Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-04 11:39:16 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 836/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 3.7.2  (landing page)
Maddy Griswold
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: devel
git_last_commit: b6d309a
git_last_commit_date: 2024-02-09 13:29:24 -0500 (Fri, 09 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for GeomxTools on merida1


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.

raw results

Summary

Package: GeomxTools
Version: 3.7.2
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_3.7.2.tar.gz
StartedAt: 2024-03-02 04:38:30 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 05:18:30 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 2400.5 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: GeomxTools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_3.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeomxTools.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.7.2’
* 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 R 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
normalize-NanoStringGeoMxSet-method  236.786  6.211   0.403
readNanoStringGeoMxSet                95.076  3.874 117.992
NanoStringGeoMxSet-class              37.740  1.527  45.679
mixedModelDE                          37.253  0.859 189.663
writeNanoStringGeoMxSet               35.358  1.600  69.700
setBioProbeQCFlags                    35.075  0.392  41.584
setQCFlags-NanoStringGeoMxSet-method  33.690  0.390  36.446
aggregateCounts                       28.759  0.369  33.949
readPKCFile                           18.814  1.488  23.542
as.SpatialExperiment                  12.421  0.587  14.816
plotConcordance                       10.740  0.630  14.174
as.Seurat                              8.655  0.263  11.135
plotNormFactorConcordance              5.660  0.064   7.144
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

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)

Tests output

GeomxTools.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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, 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

Attaching package: 'SeuratObject'

The following object is masked from 'package:S4Vectors':

    intersect

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

    intersect

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

    intersect

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')
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Example timings

GeomxTools.Rcheck/GeomxTools-Ex.timings

nameusersystemelapsed
NanoStringGeoMxSet-class37.740 1.52745.679
aggregateCounts28.759 0.36933.949
as.Seurat 8.655 0.26311.135
as.SpatialExperiment12.421 0.58714.816
checkQCFlags-NanoStringGeoMxSet-method0.1020.0040.113
checkQCFlags0.1450.0040.167
computeNormalizationFactors0.0390.0030.049
countsShiftedByOne0.1000.0030.111
logtBase0.0010.0000.001
mixedModelDE 37.253 0.859189.663
ngeoMean0.0000.0010.001
ngeoSD0.0000.0010.001
normalize-NanoStringGeoMxSet-method236.786 6.211 0.403
plotConcordance10.740 0.63014.174
plotNormFactorConcordance5.6600.0647.144
qcProteinSignal0.3180.0400.450
qcProteinSignalNames0.0330.0030.046
readDccFile1.0800.0281.468
readNanoStringGeoMxSet 95.076 3.874117.992
readPKCFile18.814 1.48823.542
setBackgroundQCFlags0.2480.0060.300
setBioProbeQCFlags35.075 0.39241.584
setGeoMxQCFlags0.1400.0050.166
setQCFlags-NanoStringGeoMxSet-method33.690 0.39036.446
setSegmentQCFlags0.3350.0110.418
setSeqQCFlags0.2020.0080.239
shiftCountsOne0.1250.0080.141
summarizeNegatives1.4990.0311.549
writeNanoStringGeoMxSet35.358 1.60069.700