##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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 24.04.2 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 5.338  0.955   6.122
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SpectriPy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SpectriPy’ ...
** this is package ‘SpectriPy’ version ‘0.99.8’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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
** testing if installed package can be loaded from final location
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
** testing if installed package keeps a record of temporary installation path
* DONE (SpectriPy)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> library(testthat)
> library(Spectra)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
> library(SpectriPy)
Loading required package: reticulate
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

> 
> test_check("SpectriPy")

Calculating similarities:   0%|          | 0/4 [00:00<?, ?it/s]
Calculating similarities:  25%|██▌       | 1/4 [00:02<00:07,  2.58s/it]
Calculating similarities: 100%|██████████| 4/4 [00:02<00:00,  1.55it/s]

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Calculating similarities:  50%|█████     | 1/2 [00:00<00:00,  1.50it/s]
Calculating similarities: 100%|██████████| 2/2 [00:00<00:00,  3.00it/s]

Calculating similarities:   0%|          | 0/2 [00:00<?, ?it/s]
Calculating similarities:  50%|█████     | 1/2 [00:00<00:00,  1.09it/s]
Calculating similarities: 100%|██████████| 2/2 [00:00<00:00,  2.19it/s]
2025-08-09 03:10:41,645:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,695:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,696:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,697:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,849:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,850:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,851:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,880:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,880:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:41,881:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:42,151:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:42,152:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:42,153:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:42,166:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:42,167:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-09 03:10:42,168:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.

Processing spectra:   0%|          | 0/4 [00:00<?, ?it/s]
Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3219.58it/s]

Processing spectra:   0%|          | 0/4 [00:00<?, ?it/s]
Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3443.60it/s]

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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3484.36it/s]

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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3706.85it/s]

Processing spectra:   0%|          | 0/4 [00:00<?, ?it/s]
Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3445.72it/s]
[ FAIL 3 | WARN 2 | SKIP 1 | PASS 461 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_zzz.R:14:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_conversion.R:253:5'): pyspec_to_rspec and .single_pyspec_to_rspec work ──
rtime(res) not equal to rtime(sps).
3/3 mismatches (average diff: 9.54e-08)
[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