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This page was generated on 2025-10-03 12:05 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1269/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetMashR 1.3.3  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/MetMashR
git_branch: devel
git_last_commit: 38b08fe
git_last_commit_date: 2025-10-02 10:11:10 -0400 (Thu, 02 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-10-02 22:41:26 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 22:45:38 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 251.4 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 
 17.972   1.241  30.013 

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

nameusersystemelapsed
AnnotationDb_database0.0200.0000.021
AnnotationDb_select0.0150.0010.017
BiocFileCache_database0.0190.0010.021
CompoundDb_source0.0110.0000.011
GO_database0.0090.0000.010
MTox700plus_database0.0190.0010.020
PathBank_metabolite_database0.0150.0000.016
add_columns0.0070.0010.007
add_labels0.0090.0000.009
annotation_bar_chart0.0120.0010.013
annotation_database0.0090.0000.009
annotation_histogram0.0130.0010.014
annotation_histogram2d0.0120.0010.013
annotation_pie_chart0.0160.0010.017
annotation_source0.0090.0000.010
annotation_table0.0120.0000.013
annotation_upset_chart0.0300.0010.032
annotation_venn_chart0.0130.0010.013
cache_as_is0.0160.0010.017
calc_ppm_diff0.0080.0000.009
calc_rt_diff0.0090.0000.008
cd_source0.0180.0000.018
chart_plot0.0150.0010.016
check_for_columns0.0080.0010.008
classyfire_lookup0.0130.0020.015
combine_columns0.7090.0050.717
combine_records0.010.000.01
combine_records_helper_functions0.0390.0020.041
combine_sources0.0200.0000.019
compute_column0.0090.0000.009
compute_record0.0060.0000.006
database_lookup0.0160.0000.016
eutils_lookup0.0190.0000.019
excel_database0.0180.0000.019
filter_labels0.0070.0000.007
filter_na0.0040.0010.005
filter_range0.0060.0000.007
filter_records0.0070.0010.009
filter_venn0.010.000.01
github_file0.0200.0000.022
greek_dictionary0.0070.0000.008
hmdb_lookup0.0160.0000.016
id_counts0.0080.0000.007
import_source0.0010.0000.001
is_writable0.0080.0000.008
kegg_lookup0.0100.0010.010
lcms_table0.0120.0000.012
lipidmaps_lookup0.0160.0000.016
ls_source0.0120.0000.013
model_apply0.1570.0030.162
mspurity_source0.0100.0000.011
mwb_compound_lookup0.0140.0010.015
mwb_refmet_database0.0150.0030.017
mwb_structure0.0070.0020.009
mz_match0.0100.0010.011
mzrt_match0.0130.0020.014
normalise_lipids0.0080.0020.010
normalise_strings0.0060.0010.007
opsin_lookup0.0130.0020.014
pivot_columns0.0060.0010.007
prioritise_columns0.0120.0020.014
pubchem_compound_lookup0.0150.0020.018
pubchem_property_lookup0.0160.0030.019
pubchem_structure0.0080.0020.010
pubchem_widget0.0150.0030.017
racemic_dictionary0.0050.0010.007
rdata_database0.0120.0020.014
rds_cache0.0130.0020.014
rds_database0.0100.0010.011
read_database0.0090.0010.010
read_source0.0140.0030.016
remove_columns0.0070.0010.008
rename_columns0.0070.0010.008
required_cols0.0100.0020.012
rest_api0.0130.0020.014
rt_match0.0080.0010.009
select_columns0.0050.0010.007
split_column0.0120.0020.013
split_records0.0080.0020.009
sqlite_database0.0120.0020.015
trim_whitespace0.0080.0010.010
tripeptide_dictionary0.0070.0010.008
unique_records0.0010.0000.001
unzip_before_cache0.0110.0030.013
upset_filters0.0000.0000.001
vertical_join0.1320.0220.155
wherever0.0380.0050.044
write_database0.0060.0010.007