| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:08 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| 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 847/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeomxTools 3.13.0 (landing page) Maddy Griswold
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | 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: 3.13.0 |
| 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_3.13.0.tar.gz |
| StartedAt: 2025-08-03 21:23:51 -0400 (Sun, 03 Aug 2025) |
| EndedAt: 2025-08-03 21:48:20 -0400 (Sun, 03 Aug 2025) |
| EllapsedTime: 1468.3 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_3.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GeomxTools.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘3.13.0’
* 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 19.3Mb
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 ... 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
normalize-NanoStringGeoMxSet-method 123.564 2.922 0.248
readNanoStringGeoMxSet 60.959 4.148 65.669
NanoStringGeoMxSet-class 22.537 1.524 24.283
writeNanoStringGeoMxSet 20.380 1.449 22.032
setBioProbeQCFlags 17.910 0.276 18.335
setQCFlags-NanoStringGeoMxSet-method 17.521 0.260 17.899
mixedModelDE 16.812 0.355 80.699
aggregateCounts 13.869 0.211 14.199
readPKCFile 12.490 1.349 13.971
as.SpatialExperiment 6.258 0.433 6.743
plotConcordance 5.156 0.259 5.452
* 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
‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/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)
GeomxTools.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13) -- "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':
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 under R 4.5.0 but the current version is
4.5.1; it is recomended that you reinstall 'SeuratObject' as the ABI
for R 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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[ 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
GeomxTools.Rcheck/GeomxTools-Ex.timings
| name | user | system | elapsed | |
| NanoStringGeoMxSet-class | 22.537 | 1.524 | 24.283 | |
| aggregateCounts | 13.869 | 0.211 | 14.199 | |
| as.Seurat | 4.147 | 0.151 | 4.335 | |
| as.SpatialExperiment | 6.258 | 0.433 | 6.743 | |
| checkQCFlags-NanoStringGeoMxSet-method | 0.068 | 0.002 | 0.071 | |
| checkQCFlags | 0.079 | 0.002 | 0.083 | |
| computeNormalizationFactors | 0.013 | 0.001 | 0.015 | |
| countsShiftedByOne | 0.059 | 0.001 | 0.061 | |
| logtBase | 0 | 0 | 0 | |
| mixedModelDE | 16.812 | 0.355 | 80.699 | |
| ngeoMean | 0 | 0 | 0 | |
| ngeoSD | 0 | 0 | 0 | |
| normalize-NanoStringGeoMxSet-method | 123.564 | 2.922 | 0.248 | |
| plotConcordance | 5.156 | 0.259 | 5.452 | |
| plotNormFactorConcordance | 2.505 | 0.023 | 2.540 | |
| qcProteinSignal | 0.141 | 0.016 | 0.157 | |
| qcProteinSignalNames | 0.012 | 0.001 | 0.013 | |
| readDccFile | 0.519 | 0.014 | 0.537 | |
| readNanoStringGeoMxSet | 60.959 | 4.148 | 65.669 | |
| readPKCFile | 12.490 | 1.349 | 13.971 | |
| setBackgroundQCFlags | 0.135 | 0.003 | 0.140 | |
| setBioProbeQCFlags | 17.910 | 0.276 | 18.335 | |
| setGeoMxQCFlags | 0.080 | 0.003 | 0.084 | |
| setQCFlags-NanoStringGeoMxSet-method | 17.521 | 0.260 | 17.899 | |
| setSegmentQCFlags | 0.169 | 0.003 | 0.173 | |
| setSeqQCFlags | 0.124 | 0.003 | 0.127 | |
| shiftCountsOne | 0.086 | 0.003 | 0.089 | |
| summarizeNegatives | 0.768 | 0.027 | 0.800 | |
| writeNanoStringGeoMxSet | 20.380 | 1.449 | 22.032 | |