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CHECK report for HPAStainR on merida1

This page was generated on 2021-05-06 12:35:19 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the HPAStainR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 848/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAStainR 1.0.3  (landing page)
Tim O. Nieuwenhuis
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/HPAStainR
Branch: RELEASE_3_12
Last Commit: ead97ed
Last Changed Date: 2021-02-03 14:12:37 -0400 (Wed, 03 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: HPAStainR
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HPAStainR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HPAStainR_1.0.3.tar.gz
StartedAt: 2021-05-06 02:43:27 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:46:36 -0400 (Thu, 06 May 2021)
EllapsedTime: 188.9 seconds
RetCode: 0
Status:   OK  
CheckDir: HPAStainR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HPAStainR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HPAStainR_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/HPAStainR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HPAStainR/DESCRIPTION’ ... OK
* this is package ‘HPAStainR’ version ‘1.0.3’
* 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 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           10.278  1.007  18.059
HPA_data_downloader  6.227  3.297  16.657
hpa_summary_maker    4.102  0.544   9.359
shiny_HPAStainR      3.348  0.393   8.063
* 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

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HPAStainR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.5 (2021-03-31) -- "Shake and Throw"
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(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 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5110246 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://www.proteinatlas.org/download/pathology.tsv.zip'
Content type 'application/zip' length 3565496 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 23.145   4.526  80.943 

Example timings

HPAStainR.Rcheck/HPAStainR-Ex.timings

nameusersystemelapsed
HPA_data_downloader 6.227 3.29716.657
HPAstainR10.278 1.00718.059
hpa_summary_maker4.1020.5449.359
shiny_HPAStainR3.3480.3938.063