Marcel Ramos
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/VisiumIO |
| git_branch: RELEASE_3_20 |
| git_last_commit: 6f8771a |
| git_last_commit_date: 2024-10-29 11:26:46 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 2252/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VisiumIO 1.2.0 (landing page) Marcel Ramos
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the VisiumIO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VisiumIO.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: VisiumIO |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VisiumIO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VisiumIO_1.2.0.tar.gz |
| StartedAt: 2024-12-21 13:08:01 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 13:11:26 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 205.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VisiumIO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VisiumIO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VisiumIO_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/VisiumIO.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VisiumIO/DESCRIPTION’ ... OK
* this is package ‘VisiumIO’ version ‘1.2.0’
* 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 ‘VisiumIO’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.file_or_filelist: no visible global function definition for ‘TENxH5’
.file_or_filelist: no visible global function definition for
‘TENxFileList’
.find_file_or_dir: no visible global function definition for ‘TENxH5’
.find_file_or_dir: no visible global function definition for
‘TENxFileList’
TENxSpatialList: no visible global function definition for
‘TENxFileList’
TENxVisium: no visible global function definition for ‘TENxH5’
TENxVisium: no visible global function definition for ‘TENxFileList’
TENxVisiumHD: no visible global function definition for ‘TENxH5’
TENxVisiumHD: no visible global function definition for ‘TENxFileList’
Undefined global functions or variables:
TENxFileList TENxH5
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/VisiumIO.Rcheck/00check.log’
for details.
VisiumIO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VisiumIO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘VisiumIO’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 (VisiumIO)
VisiumIO.Rcheck/tests/tinytest.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.
> if (requireNamespace("tinytest", quietly = TRUE))
+ tinytest::test_package("VisiumIO")
Loading required package: TENxIO
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, saveRDS, 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_TENxSpatialList-class.R.. 0 tests
test_TENxSpatialList-class.R.. 0 tests
test_TENxSpatialList-class.R.. 1 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 2 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 3 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 4 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 5 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 6 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 6 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 7 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 7 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 8 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 8 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 9 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 10 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 10 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 10 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 11 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 12 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 13 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 14 tests [0;32mOK[0m
test_TENxSpatialList-class.R.. 15 tests [0;32mOK[0m [0;34m0.3s[0m
test_TENxSpaticalCSV.R........ 0 tests
test_TENxSpaticalCSV.R........ 1 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 1 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 1 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 2 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 3 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 4 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 5 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 6 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 6 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 6 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 6 tests [0;32mOK[0m
test_TENxSpaticalCSV.R........ 7 tests [0;32mOK[0m [0;34m1.0s[0m
test_TENxVisium-class.R....... 0 tests
test_TENxVisium-class.R....... 0 tests
test_TENxVisium-class.R....... 1 tests [0;32mOK[0m
test_TENxVisium-class.R....... 2 tests [0;32mOK[0m
test_TENxVisium-class.R....... 3 tests [0;32mOK[0m
test_TENxVisium-class.R....... 3 tests [0;32mOK[0m
test_TENxVisium-class.R....... 4 tests [0;32mOK[0m
test_TENxVisium-class.R....... 5 tests [0;32mOK[0m
test_TENxVisium-class.R....... 5 tests [0;32mOK[0m
test_TENxVisium-class.R....... 6 tests [0;32mOK[0m
test_TENxVisium-class.R....... 7 tests [0;32mOK[0m
test_TENxVisium-class.R....... 8 tests [0;32mOK[0m
test_TENxVisium-class.R....... 8 tests [0;32mOK[0m
test_TENxVisium-class.R....... 9 tests [0;32mOK[0m
test_TENxVisium-class.R....... 10 tests [0;32mOK[0m
test_TENxVisium-class.R....... 11 tests [0;32mOK[0m
test_TENxVisium-class.R....... 12 tests [0;32mOK[0m
test_TENxVisium-class.R....... 13 tests [0;32mOK[0m [0;34m1.6s[0m
test_TENxVisiumList-class.R... 0 tests
test_TENxVisiumList-class.R... 0 tests
test_TENxVisiumList-class.R... 1 tests [0;32mOK[0m
test_TENxVisiumList-class.R... 2 tests [0;32mOK[0m
test_TENxVisiumList-class.R... 3 tests [0;32mOK[0m
test_TENxVisiumList-class.R... 4 tests [0;32mOK[0m
test_TENxVisiumList-class.R... 4 tests [0;32mOK[0m
test_TENxVisiumList-class.R... 5 tests [0;32mOK[0m [0;34m1.1s[0m
All ok, 40 results (4.0s)
>
> proc.time()
user system elapsed
12.935 0.572 13.657
VisiumIO.Rcheck/VisiumIO-Ex.timings
| name | user | system | elapsed | |
| TENxSpatialCSV-class | 0.058 | 0.003 | 0.062 | |
| TENxSpatialList-class | 0.048 | 0.001 | 0.051 | |
| TENxSpatialParquet-class | 0.387 | 0.029 | 0.419 | |
| TENxVisium-class | 3.530 | 0.148 | 3.691 | |
| TENxVisiumHD-class | 1.818 | 0.085 | 1.912 | |
| TENxVisiumList-class | 0.729 | 0.022 | 0.756 | |
| compareBarcodes | 0.001 | 0.000 | 0.001 | |