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This page was generated on 2024-06-19 12:10 -0400 (Wed, 19 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4402
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4351
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

Package 1003/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunotation 1.13.0  (landing page)
Katharina Imkeller
Snapshot Date: 2024-06-18 14:00 -0400 (Tue, 18 Jun 2024)
git_url: https://git.bioconductor.org/packages/immunotation
git_branch: devel
git_last_commit: aebf955
git_last_commit_date: 2024-04-30 11:33:53 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for immunotation on nebbiolo2

To the developers/maintainers of the immunotation package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: immunotation
Version: 1.13.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:immunotation.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings immunotation_1.13.0.tar.gz
StartedAt: 2024-06-19 00:11:24 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 00:15:27 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 242.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: immunotation.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:immunotation.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings immunotation_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/immunotation.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘immunotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunotation’ version ‘1.13.0’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    R         3.2Mb
    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 code 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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘immunotation-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: decode_MAC
> ### Title: Decode MAC
> ### Aliases: decode_MAC
> 
> ### ** Examples
> 
> MAC <- "A*01:ATJNV"
> decode_MAC(MAC)
Error in curl::curl_fetch_memory(url, handle = h) : 
  Timeout was reached: [hml.nmdp.org] SSL connection timeout
Calls: decode_MAC -> fetch_decoded_MAC -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_3_name_conversions.R:77:5'): encode_MAC() returns expected results ──
  Error in `curl::curl_fetch_memory("https://hml.nmdp.org/mac/api/encode", 
      handle = handle)`: Timeout was reached: [hml.nmdp.org] SSL connection timeout
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(encode_MAC("A*01:01"), "A*01:01") at test_3_name_conversions.R:77:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─immunotation::encode_MAC("A*01:01")
   5.   └─immunotation:::fetch_encoded_MAC(handle)
   6.     └─curl::curl_fetch_memory(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 141 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/immunotation.Rcheck/00check.log’
for details.


Installation output

immunotation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL immunotation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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.fail


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 2 | WARN 1 | SKIP 0 | PASS 141 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_3_name_conversions.R:68:5'): encode_MAC() returns error when arguments not adequate ──
Error in `curl::curl_fetch_memory("https://hml.nmdp.org/mac/api/encode", 
    handle = handle)`: Timeout was reached: [hml.nmdp.org] SSL connection timeout
Backtrace:
    ▆
 1. ├─testthat::expect_equal(encode_MAC(""), "glstring is empty") at test_3_name_conversions.R:68:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─immunotation::encode_MAC("")
 5.   └─immunotation:::fetch_encoded_MAC(handle)
 6.     └─curl::curl_fetch_memory(...)
── Error ('test_3_name_conversions.R:77:5'): encode_MAC() returns expected results ──
Error in `curl::curl_fetch_memory("https://hml.nmdp.org/mac/api/encode", 
    handle = handle)`: Timeout was reached: [hml.nmdp.org] SSL connection timeout
Backtrace:
    ▆
 1. ├─testthat::expect_equal(encode_MAC("A*01:01"), "A*01:01") at test_3_name_conversions.R:77:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─immunotation::encode_MAC("A*01:01")
 5.   └─immunotation:::fetch_encoded_MAC(handle)
 6.     └─curl::curl_fetch_memory(...)

[ FAIL 2 | WARN 1 | SKIP 0 | PASS 141 ]
Error: Test failures
Execution halted

Example timings

immunotation.Rcheck/immunotation-Ex.timings

nameusersystemelapsed
assemble_protein_complex1.6980.1481.845
build_allele_group0.8730.0040.877