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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:immApex.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings immApex_1.0.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/immApex.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘immApex/DESCRIPTION’ ... OK
* this is package ‘immApex’ version ‘1.0.4’
* 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 loading without being on the library search path ... 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: onehotEncoder
> ### Title: One Hot Encoder from Amino Acid or Nucleotide Strings
> ### Aliases: onehotEncoder
> 
> ### ** Examples
> 
> new.sequences <- generateSequences(prefix.motif = "CAS",
+                                    suffix.motif = "YF",
+                                    number.of.sequences = 100,
+                                    min.length = 8,
+                                    max.length = 16)
>                           
> sequence.matrix <- onehotEncoder(new.sequences, 
+                                  convert.to.matrix = TRUE)
Padding sequences...
One Hot Encoding sequences...
Preparing a matrix...
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'numpy'
Run `reticulate::py_last_error()` for details.
Calls: onehotEncoder -> array_reshape -> import -> py_module_import
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:
  ── Error ('test-sequenceDecoder.R:7:3'): sequenceDecoder works ─────────────────
  <python.builtin.ModuleNotFoundError/python.builtin.ImportError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
  Error in `py_module_import(module, convert = convert)`: ModuleNotFoundError: No module named 'numpy'
  Run `reticulate::py_last_error()` for details.
  Backtrace:
      ▆
   1. └─immApex::sequenceDecoder(sequence.matrix) at test-sequenceDecoder.R:7:3
   2.   └─immApex:::.onehotDecoder(...)
   3.     └─reticulate::array_reshape(...)
   4.       └─reticulate::import("numpy", convert = !is_py_object(x))
   5.         └─reticulate:::py_module_import(module, convert = convert)
  
  [ FAIL 3 | WARN 0 | SKIP 2 | PASS 39 ]
  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
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/immApex.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL immApex
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.145   0.035   0.168 

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> # 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 3 | WARN 0 | SKIP 2 | PASS 39 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-getIR.R:3:1', 'test-variationalSequences.R:3:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-onehotEncoder.R:7:3'): onehotEncoder works ─────────────────────
<python.builtin.ModuleNotFoundError/python.builtin.ImportError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_module_import(module, convert = convert)`: ModuleNotFoundError: No module named 'numpy'
Run `reticulate::py_last_error()` for details.
Backtrace:
    ▆
 1. └─immApex::onehotEncoder(sequences) at test-onehotEncoder.R:7:3
 2.   └─reticulate::array_reshape(...)
 3.     └─reticulate::import("numpy", convert = !is_py_object(x))
 4.       └─reticulate:::py_module_import(module, convert = convert)
── Error ('test-propertyEncoder.R:8:3'): propertyEncoder works ─────────────────
<python.builtin.ModuleNotFoundError/python.builtin.ImportError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_module_import(module, convert = convert)`: ModuleNotFoundError: No module named 'numpy'
Run `reticulate::py_last_error()` for details.
Backtrace:
    ▆
 1. └─immApex::propertyEncoder(...) at test-propertyEncoder.R:8:3
 2.   └─reticulate::array_reshape(...)
 3.     └─reticulate::import("numpy", convert = !is_py_object(x))
 4.       └─reticulate:::py_module_import(module, convert = convert)
── Error ('test-sequenceDecoder.R:7:3'): sequenceDecoder works ─────────────────
<python.builtin.ModuleNotFoundError/python.builtin.ImportError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_module_import(module, convert = convert)`: ModuleNotFoundError: No module named 'numpy'
Run `reticulate::py_last_error()` for details.
Backtrace:
    ▆
 1. └─immApex::sequenceDecoder(sequence.matrix) at test-sequenceDecoder.R:7:3
 2.   └─immApex:::.onehotDecoder(...)
 3.     └─reticulate::array_reshape(...)
 4.       └─reticulate::import("numpy", convert = !is_py_object(x))
 5.         └─reticulate:::py_module_import(module, convert = convert)

[ FAIL 3 | WARN 0 | SKIP 2 | PASS 39 ]
Error: Test failures
Execution halted