Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:04:47 -0500 (Fri, 26 Nov 2021).

CHECK results for censcyt on nebbiolo2

To the developers/maintainers of the censcyt package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/censcyt.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 278/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
censcyt 1.2.0  (landing page)
Reto Gerber
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/censcyt
git_branch: RELEASE_3_14
git_last_commit: b70a2f8
git_last_commit_date: 2021-10-26 13:05:50 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: censcyt
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:censcyt.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings censcyt_1.2.0.tar.gz
StartedAt: 2021-11-25 08:43:06 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 08:48:41 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 335.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: censcyt.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:censcyt.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings censcyt_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/censcyt.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 ‘censcyt/DESCRIPTION’ ... OK
* this is package ‘censcyt’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘censcyt’ 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 ... NOTE
mean_residual_life_imputation: no visible binding for global variable
  ‘hazard’
Undefined global functions or variables:
  hazard
* 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
censcyt 21.841  0.316  22.156
* 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:
  Backtrace:
      █
   1. └─censcyt:::test_testDA_censoredGLMM(method) test-testDA_censoredGLMM.R:47:2
   2.   ├─base::suppressWarnings(...) test-testDA_censoredGLMM.R:24:2
   3.   │ └─base::withCallingHandlers(...)
   4.   ├─base::suppressMessages(...) test-testDA_censoredGLMM.R:24:2
   5.   │ └─base::withCallingHandlers(...)
   6.   └─censcyt::testDA_censoredGLMM(...) test-testDA_censoredGLMM.R:24:2
   7.     └─censcyt:::maybe_parallel_lapply(...)
   8.       ├─BiocParallel::bplapply(X, FUN, BPPARAM = BPPARAM)
   9.       └─BiocParallel::bplapply(X, FUN, BPPARAM = BPPARAM)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 672 ]
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/censcyt.Rcheck/00check.log’
for details.


Installation output

censcyt.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘censcyt’ ...
** 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 (censcyt)

Tests output

censcyt.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(censcyt)
Loading required package: diffcyt

Attaching package: 'censcyt'

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

    createFormula

> 
> test_check("censcyt")
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-testDA_censoredGLMM.R:47:3): (code run outside of `test_that()`) ──
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 4
  6 unevaluated and other errors
  first remote error: $ operator is invalid for atomic vectors
Backtrace:
    █
 1. └─censcyt:::test_testDA_censoredGLMM(method) test-testDA_censoredGLMM.R:47:2
 2.   ├─base::suppressWarnings(...) test-testDA_censoredGLMM.R:24:2
 3.   │ └─base::withCallingHandlers(...)
 4.   ├─base::suppressMessages(...) test-testDA_censoredGLMM.R:24:2
 5.   │ └─base::withCallingHandlers(...)
 6.   └─censcyt::testDA_censoredGLMM(...) test-testDA_censoredGLMM.R:24:2
 7.     └─censcyt:::maybe_parallel_lapply(...)
 8.       ├─BiocParallel::bplapply(X, FUN, BPPARAM = BPPARAM)
 9.       └─BiocParallel::bplapply(X, FUN, BPPARAM = BPPARAM)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 672 ]
Error: Test failures
Execution halted

Example timings

censcyt.Rcheck/censcyt-Ex.timings

nameusersystemelapsed
censcyt21.841 0.31622.156
conditional_multiple_imputation0.4170.0010.417
createFormula0.0040.0000.004
simulate_multicluster0.4780.0670.548
simulate_singlecluster0.1250.0000.126
testDA_censoredGLMM3.2950.0083.303