Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-06 11:35:31 -0400 (Fri, 06 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 823/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 3.4.0  (landing page)
Nicole Ortogero
Snapshot Date: 2023-10-05 14:00:15 -0400 (Thu, 05 Oct 2023)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: RELEASE_3_17
git_last_commit: 776a43c
git_last_commit_date: 2023-04-25 11:26:17 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    ERROR  skippedskipped

CHECK results for GeomxTools on nebbiolo1


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: 3.4.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GeomxTools_3.4.0.tar.gz
StartedAt: 2023-10-05 21:35:07 -0400 (Thu, 05 Oct 2023)
EndedAt: 2023-10-05 21:58:29 -0400 (Thu, 05 Oct 2023)
EllapsedTime: 1402.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GeomxTools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GeomxTools_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeomxTools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘3.4.0’
* 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 13.5Mb
  sub-directories of 1Mb or more:
    extdata  12.7Mb
* 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 Module RTS_ID TargetName analtye assayDataElement2 qtable
  setSigFuncs<-
* checking Rd files ... WARNING
checkRd: (5) NanoStringGeoMxSet-class.Rd:109-112: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:113-116: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:117-120: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:121-124: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:125-128: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:129-132: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:133-136: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:137-140: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:141-144: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:145-149: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:150-154: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:163-166: \item in \describe must have non-empty label
* 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                         62.162  0.716  63.287
normalize-NanoStringGeoMxSet-method  48.788  0.600   0.157
readNanoStringGeoMxSet               40.772  0.664  41.438
NanoStringGeoMxSet-class             17.357  0.628  18.029
writeNanoStringGeoMxSet              16.263  0.384  16.647
setQCFlags-NanoStringGeoMxSet-method 14.477  0.076  14.547
setBioProbeQCFlags                   14.436  0.048  14.478
aggregateCounts                      11.317  0.196  11.514
readPKCFile                           8.996  0.163   9.161
as.SpatialExperiment                  5.989  0.308   6.297
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GeomxTools.Rcheck/00check.log’
for details.

Installation output

GeomxTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GeomxTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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':

    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, 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':

    I, expand.grid, unname

Loading required package: ggplot2
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
> 
> test_check("GeomxTools")

Attaching package: 'EnvStats'

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

    predict, predict.lm

Attaching SeuratObject
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
Loading required package: GenomeInfoDb

Attaching package: 'SummarizedExperiment'

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

    Assays

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

    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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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')
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boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 290 ]
> 
> proc.time()
   user  system elapsed 
589.428   8.532 622.376

Example timings

GeomxTools.Rcheck/GeomxTools-Ex.timings

nameusersystemelapsed
NanoStringGeoMxSet-class17.357 0.62818.029
aggregateCounts11.317 0.19611.514
as.Seurat2.9940.0803.074
as.SpatialExperiment5.9890.3086.297
checkQCFlags-NanoStringGeoMxSet-method0.0630.0040.066
checkQCFlags0.0730.0120.085
computeNormalizationFactors0.0180.0000.019
countsShiftedByOne0.0610.0040.065
logtBase000
mixedModelDE62.162 0.71663.287
ngeoMean0.0010.0000.001
ngeoSD000
normalize-NanoStringGeoMxSet-method48.788 0.600 0.157
plotConcordance4.1780.1484.326
plotNormFactorConcordance2.3080.0122.320
qcProteinSignal0.2410.0040.245
qcProteinSignalNames0.0120.0000.012
readDccFile0.3900.0160.406
readNanoStringGeoMxSet40.772 0.66441.438
readPKCFile8.9960.1639.161
setBackgroundQCFlags0.1250.0000.125
setBioProbeQCFlags14.436 0.04814.478
setGeoMxQCFlags0.0780.0000.079
setQCFlags-NanoStringGeoMxSet-method14.477 0.07614.547
setSegmentQCFlags0.1510.0040.156
setSeqQCFlags0.1030.0000.104
shiftCountsOne0.0780.0040.083
summarizeNegatives0.6490.0000.649
writeNanoStringGeoMxSet16.263 0.38416.647