Multiple platform build/check report for BioC 3.20 - CHECK results for tidySpatialExperiment on palomino4

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4666
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4401
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4428
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: tidySpatialExperiment

Version: 1.1.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tidySpatialExperiment.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings tidySpatialExperiment_1.1.0.tar.gz

StartedAt: 2024-05-18 05:56:34 -0400 (Sat, 18 May 2024)

EndedAt: 2024-05-18 06:01:36 -0400 (Sat, 18 May 2024)

EllapsedTime: 301.4 seconds

RetCode: 0

Status: OK

CheckDir: tidySpatialExperiment.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tidySpatialExperiment.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings tidySpatialExperiment_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/tidySpatialExperiment.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'tidySpatialExperiment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tidySpatialExperiment' version '1.1.0'
* 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 whether package 'tidySpatialExperiment' 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
select_helper: no visible global function definition for 'all_of'
join_features,SpatialExperiment: no visible binding for global variable
  'index'
Undefined global functions or variables:
  all_of index
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
aggregate_cells 5.28   0.25    6.21
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/tidySpatialExperiment.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL tidySpatialExperiment
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'tidySpatialExperiment' ...
** using staged installation
** R
** 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 (tidySpatialExperiment)


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(tidySpatialExperiment)
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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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

Loading required package: tidySingleCellExperiment

Attaching package: 'tidySpatialExperiment'

The following object is masked from 'package:tidySingleCellExperiment':

    unnest_single_cell_experiment

> 
> test_check("tidySpatialExperiment")

rd10xV> dir <- system.file(
rd10xV+   file.path("extdata", "10xVisium"), 
rd10xV+   package = "SpatialExperiment")

rd10xV> sample_ids <- c("section1", "section2")

rd10xV> samples <- file.path(dir, sample_ids, "outs")

rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"              

rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json"    "tissue_lowres_image.png"  
[3] "tissue_positions_list.csv"

rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "F:/biocbuild/bbs-3.20-bioc/R/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"

rd10xV> (spe <- read10xVisium(samples, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# [90mFeatures=50 | Cells=99 | Assays=counts[0m
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
rd10xV> samples2 <- file.path(dir, sample_ids)

rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# [90mFeatures=50 | Cells=99 | Assays=counts[0m
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # tabulate number of spots mapped to tissue
rd10xV> cd <- colData(spe)

rd10xV> table(
rd10xV+   in_tissue = cd$in_tissue, 
rd10xV+   sample_id = cd$sample_id)
         sample_id
in_tissue section1 section2
    FALSE       28       27
    TRUE        22       22

rd10xV> # view available images
rd10xV> imgData(spe)
DataFrame with 2 rows and 4 columns
    sample_id    image_id   data scaleFactor
  <character> <character> <list>   <numeric>
1    section1      lowres   ####   0.0510334
2    section2      lowres   ####   0.0510334

rd10xV> dir <- system.file(
rd10xV+   file.path("extdata", "10xVisium"), 
rd10xV+   package = "SpatialExperiment")

rd10xV> sample_ids <- c("section1", "section2")

rd10xV> samples <- file.path(dir, sample_ids, "outs")

rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"              

rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json"    "tissue_lowres_image.png"  
[3] "tissue_positions_list.csv"

rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "F:/biocbuild/bbs-3.20-bioc/R/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"

rd10xV> (spe <- read10xVisium(samples, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# [90mFeatures=50 | Cells=99 | Assays=counts[0m
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
rd10xV> samples2 <- file.path(dir, sample_ids)

rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# [90mFeatures=50 | Cells=99 | Assays=counts[0m
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # tabulate number of spots mapped to tissue
rd10xV> cd <- colData(spe)

rd10xV> table(
rd10xV+   in_tissue = cd$in_tissue, 
rd10xV+   sample_id = cd$sample_id)
         sample_id
in_tissue section1 section2
    FALSE       28       27
    TRUE        22       22

rd10xV> # view available images
rd10xV> imgData(spe)
DataFrame with 2 rows and 4 columns
    sample_id    image_id   data scaleFactor
  <character> <character> <list>   <numeric>
1    section1      lowres   ####   0.0510334
2    section2      lowres   ####   0.0510334

rd10xV> dir <- system.file(
rd10xV+   file.path("extdata", "10xVisium"), 
rd10xV+   package = "SpatialExperiment")

rd10xV> sample_ids <- c("section1", "section2")

rd10xV> samples <- file.path(dir, sample_ids, "outs")

rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"              

rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json"    "tissue_lowres_image.png"  
[3] "tissue_positions_list.csv"

rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "F:/biocbuild/bbs-3.20-bioc/R/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"

rd10xV> (spe <- read10xVisium(samples, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# [90mFeatures=50 | Cells=99 | Assays=counts[0m
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
rd10xV> samples2 <- file.path(dir, sample_ids)

rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
# A SpatialExperiment-tibble abstraction: 99 × 7
# [90mFeatures=50 | Cells=99 | Assays=counts[0m
   .cell              in_tissue array_row array_col sample_id pxl_col_in_fullres
   <chr>              <lgl>         <int>     <int> <chr>                  <int>
 1 AAACAACGAATAGTTC-1 FALSE             0        16 section1                2312
 2 AAACAAGTATCTCCCA-1 TRUE             50       102 section1                8230
 3 AAACAATCTACTAGCA-1 TRUE              3        43 section1                4170
 4 AAACACCAATAACTGC-1 TRUE             59        19 section1                2519
 5 AAACAGAGCGACTCCT-1 TRUE             14        94 section1                7679
 6 AAACAGCTTTCAGAAG-1 FALSE            43         9 section1                1831
 7 AAACAGGGTCTATATT-1 FALSE            47        13 section1                2106
 8 AAACAGTGTTCCTGGG-1 FALSE            73        43 section1                4170
 9 AAACATGGTGAGAGGA-1 FALSE            62         0 section1                1212
10 AAACATTTCCCGGATT-1 FALSE            61        97 section1                7886
# ℹ 89 more rows
# ℹ 1 more variable: pxl_row_in_fullres <int>

rd10xV> # tabulate number of spots mapped to tissue
rd10xV> cd <- colData(spe)

rd10xV> table(
rd10xV+   in_tissue = cd$in_tissue, 
rd10xV+   sample_id = cd$sample_id)
         sample_id
in_tissue section1 section2
    FALSE       28       27
    TRUE        22       22

rd10xV> # view available images
rd10xV> imgData(spe)
DataFrame with 2 rows and 4 columns
    sample_id    image_id   data scaleFactor
  <character> <character> <list>   <numeric>
1    section1      lowres   ####   0.0510334
2    section2      lowres   ####   0.0510334
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  25.31    2.21   26.42

name	user	system	elapsed
aggregate_cells	5.28	0.25	6.21
arrange	2.74	0.08	2.82
as_tibble	2.49	0.05	2.56
bind_cols	2.62	0.11	2.74
bind_rows	2.63	0.03	2.71
count	2.51	0.12	2.68
distinct	2.57	0.05	2.64
ellipse	2.68	0.05	2.78
extract	2.44	0.03	2.55
filter	2.49	0.06	2.61
formatting	2.25	0.06	2.34
ggplot	2.31	0.11	2.47
glimpse	2.0	0.1	2.1
group_by	2.12	0.10	2.25
inner_join	2.75	0.05	2.86
join_features	2.28	0.06	2.43
left_join	2.33	0.08	2.43
mutate	2.65	0.06	2.72
nest	2.13	0.07	2.23
pivot_longer	2.34	0.04	2.43
plot_ly	2.39	0.10	2.49
pull	2.20	0.08	2.36
rectangle	2.28	0.06	2.37
rename	2.39	0.10	2.48
right_join	3.20	0.12	3.34
rowwise	1.97	0.02	1.98
sample_n	2.33	0.08	2.45
select	2.12	0.11	2.27
separate	2.25	0.04	2.31
slice	2.08	0.08	2.17
summarise	2.27	0.14	2.44
tbl_format_header	0	0	0
unite	2.50	0.05	2.61
unnest	2.61	0.08	2.69

CHECK results for tidySpatialExperiment on palomino4

Summary

Command output

Installation output

Tests output

Example timings