##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/immApex.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.0.5’
* 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 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: variationalSequences
> ### Title: Generate Similar Sequences using Variational Autoencoder
> ### Aliases: variationalSequences
> 
> ### ** Examples
> 
> sequences <- generateSequences(prefix.motif = "CAS",
+                                suffix.motif = "YF",
+                                number.of.sequences = 100,
+                                min.length = 8,
+                                max.length = 16)
> 
> if(reticulate::py_module_available("keras")) {                                 
+ new.sequences <- variationalSequences(sequences, 
+                                       encoder = "onehotEncoder",
+                                       encoder.hidden.dim = c(256, 128),
+                                       latent.dim = 16,
+                                       batch.size = 16)
+ }
Converting to matrix....
Padding sequences...
One Hot Encoding sequences...
Preparing a matrix...
Error in UseMethod("compile") : 
  no applicable method for 'compile' applied to an object of class "c('keras.engine.functional.Functional', 'keras.engine.training.Model', 'keras.engine.base_layer.Layer', 'tensorflow.python.module.module.Module', 'tensorflow.python.trackable.autotrackable.AutoTrackable', 'tensorflow.python.trackable.base.Trackable', 'keras.utils.version_utils.LayerVersionSelector', 'keras.utils.version_utils.ModelVersionSelector', 'python.builtin.object')"
Calls: variationalSequences -> %>% -> <Anonymous>
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:
  `TRBV_human_inframe_aa` not equal to getdata("getIMGT", "getIMGT_TRBV_human_inframe_aa").
  Component "sequences": Names: 124 string mismatches
  Component "sequences": Length mismatch: comparison on first 147 components
  Component "sequences": Component 24: 1 string mismatch
  Component "sequences": Component 25: 1 string mismatch
  Component "sequences": Component 26: 1 string mismatch
  Component "sequences": Component 27: 1 string mismatch
  Component "sequences": Component 28: 1 string mismatch
  Component "sequences": Component 29: 1 string mismatch
  Component "sequences": Component 30: 1 string mismatch
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 54 ]
  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-3.20-bioc/meat/immApex.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL immApex
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  0.344   0.116   0.430 

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 54 ]

══ 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: 124 string mismatches
Component "sequences": Length mismatch: comparison on first 147 components
Component "sequences": Component 24: 1 string mismatch
Component "sequences": Component 25: 1 string mismatch
Component "sequences": Component 26: 1 string mismatch
Component "sequences": Component 27: 1 string mismatch
Component "sequences": Component 28: 1 string mismatch
Component "sequences": Component 29: 1 string mismatch
Component "sequences": Component 30: 1 string mismatch
...

[ FAIL 1 | WARN 0 | SKIP 2 | PASS 54 ]
Error: Test failures
Execution halted