Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:06:19 -0500 (Wed, 26 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" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 censcyt on tokay2


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: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
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 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:censcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings censcyt_1.2.0.tar.gz
StartedAt: 2022-01-25 17:06:16 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 17:14:14 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 478.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: censcyt.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:censcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings censcyt_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/censcyt.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
censcyt 16.05   1.55   17.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
censcyt 18.66   1.25    19.9
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      x
   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
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      x
   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: 2 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/censcyt.Rcheck/00check.log'
for details.


Installation output

censcyt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/censcyt_1.2.0.tar.gz && rm -rf censcyt.buildbin-libdir && mkdir censcyt.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=censcyt.buildbin-libdir censcyt_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL censcyt_1.2.0.zip && rm censcyt_1.2.0.tar.gz censcyt_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 59347  100 59347    0     0   385k      0 --:--:-- --:--:-- --:--:--  386k

install for i386

* installing *source* package 'censcyt' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'censcyt'
    finding HTML links ... done
    censcyt                                 html  
    finding level-2 HTML links ... done

    conditional_multiple_imputation         html  
    createFormula                           html  
    simulate_multicluster                   html  
    simulate_singlecluster                  html  
    testDA_censoredGLMM                     html  
** 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

install for x64

* installing *source* package 'censcyt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'censcyt' as censcyt_1.2.0.zip
* DONE (censcyt)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'censcyt' successfully unpacked and MD5 sums checked

Tests output

censcyt.Rcheck/tests_i386/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 672 ]

== 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: 7
  3 unevaluated and other errors
  first remote error: $ operator is invalid for atomic vectors
Backtrace:
    x
 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

censcyt.Rcheck/tests_x64/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-w64-mingw32/x64 (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")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 672 ]

== 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: 7
  3 unevaluated and other errors
  first remote error: $ operator is invalid for atomic vectors
Backtrace:
    x
 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/examples_i386/censcyt-Ex.timings

nameusersystemelapsed
censcyt16.05 1.5517.86
conditional_multiple_imputation0.330.000.32
createFormula0.000.020.02
simulate_multicluster0.620.120.78
simulate_singlecluster0.110.000.11
testDA_censoredGLMM2.480.002.48

censcyt.Rcheck/examples_x64/censcyt-Ex.timings

nameusersystemelapsed
censcyt18.66 1.2519.90
conditional_multiple_imputation0.520.000.56
createFormula000
simulate_multicluster0.780.140.92
simulate_singlecluster0.130.000.13
testDA_censoredGLMM3.250.013.26