| Back to Build/check report for BioC 3.21 experimental data |
|
This page was generated on 2025-10-16 15:01 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| 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 379/432 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| spatialLIBD 1.20.1 (landing page) Leonardo Collado-Torres
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||
|
To the developers/maintainers of the spatialLIBD 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: spatialLIBD |
| Version: 1.20.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings spatialLIBD_1.20.1.tar.gz |
| StartedAt: 2025-10-16 12:58:57 -0400 (Thu, 16 Oct 2025) |
| EndedAt: 2025-10-16 13:16:53 -0400 (Thu, 16 Oct 2025) |
| EllapsedTime: 1075.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: spatialLIBD.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings spatialLIBD_1.20.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/spatialLIBD.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘spatialLIBD/DESCRIPTION’ ... OK
* this is package ‘spatialLIBD’ version ‘1.20.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘spatialLIBD’ 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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
check_sce.Rd: SingleCellExperiment-class
check_sce_layer.Rd: SingleCellExperiment-class
fetch_data.Rd: SingleCellExperiment-class
layer_boxplot.Rd: SingleCellExperiment-class
read10xVisiumWrapper.Rd: SpatialExperiment-class
run_app.Rd: SingleCellExperiment-class
sce_to_spe.Rd: SingleCellExperiment-class
sig_genes_extract.Rd: SingleCellExperiment-class
sig_genes_extract_all.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘spatialLIBD-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vis_clus_p
> ### Title: Sample spatial cluster visualization workhorse function
> ### Aliases: vis_clus_p
>
> ### ** Examples
>
>
> if (enough_ram()) {
+ ## Obtain the necessary data
+ if (!exists("spe")) spe <- fetch_data("spe")
+ spe_sub <- spe[, spe$sample_id == "151673"]
+
+ ## Use the manual color palette by Lukas M Weber
+ ## Don't plot the histology information
+ p <- vis_clus_p(
+ spe = spe_sub,
+ d = as.data.frame(cbind(colData(spe_sub), SpatialExperiment::spatialCoords(spe_sub)), optional = TRUE),
+ clustervar = "layer_guess_reordered",
+ sampleid = "151673",
+ colors = libd_layer_colors,
+ title = "151673 LIBD Layers",
+ spatial = FALSE
+ )
+ print(p)
+
+ ## Clean up
+ rm(spe_sub)
+ }
Error in readRDS(.db_index_file(x)) : error reading from connection
Calls: fetch_data ... <Anonymous> -> <Anonymous> -> .local -> .db_index_load -> readRDS
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
vis_clus 21.884 3.354 25.712
add_images 20.091 2.762 24.639
img_update_all 19.082 2.409 21.627
add_qc_metrics 16.962 2.411 19.524
add_key 16.817 2.386 19.846
cluster_import 16.193 2.011 19.015
cluster_export 15.733 2.010 18.215
check_spe 14.208 1.848 16.632
frame_limits 14.141 1.788 16.410
sce_to_spe 14.009 1.450 16.066
img_edit 13.425 1.721 15.601
geom_spatial 13.464 1.510 15.448
img_update 13.388 1.428 15.395
gene_set_enrichment_plot 7.105 0.808 8.214
layer_stat_cor_plot 4.382 0.688 5.430
* 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:
▆
1. └─spatialLIBD::fetch_data("spe") at test-vis_gene.R:4:9
2. └─spatialLIBD::sce_to_spe(...)
3. └─base::lapply(url_scaleFactors, jsonlite::read_json)
4. └─jsonlite (local) FUN(X[[i]], ...)
5. └─jsonlite::parse_json(...)
6. └─jsonlite:::parse_and_simplify(...)
7. └─jsonlite:::parseJSON(txt, bigint_as_char)
8. └─jsonlite:::parse_con(txt, bigint_as_char)
9. ├─base::open(con, "rb")
10. └─base::open.connection(con, "rb")
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 38 ]
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-3.21-data-experiment/meat/spatialLIBD.Rcheck/00check.log’
for details.
spatialLIBD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL spatialLIBD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘spatialLIBD’ ... ** this is package ‘spatialLIBD’ version ‘1.20.1’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (spatialLIBD)
spatialLIBD.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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.
> library(testthat)
> library(spatialLIBD)
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("spatialLIBD")
rgstr_> ## Ensure reproducibility of example data
rgstr_> set.seed(20220907)
rgstr_> ## Generate example data
rgstr_> sce <- scuttle::mockSCE()
rgstr_> ## Add some sample IDs
rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE)
rgstr_> ## Add a sample-level covariate: age
rgstr_> ages <- rnorm(5, mean = 20, sd = 4)
rgstr_> names(ages) <- LETTERS[1:5]
rgstr_> sce$age <- ages[sce$sample_id]
rgstr_> ## Add gene-level information
rgstr_> rowData(sce)$ensembl <- paste0("ENSG", seq_len(nrow(sce)))
rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))
rgstr_> ## Pseudo-bulk
rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL)
rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 8 columns
Mutation_Status Cell_Cycle Treatment sample_id age
<character> <character> <character> <character> <numeric>
A_G0 NA G0 NA A 19.1872
B_G0 NA G0 NA B 25.3496
C_G0 NA G0 NA C 24.1802
D_G0 NA G0 NA D 15.5211
E_G0 NA G0 NA E 20.9701
... ... ... ... ... ...
A_S NA S NA A 19.1872
B_S NA S NA B 25.3496
C_S NA S NA C 24.1802
D_S NA S NA D 15.5211
E_S NA S NA E 20.9701
registration_variable registration_sample_id ncells
<character> <character> <integer>
A_G0 G0 A 8
B_G0 G0 B 13
C_G0 G0 C 9
D_G0 G0 D 7
E_G0 G0 E 10
... ... ... ...
A_S S A 12
B_S S B 8
C_S S C 7
D_S S D 14
E_S S E 11
rgstr_> ## Ensure reproducibility of example data
rgstr_> set.seed(20220907)
rgstr_> ## Generate example data
rgstr_> sce <- scuttle::mockSCE()
rgstr_> ## Add some sample IDs
rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE)
rgstr_> ## Add a sample-level covariate: age
rgstr_> ages <- rnorm(5, mean = 20, sd = 4)
rgstr_> names(ages) <- LETTERS[1:5]
rgstr_> sce$age <- ages[sce$sample_id]
rgstr_> ## Add gene-level information
rgstr_> rowData(sce)$ensembl <- paste0("ENSG", seq_len(nrow(sce)))
rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))
rgstr_> ## Pseudo-bulk
rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL)
rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 8 columns
Mutation_Status Cell_Cycle Treatment sample_id age
<character> <character> <character> <character> <numeric>
A_G0 NA G0 NA A 19.1872
B_G0 NA G0 NA B 25.3496
C_G0 NA G0 NA C 24.1802
D_G0 NA G0 NA D 15.5211
E_G0 NA G0 NA E 20.9701
... ... ... ... ... ...
A_S NA S NA A 19.1872
B_S NA S NA B 25.3496
C_S NA S NA C 24.1802
D_S NA S NA D 15.5211
E_S NA S NA E 20.9701
registration_variable registration_sample_id ncells
<character> <character> <integer>
A_G0 G0 A 8
B_G0 G0 B 13
C_G0 G0 C 9
D_G0 G0 D 7
E_G0 G0 E 10
... ... ... ...
A_S S A 12
B_S S B 8
C_S S C 7
D_S S D 14
E_S S E 11
rgst__> example("registration_model", package = "spatialLIBD")
rgstr_> example("registration_pseudobulk", package = "spatialLIBD")
rgstr_> ## Ensure reproducibility of example data
rgstr_> set.seed(20220907)
rgstr_> ## Generate example data
rgstr_> sce <- scuttle::mockSCE()
rgstr_> ## Add some sample IDs
rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE)
rgstr_> ## Add a sample-level covariate: age
rgstr_> ages <- rnorm(5, mean = 20, sd = 4)
rgstr_> names(ages) <- LETTERS[1:5]
rgstr_> sce$age <- ages[sce$sample_id]
rgstr_> ## Add gene-level information
rgstr_> rowData(sce)$ensembl <- paste0("ENSG", seq_len(nrow(sce)))
rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))
rgstr_> ## Pseudo-bulk
rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL)
rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 8 columns
Mutation_Status Cell_Cycle Treatment sample_id age
<character> <character> <character> <character> <numeric>
A_G0 NA G0 NA A 19.1872
B_G0 NA G0 NA B 25.3496
C_G0 NA G0 NA C 24.1802
D_G0 NA G0 NA D 15.5211
E_G0 NA G0 NA E 20.9701
... ... ... ... ... ...
A_S NA S NA A 19.1872
B_S NA S NA B 25.3496
C_S NA S NA C 24.1802
D_S NA S NA D 15.5211
E_S NA S NA E 20.9701
registration_variable registration_sample_id ncells
<character> <character> <integer>
A_G0 G0 A 8
B_G0 G0 B 13
C_G0 G0 C 9
D_G0 G0 D 7
E_G0 G0 E 10
... ... ... ...
A_S S A 12
B_S S B 8
C_S S C 7
D_S S D 14
E_S S E 11
rgstr_> registration_mod <- registration_model(sce_pseudo, "age")
rgstr_> head(registration_mod)
registration_variableG0 registration_variableG1 registration_variableG2M
A_G0 1 0 0
B_G0 1 0 0
C_G0 1 0 0
D_G0 1 0 0
E_G0 1 0 0
A_G1 0 1 0
registration_variableS age
A_G0 0 19.18719
B_G0 0 25.34965
C_G0 0 24.18019
D_G0 0 15.52107
E_G0 0 20.97006
A_G1 0 19.18719
rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod)
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 38 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-vis_clus.R:4:9'): vis_clus ─────────────────────────────────────
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json'
Backtrace:
▆
1. └─spatialLIBD::fetch_data("spe") at test-vis_clus.R:4:9
2. └─spatialLIBD::sce_to_spe(...)
3. └─base::lapply(url_scaleFactors, jsonlite::read_json)
4. └─jsonlite (local) FUN(X[[i]], ...)
5. └─jsonlite::parse_json(...)
6. └─jsonlite:::parse_and_simplify(...)
7. └─jsonlite:::parseJSON(txt, bigint_as_char)
8. └─jsonlite:::parse_con(txt, bigint_as_char)
9. ├─base::open(con, "rb")
10. └─base::open.connection(con, "rb")
── Error ('test-vis_gene.R:4:9'): vis_gene ─────────────────────────────────────
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json'
Backtrace:
▆
1. └─spatialLIBD::fetch_data("spe") at test-vis_gene.R:4:9
2. └─spatialLIBD::sce_to_spe(...)
3. └─base::lapply(url_scaleFactors, jsonlite::read_json)
4. └─jsonlite (local) FUN(X[[i]], ...)
5. └─jsonlite::parse_json(...)
6. └─jsonlite:::parse_and_simplify(...)
7. └─jsonlite:::parseJSON(txt, bigint_as_char)
8. └─jsonlite:::parse_con(txt, bigint_as_char)
9. ├─base::open(con, "rb")
10. └─base::open.connection(con, "rb")
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 38 ]
Error: Test failures
Execution halted
spatialLIBD.Rcheck/spatialLIBD-Ex.timings
| name | user | system | elapsed | |
| add10xVisiumAnalysis | 0.001 | 0.000 | 0.000 | |
| add_images | 20.091 | 2.762 | 24.639 | |
| add_key | 16.817 | 2.386 | 19.846 | |
| add_qc_metrics | 16.962 | 2.411 | 19.524 | |
| annotate_registered_clusters | 1.145 | 0.165 | 1.464 | |
| check_modeling_results | 1.127 | 0.148 | 1.455 | |
| check_sce | 3.399 | 0.265 | 3.814 | |
| check_sce_layer | 1.202 | 0.130 | 1.484 | |
| check_spe | 14.208 | 1.848 | 16.632 | |
| cluster_export | 15.733 | 2.010 | 18.215 | |
| cluster_import | 16.193 | 2.011 | 19.015 | |
| enough_ram | 0.003 | 0.007 | 0.009 | |
| fetch_data | 1.204 | 0.150 | 1.525 | |
| frame_limits | 14.141 | 1.788 | 16.410 | |
| gene_set_enrichment | 1.225 | 0.160 | 1.585 | |
| gene_set_enrichment_plot | 7.105 | 0.808 | 8.214 | |
| geom_spatial | 13.464 | 1.510 | 15.448 | |
| get_colors | 1.242 | 0.124 | 1.523 | |
| img_edit | 13.425 | 1.721 | 15.601 | |
| img_update | 13.388 | 1.428 | 15.395 | |
| img_update_all | 19.082 | 2.409 | 21.627 | |
| layer_boxplot | 3.215 | 0.460 | 3.995 | |
| layer_stat_cor | 1.074 | 0.088 | 1.315 | |
| layer_stat_cor_plot | 4.382 | 0.688 | 5.430 | |
| locate_images | 0.000 | 0.000 | 0.001 | |
| read10xVisiumAnalysis | 0 | 0 | 0 | |
| read10xVisiumWrapper | 0 | 0 | 0 | |
| registration_block_cor | 3.677 | 0.277 | 3.955 | |
| registration_model | 0.686 | 0.019 | 0.705 | |
| registration_pseudobulk | 0.574 | 0.011 | 0.585 | |
| registration_stats_anova | 2.808 | 0.112 | 2.922 | |
| registration_stats_enrichment | 2.919 | 0.039 | 2.957 | |
| registration_stats_pairwise | 2.721 | 0.020 | 2.740 | |
| registration_wrapper | 4.249 | 0.082 | 4.331 | |
| run_app | 0.000 | 0.002 | 0.001 | |
| sce_to_spe | 14.009 | 1.450 | 16.066 | |
| sig_genes_extract | 2.589 | 0.940 | 3.879 | |
| sig_genes_extract_all | 3.169 | 0.375 | 3.878 | |
| sort_clusters | 0.005 | 0.004 | 0.010 | |
| vis_clus | 21.884 | 3.354 | 25.712 | |