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This page was generated on 2025-10-18 12:03 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1275/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetMashR 1.3.3  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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  NO, package depends on 'struct' which is not available
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'struct' which is not available
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'struct' which is not available
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MetMashR on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MetMashR_1.3.3.tar.gz
StartedAt: 2025-10-18 01:45:59 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 01:54:18 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 498.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MetMashR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MetMashR_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MetMashR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

MetMashR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MetMashR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "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.

> # 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 
 15.642   0.762  25.417 

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

nameusersystemelapsed
AnnotationDb_database0.0230.0000.023
AnnotationDb_select0.0130.0000.013
BiocFileCache_database0.0170.0000.017
CompoundDb_source0.0090.0000.009
GO_database0.0110.0000.011
MTox700plus_database0.020.000.02
PathBank_metabolite_database0.0180.0000.018
add_columns0.0060.0020.008
add_labels0.0080.0000.008
annotation_bar_chart0.0080.0000.008
annotation_database0.0080.0000.008
annotation_histogram0.0120.0000.012
annotation_histogram2d0.0120.0000.012
annotation_pie_chart0.0150.0000.015
annotation_source0.0050.0010.006
annotation_table0.010.000.01
annotation_upset_chart0.0240.0000.024
annotation_venn_chart0.0120.0000.012
cache_as_is0.0110.0000.012
calc_ppm_diff0.0070.0000.007
calc_rt_diff0.0070.0000.007
cd_source0.0150.0000.015
chart_plot0.0080.0000.009
check_for_columns0.0070.0000.007
classyfire_lookup0.0160.0000.016
combine_columns0.7320.0000.732
combine_records0.0080.0000.008
combine_records_helper_functions0.0350.0010.037
combine_sources0.0170.0000.017
compute_column0.0080.0000.008
compute_record0.0060.0000.006
database_lookup0.0120.0000.012
eutils_lookup0.0170.0000.017
excel_database0.0160.0000.016
filter_labels0.0090.0000.010
filter_na0.0040.0000.004
filter_range0.0080.0000.008
filter_records0.0060.0000.006
filter_venn0.0080.0000.008
github_file0.0190.0000.020
greek_dictionary0.0080.0000.008
hmdb_lookup0.0110.0010.012
id_counts0.0060.0010.006
import_source0.0010.0000.001
is_writable0.0050.0000.004
kegg_lookup0.0070.0000.007
lcms_table0.0140.0000.014
lipidmaps_lookup0.0170.0000.016
ls_source0.0140.0000.014
model_apply0.1590.0010.161
mspurity_source0.0080.0000.008
mwb_compound_lookup0.0150.0000.015
mwb_refmet_database0.0120.0000.012
mwb_structure0.0060.0000.006
mz_match0.0070.0000.008
mzrt_match0.0080.0050.013
normalise_lipids0.0100.0010.010
normalise_strings0.0080.0000.008
opsin_lookup0.0120.0020.015
pivot_columns0.0070.0010.008
prioritise_columns0.0090.0020.011
pubchem_compound_lookup0.0150.0000.015
pubchem_property_lookup0.0120.0060.018
pubchem_structure0.0080.0010.008
pubchem_widget0.0100.0030.014
racemic_dictionary0.0050.0020.007
rdata_database0.0120.0000.011
rds_cache0.0100.0020.011
rds_database0.0080.0010.009
read_database0.0060.0000.007
read_source0.0130.0030.016
remove_columns0.0040.0020.006
rename_columns0.0070.0000.006
required_cols0.0100.0020.011
rest_api0.0100.0020.014
rt_match0.0080.0020.010
select_columns0.0050.0020.007
split_column0.0100.0010.011
split_records0.0070.0020.008
sqlite_database0.0100.0020.012
trim_whitespace0.0060.0010.006
tripeptide_dictionary0.0060.0010.007
unique_records000
unzip_before_cache0.0090.0040.013
upset_filters000
vertical_join0.1170.0280.145
wherever0.0330.0040.037
write_database0.0040.0020.006