Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:37 -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 hca on palomino3


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? 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 878/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hca 1.4.3  (landing page)
Martin Morgan
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/hca
git_branch: RELEASE_3_15
git_last_commit: 3995bfc
git_last_commit_date: 2022-07-21 10:59:05 -0400 (Thu, 21 Jul 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hca
Version: 1.4.3
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hca.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings hca_1.4.3.tar.gz
StartedAt: 2022-10-19 00:57:04 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 00:59:59 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 175.4 seconds
RetCode: 0
Status:   OK  
CheckDir: hca.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hca.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings hca_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/hca.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'hca/DESCRIPTION' ... OK
* this is package 'hca' version '1.4.3'
* 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 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
lol      21.54   0.92   30.72
files    10.22   0.20   24.85
projects  8.94   0.18   14.91
bundles   1.42   0.06    8.64
hca       0.42   0.00   10.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: OK


Installation output

hca.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL hca
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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(hca)

Attaching package: 'hca'

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

    summary

> 
> test_check("hca")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 157 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• manifest() generates an internal server 500 error, 7 February, 2022 (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 157 ]
> 
> proc.time()
   user  system elapsed 
   4.89    0.51   12.79 

Example timings

hca.Rcheck/hca-Ex.timings

nameusersystemelapsed
bundles1.420.068.64
catalogs000
files10.22 0.2024.85
filters000
hca 0.42 0.0010.83
list_hca0.610.221.53
lol21.54 0.9230.72
manifest-internal000
manifest000
projects 8.94 0.1814.91
samples1.440.022.92
summary0.220.022.48
tbl_hca0.550.001.31