##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immApex.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings immApex_1.0.5.tar.gz
###
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##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/immApex.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'immApex/DESCRIPTION' ... OK
* this is package 'immApex' version '1.0.5'
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
variationalSequences 32.10  12.19  129.08
onehotEncoder         0.43   0.31   49.15
* 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:
  `TRAJ_mouse_inframe_aa` not equal to getdata("getIMGT", "getIMGT_TRAJ_mouse_inframe_aa").
  Component "sequences": names for current but not for target
  Component "sequences": Length mismatch: comparison on first 0 components
  ── Failure ('test-getIMGT.R:48:3'): getIMGT works when IMGT website is available ──
  `IGHV_rat_all_nt` not equal to getdata("getIMGT", "getIMGT_IGHV_rat_all_nt").
  Component "sequences": names for current but not for target
  Component "sequences": Length mismatch: comparison on first 0 components
  ── Failure ('test-getIMGT.R:59:3'): getIMGT works when IMGT website is available ──
  `TRBV_rabbit_gap_aa` not equal to getdata("getIMGT", "getIMGT_TRBV_rabbit_gap_aa").
  Component "sequences": names for current but not for target
  Component "sequences": Length mismatch: comparison on first 0 components
  
  [ FAIL 4 | WARN 0 | SKIP 2 | PASS 51 ]
  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: 1 ERROR
See
  'F:/biocbuild/bbs-3.20-bioc/meat/immApex.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL immApex
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'immApex' ...
** using staged installation
** R
** data
** 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 (immApex)

R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.18    0.07    0.35 

R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(immApex)
> 
> test_check("immApex")
2025-04-01 02:43:13.595417: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2025-04-01 02:43:15.651536: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
[ FAIL 4 | WARN 0 | SKIP 2 | PASS 51 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• Required Python modules (Keras, NumPy) are not available. (1):
  'test-variationalSequences.R:10:5'
• empty test (1): 'test-getIR.R:3:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-getIMGT.R:26:3'): getIMGT works when IMGT website is available ──
`TRBV_human_inframe_aa` not equal to getdata("getIMGT", "getIMGT_TRBV_human_inframe_aa").
Component "sequences": names for current but not for target
Component "sequences": Length mismatch: comparison on first 0 components
── Failure ('test-getIMGT.R:37:3'): getIMGT works when IMGT website is available ──
`TRAJ_mouse_inframe_aa` not equal to getdata("getIMGT", "getIMGT_TRAJ_mouse_inframe_aa").
Component "sequences": names for current but not for target
Component "sequences": Length mismatch: comparison on first 0 components
── Failure ('test-getIMGT.R:48:3'): getIMGT works when IMGT website is available ──
`IGHV_rat_all_nt` not equal to getdata("getIMGT", "getIMGT_IGHV_rat_all_nt").
Component "sequences": names for current but not for target
Component "sequences": Length mismatch: comparison on first 0 components
── Failure ('test-getIMGT.R:59:3'): getIMGT works when IMGT website is available ──
`TRBV_rabbit_gap_aa` not equal to getdata("getIMGT", "getIMGT_TRBV_rabbit_gap_aa").
Component "sequences": names for current but not for target
Component "sequences": Length mismatch: comparison on first 0 components

[ FAIL 4 | WARN 0 | SKIP 2 | PASS 51 ]
Error: Test failures
Execution halted