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This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
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 378/430HostnameOS / ArchINSTALLBUILDCHECK
spatialLIBD 1.16.2  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-07-02 07:30 -0400 (Tue, 02 Jul 2024)
git_url: https://git.bioconductor.org/packages/spatialLIBD
git_branch: RELEASE_3_19
git_last_commit: c54a0e5
git_last_commit_date: 2024-05-24 13:36:48 -0400 (Fri, 24 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for spatialLIBD on nebbiolo1

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.

raw results


Summary

Package: spatialLIBD
Version: 1.16.2
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings spatialLIBD_1.16.2.tar.gz
StartedAt: 2024-07-02 12:06:10 -0400 (Tue, 02 Jul 2024)
EndedAt: 2024-07-02 12:26:13 -0400 (Tue, 02 Jul 2024)
EllapsedTime: 1202.6 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialLIBD.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings spatialLIBD_1.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/spatialLIBD.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘spatialLIBD/DESCRIPTION’ ... OK
* this is package ‘spatialLIBD’ version ‘1.16.2’
* 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 ‘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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
vis_gene       43.004  2.220  45.780
vis_clus       31.235  1.889  33.625
add_images     28.310  2.205  33.517
img_update_all 27.201  1.514  28.919
vis_grid_gene  25.869  2.126  28.558
vis_grid_clus  24.860  1.833  27.262
vis_clus_p     23.807  1.675  26.013
add_key        23.807  1.546  25.874
cluster_import 24.062  1.225  25.868
vis_gene_p     23.741  1.247  25.638
img_edit       23.380  1.447  25.339
check_spe      23.571  1.205  25.407
geom_spatial   23.322  1.132  25.128
cluster_export 23.054  1.377  25.027
frame_limits   22.329  1.484  24.412
sce_to_spe     22.238  1.478  24.332
img_update     22.348  1.252  24.121
* 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: OK


Installation output

spatialLIBD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL spatialLIBD
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘spatialLIBD’ ...
** 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)

Tests output

spatialLIBD.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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.

> 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 54.746   4.221  59.811 

Example timings

spatialLIBD.Rcheck/spatialLIBD-Ex.timings

nameusersystemelapsed
add10xVisiumAnalysis0.0010.0000.000
add_images28.310 2.20533.517
add_key23.807 1.54625.874
annotate_registered_clusters1.3120.1231.659
check_modeling_results1.1730.0971.483
check_sce3.3820.1073.670
check_sce_layer1.2260.0881.493
check_spe23.571 1.20525.407
cluster_export23.054 1.37725.027
cluster_import24.062 1.22525.868
enough_ram0.0060.0000.007
fetch_data1.2320.0761.532
frame_limits22.329 1.48424.412
gene_set_enrichment1.3170.1111.533
gene_set_enrichment_plot1.4310.1241.764
geom_spatial23.322 1.13225.128
get_colors1.2350.0801.524
img_edit23.380 1.44725.339
img_update22.348 1.25224.121
img_update_all27.201 1.51428.919
layer_boxplot3.0710.1653.641
layer_matrix_plot0.0100.0040.014
layer_stat_cor1.2090.0881.475
layer_stat_cor_plot1.1180.0561.352
locate_images000
read10xVisiumAnalysis000
read10xVisiumWrapper0.0000.0010.000
registration_block_cor3.8890.1864.076
registration_model0.8680.0040.872
registration_pseudobulk0.8000.0000.801
registration_stats_anova3.0270.0083.035
registration_stats_enrichment3.1540.0113.166
registration_stats_pairwise2.9930.0163.009
registration_wrapper4.3130.0124.325
run_app0.0010.0000.002
sce_to_spe22.238 1.47824.332
sig_genes_extract2.5700.7843.779
sig_genes_extract_all3.0180.1513.557
sort_clusters0.0030.0010.004
vis_clus31.235 1.88933.625
vis_clus_p23.807 1.67526.013
vis_gene43.004 2.22045.780
vis_gene_p23.741 1.24725.638
vis_grid_clus24.860 1.83327.262
vis_grid_gene25.869 2.12628.558