Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:05:27 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 muscat on nebbiolo2


To the developers/maintainers of the muscat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/muscat.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 1253/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
muscat 1.8.1  (landing page)
Helena L. Crowell
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/muscat
git_branch: RELEASE_3_14
git_last_commit: 06006c2
git_last_commit_date: 2022-01-14 03:51:16 -0500 (Fri, 14 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: muscat
Version: 1.8.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings muscat_1.8.1.tar.gz
StartedAt: 2022-01-20 08:35:09 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 08:42:48 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 459.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: muscat.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings muscat_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/muscat.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘muscat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscat’ version ‘1.8.1’
* 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 ‘muscat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
simData       10.657  0.152  10.810
mmDS          10.019  0.332  10.351
pbHeatmap      8.324  0.385   8.691
prepSim        5.736  0.160   5.896
aggregateData  4.631  0.684   5.315
* 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:
  TMB was built with Matrix version 1.3.4
  Current Matrix version is 1.4.0
  Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
  > 
  > test_check("muscat")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-resDS.R:66:5): resDS() - 'cpm = TRUE' ─────────────────────────
  all(u%%2 == 0 | is.na(u)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 550 ]
  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
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/muscat.Rcheck/00check.log’
for details.


Installation output

muscat.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL muscat
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘muscat’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** testing if installed package can be loaded from final location
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** testing if installed package keeps a record of temporary installation path
* DONE (muscat)

Tests output

muscat.Rcheck/tests/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(muscat)
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
> 
> test_check("muscat")
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-resDS.R:66:5): resDS() - 'cpm = TRUE' ─────────────────────────
all(u%%2 == 0 | is.na(u)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 550 ]
Error: Test failures
Execution halted

Example timings

muscat.Rcheck/muscat-Ex.timings

nameusersystemelapsed
aggregateData4.6310.6845.315
calcExprFreqs1.1000.0791.166
data0.0000.0000.001
mmDS10.019 0.33210.351
pbDS2.1710.0512.223
pbFlatten1.5460.0241.571
pbHeatmap8.3240.3858.691
pbMDS1.2050.0161.221
prepSCE0.8620.0480.910
prepSim5.7360.1605.896
resDS4.3270.0564.371
simData10.657 0.15210.810