Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-06 13:05:59 -0500 (Mon, 06 Dec 2021).

CHECK results for hca on machv2

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: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 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    TIMEOUT  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: hca
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hca.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hca_1.2.0.tar.gz
StartedAt: 2021-12-05 15:27:58 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 15:30:31 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 152.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: hca.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hca.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hca_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/hca.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ... ERROR
Running examples in ‘hca-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bundles
> ### Title: HCA Bundle Querying
> ### Aliases: bundles bundles_facets bundles_default_columns bundles_detail
> 
> ### ** Examples
> 
> title <- paste(
+     "Tabula Muris: Transcriptomic characterization of 20 organs and",
+     "tissues from Mus musculus at single cell resolution"
+ )
> filters <- filters( projectTitle = list(is = title) )
> bundles(filters = filters)
# A tibble: 1,000 × 6
   projectTitle        genusSpecies samples    files bundleUuid   bundleVersion 
   <chr>               <chr>        <chr>      <lis> <chr>        <chr>         
 1 Tabula Muris: Tran… Mus musculus 3_38_F_Ma… <chr… 00004ffa-a7… 2019-08-01T20…
 2 Tabula Muris: Tran… Mus musculus 3_10_M_Br… <chr… 00007f4c-13… 2019-08-01T20…
 3 Tabula Muris: Tran… Mus musculus 3_8_M_Tra… <chr… 0000984f-3f… 2019-08-01T20…
 4 Tabula Muris: Tran… Mus musculus 3_57_F_Ma… <chr… 00031982-f8… 2019-08-01T20…
 5 Tabula Muris: Tran… Mus musculus 3_8_M_Spl… <chr… 0004846a-81… 2019-08-01T20…
 6 Tabula Muris: Tran… Mus musculus 3_9_M_Liv… <chr… 000598de-22… 2019-08-01T20…
 7 Tabula Muris: Tran… Mus musculus 3_10_M_Ki… <chr… 00071db7-72… 2019-08-01T20…
 8 Tabula Muris: Tran… Mus musculus 3_38_F_Bl… <chr… 00073cfb-c3… 2019-08-01T20…
 9 Tabula Muris: Tran… Mus musculus 3_57_F_Ma… <chr… 00075c23-ee… 2019-08-01T20…
10 Tabula Muris: Tran… Mus musculus 3_39_F_To… <chr… 0008b864-59… 2019-08-01T20…
# … with 990 more rows
> 
> bundles_facets()
Error in .hca_GET(index_path) : Internal Server Error (HTTP 500).
Calls: bundles_facets ... bundles -> .index_GET -> .hca_GET -> stop_for_status
Execution halted
* 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:
  requesting manifest
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_bundles.R:2:5): 'bundles()' works with small size and default arguments ──
  <http_500/http_error/error/condition>
  Error in `.hca_GET(index_path)`: Internal Server Error (HTTP 500).
  Backtrace:
      █
   1. └─hca::bundles(size = 4) test_bundles.R:2:4
   2.   └─hca:::.index_GET(...)
   3.     └─hca:::.hca_GET(index_path)
   4.       └─httr::stop_for_status(response)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 155 ]
  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
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/hca.Rcheck/00check.log’
for details.


Installation output

hca.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hca
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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")
requesting manifest
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_bundles.R:2:5): 'bundles()' works with small size and default arguments ──
<http_500/http_error/error/condition>
Error in `.hca_GET(index_path)`: Internal Server Error (HTTP 500).
Backtrace:
    █
 1. └─hca::bundles(size = 4) test_bundles.R:2:4
 2.   └─hca:::.index_GET(...)
 3.     └─hca:::.hca_GET(index_path)
 4.       └─httr::stop_for_status(response)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 155 ]
Error: Test failures
Execution halted

Example timings

hca.Rcheck/hca-Ex.timings

nameusersystemelapsed