Maddy Griswold
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/GeomxTools |
| git_branch: RELEASE_3_21 |
| git_last_commit: b5554ad |
| git_last_commit_date: 2025-09-12 13:20:26 -0400 (Fri, 12 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:39 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 855/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeomxTools 3.12.1 (landing page) Maddy Griswold
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 3.12.1 |
| 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_3.12.1.tar.gz |
| StartedAt: 2025-09-23 04:10:30 -0400 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 04:50:30 -0400 (Tue, 23 Sep 2025) |
| EllapsedTime: 2400.2 seconds |
| RetCode: None |
| Status: TIMEOUT |
| 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_3.12.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeomxTools.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.12.1’
* 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 ... INFO
installed size is 19.4Mb
sub-directories of 1Mb or more:
extdata 18.5Mb
* 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’
readNanoStringGeoMxSet: no visible global function definition for
‘read.table’
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
read.table setSigFuncs<-
Consider adding
importFrom("utils", "read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
NanoStringGeoMxSet-class.Rd: ExpressionSet-class, AnnotatedDataFrame,
MIAME, SignatureSet, ExpressionSet
readPKCFile.Rd: DataFrame-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 162.997 3.057 180.106
normalize-NanoStringGeoMxSet-method 126.660 2.581 0.350
readNanoStringGeoMxSet 109.791 8.001 120.382
NanoStringGeoMxSet-class 41.950 2.766 45.228
writeNanoStringGeoMxSet 40.721 2.898 44.002
setQCFlags-NanoStringGeoMxSet-method 34.783 0.322 35.359
setBioProbeQCFlags 34.378 0.468 35.238
aggregateCounts 28.289 0.194 28.597
readPKCFile 23.501 2.914 27.726
plotConcordance 15.700 0.572 16.942
as.SpatialExperiment 12.678 0.613 13.911
as.Seurat 8.530 0.166 8.780
plotNormFactorConcordance 8.597 0.053 8.860
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
GeomxTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeomxTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘GeomxTools’ ... ** this is package ‘GeomxTools’ version ‘3.12.1’ ** 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
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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(GeomxTools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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':
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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
The following object is masked from 'package:base':
print.default
Loading required package: SeuratObject
Loading required package: sp
'SeuratObject' was built with package 'Matrix' 1.7.3 but the current
version is 1.7.4; 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: 'lme4'
The following object is masked from 'package:generics':
refit
Attaching package: 'lmerTest'
The following object is masked from 'package:lme4':
lmer
The following object is masked from 'package:stats':
step
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GeomxTools.Rcheck/GeomxTools-Ex.timings
| name | user | system | elapsed | |
| NanoStringGeoMxSet-class | 41.950 | 2.766 | 45.228 | |
| aggregateCounts | 28.289 | 0.194 | 28.597 | |
| as.Seurat | 8.530 | 0.166 | 8.780 | |
| as.SpatialExperiment | 12.678 | 0.613 | 13.911 | |
| checkQCFlags-NanoStringGeoMxSet-method | 0.104 | 0.003 | 0.107 | |
| checkQCFlags | 0.157 | 0.009 | 0.167 | |
| computeNormalizationFactors | 0.043 | 0.008 | 0.050 | |
| countsShiftedByOne | 0.111 | 0.003 | 0.114 | |
| logtBase | 0.000 | 0.000 | 0.001 | |
| mixedModelDE | 162.997 | 3.057 | 180.106 | |
| ngeoMean | 0.000 | 0.001 | 0.001 | |
| ngeoSD | 0.000 | 0.001 | 0.001 | |
| normalize-NanoStringGeoMxSet-method | 126.660 | 2.581 | 0.350 | |
| plotConcordance | 15.700 | 0.572 | 16.942 | |
| plotNormFactorConcordance | 8.597 | 0.053 | 8.860 | |
| qcProteinSignal | 0.320 | 0.039 | 0.362 | |
| qcProteinSignalNames | 0.033 | 0.001 | 0.036 | |
| readDccFile | 1.063 | 0.020 | 1.094 | |
| readNanoStringGeoMxSet | 109.791 | 8.001 | 120.382 | |
| readPKCFile | 23.501 | 2.914 | 27.726 | |
| setBackgroundQCFlags | 0.259 | 0.009 | 0.269 | |
| setBioProbeQCFlags | 34.378 | 0.468 | 35.238 | |
| setGeoMxQCFlags | 0.151 | 0.004 | 0.155 | |
| setQCFlags-NanoStringGeoMxSet-method | 34.783 | 0.322 | 35.359 | |
| setSegmentQCFlags | 0.329 | 0.004 | 0.335 | |
| setSeqQCFlags | 0.209 | 0.005 | 0.217 | |
| shiftCountsOne | 0.144 | 0.004 | 0.149 | |
| summarizeNegatives | 1.802 | 0.006 | 1.812 | |
| writeNanoStringGeoMxSet | 40.721 | 2.898 | 44.002 | |