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This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1233/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetMashR 1.1.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/MetMashR
git_branch: devel
git_last_commit: e797206
git_last_commit_date: 2024-10-29 11:34:47 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped


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: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2024-12-23 21:32:34 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 21:36:26 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 232.7 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MetMashR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.1.0’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-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’ ...
** 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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 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 
 16.700   1.169  29.247 

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

nameusersystemelapsed
AnnotationDb_database0.0210.0000.021
AnnotationDb_select0.0120.0010.013
BiocFileCache_database0.0200.0010.021
CompoundDb_source0.0100.0010.010
GO_database0.0110.0010.012
MTox700plus_database0.0220.0010.023
PathBank_metabolite_database0.0220.0000.024
add_columns0.0090.0010.009
add_labels0.0110.0010.011
annotation_bar_chart0.0110.0010.011
annotation_database0.0100.0010.011
annotation_histogram0.0160.0000.017
annotation_histogram2d0.0180.0020.020
annotation_pie_chart0.0180.0020.021
annotation_source0.0080.0020.009
annotation_table0.0120.0020.013
annotation_upset_chart0.0160.0030.019
annotation_venn_chart0.0110.0020.013
cache_as_is0.0280.0040.032
calc_ppm_diff0.0090.0010.010
calc_rt_diff0.0070.0010.008
cd_source0.0160.0030.017
chart_plot0.0100.0020.011
check_for_columns0.0090.0020.011
classyfire_lookup0.0170.0030.019
combine_columns0.0100.0020.010
combine_records0.0100.0020.012
combine_records_helper_functions0.0450.0080.053
combine_sources0.0230.0030.026
compute_column0.0080.0010.010
compute_record0.0050.0010.006
database_lookup0.0110.0010.012
eutils_lookup0.0140.0020.017
excel_database0.0130.0020.015
filter_labels0.0090.0010.010
filter_na0.0050.0010.006
filter_range0.0100.0020.011
filter_records0.0050.0010.007
filter_venn0.0120.0010.013
github_file0.0210.0030.023
greek_dictionary0.0090.0020.010
hmdb_lookup0.0150.0020.017
id_counts0.0090.0010.010
import_source0.0010.0000.001
is_writable0.0140.0020.016
kegg_lookup0.0100.0020.012
lcms_table0.0110.0020.013
lipidmaps_lookup0.0140.0020.016
ls_source0.0140.0020.016
model_apply0.2560.0120.270
mspurity_source0.0090.0000.010
mwb_compound_lookup0.0160.0000.017
mwb_refmet_database0.010.000.01
mwb_structure0.0050.0000.006
mz_match0.010.000.01
mzrt_match0.010.000.01
normalise_lipids0.0090.0000.009
normalise_strings0.0180.0000.018
openbabel_structure0.0200.0010.022
opsin_lookup0.0190.0010.019
pivot_columns0.0060.0000.006
prioritise_columns0.0080.0000.008
pubchem_compound_lookup0.0150.0010.015
pubchem_property_lookup0.0150.0000.015
pubchem_structure0.0090.0000.010
pubchem_widget0.0170.0000.017
racemic_dictionary0.0060.0000.006
rdata_database0.0090.0000.010
rds_cache0.010.000.01
rds_database0.0080.0000.008
read_database0.0190.0020.021
read_source0.0400.0010.041
remove_columns0.0070.0010.009
rename_columns0.0050.0000.006
required_cols0.0270.0000.028
rest_api0.0130.0000.013
rt_match0.0090.0000.008
select_columns0.0080.0010.008
split_column0.0100.0000.009
split_records0.0080.0000.008
sqlite_database0.0110.0000.011
trim_whitespace0.0070.0000.007
tripeptide_dictionary0.0080.0010.008
unique_records0.0010.0000.001
unzip_before_cache0.0150.0000.016
vertical_join0.1490.0080.159
wherever0.0490.0020.050
write_database0.0060.0010.006