Maddy Griswold
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/GeomxTools |
| git_branch: RELEASE_3_20 |
| git_last_commit: 234c5d0 |
| git_last_commit_date: 2024-10-29 10:55:05 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:34 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 840/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeomxTools 3.10.0 (landing page) Maddy Griswold
| 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 | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the GeomxTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeomxTools.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: GeomxTools |
| Version: 3.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeomxTools_3.10.0.tar.gz |
| StartedAt: 2025-04-01 20:29:46 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 20:49:50 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 1203.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeomxTools.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeomxTools_3.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeomxTools.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.10.0’
* 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 ‘GeomxTools’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.3Mb
sub-directories of 1Mb or more:
extdata 18.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
aggregateCounts: no visible binding for global variable ‘TargetName’
hkNorm: no visible binding for global variable ‘TargetName’
mixedModelDE: multiple local function definitions for ‘deFunc’ with
different formal arguments
qgrubbs: no visible global function definition for ‘qtable’
readPKCFile: no visible binding for global variable ‘RTS_ID’
readPKCFile: no visible binding for global variable ‘Module’
setGrubbsFlags: no visible binding for global variable ‘TargetName’
setGrubbsFlags : <anonymous>: no visible binding for global variable
‘Module’
setProbeRatioFlags: no visible binding for global variable ‘TargetName’
setTargetFlags: no visible global function definition for ‘analtye’
subtractBackground : <anonymous>: no visible binding for global
variable ‘Module’
setSignatureFuncs<-,NanoStringGeoMxSet-character: no visible global
function definition for ‘setSigFuncs<-’
signatureScores,NanoStringGeoMxSet: no visible global function
definition for ‘assayDataElement2’
signatureScores,NanoStringGeoMxSet: no visible global function
definition for ‘.sigCalc’
Undefined global functions or variables:
.sigCalc Module RTS_ID TargetName analtye assayDataElement2 qtable
setSigFuncs<-
* 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
mixedModelDE 66.128 1.237 68.333
readNanoStringGeoMxSet 51.593 5.535 57.605
normalize-NanoStringGeoMxSet-method 52.396 0.984 0.196
NanoStringGeoMxSet-class 24.171 1.661 26.014
writeNanoStringGeoMxSet 22.422 1.779 24.486
setQCFlags-NanoStringGeoMxSet-method 14.563 0.253 14.712
setBioProbeQCFlags 13.356 0.316 13.515
readPKCFile 10.720 1.654 12.400
aggregateCounts 10.960 0.156 11.158
as.SpatialExperiment 5.992 0.284 6.276
* 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:
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_GeoMxSet_probeCollapse.R:61:3'): test that collapsed probe count is equal to the geomean of probes for each target ──
sum(matches) == nrow(aggTestData@assayData$exprs) * numDCC is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]
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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/GeomxTools.Rcheck/00check.log’
for details.
GeomxTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeomxTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘GeomxTools’ ... ** 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 (GeomxTools)
GeomxTools.Rcheck/tests/testthat.Rout.fail
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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(GeomxTools)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: NanoStringNCTools
Loading required package: S4Vectors
Loading required package: stats4
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: ggplot2
>
> test_check("GeomxTools")
Attaching package: 'EnvStats'
The following objects are masked from 'package:stats':
predict, predict.lm
Coercing raw data, it is NOT recommended to use Seurat's normalization for GeoMx data.
Loading required package: SeuratObject
Loading required package: sp
'SeuratObject' was built under R 4.4.0 but the current version is
4.4.3; it is recomended that you reinstall 'SeuratObject' as the ABI
for R may have changed
'SeuratObject' was built with package 'Matrix' 1.7.0 but the current
version is 1.7.3; it is recomended that you reinstall 'SeuratObject' as
the ABI for 'Matrix' may have changed
Attaching package: 'SeuratObject'
The following object is masked from 'package:S4Vectors':
intersect
The following object is masked from 'package:BiocGenerics':
intersect
The following objects are masked from 'package:base':
intersect, t
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following object is masked from 'package:EnvStats':
iqr
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
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
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:sp':
%over%
Loading required package: GenomeInfoDb
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:Seurat':
Assays
The following object is masked from 'package:SeuratObject':
Assays
Attaching package: 'SingleCellExperiment'
The following object is masked from 'package:NanoStringNCTools':
weights<-
Loading required package: lme4
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'lmerTest'
The following object is masked from 'package:lme4':
lmer
The following object is masked from 'package:stats':
step
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
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[ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_GeoMxSet_probeCollapse.R:61:3'): test that collapsed probe count is equal to the geomean of probes for each target ──
sum(matches) == nrow(aggTestData@assayData$exprs) * numDCC is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]
Error: Test failures
Execution halted
GeomxTools.Rcheck/GeomxTools-Ex.timings
| name | user | system | elapsed | |
| NanoStringGeoMxSet-class | 24.171 | 1.661 | 26.014 | |
| aggregateCounts | 10.960 | 0.156 | 11.158 | |
| as.Seurat | 3.647 | 0.111 | 3.759 | |
| as.SpatialExperiment | 5.992 | 0.284 | 6.276 | |
| checkQCFlags-NanoStringGeoMxSet-method | 0.082 | 0.002 | 0.084 | |
| checkQCFlags | 0.100 | 0.005 | 0.104 | |
| computeNormalizationFactors | 0.008 | 0.001 | 0.011 | |
| countsShiftedByOne | 0.033 | 0.003 | 0.038 | |
| logtBase | 0.000 | 0.001 | 0.000 | |
| mixedModelDE | 66.128 | 1.237 | 68.333 | |
| ngeoMean | 0.000 | 0.000 | 0.001 | |
| ngeoSD | 0.000 | 0.001 | 0.000 | |
| normalize-NanoStringGeoMxSet-method | 52.396 | 0.984 | 0.196 | |
| plotConcordance | 3.990 | 0.330 | 4.335 | |
| plotNormFactorConcordance | 1.859 | 0.024 | 1.888 | |
| qcProteinSignal | 0.110 | 0.012 | 0.123 | |
| qcProteinSignalNames | 0.012 | 0.001 | 0.014 | |
| readDccFile | 0.520 | 0.026 | 0.550 | |
| readNanoStringGeoMxSet | 51.593 | 5.535 | 57.605 | |
| readPKCFile | 10.720 | 1.654 | 12.400 | |
| setBackgroundQCFlags | 0.141 | 0.003 | 0.145 | |
| setBioProbeQCFlags | 13.356 | 0.316 | 13.515 | |
| setGeoMxQCFlags | 0.101 | 0.004 | 0.105 | |
| setQCFlags-NanoStringGeoMxSet-method | 14.563 | 0.253 | 14.712 | |
| setSegmentQCFlags | 0.177 | 0.003 | 0.181 | |
| setSeqQCFlags | 0.129 | 0.003 | 0.132 | |
| shiftCountsOne | 0.098 | 0.007 | 0.106 | |
| summarizeNegatives | 0.685 | 0.016 | 0.701 | |
| writeNanoStringGeoMxSet | 22.422 | 1.779 | 24.486 | |