Back to Multiple platform build/check report for BioC 3.13
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:39 -0400 (Fri, 15 Oct 2021).

CHECK results for immunotation on machv2

To the developers/maintainers of the immunotation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immunotation.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 916/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunotation 1.0.1  (landing page)
Katharina Imkeller
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/immunotation
git_branch: RELEASE_3_13
git_last_commit: 050aa59
git_last_commit_date: 2021-08-16 10:37:19 -0400 (Mon, 16 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: immunotation
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:immunotation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings immunotation_1.0.1.tar.gz
StartedAt: 2021-10-14 20:10:12 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:13:19 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 187.0 seconds
RetCode: 0
Status:   OK  
CheckDir: immunotation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:immunotation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings immunotation_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/immunotation.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘immunotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunotation’ version ‘1.0.1’
* 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 ‘immunotation’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         4.0Mb
    extdata   2.2Mb
* 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
plot_allele_frequency       2.873  0.241  18.038
query_haplotype_frequencies 0.678  0.077  13.495
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/immunotation.Rcheck/00check.log’
for details.



Installation output

immunotation.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘immunotation’ ...
** using staged installation
** R
** inst
** 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 (immunotation)

Tests output

immunotation.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(immunotation)
> 
> test_check("immunotation")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 146 ]
Warning messages:
1: closing unused connection 9 (https://iamnotanurl) 
2: closing unused connection 8 (https://iamnotanurl) 
3: closing unused connection 6 (https://iamnotanurl) 
4: closing unused connection 5 (https://iamnotanurl) 
5: closing unused connection 4 (https://iamnotanurl) 
> 
> 
> proc.time()
   user  system elapsed 
 53.247   5.876 108.447 

Example timings

immunotation.Rcheck/immunotation-Ex.timings

nameusersystemelapsed
assemble_protein_complex2.4360.1732.610
build_allele_group1.9430.0131.957
decode_MAC0.0960.0100.292
encode_MAC0.0020.0000.060
get_G_group0.0180.0000.019
get_P_group0.0030.0000.003
get_mhcpan_input0.0190.0010.019
get_serotypes0.0320.0020.034
get_valid_organisms0.0040.0010.004
human_protein_complex_table0.8020.7781.627
plot_allele_frequency 2.873 0.24118.038
query_allele_frequencies0.1470.0111.548
query_haplotype_frequencies 0.678 0.07713.495
query_population_detail0.0250.0020.352
retrieve_chain_lookup_table1.0840.0171.102