##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialLIBD_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/spatialLIBD.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
 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
  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: add_images
> ### Title: Add non-standard images with the same dimensions as current ones
> ### Aliases: add_images
> 
> ### ** Examples
> 
> if (enough_ram()) {
+     ## Obtain the necessary data
+     if (!exists("spe")) spe <- fetch_data("spe")
+ 
+     ## Add an image
+     SpatialExperiment::imgData(add_images(
+         spe,
+         image_id_current = "lowres",
+         image_id = "lowres_aws",
+         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
+     ))
+ }
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Calls: fetch_data ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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:2:5
   2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
   3.   ├─methods::is(eh, "ExperimentHub")
   4.   └─ExperimentHub::ExperimentHub()
   5.     └─AnnotationHub::.Hub(...)
   6.       └─base::tryCatch(...)
   7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.             └─value[[3L]](cond)
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 25 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘TenX_data_download.Rmd’ using rmarkdown
--- finished re-building ‘TenX_data_download.Rmd’

--- re-building ‘guide_to_spatial_registration.Rmd’ using rmarkdown
--- finished re-building ‘guide_to_spatial_registration.Rmd’

--- re-building ‘multi_gene_plots.Rmd’ using rmarkdown

Quitting from multi_gene_plots.Rmd:81-85 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'multi_gene_plots.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘multi_gene_plots.Rmd’

--- re-building ‘spatialLIBD.Rmd’ using rmarkdown

Quitting from spatialLIBD.Rmd:202-205 [experiment_hub]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─ExperimentHub::ExperimentHub()
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spatialLIBD.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘spatialLIBD.Rmd’

SUMMARY: processing the following files failed:
  ‘multi_gene_plots.Rmd’ ‘spatialLIBD.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/spatialLIBD.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL spatialLIBD
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘spatialLIBD’ ...
** this is package ‘spatialLIBD’ version ‘1.22.0’
** 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)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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: Seqinfo
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")
Saving _problems/test-add_qc_metrics-4.R
Saving _problems/test-annotate_registered_cluster-3.R
Saving _problems/test-gene_set_enrichment-19.R
Saving _problems/test-layer_stat_cor_plot-4.R
Saving _problems/test-prep_stitched_data-4.R

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)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))

rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))

rgstr_> ## Pseudo-bulk by Cell Cycle
rgstr_> sce_pseudo <- registration_pseudobulk(
rgstr_+     sce,
rgstr_+     var_registration = "Cell_Cycle",
rgstr_+     var_sample_id = "sample_id",
rgstr_+     covars = c("age"),
rgstr_+     min_ncells = NULL
rgstr_+ )

rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 9 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 pseudo_sum_umi
               <character>            <character> <integer>      <numeric>
A_G0                    G0                      A         8        2946915
B_G0                    G0                      B        13        4922867
C_G0                    G0                      C         9        3398888
D_G0                    G0                      D         7        2630651
E_G0                    G0                      E        10        3761710
...                    ...                    ...       ...            ...
A_S                      S                      A        12        4516334
B_S                      S                      B         8        2960685
C_S                      S                      C         7        2595774
D_S                      S                      D        14        5233560
E_S                      S                      E        11        4151818

rgstr_> rowData(sce_pseudo)
DataFrame with 2000 rows and 3 columns
              gene_id   gene_name        gene_search
          <character> <character>        <character>
Gene_0001       ENSG1       gene1       gene1; ENSG1
Gene_0002       ENSG2       gene2       gene2; ENSG2
Gene_0003       ENSG3       gene3       gene3; ENSG3
Gene_0004       ENSG4       gene4       gene4; ENSG4
Gene_0005       ENSG5       gene5       gene5; ENSG5
...               ...         ...                ...
Gene_1996    ENSG1996    gene1996 gene1996; ENSG1996
Gene_1997    ENSG1997    gene1997 gene1997; ENSG1997
Gene_1998    ENSG1998    gene1998 gene1998; ENSG1998
Gene_1999    ENSG1999    gene1999 gene1999; ENSG1999
Gene_2000    ENSG2000    gene2000 gene2000; ENSG2000

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)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))

rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))

rgstr_> ## Pseudo-bulk by Cell Cycle
rgstr_> sce_pseudo <- registration_pseudobulk(
rgstr_+     sce,
rgstr_+     var_registration = "Cell_Cycle",
rgstr_+     var_sample_id = "sample_id",
rgstr_+     covars = c("age"),
rgstr_+     min_ncells = NULL
rgstr_+ )

rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 9 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 pseudo_sum_umi
               <character>            <character> <integer>      <numeric>
A_G0                    G0                      A         8        2946915
B_G0                    G0                      B        13        4922867
C_G0                    G0                      C         9        3398888
D_G0                    G0                      D         7        2630651
E_G0                    G0                      E        10        3761710
...                    ...                    ...       ...            ...
A_S                      S                      A        12        4516334
B_S                      S                      B         8        2960685
C_S                      S                      C         7        2595774
D_S                      S                      D        14        5233560
E_S                      S                      E        11        4151818

rgstr_> rowData(sce_pseudo)
DataFrame with 2000 rows and 3 columns
              gene_id   gene_name        gene_search
          <character> <character>        <character>
Gene_0001       ENSG1       gene1       gene1; ENSG1
Gene_0002       ENSG2       gene2       gene2; ENSG2
Gene_0003       ENSG3       gene3       gene3; ENSG3
Gene_0004       ENSG4       gene4       gene4; ENSG4
Gene_0005       ENSG5       gene5       gene5; ENSG5
...               ...         ...                ...
Gene_1996    ENSG1996    gene1996 gene1996; ENSG1996
Gene_1997    ENSG1997    gene1997 gene1997; ENSG1997
Gene_1998    ENSG1998    gene1998 gene1998; ENSG1998
Gene_1999    ENSG1999    gene1999 gene1999; ENSG1999
Gene_2000    ENSG2000    gene2000 gene2000; ENSG2000

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)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))

rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))

rgstr_> ## Pseudo-bulk by Cell Cycle
rgstr_> sce_pseudo <- registration_pseudobulk(
rgstr_+     sce,
rgstr_+     var_registration = "Cell_Cycle",
rgstr_+     var_sample_id = "sample_id",
rgstr_+     covars = c("age"),
rgstr_+     min_ncells = NULL
rgstr_+ )

rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 9 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 pseudo_sum_umi
               <character>            <character> <integer>      <numeric>
A_G0                    G0                      A         8        2946915
B_G0                    G0                      B        13        4922867
C_G0                    G0                      C         9        3398888
D_G0                    G0                      D         7        2630651
E_G0                    G0                      E        10        3761710
...                    ...                    ...       ...            ...
A_S                      S                      A        12        4516334
B_S                      S                      B         8        2960685
C_S                      S                      C         7        2595774
D_S                      S                      D        14        5233560
E_S                      S                      E        11        4151818

rgstr_> rowData(sce_pseudo)
DataFrame with 2000 rows and 3 columns
              gene_id   gene_name        gene_search
          <character> <character>        <character>
Gene_0001       ENSG1       gene1       gene1; ENSG1
Gene_0002       ENSG2       gene2       gene2; ENSG2
Gene_0003       ENSG3       gene3       gene3; ENSG3
Gene_0004       ENSG4       gene4       gene4; ENSG4
Gene_0005       ENSG5       gene5       gene5; ENSG5
...               ...         ...                ...
Gene_1996    ENSG1996    gene1996 gene1996; ENSG1996
Gene_1997    ENSG1997    gene1997 gene1997; ENSG1997
Gene_1998    ENSG1998    gene1998 gene1998; ENSG1998
Gene_1999    ENSG1999    gene1999 gene1999; ENSG1999
Gene_2000    ENSG2000    gene2000 gene2000; ENSG2000

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)
Saving _problems/test-sig_genes_extract-3.R
Saving _problems/test-vis_clus-4.R
Saving _problems/test-vis_gene-2.R
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 25 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-add_qc_metrics.R:4:9'): add_qc_metrics returns modified spe ────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data("spe") at test-add_qc_metrics.R:4:9
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
── Error ('test-annotate_registered_cluster.R:3:5'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data(type = "modeling_results") at test-annotate_registered_cluster.R:3:5
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
── Error ('test-gene_set_enrichment.R:19:5'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data(type = "modeling_results") at test-gene_set_enrichment.R:19:5
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
── Error ('test-layer_stat_cor_plot.R:4:5'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data(type = "modeling_results") at test-layer_stat_cor_plot.R:4:5
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
── Error ('test-prep_stitched_data.R:4:9'): prep_stitched_data ─────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data("spe") at test-prep_stitched_data.R:4:9
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
── Error ('test-sig_genes_extract.R:3:5'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data(type = "modeling_results") at test-sig_genes_extract.R:3:5
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
── Error ('test-vis_clus.R:4:9'): vis_clus ─────────────────────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data("spe") at test-vis_clus.R:4:9
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)
── Error ('test-vis_gene.R:2:5'): vis_gene ─────────────────────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data("spe") at test-vis_gene.R:2:5
 2.   ├─base::stopifnot(methods::is(eh, "ExperimentHub"))
 3.   ├─methods::is(eh, "ExperimentHub")
 4.   └─ExperimentHub::ExperimentHub()
 5.     └─AnnotationHub::.Hub(...)
 6.       └─base::tryCatch(...)
 7.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.             └─value[[3L]](cond)

[ FAIL 8 | WARN 0 | SKIP 0 | PASS 25 ]
Error:
! Test failures.
Execution halted