Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:53 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for GeomxTools on nebbiolo1


To the developers/maintainers of the GeomxTools package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 764/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 2.1.0  (landing page)
Nicole Ortogero
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: master
git_last_commit: f786ad8
git_last_commit_date: 2021-10-26 13:06:34 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeomxTools
Version: 2.1.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeomxTools_2.1.0.tar.gz
StartedAt: 2022-01-21 19:22:38 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 19:35:41 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 783.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GeomxTools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeomxTools_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GeomxTools.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* this is package ‘GeomxTools’ version ‘2.1.0’
* 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  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* 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
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’
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 TargetName assayDataElement2 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
readNanoStringGeoMxSet               41.604  0.496  42.100
setQCFlags-NanoStringGeoMxSet-method 38.918  0.088  38.999
setBioProbeQCFlags                   38.460  0.096  38.546
mixedModelDE                         20.341  2.653  15.183
NanoStringGeoMxSet-class             16.498  0.792  17.352
writeNanoStringGeoMxSet              15.159  0.240  15.401
aggregateCounts                      15.215  0.004  15.222
readPKCFile                           9.112  0.055   9.167
* 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 0 | SKIP 0 | PASS 148 ]
  
  ══ 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(...) test_de.R:38:0
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 148 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/GeomxTools.Rcheck/00check.log’
for details.


Installation output

GeomxTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GeomxTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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, 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 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

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 ?isSingular
boundary (singular) fit: see ?isSingular
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boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 148 ]

══ 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(...) test_de.R:38:0
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 148 ]
Error: Test failures
Execution halted

Example timings

GeomxTools.Rcheck/GeomxTools-Ex.timings

nameusersystemelapsed
NanoStringGeoMxSet-class16.498 0.79217.352
aggregateCounts15.215 0.00415.222
checkQCFlags-NanoStringGeoMxSet-method0.0550.0000.055
checkQCFlags0.0720.0000.073
countsShiftedByOne0.0440.0120.057
logtBase000
mixedModelDE20.341 2.65315.183
ngeoMean0.0010.0000.000
ngeoSD000
normalize-NanoStringGeoMxSet-method1.6690.4570.147
readDccFile3.7840.0683.853
readNanoStringGeoMxSet41.604 0.49642.100
readPKCFile9.1120.0559.167
setBackgroundQCFlags0.1690.0000.169
setBioProbeQCFlags38.460 0.09638.546
setGeoMxQCFlags0.0580.0040.062
setQCFlags-NanoStringGeoMxSet-method38.918 0.08838.999
setSegmentQCFlags0.2320.0040.236
setSeqQCFlags0.0890.0000.089
shiftCountsOne0.0600.0120.072
summarizeNegatives0.5900.0080.598
writeNanoStringGeoMxSet15.159 0.24015.401