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This page was generated on 2024-12-09 11:46 -0500 (Mon, 09 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4749
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4461
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4411
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4366
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4241
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 1231/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetMashR 1.1.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-12-08 13:40 -0500 (Sun, 08 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    OK    OK  


CHECK results for MetMashR on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MetMashR
Version: 1.1.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetMashR_1.1.0.tar.gz
StartedAt: 2024-12-09 07:29:24 -0000 (Mon, 09 Dec 2024)
EndedAt: 2024-12-09 07:33:46 -0000 (Mon, 09 Dec 2024)
EllapsedTime: 262.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MetMashR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetMashR_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MetMashR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (conda-forge gcc 14.2.0-1) 14.2.0
    GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MetMashR.Rcheck/00check.log’
for details.


Installation output

MetMashR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MetMashR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 19.775   0.992  29.872 

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

nameusersystemelapsed
AnnotationDb_database0.030.000.03
AnnotationDb_select0.0160.0000.016
BiocFileCache_database0.0220.0000.022
CompoundDb_source0.0110.0000.011
GO_database0.0130.0000.014
MTox700plus_database0.0250.0000.026
PathBank_metabolite_database0.030.000.03
add_columns0.010.000.01
add_labels0.0110.0000.011
annotation_bar_chart0.0110.0000.011
annotation_database0.0100.0000.011
annotation_histogram0.0160.0000.016
annotation_histogram2d0.0130.0040.017
annotation_pie_chart0.0180.0000.019
annotation_source0.0090.0000.010
annotation_table0.0100.0040.014
annotation_upset_chart0.0220.0000.021
annotation_venn_chart0.0160.0000.016
cache_as_is0.0360.0000.036
calc_ppm_diff0.0090.0000.010
calc_rt_diff0.0110.0000.010
cd_source0.0220.0000.022
chart_plot0.0150.0000.015
check_for_columns0.0120.0040.016
classyfire_lookup0.0060.0160.022
combine_columns0.0130.0040.017
combine_records0.0120.0000.012
combine_records_helper_functions0.0520.0150.068
combine_sources0.0270.0000.027
compute_column0.0110.0000.011
compute_record0.0070.0000.007
database_lookup0.0170.0000.018
eutils_lookup0.0170.0070.025
excel_database0.0180.0050.021
filter_labels0.0150.0000.015
filter_na0.0060.0000.007
filter_range0.0130.0000.012
filter_records0.0090.0000.008
filter_venn0.0130.0030.016
github_file0.0330.0050.037
greek_dictionary0.0080.0040.012
hmdb_lookup0.0190.0000.020
id_counts0.0060.0040.010
import_source0.0000.0000.001
is_writable0.0170.0060.024
kegg_lookup0.0100.0000.011
lcms_table0.0190.0000.019
lipidmaps_lookup0.0150.0070.023
ls_source0.0200.0010.020
model_apply0.2290.0070.236
mspurity_source0.0130.0000.012
mwb_compound_lookup0.0230.0000.024
mwb_refmet_database0.0370.0000.037
mwb_structure0.0090.0000.009
mz_match0.0120.0000.012
mzrt_match0.0150.0000.015
normalise_lipids0.0120.0000.012
normalise_strings0.0180.0000.018
openbabel_structure0.0210.0000.021
opsin_lookup0.0180.0000.018
pivot_columns0.0080.0000.009
prioritise_columns0.0140.0000.014
pubchem_compound_lookup0.0190.0000.019
pubchem_property_lookup0.0210.0000.022
pubchem_structure0.0110.0000.011
pubchem_widget0.0180.0000.018
racemic_dictionary0.0080.0000.009
rdata_database0.0140.0000.014
rds_cache0.0130.0000.013
rds_database0.0110.0000.012
read_database0.0280.0000.028
read_source0.0480.0040.052
remove_columns0.0080.0000.008
rename_columns0.0040.0040.008
required_cols0.0380.0000.038
rest_api0.0170.0000.017
rt_match0.0120.0000.013
select_columns0.0080.0000.008
split_column0.0130.0000.013
split_records0.010.000.01
sqlite_database0.0150.0000.015
trim_whitespace0.0050.0040.008
tripeptide_dictionary0.0090.0000.009
unique_records0.0010.0000.001
unzip_before_cache0.0160.0000.016
vertical_join0.1600.0040.164
wherever0.0540.0000.054
write_database0.0070.0000.008