Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:04:53 -0500 (Fri, 26 Nov 2021).

CHECK results for hca on nebbiolo2

To the developers/maintainers of the hca package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hca.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 854/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hca 1.2.0  (landing page)
Martin Morgan
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/hca
git_branch: RELEASE_3_14
git_last_commit: 83b5cdb
git_last_commit_date: 2021-10-26 13:07:17 -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: hca
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hca.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hca_1.2.0.tar.gz
StartedAt: 2021-11-25 09:45:14 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 09:47:59 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 165.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: hca.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hca.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hca_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/hca.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 ‘hca/DESCRIPTION’ ... OK
* this is package ‘hca’ version ‘1.2.0’
* 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 ‘hca’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
bundles  9.861  0.356  30.283
files    8.433  0.240  21.039
lol      4.854  0.188  15.255
projects 4.588  0.208  14.347
* 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:
  
      summary
  
  > 
  > test_check("hca")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_manifest.R:5:5): 'manifest()' works with default arguments ────
  nrow(test_manifest) > 0L is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 157 ]
  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/hca.Rcheck/00check.log’
for details.


Installation output

hca.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘hca’ ...
** using staged installation
** R
** 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 (hca)

Tests output

hca.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(hca)

Attaching package: 'hca'

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

    summary

> 
> test_check("hca")
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test_manifest.R:5:5): 'manifest()' works with default arguments ────
nrow(test_manifest) > 0L is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 157 ]
Error: Test failures
Execution halted

Example timings

hca.Rcheck/hca-Ex.timings

nameusersystemelapsed
bundles 9.861 0.35630.283
catalogs000
files 8.433 0.24021.039
filters0.0040.0000.004
hca0.2280.0124.875
lol 4.854 0.18815.255
manifest-internal0.0050.0000.005
manifest0.0000.0020.003
projects 4.588 0.20814.347
samples0.8580.0604.031
summary0.1870.0032.310
tbl_hca0.6110.0684.298