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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpectriPy.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpectriPy_0.99.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpectriPy.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SpectriPy/DESCRIPTION’ ... OK
* this is package ‘SpectriPy’ version ‘0.99.8’
* 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 ‘SpectriPy’ 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 ... NOTE
python:         /home/biocbuild/.virtualenvs/r-reticulate/bin/python
libpython:      /usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so
pythonhome:     /home/biocbuild/.virtualenvs/r-reticulate:/home/biocbuild/.virtualenvs/r-reticulate
version:        3.12.3 (main, Jun 18 2025, 17:59:45) [GCC 13.3.0]
numpy:          /home/biocbuild/.virtualenvs/r-reticulate/lib/python3.12/site-packages/numpy
numpy_version:  2.2.6

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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 ... NOTE
File ‘SpectriPy/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(print(py_config()))
    print(py_config())

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

python:         /home/biocbuild/.virtualenvs/r-reticulate/bin/python
libpython:      /usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so
pythonhome:     /home/biocbuild/.virtualenvs/r-reticulate:/home/biocbuild/.virtualenvs/r-reticulate
version:        3.12.3 (main, Jun 18 2025, 17:59:45) [GCC 13.3.0]
numpy:          /home/biocbuild/.virtualenvs/r-reticulate/lib/python3.12/site-packages/numpy
numpy_version:  2.2.6
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
MsBackendPy 5.169  0.736   5.749
* 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:
  [1] 1.2 - 1.2 ==  4.77e-08
  [2] 3.2 - 3.2 ==  4.77e-08
  [3] 5.2 - 5.2 == -1.91e-07
  ── Failure ('test_conversion.R:379:5'): .py_spectrum_utils_spectrum_spectra_data works ──
  res$rtime not equal to sps$rtime[1L].
  1/1 mismatches
  [1] 1.2 - 1.2 == 4.77e-08
  ── Failure ('test_conversion.R:388:5'): .py_spectrum_utils_spectrum_spectra_data works ──
  res$precursorCharge not identical to NA_integer_.
  1/1 mismatches
  [1] 0 - NA == NA
  
  [ FAIL 3 | WARN 2 | SKIP 1 | PASS 461 ]
  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: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SpectriPy.Rcheck/00check.log’
for details.