| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:34 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
To the developers/maintainers of the imcRtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/imcRtools.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 975/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| imcRtools 1.7.0 (landing page) Nils Eling
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: imcRtools |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings imcRtools_1.7.0.tar.gz |
| StartedAt: 2023-06-06 00:23:02 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 00:54:50 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 1907.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: imcRtools.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings imcRtools_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/imcRtools.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘imcRtools/DESCRIPTION’ ... OK
* this is package ‘imcRtools’ 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 ‘imcRtools’ 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 R 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
testInteractions 208.465 1.949 204.987
read_steinbock 32.303 4.911 29.631
buildSpatialGraph 16.787 0.727 17.343
plotSpatial 7.596 0.199 7.809
* 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:
`cur_out <- plotSpotHeatmap(cur_sce, order_metals = FALSE, cluster_cols = TRUE)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:97:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, color = viridis::inferno(50))` produced warnings.
── Failure ('test_plotSpotHeatmap.R:98:5'): plotSpotHeatmap function works. ────
`... <- NULL` produced warnings.
── Failure ('test_plotSpotHeatmap.R:100:5'): plotSpotHeatmap function works. ───
`... <- NULL` produced warnings.
── Failure ('test_plotSpotHeatmap.R:102:5'): plotSpotHeatmap function works. ───
`cur_out <- plotSpotHeatmap(cur_sce, cellwidth = 5)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:103:5'): plotSpotHeatmap function works. ───
`... <- NULL` produced warnings.
[ FAIL 17 | WARN 1850 | SKIP 0 | PASS 2012 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘imcRtools.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.18-bioc/meat/imcRtools.Rcheck/00check.log’
for details.
imcRtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL imcRtools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘imcRtools’ ... ** 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 (imcRtools)
imcRtools.Rcheck/tests/testthat.Rout.fail
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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(imcRtools)
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, sort, 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
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
>
> test_check("imcRtools")
[ FAIL 17 | WARN 1850 | SKIP 0 | PASS 2012 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plotSpotHeatmap.R:8:5'): plotSpotHeatmap function works. ─────
`cur_out <- plotSpotHeatmap(cur_sce)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:21:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, log = FALSE)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:32:5'): plotSpotHeatmap function works. ────
`... <- NULL` produced warnings.
── Failure ('test_plotSpotHeatmap.R:43:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, threshold = 200)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:44:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, threshold = 0)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:45:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, log = FALSE, threshold = 200)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:56:5'): plotSpotHeatmap function works. ────
`cur_out_2 <- plotSpotHeatmap(cur_sce, log = TRUE, threshold = log10(200))` produced warnings.
── Failure ('test_plotSpotHeatmap.R:61:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, spot_id = "test_spot")` produced warnings.
── Failure ('test_plotSpotHeatmap.R:73:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, channel_id = "test_channel")` produced warnings.
── Failure ('test_plotSpotHeatmap.R:78:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, assay_type = "exprs", log = FALSE)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:93:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, order_metals = FALSE, cluster_rows = TRUE)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:95:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, order_metals = FALSE, cluster_cols = TRUE)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:97:5'): plotSpotHeatmap function works. ────
`cur_out <- plotSpotHeatmap(cur_sce, color = viridis::inferno(50))` produced warnings.
── Failure ('test_plotSpotHeatmap.R:98:5'): plotSpotHeatmap function works. ────
`... <- NULL` produced warnings.
── Failure ('test_plotSpotHeatmap.R:100:5'): plotSpotHeatmap function works. ───
`... <- NULL` produced warnings.
── Failure ('test_plotSpotHeatmap.R:102:5'): plotSpotHeatmap function works. ───
`cur_out <- plotSpotHeatmap(cur_sce, cellwidth = 5)` produced warnings.
── Failure ('test_plotSpotHeatmap.R:103:5'): plotSpotHeatmap function works. ───
`... <- NULL` produced warnings.
[ FAIL 17 | WARN 1850 | SKIP 0 | PASS 2012 ]
Error: Test failures
Execution halted
imcRtools.Rcheck/imcRtools-Ex.timings
| name | user | system | elapsed | |
| aggregateNeighbors | 1.542 | 0.132 | 1.674 | |
| binAcrossPixels | 1.652 | 0.128 | 1.752 | |
| buildSpatialGraph | 16.787 | 0.727 | 17.343 | |
| countInteractions | 1.117 | 0.012 | 1.126 | |
| detectCommunity | 1.717 | 0.027 | 1.749 | |
| detectSpatialContext | 3.059 | 0.008 | 3.073 | |
| filterPixels | 2.920 | 0.139 | 3.033 | |
| filterSpatialContext | 4.752 | 0.056 | 4.816 | |
| findBorderCells | 0.588 | 0.000 | 0.588 | |
| minDistToCells | 3.717 | 0.104 | 3.832 | |
| patchDetection | 3.887 | 0.040 | 3.927 | |
| patchSize | 1.862 | 0.016 | 1.868 | |
| plotSpatial | 7.596 | 0.199 | 7.809 | |
| plotSpatialContext | 4.830 | 0.072 | 4.909 | |
| plotSpotHeatmap | 1.088 | 0.104 | 1.162 | |
| readImagefromTXT | 0.498 | 0.153 | 0.453 | |
| readSCEfromTXT | 0.643 | 0.071 | 0.684 | |
| read_cpout | 1.729 | 0.408 | 1.961 | |
| read_steinbock | 32.303 | 4.911 | 29.631 | |
| show_cpout_features | 0.195 | 0.068 | 0.259 | |
| testInteractions | 208.465 | 1.949 | 204.987 | |