| Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:36 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 1026/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| imcRtools 1.10.0 (landing page) Daniel Schulz
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the imcRtools package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: imcRtools |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imcRtools_1.10.0.tar.gz |
| StartedAt: 2024-05-06 22:20:28 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 22:26:51 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 383.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: imcRtools.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imcRtools_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/imcRtools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imcRtools/DESCRIPTION’ ... OK
* this is package ‘imcRtools’ version ‘1.10.0’
* 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) aggregateNeighbors.Rd:52: Lost braces; missing escapes or markup?
52 | \code{summarize_by = "metadata"} or "{statistic}_aggregatedExpression" when
| ^
checkRd: (-1) testInteractions.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
* 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 40.675 0.482 41.158
read_steinbock 7.729 1.813 7.365
* 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:
`actual`: FALSE
`expected`: TRUE
── Failure ('test_countInteractions.R:396:5'): countInteractions function works ──
all(cur_out$ct[!is.na(cur_out$ct)] == 1) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test_integration_interactions.R:351:5'): testInteractions gives same results as neighbouRhood ──
dat_p$p_gt[!is.na(imcRtools_classic$ct)] not equal to imcRtools_classic_perm$p_gt[!is.na(imcRtools_classic$ct)].
1/22 mismatches
[8] 0.881 - 0.901 == -0.0198
[ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ]
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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/imcRtools.Rcheck/00check.log’
for details.
imcRtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL imcRtools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup"
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.
> 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':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, 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':
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("imcRtools")
[ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_aggregateNeighbors.R:36:5'): aggregateNeighbors function works ──
all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test_aggregateNeighbors.R:116:5'): aggregateNeighbors function works ──
all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test_aggregateNeighbors.R:545:5'): aggregateNeighbors function works ──
all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test_countInteractions.R:396:5'): countInteractions function works ──
all(cur_out$ct[!is.na(cur_out$ct)] == 1) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test_integration_interactions.R:351:5'): testInteractions gives same results as neighbouRhood ──
dat_p$p_gt[!is.na(imcRtools_classic$ct)] not equal to imcRtools_classic_perm$p_gt[!is.na(imcRtools_classic$ct)].
1/22 mismatches
[8] 0.881 - 0.901 == -0.0198
[ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ]
Error: Test failures
Execution halted
imcRtools.Rcheck/imcRtools-Ex.timings
| name | user | system | elapsed | |
| aggregateNeighbors | 0.302 | 0.016 | 0.318 | |
| binAcrossPixels | 0.368 | 0.034 | 0.393 | |
| buildSpatialGraph | 3.233 | 0.201 | 3.337 | |
| countInteractions | 0.225 | 0.009 | 0.235 | |
| detectCommunity | 0.535 | 0.017 | 0.553 | |
| detectSpatialContext | 0.548 | 0.006 | 0.554 | |
| filterPixels | 0.735 | 0.079 | 0.800 | |
| filterSpatialContext | 0.930 | 0.010 | 0.942 | |
| findBorderCells | 0.118 | 0.003 | 0.121 | |
| minDistToCells | 0.759 | 0.016 | 0.772 | |
| patchDetection | 0.760 | 0.019 | 0.778 | |
| patchSize | 0.839 | 0.005 | 0.840 | |
| plotSpatial | 1.556 | 0.041 | 1.598 | |
| plotSpatialContext | 0.994 | 0.013 | 1.009 | |
| plotSpotHeatmap | 0.215 | 0.026 | 0.227 | |
| readImagefromTXT | 0.165 | 0.064 | 0.119 | |
| readSCEfromTXT | 0.129 | 0.024 | 0.139 | |
| read_cpout | 0.374 | 0.119 | 0.414 | |
| read_steinbock | 7.729 | 1.813 | 7.365 | |
| show_cpout_features | 0.060 | 0.027 | 0.087 | |
| testInteractions | 40.675 | 0.482 | 41.158 | |