Maddy Griswold
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:09 -0400 (Mon, 10 Mar 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" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| 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 | OK | 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: 2025-03-07 04:12:38 -0500 (Fri, 07 Mar 2025) |
| EndedAt: 2025-03-07 04:52:38 -0500 (Fri, 07 Mar 2025) |
| EllapsedTime: 2400.8 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_3.10.0.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: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.10.0’
* 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 152.451 3.176 165.557
readNanoStringGeoMxSet 89.992 4.432 99.727
NanoStringGeoMxSet-class 37.063 1.815 41.005
writeNanoStringGeoMxSet 34.758 1.776 46.700
setQCFlags-NanoStringGeoMxSet-method 35.557 0.254 36.747
setBioProbeQCFlags 34.892 0.375 35.998
aggregateCounts 28.518 0.304 29.229
readPKCFile 18.471 2.125 20.928
as.SpatialExperiment 11.062 0.433 11.859
plotConcordance 10.559 0.556 12.032
as.Seurat 7.874 0.178 8.109
plotNormFactorConcordance 5.772 0.050 6.544
* 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/4.4-x86_64/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
R version 4.4.3 (2025-02-28) -- "Trophy Case"
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
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 1.7.2; 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
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GeomxTools.Rcheck/GeomxTools-Ex.timings
| name | user | system | elapsed | |
| NanoStringGeoMxSet-class | 37.063 | 1.815 | 41.005 | |
| aggregateCounts | 28.518 | 0.304 | 29.229 | |
| as.Seurat | 7.874 | 0.178 | 8.109 | |
| as.SpatialExperiment | 11.062 | 0.433 | 11.859 | |
| checkQCFlags-NanoStringGeoMxSet-method | 0.102 | 0.002 | 0.105 | |
| checkQCFlags | 0.135 | 0.005 | 0.141 | |
| computeNormalizationFactors | 0.045 | 0.007 | 0.138 | |
| countsShiftedByOne | 0.091 | 0.003 | 0.094 | |
| logtBase | 0.000 | 0.000 | 0.001 | |
| mixedModelDE | 152.451 | 3.176 | 165.557 | |
| ngeoMean | 0.000 | 0.004 | 0.006 | |
| ngeoSD | 0.000 | 0.003 | 0.003 | |
| normalize-NanoStringGeoMxSet-method | 0.176 | 0.096 | 0.275 | |
| plotConcordance | 10.559 | 0.556 | 12.032 | |
| plotNormFactorConcordance | 5.772 | 0.050 | 6.544 | |
| qcProteinSignal | 0.327 | 0.040 | 0.381 | |
| qcProteinSignalNames | 0.033 | 0.002 | 0.036 | |
| readDccFile | 1.111 | 0.032 | 1.218 | |
| readNanoStringGeoMxSet | 89.992 | 4.432 | 99.727 | |
| readPKCFile | 18.471 | 2.125 | 20.928 | |
| setBackgroundQCFlags | 0.257 | 0.005 | 0.263 | |
| setBioProbeQCFlags | 34.892 | 0.375 | 35.998 | |
| setGeoMxQCFlags | 0.145 | 0.004 | 0.150 | |
| setQCFlags-NanoStringGeoMxSet-method | 35.557 | 0.254 | 36.747 | |
| setSegmentQCFlags | 0.337 | 0.005 | 0.348 | |
| setSeqQCFlags | 0.206 | 0.004 | 0.229 | |
| shiftCountsOne | 0.129 | 0.004 | 0.141 | |
| summarizeNegatives | 1.997 | 0.008 | 2.082 | |
| writeNanoStringGeoMxSet | 34.758 | 1.776 | 46.700 | |