Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:28 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 HPAStainR on nebbiolo2


To the developers/maintainers of the HPAStainR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HPAStainR.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 885/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAStainR 1.4.1  (landing page)
Tim O. Nieuwenhuis
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/HPAStainR
git_branch: RELEASE_3_14
git_last_commit: 70ebd09
git_last_commit_date: 2021-11-25 09:56:16 -0400 (Thu, 25 Nov 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    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: HPAStainR
Version: 1.4.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:HPAStainR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings HPAStainR_1.4.1.tar.gz
StartedAt: 2022-04-12 07:48:58 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:53:03 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 245.1 seconds
RetCode: 0
Status:   OK  
CheckDir: HPAStainR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:HPAStainR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings HPAStainR_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/HPAStainR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HPAStainR/DESCRIPTION’ ... OK
* this is package ‘HPAStainR’ version ‘1.4.1’
* 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 ‘HPAStainR’ 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
HPAstainR           7.626  0.913  20.779
HPA_data_downloader 3.668  0.779  36.494
shiny_HPAStainR     3.017  0.363  16.102
hpa_summary_maker   3.052  0.230  15.464
* 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

HPAStainR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘HPAStainR’ ...
** 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 (HPAStainR)

Tests output

HPAStainR.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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(HPAStainR)
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

Loading required package: tidyr

Attaching package: 'tidyr'

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

    matches

> 
> test_check("HPAStainR")
trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5596382 bytes (5.3 MB)
==================================================
downloaded 5.3 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3609266 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 22.088   2.546 124.045 

Example timings

HPAStainR.Rcheck/HPAStainR-Ex.timings

nameusersystemelapsed
HPA_data_downloader 3.668 0.77936.494
HPAstainR 7.626 0.91320.779
hpa_summary_maker 3.052 0.23015.464
shiny_HPAStainR 3.017 0.36316.102