Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2023-11-02 11:40:56 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 1251/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiomeProfiler 1.8.0  (landing page)
Meijun Chen
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/MicrobiomeProfiler
git_branch: RELEASE_3_18
git_last_commit: 4aff8e7
git_last_commit_date: 2023-10-24 11:37:01 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for MicrobiomeProfiler on kunpeng2


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

raw results


Summary

Package: MicrobiomeProfiler
Version: 1.8.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:MicrobiomeProfiler.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings MicrobiomeProfiler_1.8.0.tar.gz
StartedAt: 2023-11-02 12:08:54 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 12:17:46 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 532.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiomeProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:MicrobiomeProfiler.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings MicrobiomeProfiler_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MicrobiomeProfiler.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiomeProfiler/DESCRIPTION’ ... OK
* this is package ‘MicrobiomeProfiler’ version ‘1.8.0’
* 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 R 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 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 in ‘inst/doc’ ... 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:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL MicrobiomeProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘MicrobiomeProfiler’ ...
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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: 5.3.1.1,4.1.2.13,1.1.2.7,2.3.3.3,6.2.1.5,1.3.5.1
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG0007,COG0066,COG0029,COG0022,COG0049,COG0005
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 41211,904,53246,218538,46506,821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C001104,PW_C001441,PW_C000040,PW_C001148,PW_C000134,PW_C000029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C00036,C05378,C00216,C15972,C00221,C00231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0000208,HMDB0001554,HMDB0001303,HMDB0001377,HMDB0000045,HMDB0011111
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 17.603   1.365  25.099 

Example timings

MicrobiomeProfiler.Rcheck/MicrobiomeProfiler-Ex.timings

nameusersystemelapsed
Psoriasis_data0.0030.0000.003
Rat_data0.0010.0000.002
enrichCOG0.2620.0110.276
enrichHMDB0.0450.0030.050
enrichKO1.1430.0191.171
enrichMBKEGG0.1370.0000.139
enrichMDA0.1940.0000.195
enrichModule0.0540.0030.057
enrichSMPDB0.1520.0000.153
microbiota_taxlist0.0010.0000.001
run_MicrobiomeProfiler000