Multiple platform build/check report for BioC 3.22 - CHECK results for MetMashR on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4883
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4607
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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*

CHECK results for MetMashR on merida1

To the developers/maintainers of the MetMashR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetMashR.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: MetMashR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetMashR_1.4.0.tar.gz

StartedAt: 2025-12-19 06:56:44 -0500 (Fri, 19 Dec 2025)

EndedAt: 2025-12-19 07:05:15 -0500 (Fri, 19 Dec 2025)

EllapsedTime: 510.8 seconds

RetCode: 0

Status: OK

CheckDir: MetMashR.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetMashR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MetMashR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetMashR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetMashR’ version ‘1.4.0’
* 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 ... NOTE
Found the following non-portable file paths:
  MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/PE%2816%3A0_18%3A1%29/inchi_key%2Chmdb_id/json.json
  MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/TG%2816%3A0_16%3A1_18%3A2%29/inchi_key%2Chmdb_id/json.json
  MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/TG%2816%3A0_16%3A1_18%3A2%29/inchi_key%2Chmdb_id

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MetMashR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.get_limits: no visible global function definition for ‘ggplot_build’
scale_color_Publication: no visible global function definition for
  ‘discrete_scale’
scale_fill_Publication: no visible global function definition for
  ‘discrete_scale’
theme_Publication: no visible global function definition for ‘theme’
theme_Publication: no visible global function definition for
  ‘element_text’
theme_Publication: no visible global function definition for ‘rel’
theme_Publication: no visible global function definition for
  ‘element_rect’
theme_Publication: no visible global function definition for
  ‘element_line’
theme_Publication: no visible global function definition for
  ‘element_blank’
theme_Publication: no visible global function definition for ‘unit’
venn_this: no visible global function definition for ‘aes’
venn_this: no visible global function definition for ‘ggplot’
venn_this: no visible binding for global variable ‘geom_polygon’
venn_this: no visible binding for global variable ‘geom_path’
venn_this: no visible global function definition for ‘geom_text’
venn_this: no visible global function definition for ‘theme_void’
venn_this: no visible global function definition for
  ‘scale_x_continuous’
venn_this: no visible global function definition for ‘expansion’
venn_this: no visible global function definition for ‘theme’
venn_this: no visible global function definition for ‘coord_fixed’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘ggplot’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘aes’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘geom_bar’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘geom_text’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘coord_cartesian’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘theme’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘element_rect’
chart_plot,annotation_bar_chart-annotation_source: no visible global
  function definition for ‘element_blank’
chart_plot,annotation_histogram-annotation_source: no visible global
  function definition for ‘ggplot’
chart_plot,annotation_histogram-annotation_source: no visible global
  function definition for ‘geom_histogram’
chart_plot,annotation_histogram-annotation_source: no visible global
  function definition for ‘aes’
chart_plot,annotation_histogram-annotation_source: no visible global
  function definition for ‘geom_vline’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘ggplot’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘aes’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘geom_bin2d’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘theme’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘unit’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘element_rect’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘xlab’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘ylab’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘element_blank’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘coord_cartesian’
chart_plot,annotation_histogram2d-annotation_source: no visible global
  function definition for ‘coord_flip’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘ggplot’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘aes’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘geom_bar’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘coord_polar’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘theme_void’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘geom_text’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘position_stack’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘theme’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘unit’
chart_plot,annotation_pie_chart-annotation_source: no visible global
  function definition for ‘xlim’
Undefined global functions or variables:
  aes coord_cartesian coord_fixed coord_flip coord_polar discrete_scale
  element_blank element_line element_rect element_text expansion
  geom_bar geom_bin2d geom_histogram geom_path geom_polygon geom_text
  geom_vline ggplot ggplot_build position_stack rel scale_x_continuous
  theme theme_void unit xlab xlim ylab
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/MetMashR.Rcheck/00check.log’
for details.

Installation output

MetMashR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MetMashR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MetMashR’ ...
** this is package ‘MetMashR’ version ‘1.4.0’
** using staged installation
** R
** 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 (MetMashR)

Tests output

MetMashR.Rcheck/tests/testthat.Rout


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(MetMashR)
Loading required package: struct
> 
> test_check("MetMashR")
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 249 ]
> 
> proc.time()
   user  system elapsed 
 33.505   2.203  51.677

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

name	user	system	elapsed
AnnotationDb_database	0.043	0.001	0.067
AnnotationDb_select	0.028	0.002	0.034
BiocFileCache_database	0.039	0.001	0.046
CompoundDb_source	0.022	0.001	0.051
GO_database	0.026	0.002	0.036
MTox700plus_database	0.048	0.002	0.061
PathBank_metabolite_database	0.045	0.002	0.070
add_columns	0.017	0.001	0.023
add_labels	0.021	0.002	0.035
annotation_bar_chart	0.020	0.001	0.028
annotation_database	0.021	0.000	0.023
annotation_histogram	0.030	0.002	0.037
annotation_histogram2d	0.031	0.002	0.046
annotation_pie_chart	0.033	0.001	0.040
annotation_source	0.019	0.001	0.023
annotation_table	0.026	0.001	0.030
annotation_upset_chart	0.068	0.003	0.083
annotation_venn_chart	0.030	0.001	0.040
cache_as_is	0.031	0.001	0.037
calc_ppm_diff	0.018	0.001	0.023
calc_rt_diff	0.020	0.001	0.027
cd_source	0.042	0.002	0.047
chart_plot	0.024	0.002	0.031
check_for_columns	0.018	0.001	0.022
classyfire_lookup	0.039	0.003	0.049
combine_columns	0.032	0.005	0.067
combine_records	0.020	0.003	0.038
combine_records_helper_functions	0.105	0.019	0.152
combine_sources	0.053	0.009	0.076
compute_column	0.020	0.004	0.026
compute_record	0.013	0.003	0.016
database_lookup	0.034	0.006	0.051
eutils_lookup	0.049	0.008	0.070
excel_database	0.041	0.007	0.055
filter_labels	0.030	0.005	0.042
filter_na	0.013	0.002	0.016
filter_range	0.024	0.004	0.033
filter_records	0.014	0.002	0.018
filter_venn	0.024	0.004	0.034
github_file	0.084	0.011	0.111
greek_dictionary	0.020	0.001	0.023
hmdb_lookup	0.035	0.001	0.044
id_counts	0.016	0.001	0.020
import_source	0.002	0.000	0.001
is_writable	0.012	0.000	0.015
kegg_lookup	0.017	0.001	0.021
lcms_table	0.033	0.001	0.038
lipidmaps_lookup	0.044	0.002	0.052
ls_source	0.035	0.001	0.044
model_apply	0.334	0.004	0.392
mspurity_source	0.021	0.001	0.026
mwb_compound_lookup	0.042	0.002	0.051
mwb_refmet_database	0.031	0.001	0.040
mwb_structure	0.017	0.001	0.022
mz_match	0.024	0.000	0.028
mzrt_match	0.034	0.001	0.042
normalise_lipids	0.024	0.001	0.031
normalise_strings	0.018	0.001	0.020
opsin_lookup	0.037	0.001	0.044
pivot_columns	0.016	0.001	0.021
prioritise_columns	0.027	0.001	0.031
pubchem_compound_lookup	0.035	0.000	0.039
pubchem_property_lookup	0.042	0.001	0.049
pubchem_structure	0.019	0.001	0.023
pubchem_widget	0.033	0.001	0.039
racemic_dictionary	0.016	0.001	0.019
rdata_database	0.026	0.000	0.032
rds_cache	0.024	0.001	0.028
rds_database	0.021	0.000	0.022
read_database	0.017	0.002	0.023
read_source	0.037	0.001	0.043
remove_columns	0.011	0.001	0.014
rename_columns	0.012	0.001	0.014
required_cols	0.028	0.001	0.035
rest_api	0.032	0.001	0.041
rt_match	0.022	0.001	0.027
select_columns	0.013	0.001	0.014
split_column	0.026	0.000	0.032
split_records	0.020	0.001	0.027
sqlite_database	0.029	0.001	0.037
trim_whitespace	0.016	0.001	0.018
tripeptide_dictionary	0.017	0.001	0.020
unique_records	0.002	0.000	0.003
unzip_before_cache	0.032	0.001	0.038
upset_filters	0.000	0.002	0.001
vertical_join	0.302	0.038	0.399
wherever	0.080	0.013	0.106
write_database	0.015	0.004	0.022