Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-15 12:06 -0400 (Mon, 15 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 852/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 3.13.1  (landing page)
Maddy Griswold
Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 2025)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: devel
git_last_commit: 8bb08d5
git_last_commit_date: 2025-09-12 13:22:55 -0400 (Fri, 12 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  

CHECK results for GeomxTools on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GeomxTools
Version: 3.13.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeomxTools_3.13.0.tar.gz
StartedAt: 2025-09-12 07:52:07 -0000 (Fri, 12 Sep 2025)
EndedAt: 2025-09-12 08:16:04 -0000 (Fri, 12 Sep 2025)
EllapsedTime: 1437.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GeomxTools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeomxTools_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeomxTools.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.13.0’
* 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 ... INFO
  installed size is 19.4Mb
  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 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 ... 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 ... 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                         93.207  1.431  95.611
normalize-NanoStringGeoMxSet-method  72.392  1.389   0.142
readNanoStringGeoMxSet               52.318  2.378  54.850
setBioProbeQCFlags                   21.359  0.671  22.076
NanoStringGeoMxSet-class             21.140  0.862  22.292
setQCFlags-NanoStringGeoMxSet-method 21.413  0.303  21.770
writeNanoStringGeoMxSet              19.040  0.344  19.428
aggregateCounts                      17.432  0.373  17.909
readPKCFile                          10.956  0.259  11.239
plotConcordance                       9.771  1.021  10.821
as.SpatialExperiment                  7.312  0.310   7.666
plotNormFactorConcordance             5.406  0.192   5.612
as.Seurat                             4.992  0.167   5.192
* 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:
  `expected`: TRUE 
  ── Failure ('test_protein.R:158:3'): Concordance plots are plotted ─────────────
  class(fig)[1] == "gg" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test_protein.R:210:3'): QC plots are plotted ──────────────────────
  class(fig)[1] == "gg" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 286 ]
  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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GeomxTools.Rcheck/00check.log’
for details.

Installation output

GeomxTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GeomxTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘GeomxTools’ ...
** this is package ‘GeomxTools’ version ‘3.13.0’
** 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)

Tests output

GeomxTools.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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':

    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

The following object is masked from 'package:base':

    print.default

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 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: Seqinfo

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

boundary (singular) fit: see help('isSingular')
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boundary (singular) fit: see help('isSingular')
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boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 286 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_protein.R:150:3'): Concordance plots are plotted ─────────────
class(fig)[1] == "gg" is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_protein.R:154:3'): Concordance plots are plotted ─────────────
class(fig)[1] == "gg" is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_protein.R:158:3'): Concordance plots are plotted ─────────────
class(fig)[1] == "gg" is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_protein.R:210:3'): QC plots are plotted ──────────────────────
class(fig)[1] == "gg" is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 4 | WARN 1 | SKIP 0 | PASS 286 ]
Error: Test failures
Execution halted

Example timings

GeomxTools.Rcheck/GeomxTools-Ex.timings

nameusersystemelapsed
NanoStringGeoMxSet-class21.140 0.86222.292
aggregateCounts17.432 0.37317.909
as.Seurat4.9920.1675.192
as.SpatialExperiment7.3120.3107.666
checkQCFlags-NanoStringGeoMxSet-method0.0580.0040.061
checkQCFlags0.0830.0040.087
computeNormalizationFactors0.0220.0000.024
countsShiftedByOne0.060.000.06
logtBase000
mixedModelDE93.207 1.43195.611
ngeoMean0.0010.0000.001
ngeoSD000
normalize-NanoStringGeoMxSet-method72.392 1.389 0.142
plotConcordance 9.771 1.02110.821
plotNormFactorConcordance5.4060.1925.612
qcProteinSignal0.2150.0040.219
qcProteinSignalNames0.0170.0000.017
readDccFile0.4790.0160.496
readNanoStringGeoMxSet52.318 2.37854.850
readPKCFile10.956 0.25911.239
setBackgroundQCFlags0.1440.0080.153
setBioProbeQCFlags21.359 0.67122.076
setGeoMxQCFlags0.0820.0000.082
setQCFlags-NanoStringGeoMxSet-method21.413 0.30321.770
setSegmentQCFlags0.1910.0000.191
setSeqQCFlags0.1170.0040.122
shiftCountsOne0.0690.0120.082
summarizeNegatives0.9440.0320.978
writeNanoStringGeoMxSet19.040 0.34419.428