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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 lconway

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: 1.3.3

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_1.3.3.tar.gz

StartedAt: 2025-10-23 22:20:45 -0400 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 22:24:50 -0400 (Thu, 23 Oct 2025)

EllapsedTime: 245.0 seconds

RetCode: 0

Status: OK

CheckDir: MetMashR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MetMashR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.3.3’
* 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 ‘1.3.3’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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 
 17.793   1.149  29.794

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

name	user	system	elapsed
AnnotationDb_database	0.022	0.001	0.023
AnnotationDb_select	0.016	0.001	0.018
BiocFileCache_database	0.019	0.001	0.021
CompoundDb_source	0.011	0.001	0.012
GO_database	0.013	0.001	0.014
MTox700plus_database	0.018	0.001	0.019
PathBank_metabolite_database	0.023	0.001	0.025
add_columns	0.007	0.001	0.007
add_labels	0.010	0.001	0.011
annotation_bar_chart	0.010	0.001	0.010
annotation_database	0.010	0.001	0.010
annotation_histogram	0.018	0.000	0.018
annotation_histogram2d	0.015	0.001	0.015
annotation_pie_chart	0.014	0.001	0.014
annotation_source	0.009	0.000	0.009
annotation_table	0.012	0.000	0.013
annotation_upset_chart	0.031	0.001	0.032
annotation_venn_chart	0.015	0.001	0.015
cache_as_is	0.015	0.001	0.016
calc_ppm_diff	0.010	0.000	0.011
calc_rt_diff	0.010	0.000	0.011
cd_source	0.022	0.000	0.023
chart_plot	0.013	0.001	0.014
check_for_columns	0.007	0.001	0.007
classyfire_lookup	0.019	0.002	0.021
combine_columns	0.695	0.005	0.703
combine_records	0.009	0.001	0.009
combine_records_helper_functions	0.040	0.002	0.042
combine_sources	0.020	0.000	0.021
compute_column	0.010	0.000	0.011
compute_record	0.006	0.001	0.007
database_lookup	0.013	0.001	0.014
eutils_lookup	0.019	0.001	0.020
excel_database	0.019	0.001	0.018
filter_labels	0.01	0.00	0.01
filter_na	0.007	0.000	0.006
filter_range	0.011	0.000	0.011
filter_records	0.007	0.000	0.008
filter_venn	0.009	0.000	0.010
github_file	0.022	0.000	0.022
greek_dictionary	0.011	0.000	0.011
hmdb_lookup	0.015	0.000	0.015
id_counts	0.009	0.000	0.010
import_source	0.000	0.001	0.001
is_writable	0.004	0.000	0.004
kegg_lookup	0.007	0.000	0.008
lcms_table	0.016	0.000	0.016
lipidmaps_lookup	0.019	0.000	0.020
ls_source	0.016	0.000	0.016
model_apply	0.175	0.004	0.180
mspurity_source	0.012	0.001	0.012
mwb_compound_lookup	0.019	0.001	0.021
mwb_refmet_database	0.015	0.002	0.017
mwb_structure	0.008	0.001	0.010
mz_match	0.009	0.002	0.011
mzrt_match	0.013	0.002	0.015
normalise_lipids	0.012	0.001	0.013
normalise_strings	0.008	0.001	0.009
opsin_lookup	0.017	0.003	0.020
pivot_columns	0.009	0.001	0.011
prioritise_columns	0.014	0.002	0.016
pubchem_compound_lookup	0.018	0.003	0.020
pubchem_property_lookup	0.020	0.003	0.023
pubchem_structure	0.011	0.002	0.012
pubchem_widget	0.016	0.003	0.018
racemic_dictionary	0.008	0.001	0.009
rdata_database	0.014	0.002	0.016
rds_cache	0.012	0.002	0.013
rds_database	0.009	0.001	0.011
read_database	0.010	0.002	0.012
read_source	0.016	0.002	0.020
remove_columns	0.006	0.001	0.008
rename_columns	0.006	0.001	0.007
required_cols	0.012	0.002	0.014
rest_api	0.014	0.002	0.016
rt_match	0.010	0.002	0.012
select_columns	0.007	0.002	0.008
split_column	0.014	0.002	0.016
split_records	0.008	0.002	0.009
sqlite_database	0.012	0.002	0.015
trim_whitespace	0.007	0.001	0.008
tripeptide_dictionary	0.008	0.001	0.009
unique_records	0.001	0.000	0.002
unzip_before_cache	0.012	0.002	0.014
upset_filters	0	0	0
vertical_join	0.132	0.019	0.152
wherever	0.038	0.005	0.044
write_database	0.006	0.001	0.007