Back to Multiple platform build/check report for BioC 3.15
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:19:58 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 AnVIL on nebbiolo1


To the developers/maintainers of the AnVIL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnVIL.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 67/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnVIL 1.8.8  (landing page)
Martin Morgan
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/AnVIL
git_branch: RELEASE_3_15
git_last_commit: a08a6ac
git_last_commit_date: 2022-10-11 19:37:36 -0400 (Tue, 11 Oct 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: AnVIL
Version: 1.8.8
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:AnVIL.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings AnVIL_1.8.8.tar.gz
StartedAt: 2022-10-18 18:33:41 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:34:20 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 39.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: AnVIL.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:AnVIL.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings AnVIL_1.8.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/AnVIL.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnVIL/DESCRIPTION’ ... OK
* this is package ‘AnVIL’ version ‘1.8.8’
* 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 ‘AnVIL’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘rapiclient:::build_op_url’ ‘rapiclient:::get_parameters’
  See the note in ?`:::` about the use of this operator.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  > 
  > test_check("AnVIL")
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 38 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • !gcloud_exists() is TRUE (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_api.R:25'): 'accept' defaults to */* ─────────────────────────
  .api_get_accept(op_def) not identical to httr::accept(produces).
  Component "headers": 1 string mismatch
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 38 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/AnVIL.Rcheck/00check.log’
for details.


Installation output

AnVIL.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘AnVIL’ ...
** 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 (AnVIL)

Tests output

AnVIL.Rcheck/tests/testthat.Rout.fail


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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(AnVIL)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("AnVIL")
[ FAIL 1 | WARN 0 | SKIP 3 | PASS 38 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• !gcloud_exists() is TRUE (3)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_api.R:25'): 'accept' defaults to */* ─────────────────────────
.api_get_accept(op_def) not identical to httr::accept(produces).
Component "headers": 1 string mismatch

[ FAIL 1 | WARN 0 | SKIP 3 | PASS 38 ]
Error: Test failures
Execution halted

Example timings

AnVIL.Rcheck/AnVIL-Ex.timings

nameusersystemelapsed
Response0.0080.0030.013
Service0.0150.0000.015
Services0.3070.0240.975
av0.0130.0040.017
avnotebooks0.0090.0030.012
avworkflow0.0100.0040.015
avworkflow_configuration0.0080.0130.020
avworkspace0.0000.0000.001
drs0.0020.0010.004
gcloud0.0070.0020.008
gsutil0.0090.0060.014
install0.1580.0050.564