Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-02-27 11:35:49 -0500 (Tue, 27 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 839/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 3.6.2  (landing page)
Maddy Griswold
Snapshot Date: 2024-02-26 14:53:20 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: RELEASE_3_18
git_last_commit: fb59586
git_last_commit_date: 2024-02-09 13:23:59 -0500 (Fri, 09 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for GeomxTools on nebbiolo2


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: 3.6.2
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GeomxTools_3.6.2.tar.gz
StartedAt: 2024-02-26 23:22:31 -0500 (Mon, 26 Feb 2024)
EndedAt: 2024-02-26 23:46:04 -0500 (Mon, 26 Feb 2024)
EllapsedTime: 1413.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GeomxTools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GeomxTools_3.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GeomxTools.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.6.2’
* 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 19.4Mb
  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 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 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 analtye assayDataElement2 Module qtable RTS_ID setSigFuncs<-
  TargetName
* 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                         62.539  1.320  65.936
normalize-NanoStringGeoMxSet-method  50.519  1.658   0.122
readNanoStringGeoMxSet               41.930  1.867  43.800
NanoStringGeoMxSet-class             16.938  0.873  17.837
writeNanoStringGeoMxSet              15.877  0.448  16.331
setQCFlags-NanoStringGeoMxSet-method 14.671  0.151  14.817
setBioProbeQCFlags                   14.564  0.172  14.730
aggregateCounts                      11.787  0.164  11.951
readPKCFile                           7.986  0.063   8.051
as.SpatialExperiment                  5.598  0.279   5.879
plotConcordance                       4.629  0.492   5.122
* 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:
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_de.R:38:1'): test output p-value is as expected ────────────────
  <subscriptOutOfBoundsError/error/condition>
  Error in `mixedOuts["lsmeans", target]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test_de.R:38:1
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using ‘UTF-8’... OK
  ‘GeomxSet_coercions.Rmd’ using ‘UTF-8’... OK
  ‘Protein_in_GeomxTools.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GeomxTools.Rcheck/00check.log’
for details.


Installation output

GeomxTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GeomxTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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.fail


R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    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':

    expand.grid, I, unname

Loading required package: ggplot2
> 
> test_check("GeomxTools")
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' 1.6.3 but the current
version is 1.6.5; 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 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 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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Attaching package: 'EnvStats'

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

    iqr

The following objects are masked from 'package:stats':

    predict, predict.lm

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_de.R:38:1'): test output p-value is as expected ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `mixedOuts["lsmeans", target]`: subscript out of bounds
Backtrace:
    ▆
 1. └─testthat::expect_equal(...) at test_de.R:38:1
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 289 ]
Error: Test failures
Execution halted

Example timings

GeomxTools.Rcheck/GeomxTools-Ex.timings

nameusersystemelapsed
NanoStringGeoMxSet-class16.938 0.87317.837
aggregateCounts11.787 0.16411.951
as.Seurat3.5490.0633.614
as.SpatialExperiment5.5980.2795.879
checkQCFlags-NanoStringGeoMxSet-method0.0600.0040.065
checkQCFlags0.0800.0000.081
computeNormalizationFactors0.0100.0030.015
countsShiftedByOne0.0630.0000.064
logtBase0.0010.0000.000
mixedModelDE62.539 1.32065.936
ngeoMean000
ngeoSD000
normalize-NanoStringGeoMxSet-method50.519 1.658 0.122
plotConcordance4.6290.4925.122
plotNormFactorConcordance2.4440.1312.577
qcProteinSignal0.2460.0090.254
qcProteinSignalNames0.0090.0030.013
readDccFile0.4130.0090.422
readNanoStringGeoMxSet41.930 1.86743.800
readPKCFile7.9860.0638.051
setBackgroundQCFlags0.1200.0040.124
setBioProbeQCFlags14.564 0.17214.730
setGeoMxQCFlags0.0740.0120.087
setQCFlags-NanoStringGeoMxSet-method14.671 0.15114.817
setSegmentQCFlags0.1560.0000.156
setSeqQCFlags0.1120.0010.112
shiftCountsOne0.0770.0040.081
summarizeNegatives0.6760.0000.676
writeNanoStringGeoMxSet15.877 0.44816.331