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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1272/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiomeProfiler 1.15.0  (landing page)
Guangchuang Yu
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/MicrobiomeProfiler
git_branch: devel
git_last_commit: 9367a71
git_last_commit_date: 2025-04-15 12:40:06 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MicrobiomeProfiler on kjohnson3

To the developers/maintainers of the MicrobiomeProfiler package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MicrobiomeProfiler.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: MicrobiomeProfiler
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MicrobiomeProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MicrobiomeProfiler_1.15.0.tar.gz
StartedAt: 2025-08-08 20:18:05 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 20:19:08 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 63.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiomeProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MicrobiomeProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MicrobiomeProfiler_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MicrobiomeProfiler.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiomeProfiler/DESCRIPTION’ ... OK
* this is package ‘MicrobiomeProfiler’ version ‘1.15.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MicrobiomeProfiler’ can be installed ... OK
* checking installed package size ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: OK


Installation output

MicrobiomeProfiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MicrobiomeProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘MicrobiomeProfiler’ ...
** this is package ‘MicrobiomeProfiler’ version ‘1.15.0’
** using staged installation
** R
** data
** 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 (MicrobiomeProfiler)

Tests output

MicrobiomeProfiler.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "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.

> library(testthat)
> library(MicrobiomeProfiler)

> test_check("MicrobiomeProfiler")
--> No gene can be mapped....
--> Expected input gene ID: 1.1.1.47,2.7.9.1,1.1.1.343,2.7.1.63,1.3.2.4,2.7.1.147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG0077,COG0003,COG0064,COG0067,COG0035,COG0063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 310298,59823,33038,46506,1338,360807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C000413,PW_C000826,PW_C040711,PW_C000721,PW_C001148,PW_C001847
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C00469,C15973,C01801,C05381,C00158,C00036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0001248,HMDB0000538,HMDB0001397,HMDB0000208,HMDB0001303,HMDB0001491
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  3.155   0.197   3.383 

Example timings

MicrobiomeProfiler.Rcheck/MicrobiomeProfiler-Ex.timings

nameusersystemelapsed
Psoriasis_data0.0010.0010.001
Rat_data0.0000.0010.000
enrichCOG0.0260.0020.029
enrichHMDB0.0150.0020.017
enrichKO0.2000.0190.218
enrichMBKEGG0.0490.0050.056
enrichMDA0.0630.0030.067
enrichModule0.0210.0010.021
enrichSMPDB0.0500.0010.051
microbiota_taxlist0.0010.0000.000
run_MicrobiomeProfiler000