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This page was generated on 2025-08-21 12:04 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2055/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpectriPy 0.99.10  (landing page)
Johannes Rainer
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 Aug 2025)
git_url: https://git.bioconductor.org/packages/SpectriPy
git_branch: devel
git_last_commit: ff8cea4
git_last_commit_date: 2025-08-20 02:14:35 -0400 (Wed, 20 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  ERROR    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for SpectriPy on nebbiolo2

To the developers/maintainers of the SpectriPy package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpectriPy.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SpectriPy
Version: 0.99.10
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_0.99.10.tar.gz
StartedAt: 2025-08-21 03:15:20 -0400 (Thu, 21 Aug 2025)
EndedAt: 2025-08-21 03:28:17 -0400 (Thu, 21 Aug 2025)
EllapsedTime: 777.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SpectriPy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_0.99.10.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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SpectriPy/DESCRIPTION’ ... OK
* this is package ‘SpectriPy’ version ‘0.99.10’
* 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/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/python3
libpython:      /home/biocbuild/.cache/R/reticulate/uv/python/cpython-3.12.11-linux-x86_64-gnu/lib/libpython3.12.so
pythonhome:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG:/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG
virtualenv:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/activate_this.py
version:        3.12.11 (main, Jul 11 2025, 22:43:48) [Clang 20.1.4 ]
numpy:          /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/lib/python3.12/site-packages/numpy
numpy_version:  2.2.6

NOTE: Python version was forced by py_require()

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/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/python3
libpython:      /home/biocbuild/.cache/R/reticulate/uv/python/cpython-3.12.11-linux-x86_64-gnu/lib/libpython3.12.so
pythonhome:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG:/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG
virtualenv:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/activate_this.py
version:        3.12.11 (main, Jul 11 2025, 22:43:48) [Clang 20.1.4 ]
numpy:          /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/lib/python3.12/site-packages/numpy
numpy_version:  2.2.6

NOTE: Python version was forced by py_require()
* 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 4.873  0.697   5.448
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SpectriPy.Rcheck/00check.log’
for details.


Installation output

SpectriPy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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 ‘0.99.10’
** 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 fastobo (2.1MiB)
 Downloading fastobo
Installed 42 packages in 102ms
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/lib/python3.12/site-packages/pubchempy.py:563: SyntaxWarning: "is not" with 'int' literal. Did you mean "!="?
  if self.charge is not 0:
python:         /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/python3
libpython:      /home/biocbuild/.cache/R/reticulate/uv/python/cpython-3.12.11-linux-x86_64-gnu/lib/libpython3.12.so
pythonhome:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG:/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG
virtualenv:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/activate_this.py
version:        3.12.11 (main, Jul 11 2025, 22:43:48) [Clang 20.1.4 ]
numpy:          /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/lib/python3.12/site-packages/numpy
numpy_version:  2.2.6

NOTE: Python version was forced by py_require()
** testing if installed package can be loaded from final location
python:         /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/python3
libpython:      /home/biocbuild/.cache/R/reticulate/uv/python/cpython-3.12.11-linux-x86_64-gnu/lib/libpython3.12.so
pythonhome:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG:/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG
virtualenv:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/activate_this.py
version:        3.12.11 (main, Jul 11 2025, 22:43:48) [Clang 20.1.4 ]
numpy:          /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/lib/python3.12/site-packages/numpy
numpy_version:  2.2.6

NOTE: Python version was forced by py_require()
** testing if installed package keeps a record of temporary installation path
* DONE (SpectriPy)

Tests output

SpectriPy.Rcheck/tests/testthat.Rout


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/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/python3
libpython:      /home/biocbuild/.cache/R/reticulate/uv/python/cpython-3.12.11-linux-x86_64-gnu/lib/libpython3.12.so
pythonhome:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG:/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG
virtualenv:     /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/bin/activate_this.py
version:        3.12.11 (main, Jul 11 2025, 22:43:48) [Clang 20.1.4 ]
numpy:          /home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/WtztdQjAnWe2-XDhMk4kG/lib/python3.12/site-packages/numpy
numpy_version:  2.2.6

NOTE: Python version was forced by py_require()

> 
> test_check("SpectriPy")

Calculating similarities:   0%|          | 0/4 [00:00<?, ?it/s]
Calculating similarities:  25%|██▌       | 1/4 [00:02<00:07,  2.43s/it]
Calculating similarities: 100%|██████████| 4/4 [00:02<00:00,  1.64it/s]

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Calculating similarities: 100%|██████████| 2/2 [00:00<00:00,  2.40it/s]
2025-08-21 03:19:53,770:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:53,817:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:53,818:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:53,819:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:53,976:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:53,977:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:53,978:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,010:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,011:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,011:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,301:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,302:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,303:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,317:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,317:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-08-21 03:19:54,318:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.

Processing spectra:   0%|          | 0/4 [00:00<?, ?it/s]
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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 4232.40it/s]

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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3932.77it/s]
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 463 ]

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

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 463 ]
> 
> proc.time()
   user  system elapsed 
 23.471   2.278  25.181 

Example timings

SpectriPy.Rcheck/SpectriPy-Ex.timings

nameusersystemelapsed
MsBackendPy4.8730.6975.448
compareSpectriPy2.3100.1662.500
conversion0.3220.2540.434
filterSpectriPy0.1730.0240.196