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###
### 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_0.99.11.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 ‘0.99.11’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
MsBackendPy 5.121  0.849    5.82
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK

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###
### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SpectriPy
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SpectriPy’ ...
** this is package ‘SpectriPy’ version ‘0.99.11’
** 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
Downloading fonttools (4.7MiB)
 Downloading fonttools
Installed 42 packages in 101ms
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/2eL-IH3a_bYhIGLGli_OV/lib/python3.12/site-packages/pubchempy.py:563: SyntaxWarning: "is not" with 'int' literal. Did you mean "!="?
  if self.charge is not 0:
** testing if installed package can be loaded from final location
** 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
> 
> test_check("SpectriPy")

Calculating similarities:   0%|          | 0/4 [00:00<?, ?it/s]
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2025-08-28 03:46:42,884:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:42,932:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:42,933:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:42,934:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:42,992:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:42,993:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:42,994:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,207:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,208:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,209:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,238:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,238:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,239:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,503:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,504:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,505:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,517:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,518:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-28 03:46:43,519:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.

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[ FAIL 0 | WARN 4 | SKIP 1 | PASS 524 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_zzz.R:16:1'

[ FAIL 0 | WARN 4 | SKIP 1 | PASS 524 ]
> 
> proc.time()
   user  system elapsed 
 23.955   2.615  26.096