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This page was generated on 2025-10-04 12:06 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
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 1271/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetMashR 1.3.3  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 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  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MetMashR on kjohnson3

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: 2025-10-03 20:21:13 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 20:22:43 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 90.1 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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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-arm64/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: aarch64-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 
  5.713   0.297  15.180 

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

nameusersystemelapsed
AnnotationDb_database0.0050.0000.006
AnnotationDb_select0.0040.0000.004
BiocFileCache_database0.0040.0000.005
CompoundDb_source0.0020.0000.002
GO_database0.0030.0000.003
MTox700plus_database0.0060.0010.005
PathBank_metabolite_database0.0050.0000.005
add_columns0.0020.0000.002
add_labels0.0020.0010.003
annotation_bar_chart0.0030.0000.002
annotation_database0.0020.0000.002
annotation_histogram0.0030.0000.004
annotation_histogram2d0.0030.0010.004
annotation_pie_chart0.0040.0000.004
annotation_source0.0020.0000.002
annotation_table0.0030.0000.003
annotation_upset_chart0.0070.0000.007
annotation_venn_chart0.0040.0000.004
cache_as_is0.0030.0000.003
calc_ppm_diff0.0020.0010.002
calc_rt_diff0.0020.0000.002
cd_source0.0040.0000.004
chart_plot0.0030.0000.004
check_for_columns0.0020.0000.002
classyfire_lookup0.0040.0000.005
combine_columns0.2990.0010.299
combine_records0.0020.0000.002
combine_records_helper_functions0.0110.0010.011
combine_sources0.0050.0000.005
compute_column0.0020.0000.003
compute_record0.0010.0000.001
database_lookup0.0030.0010.004
eutils_lookup0.0050.0000.005
excel_database0.0040.0000.004
filter_labels0.0020.0000.003
filter_na0.0010.0000.001
filter_range0.0020.0000.002
filter_records0.0010.0000.002
filter_venn0.0030.0000.003
github_file0.0060.0000.006
greek_dictionary0.0020.0010.003
hmdb_lookup0.0040.0000.004
id_counts0.0020.0000.002
import_source0.0000.0000.001
is_writable0.0010.0000.001
kegg_lookup0.0020.0010.003
lcms_table0.0040.0000.004
lipidmaps_lookup0.0040.0000.004
ls_source0.0030.0000.004
model_apply0.0450.0010.045
mspurity_source0.0030.0000.003
mwb_compound_lookup0.0050.0000.004
mwb_refmet_database0.0030.0000.003
mwb_structure0.0020.0000.002
mz_match0.0030.0000.003
mzrt_match0.0030.0010.004
normalise_lipids0.0030.0000.003
normalise_strings0.0020.0010.002
opsin_lookup0.0040.0000.004
pivot_columns0.0020.0010.002
prioritise_columns0.0030.0000.003
pubchem_compound_lookup0.0040.0010.005
pubchem_property_lookup0.0050.0000.005
pubchem_structure0.0020.0000.003
pubchem_widget0.0040.0010.004
racemic_dictionary0.0020.0000.002
rdata_database0.0030.0000.003
rds_cache0.0030.0000.003
rds_database0.0020.0000.002
read_database0.0020.0010.002
read_source0.0050.0000.005
remove_columns0.0020.0000.002
rename_columns0.0010.0000.002
required_cols0.0030.0010.003
rest_api0.0040.0000.004
rt_match0.0020.0010.003
select_columns0.0010.0000.002
split_column0.0030.0010.003
split_records0.0030.0000.003
sqlite_database0.0030.0010.004
trim_whitespace0.0020.0000.002
tripeptide_dictionary0.0020.0010.002
unique_records000
unzip_before_cache0.0030.0000.003
upset_filters000
vertical_join0.0410.0050.047
wherever0.0100.0010.012
write_database0.0020.0010.002