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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:immApex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings immApex_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/immApex.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘immApex/DESCRIPTION’ ... OK
* this is package ‘immApex’ version ‘1.1.0’
* 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 ‘immApex’ 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 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘immApex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getIMGT
> ### Title: Get IMGT Sequences for Specific Loci
> ### Aliases: getIMGT
> 
> ### ** Examples
> 
> TRBV_aa <- getIMGT(species = "human",
+                    chain = "TRB",
+                    frame = "inframe",
+                    region = "v",
+                    sequence.type = "aa", 
+                    max.retries = 3) 
Data from IMGT is under a CC BY-NC-ND 4.0 license. Attribution is required.
Getting sequences from IMGT...
Attempt 1 failed. Retrying...
Attempt 2 failed. Retrying...
Attempt 3 failed. Retrying...
Error in getIMGT(species = "human", chain = "TRB", frame = "inframe",  : 
  Failed to retrieve data after 3 attempts.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  <curl_error_operation_timedout/curl_error/error/condition>
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [www.imgt.org]: Connection timed out after 10001 milliseconds
  Backtrace:
      â–†
   1. ├─immApex::getIMGT(...) at test-getIMGT.R:6:3
   2. │ └─httr::GET(updated.url)
   3. │   └─httr:::request_perform(req, hu$handle$handle)
   4. │     ├─httr:::request_fetch(req$output, req$url, handle)
   5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   6. │       └─curl::curl_fetch_memory(url, handle = handle)
   7. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 50 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/immApex.Rcheck/00check.log’
for details.