| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:28 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
|
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. |
| Package 885/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HPAStainR 1.4.1 (landing page) Tim O. Nieuwenhuis
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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 |
##############################################################################
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###
### 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
###
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##############################################################################
* 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
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)
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
HPAStainR.Rcheck/HPAStainR-Ex.timings
| name | user | system | elapsed | |
| HPA_data_downloader | 3.668 | 0.779 | 36.494 | |
| HPAstainR | 7.626 | 0.913 | 20.779 | |
| hpa_summary_maker | 3.052 | 0.230 | 15.464 | |
| shiny_HPAStainR | 3.017 | 0.363 | 16.102 | |