = slot), GetAssayData.Seurat(data, slot = slot), .Deprecate(when = "5.0.0", what = "GetAssayData(slot = )", with = "GetAssayData(layer = )"), deprecate_stop(when = wv, what = what, with = with, env = caller, ...), deprecate_stop0(msg), cnd_signal(error_cnd(c("lifecycle_error_deprecated", "defunctError"), old = NULL, new = NULL, package = NULL, message = msg))), parent = c(0L, 0L, 2L, 2L, 2L, 5L, 6L, 7L, 8L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE), namespace = c("mastR", "mastR", "mastR", "SeuratObject", "SeuratObject", "SeuratObject", "lifecycle", "lifecycle", "rlang"), scope = c("::", "::", "::", "::", ":::", "::", "::", ":::", "::")), row.names = c(NA, -9L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, old = NULL, new = NULL, package = NULL, call = NULL, use_cli_format = TRUE), class = c("lifecycle_error_deprecated", "defunctError", "rlang_error", "error", "condition")))`: error in evaluating the argument 'data' in selecting a method for function 'sig_scatter_plot': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. ├─mastR::sig_scatter_plot(...) at test-sig_scatter_plot.R:30:3
2. ├─mastR::sig_scatter_plot(...)
3. │ ├─mastR::sig_scatter_plot(...)
4. │ ├─SeuratObject::GetAssayData(data, slot = slot)
5. │ └─SeuratObject:::GetAssayData.Seurat(data, slot = slot)
6. │ └─SeuratObject::.Deprecate(...)
7. │ └─lifecycle::deprecate_stop(...)
8. │ └─lifecycle:::deprecate_stop0(msg)
9. │ └─rlang::cnd_signal(...)
10. │ └─rlang:::signal_abort(cnd)
11. │ └─base::signalCondition(cnd)
12. └─base (local) `<fn>`(`<lfcycl__>`)
[ FAIL 11 | WARN 41 | SKIP 0 | PASS 91 ]
Error:
! Test failures.
Execution halted
mastR.Rcheck/mastR-Ex.timings
| name | user | system | elapsed | |
| ccle_2_wide | 0.125 | 0.018 | 0.144 | |
| de_analysis | 2.509 | 0.067 | 2.575 | |
| filter_subset_sig | 3.435 | 0.201 | 3.636 | |
| get_de_table | 1.744 | 0.019 | 1.763 | |
| get_degs | 1.777 | 0.004 | 1.781 | |
| get_gsc_sig | 0.014 | 0.001 | 0.015 | |
| get_lm_sig | 0.012 | 0.000 | 0.012 | |
| get_panglao_sig | 5.255 | 0.246 | 10.729 | |
| gls2gsc | 0.007 | 0.002 | 0.008 | |
| gsc_plot | 0.982 | 0.021 | 1.003 | |
| list_panglao_organs | 0.092 | 0.005 | 0.697 | |
| list_panglao_types | 0.204 | 0.004 | 1.244 | |
| merge_markers | 0.039 | 0.001 | 0.040 | |
| pca_matrix_plot | 3.017 | 0.087 | 3.104 | |
| plot_diagnostics | 9.895 | 0.214 | 10.110 | |
| plot_mean_var | 2.416 | 0.016 | 2.432 | |
| process_data | 1.509 | 0.004 | 1.514 | |
| pseudo_sample_list | 0.132 | 0.004 | 0.136 | |