| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-13 11:40:16 -0400 (Mon, 13 May 2024).
| 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" | 4663 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4394 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4425 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 1972/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialFeatureExperiment 1.7.0 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | NA | ||||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the SpatialFeatureExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialFeatureExperiment.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SpatialFeatureExperiment |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.7.0.tar.gz |
| StartedAt: 2024-05-11 12:35:25 -0400 (Sat, 11 May 2024) |
| EndedAt: 2024-05-11 13:09:34 -0400 (Sat, 11 May 2024) |
| EllapsedTime: 2049.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpatialFeatureExperiment.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialFeatureExperiment’ 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 ... WARNING
'::' or ':::' import not declared from: ‘Biobase’
Unexported objects imported by ':::' calls:
‘S4Vectors:::disableValidity’ ‘SpatialExperiment:::.get_img_idx’
‘spdep:::minmax.listw’
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
.no_raw_bytes: no visible binding for global variable ‘xoa_version’
.no_raw_bytes: no visible binding for global variable ‘major_version’
.no_raw_bytes: no visible binding for global variable ‘minor_version’
.no_raw_bytes: no visible binding for global variable
‘instrument_version’
.seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to
‘assays_sfe_out’
.seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to
‘sfe_out’
.seu_to_sfe : <anonymous>: no visible global function definition for
‘reducedDim<-’
.seu_to_sfe : <anonymous>: no visible global function definition for
‘slot<-’
.seu_to_sfe : <anonymous>: no visible global function definition for
‘altExp<-’
.seu_to_sfe: no visible binding for '<<-' assignment to ‘obj_list_test’
addTxTech: no visible binding for global variable ‘gene_col’
addTxTech: no visible binding for global variable ‘cell_col’
addTxTech: no visible binding for global variable ‘fn’
formatTxTech: no visible binding for global variable ‘gene_col’
formatTxTech: no visible binding for global variable ‘cell_col’
formatTxTech: no visible binding for global variable ‘fn’
readXenium: no visible binding for global variable ‘xoa_version’
readXenium: no visible binding for global variable ‘major_version’
readXenium: no visible binding for global variable ‘minor_version’
readXenium: no visible binding for global variable ‘instrument_version’
reducedDimFeatureData<-: no visible global function definition for
‘reducedDim<-’
Undefined global functions or variables:
altExp<- cell_col fn gene_col instrument_version major_version
minor_version reducedDim<- slot<- xoa_version
Consider adding
importFrom("methods", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SpatialFeatureExperiment-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: formatTxTech
> ### Title: Read and process transcript spots for specific commercial
> ### technologies
> ### Aliases: formatTxTech addTxTech
>
> ### ** Examples
>
> library(SFEData)
> fp <- tempdir()
> dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
Error: record not found in database
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:
Backtrace:
▆
1. └─SFEData::XeniumOutput("v2", file_path = file.path(fp, "xenium_test")) at test-read.R:727:5
2. ├─ds[[id, force = force, verbose = verbose]]
3. └─ds[[id, force = force, verbose = verbose]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
── Error ('test-utils.R:56:1'): (code run outside of `test_that()`) ────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-utils.R:56:1
[ FAIL 20 | WARN 2 | SKIP 2 | PASS 812 ]
Error: Test failures
Execution halted
* 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 ERRORs, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SpatialFeatureExperiment’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘toSpatialFeatureExperiment’ with signature ‘"Seurat"’: no definition for class “Seurat” Creating a generic function for ‘NROW’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘NCOL’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘saveRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘readRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’ ** help *** installing help indices ** 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 (SpatialFeatureExperiment)
SpatialFeatureExperiment.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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(SpatialFeatureExperiment)
Attaching package: 'SpatialFeatureExperiment'
The following object is masked from 'package:base':
scale
>
> test_check("SpatialFeatureExperiment")
Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
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 objects are masked from 'package:Matrix':
expand, unname
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
Loading required package: scuttle
Loading required package: ggplot2
Attaching package: 'ggplot2'
The following object is masked from 'package:SpatialFeatureExperiment':
unit
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
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see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
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see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> Constructing cell polygons
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 7521734 bytes (7.2 MB)
==================================================
downloaded 7.2 MB
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_spatial.tar.gz'
Content type 'application/x-tar' length 7806681 bytes (7.4 MB)
==================================================
downloaded 7.4 MB
terra 1.7.71
Attaching package: 'terra'
The following objects are masked from 'package:SummarizedExperiment':
distance, nearest, shift, trim, values, values<-, width
The following objects are masked from 'package:GenomicRanges':
distance, gaps, nearest, shift, trim, values, values<-, width
The following objects are masked from 'package:IRanges':
distance, gaps, nearest, shift, trim, width
The following objects are masked from 'package:S4Vectors':
values, values<-, width
The following object is masked from 'package:BiocGenerics':
width
The following objects are masked from 'package:SpatialFeatureExperiment':
centroids, crop, origin, rotate
The following objects are masked from 'package:testthat':
compare, describe
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
BioFormats library version 7.3.0
Attaching package: 'EBImage'
The following objects are masked from 'package:terra':
flip, rotate
The following object is masked from 'package:SummarizedExperiment':
resize
The following object is masked from 'package:Biobase':
channel
The following objects are masked from 'package:GenomicRanges':
resize, tile
The following objects are masked from 'package:IRanges':
resize, tile
The following objects are masked from 'package:SpatialFeatureExperiment':
affine, rotate, translate, transpose
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Testing dist_type none style W
Testing dist_type idw style W
Testing dist_type exp style W
Testing dist_type dpd style W
Testing dist_type idw style raw
Testing dist_type idw style W
Testing dist_type idw style B
Testing dist_type idw style C
Testing dist_type idw style U
Testing dist_type idw style minmax
Testing dist_type idw style S
Testing dist_type none style W
Testing dist_type idw style W
Testing dist_type exp style W
Testing dist_type dpd style W
Testing dist_type idw style raw
Testing dist_type idw style W
Testing dist_type idw style B
Testing dist_type idw style C
Testing dist_type idw style U
Testing dist_type idw style minmax
Testing dist_type idw style S
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 10785331 bytes (10.3 MB)
==================================================
downloaded 10.3 MB
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_spatial.tar.gz'
Content type 'application/x-tar' length 8531653 bytes (8.1 MB)
==================================================
downloaded 8.1 MB
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/hdf5s_micron_space.parquet
Removing 3 cells with area less than 15
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/multi/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/multi/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/multi/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 3 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/small/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/small/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/small/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/image/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/image/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/image/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cellpose/vizgen_cellbound_Cellpose
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/cellpose/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /private/tmp/RtmpuUkXQN/cellpose/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/empty/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/empty/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/empty/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 34 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/all/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/all/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpuUkXQN/all/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound
>>> 2 `.parquet` files exist:
/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/cool_cell_boundaries.parquet
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound_Cellpose
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> File cell_boundaries_sf.parquet found
>>> File cell_boundaries_sf.parquet found
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
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>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpuUkXQN/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
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>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'dgCMatrix'
updateObjectFromSlots(object = 'dgCMatrix' class = 'dgCMatrix')
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'numeric'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
[updateObject] Validating the updated object ... OK
heuristic updateObjectFromSlots, method 1
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] CompressedGRangesList object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of PartitioningByEnd object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 20 | WARN 2 | SKIP 2 | PASS 812 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• gdalParquetAvailable() is not TRUE (2): 'test-formatTxSpots.R:113:5',
'test-formatTxSpots.R:138:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-formatTxSpots.R:50:5'): Format MERFISH transcript spots for colGeometries ──
<Rcpp::exception/C++Error/error/condition>
Error: Cannot open "/private/tmp/RtmpuUkXQN/vizgen_test/vizgen_cellbound/tx_in_cells/NCAM1_spots.parquet"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats.
Backtrace:
▆
1. ├─sf::st_read(fn) at test-formatTxSpots.R:50:5
2. └─sf:::st_read.character(fn)
3. └─sf:::CPL_read_ogr(...)
── Error ('test-formatTxSpots.R:107:5'): Format CosMX spots for colGeometry, multiple z-planes ──
<Rcpp::exception/C++Error/error/condition>
Error: Cannot open "/private/tmp/RtmpuUkXQN/cosmx_test/cosmx/tx_spots/6330403K07Rik_spots_z0.parquet"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats.
Backtrace:
▆
1. ├─sf::st_read(fn) at test-formatTxSpots.R:107:5
2. └─sf:::st_read.character(fn)
3. └─sf:::CPL_read_ogr(...)
── Error ('test-formatTxSpots.R:130:5'): Error message when Parquet driver is unavailable ──
Error: record not found in database
Backtrace:
▆
1. └─SFEData::XeniumOutput("v2", file_path = file.path(fp, "xenium_test")) at test-formatTxSpots.R:130:5
2. ├─ds[[id, force = force, verbose = verbose]]
3. └─ds[[id, force = force, verbose = verbose]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
── Error ('test-formatTxSpots.R:161:5'): Add subset of spots, multiple files in tx spots output ──
Error in `readSelectTx(file, gene_select, z, z_option)`: GDAL Parquet driver is required to selectively read genes.
Backtrace:
▆
1. └─SpatialFeatureExperiment::addSelectTx(...) at test-formatTxSpots.R:161:5
2. └─SpatialFeatureExperiment::readSelectTx(...)
── Error ('test-geometry_operation.R:258:5'): Crop 3D geometry ─────────────────
Error in ``.rowNamesDF<-`(x, value = value)`: duplicate 'row.names' are not allowed
Backtrace:
▆
1. └─SpatialFeatureExperiment::readCosMX(...) at test-geometry_operation.R:258:5
2. └─SpatialFeatureExperiment::addTxTech(...)
3. └─SpatialFeatureExperiment::addTxSpots(...)
4. └─SpatialFeatureExperiment::formatTxSpots(...)
5. └─SpatialFeatureExperiment:::.read_tx_output(...)
6. └─base::lapply(...)
7. └─SpatialFeatureExperiment (local) FUN(X[[i]], ...)
8. └─base::`rownames<-`(`*tmp*`, value = x[[gene_col]])
9. ├─base::`row.names<-`(`*tmp*`, value = value)
10. └─base::`row.names<-.data.frame`(`*tmp*`, value = value)
11. └─base::`.rowNamesDF<-`(x, value = value)
── Error ('test-geometry_operation.R:829:5'): Transformation when there's 3D geometry ──
Error in ``.rowNamesDF<-`(x, value = value)`: duplicate 'row.names' are not allowed
Backtrace:
▆
1. └─SpatialFeatureExperiment::readCosMX(...) at test-geometry_operation.R:829:5
2. └─SpatialFeatureExperiment::addTxTech(...)
3. └─SpatialFeatureExperiment::addTxSpots(...)
4. └─SpatialFeatureExperiment::formatTxSpots(...)
5. └─SpatialFeatureExperiment:::.read_tx_output(...)
6. └─base::lapply(...)
7. └─SpatialFeatureExperiment (local) FUN(X[[i]], ...)
8. └─base::`rownames<-`(`*tmp*`, value = x[[gene_col]])
9. ├─base::`row.names<-`(`*tmp*`, value = value)
10. └─base::`row.names<-.data.frame`(`*tmp*`, value = value)
11. └─base::`.rowNamesDF<-`(x, value = value)
── Error ('test-geometry_operation.R:868:1'): (code run outside of `test_that()`) ──
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput(file_path = file.path(fp, "xenium_test")) at test-geometry_operation.R:868:1
── Error ('test-image.R:16:1'): (code run outside of `test_that()`) ────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-image.R:16:1
── Error ('test-read.R:546:5'): readXenium, XOA v1 ─────────────────────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-read.R:546:5
── Error ('test-read.R:577:5'): readXenium XOA v1, image not found ─────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-read.R:577:5
── Error ('test-read.R:587:5'): readXenium XOA v1, use parquet files, with annoying arrow raw bytes ──
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-read.R:587:5
── Error ('test-read.R:602:5'): readXenium XOA v1 when only cell but not nuclei segmentation is available ──
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-read.R:602:5
── Error ('test-read.R:614:5'): readXenium XOA v1 read the output _sf.parquet next time ──
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-read.R:614:5
── Error ('test-read.R:627:5'): readXenium XOA v1 read cell metadata parquet when csv is absent ──
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-read.R:627:5
── Error ('test-read.R:639:5'): readXenium XOA v1 flip image ───────────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-read.R:639:5
── Error ('test-read.R:657:5'): readXenium XOA v2, normal stuff ────────────────
Error: record not found in database
Backtrace:
▆
1. └─SFEData::XeniumOutput("v2", file_path = file.path(fp, "xenium_test")) at test-read.R:657:5
2. ├─ds[[id, force = force, verbose = verbose]]
3. └─ds[[id, force = force, verbose = verbose]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
── Error ('test-read.R:687:5'): readXenium XOA v2, somes images not found ──────
Error: record not found in database
Backtrace:
▆
1. └─SFEData::XeniumOutput("v2", file_path = file.path(fp, "xenium_test")) at test-read.R:687:5
2. ├─ds[[id, force = force, verbose = verbose]]
3. └─ds[[id, force = force, verbose = verbose]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
── Error ('test-read.R:696:5'): readXenium XOA v2, use csv files ───────────────
Error: record not found in database
Backtrace:
▆
1. └─SFEData::XeniumOutput("v2", file_path = file.path(fp, "xenium_test")) at test-read.R:696:5
2. ├─ds[[id, force = force, verbose = verbose]]
3. └─ds[[id, force = force, verbose = verbose]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
── Error ('test-read.R:727:5'): readXenium, flip image ─────────────────────────
Error: record not found in database
Backtrace:
▆
1. └─SFEData::XeniumOutput("v2", file_path = file.path(fp, "xenium_test")) at test-read.R:727:5
2. ├─ds[[id, force = force, verbose = verbose]]
3. └─ds[[id, force = force, verbose = verbose]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
── Error ('test-utils.R:56:1'): (code run outside of `test_that()`) ────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
▆
1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-utils.R:56:1
[ FAIL 20 | WARN 2 | SKIP 2 | PASS 812 ]
Error: Test failures
Execution halted
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
| name | user | system | elapsed | |
| SFE-image | 11.395 | 2.802 | 18.017 | |
| SFE-transform | 7.731 | 0.503 | 9.792 | |
| SpatRasterImage | 0.000 | 0.001 | 0.001 | |
| SpatialFeatureExperiment-coercion | 6.758 | 0.113 | 7.978 | |
| SpatialFeatureExperiment-subset | 4.015 | 0.255 | 5.169 | |
| SpatialFeatureExperiment | 1.792 | 0.025 | 2.219 | |
| addVisiumSpotPoly | 6.446 | 0.095 | 7.578 | |
| aggBboxes | 0.000 | 0.000 | 0.001 | |
| annotGeometries | 3.614 | 0.258 | 4.684 | |
| annotOp | 3.743 | 0.236 | 4.860 | |
| annotPred | 3.704 | 0.275 | 7.720 | |
| annotSummary | 4.020 | 0.262 | 4.993 | |
| bbox-SpatialFeatureExperiment-method | 3.587 | 0.232 | 4.575 | |
| bbox_center | 0.001 | 0.001 | 0.001 | |
| cbind-SpatialFeatureExperiment-method | 9.517 | 0.499 | 12.183 | |
| changeSampleIDs | 4.030 | 0.268 | 5.256 | |
| colFeatureData | 5.627 | 0.360 | 7.395 | |
| colGeometries | 4.009 | 0.228 | 5.125 | |
| crop | 7.298 | 0.273 | 9.052 | |
| df2sf | 0.027 | 0.006 | 0.039 | |
| dimGeometries | 12.815 | 0.542 | 16.228 | |
| findSpatialNeighbors-SpatialFeatureExperiment-method | 9.879 | 0.501 | 12.385 | |
| findVisiumGraph | 9.586 | 0.485 | 12.059 | |
| formatTxSpots | 33.832 | 1.883 | 45.738 | |