Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:20 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for MicrobiomeProfiler on machv2


To the developers/maintainers of the MicrobiomeProfiler package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1145/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiomeProfiler 1.0.0  (landing page)
Meijun Chen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MicrobiomeProfiler
git_branch: RELEASE_3_14
git_last_commit: 3740c10
git_last_commit_date: 2021-10-26 13:13:02 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MicrobiomeProfiler
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2022-04-12 15:27:38 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:32:22 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 284.6 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MicrobiomeProfiler.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiomeProfiler/DESCRIPTION’ ... OK
* this is package ‘MicrobiomeProfiler’ version ‘1.0.0’
* 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 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MicrobiomeProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: K01622,K11263,K15634,K00189,K10046,K13951
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG0078,COG0367,COG0072,COG0160,COG2125,COG1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158846,29523,1735,469,544,1743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C000500,PW_C000964,PW_C000062,PW_C000042,PW_C008133,PW_C040095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C00433,C00620,C01530,C06019,C00476,C20878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0001846,HMDB0000641,HMDB0001429,HMDB0002281,HMDB0000271,HMDB0000294
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> 
> proc.time()
   user  system elapsed 
 15.571   0.761  16.318 

Example timings

MicrobiomeProfiler.Rcheck/MicrobiomeProfiler-Ex.timings

nameusersystemelapsed
Psoriasis_data0.0050.0020.007
Rat_data0.0020.0020.004
bitr_smpdb0.1510.0140.165
enrichCOG0.0330.0030.035
enrichHMDB0.2080.0110.219
enrichKO0.4980.0300.528
enrichMBKEGG0.2560.0090.266
enrichMDA0.0970.0070.104
enrichSMPDB0.1810.0090.190
microbiota_taxlist0.0010.0010.002
run_MicrobiomeProfiler0.0000.0010.000