Gavin Rhys Lloyd
| Snapshot Date: 2025-10-13 13:45 -0400 (Mon, 13 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-14 12:03 -0400 (Tue, 14 Oct 2025).
| 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" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
| 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 1272/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MetMashR 1.3.3 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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: 2025-10-14 01:54:31 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 02:02:57 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 505.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MetMashR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Extending_MetMashR.Rmd’ using rmarkdown
--- finished re-building ‘Extending_MetMashR.Rmd’
--- re-building ‘annotate_mixtures.Rmd’ using rmarkdown
--- finished re-building ‘annotate_mixtures.Rmd’
--- re-building ‘exploring_mtox.Rmd’ using rmarkdown
--- finished re-building ‘exploring_mtox.Rmd’
--- re-building ‘using_MetMashR.Rmd’ using rmarkdown
Quitting from using_MetMashR.Rmd:394-433 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.submit_api_query()`:
! 'getURL()' failed:
URL: https://www.lipidmaps.org/rest/compound/abbrev/AcCa%2814%3A0%29/inchi_key/json
error: Timeout was reached [www.lipidmaps.org]:
Resolving timed out after 10001 milliseconds
---
Backtrace:
▆
1. ├─struct::model_apply(WF, AT)
2. └─MetMashR::model_apply(WF, AT)
3. └─MetMashR (local) .local(M, D, ...)
4. ├─struct::model_apply(M[i], D)
5. └─MetMashR::model_apply(M[i], D)
6. └─MetMashR (local) .local(M, D, ...)
7. └─MetMashR:::.submit_api_query(URL = u, FUN = .submit_fun, params = param_list(M))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'using_MetMashR.Rmd' failed with diagnostics:
'getURL()' failed:
URL: https://www.lipidmaps.org/rest/compound/abbrev/AcCa%2814%3A0%29/inchi_key/json
error: Timeout was reached [www.lipidmaps.org]:
Resolving timed out after 10001 milliseconds
--- failed re-building ‘using_MetMashR.Rmd’
SUMMARY: processing the following file failed:
‘using_MetMashR.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/MetMashR.Rcheck/00check.log’
for details.
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)
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
14.595 0.763 24.373
MetMashR.Rcheck/MetMashR-Ex.timings
| name | user | system | elapsed | |
| AnnotationDb_database | 0.021 | 0.001 | 0.021 | |
| AnnotationDb_select | 0.016 | 0.000 | 0.015 | |
| BiocFileCache_database | 0.018 | 0.001 | 0.019 | |
| CompoundDb_source | 0.010 | 0.001 | 0.010 | |
| GO_database | 0.012 | 0.000 | 0.011 | |
| MTox700plus_database | 0.021 | 0.000 | 0.021 | |
| PathBank_metabolite_database | 0.018 | 0.001 | 0.019 | |
| add_columns | 0.009 | 0.000 | 0.009 | |
| add_labels | 0.011 | 0.000 | 0.011 | |
| annotation_bar_chart | 0.011 | 0.000 | 0.011 | |
| annotation_database | 0.01 | 0.00 | 0.01 | |
| annotation_histogram | 0.015 | 0.000 | 0.015 | |
| annotation_histogram2d | 0.015 | 0.001 | 0.016 | |
| annotation_pie_chart | 0.016 | 0.001 | 0.017 | |
| annotation_source | 0.009 | 0.000 | 0.008 | |
| annotation_table | 0.012 | 0.000 | 0.012 | |
| annotation_upset_chart | 0.025 | 0.004 | 0.028 | |
| annotation_venn_chart | 0.013 | 0.000 | 0.013 | |
| cache_as_is | 0.013 | 0.001 | 0.014 | |
| calc_ppm_diff | 0.009 | 0.000 | 0.009 | |
| calc_rt_diff | 0.009 | 0.000 | 0.010 | |
| cd_source | 0.021 | 0.000 | 0.021 | |
| chart_plot | 0.014 | 0.000 | 0.014 | |
| check_for_columns | 0.009 | 0.001 | 0.009 | |
| classyfire_lookup | 0.018 | 0.001 | 0.019 | |
| combine_columns | 0.943 | 0.000 | 0.943 | |
| combine_records | 0.008 | 0.000 | 0.008 | |
| combine_records_helper_functions | 0.038 | 0.000 | 0.038 | |
| combine_sources | 0.018 | 0.000 | 0.018 | |
| compute_column | 0.008 | 0.000 | 0.008 | |
| compute_record | 0.005 | 0.000 | 0.005 | |
| database_lookup | 0.012 | 0.000 | 0.012 | |
| eutils_lookup | 0.017 | 0.001 | 0.017 | |
| excel_database | 0.015 | 0.000 | 0.014 | |
| filter_labels | 0.01 | 0.00 | 0.01 | |
| filter_na | 0.005 | 0.000 | 0.005 | |
| filter_range | 0.008 | 0.001 | 0.009 | |
| filter_records | 0.007 | 0.000 | 0.007 | |
| filter_venn | 0.009 | 0.000 | 0.009 | |
| github_file | 0.021 | 0.000 | 0.021 | |
| greek_dictionary | 0.008 | 0.000 | 0.008 | |
| hmdb_lookup | 0.013 | 0.000 | 0.013 | |
| id_counts | 0.007 | 0.000 | 0.007 | |
| import_source | 0.001 | 0.000 | 0.001 | |
| is_writable | 0.005 | 0.000 | 0.005 | |
| kegg_lookup | 0.007 | 0.000 | 0.007 | |
| lcms_table | 0.012 | 0.001 | 0.013 | |
| lipidmaps_lookup | 0.016 | 0.000 | 0.016 | |
| ls_source | 0.013 | 0.000 | 0.013 | |
| model_apply | 0.155 | 0.000 | 0.155 | |
| mspurity_source | 0.011 | 0.000 | 0.010 | |
| mwb_compound_lookup | 0.018 | 0.000 | 0.018 | |
| mwb_refmet_database | 0.013 | 0.000 | 0.013 | |
| mwb_structure | 0.007 | 0.000 | 0.008 | |
| mz_match | 0.01 | 0.00 | 0.01 | |
| mzrt_match | 0.011 | 0.003 | 0.014 | |
| normalise_lipids | 0.010 | 0.002 | 0.011 | |
| normalise_strings | 0.005 | 0.002 | 0.008 | |
| opsin_lookup | 0.011 | 0.006 | 0.017 | |
| pivot_columns | 0.007 | 0.001 | 0.008 | |
| prioritise_columns | 0.009 | 0.003 | 0.012 | |
| pubchem_compound_lookup | 0.012 | 0.004 | 0.016 | |
| pubchem_property_lookup | 0.016 | 0.003 | 0.019 | |
| pubchem_structure | 0.006 | 0.003 | 0.010 | |
| pubchem_widget | 0.014 | 0.001 | 0.015 | |
| racemic_dictionary | 0.005 | 0.002 | 0.008 | |
| rdata_database | 0.011 | 0.001 | 0.013 | |
| rds_cache | 0.009 | 0.003 | 0.012 | |
| rds_database | 0.009 | 0.002 | 0.011 | |
| read_database | 0.006 | 0.002 | 0.008 | |
| read_source | 0.010 | 0.007 | 0.017 | |
| remove_columns | 0.007 | 0.000 | 0.007 | |
| rename_columns | 0.007 | 0.000 | 0.007 | |
| required_cols | 0.010 | 0.003 | 0.013 | |
| rest_api | 0.013 | 0.001 | 0.014 | |
| rt_match | 0.009 | 0.001 | 0.010 | |
| select_columns | 0.006 | 0.000 | 0.007 | |
| split_column | 0.010 | 0.002 | 0.012 | |
| split_records | 0.007 | 0.003 | 0.010 | |
| sqlite_database | 0.011 | 0.002 | 0.013 | |
| trim_whitespace | 0.006 | 0.001 | 0.007 | |
| tripeptide_dictionary | 0.008 | 0.000 | 0.007 | |
| unique_records | 0.001 | 0.000 | 0.001 | |
| unzip_before_cache | 0.013 | 0.001 | 0.014 | |
| upset_filters | 0 | 0 | 0 | |
| vertical_join | 0.118 | 0.027 | 0.146 | |
| wherever | 0.029 | 0.008 | 0.037 | |
| write_database | 0.006 | 0.000 | 0.007 | |