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This page was generated on 2022-03-18 11:08:01 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 1150/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiomeProfiler 1.1.3  (landing page)
Meijun Chen
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/MicrobiomeProfiler
git_branch: master
git_last_commit: bd2ad9f
git_last_commit_date: 2022-03-15 05:00:40 -0400 (Tue, 15 Mar 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MicrobiomeProfiler
Version: 1.1.3
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiomeProfiler.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiomeProfiler_1.1.3.tar.gz
StartedAt: 2022-03-17 19:34:54 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:37:39 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 164.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiomeProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiomeProfiler.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiomeProfiler_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MicrobiomeProfiler.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MicrobiomeProfiler/DESCRIPTION' ... OK
* this is package 'MicrobiomeProfiler' version '1.1.3'
* 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 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:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MicrobiomeProfiler
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MicrobiomeProfiler' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MicrobiomeProfiler'
    finding HTML links ... done
    MicrobiomeProfiler-package              html  
    Psoriasis_data                          html  
    Rat_data                                html  
    bitr_smpdb                              html  
    enrichCOG                               html  
    enrichHMDB                              html  
    enrichKO                                html  
    enrichMBKEGG                            html  
    enrichMDA                               html  
    enrichSMPDB                             html  
    microbiota_taxlist                      html  
    run_MicrobiomeProfiler                  html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MACPET' is missing or broken
 done

Tests output

MicrobiomeProfiler.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: K00971,K07515,K17743,K00041,K00208,K00116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG2174,COG1527,COG2167,COG0134,COG4830,COG1997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 41978,59823,135858,41978,1737406,239935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C000964,PW_C000414,PW_C009794,PW_C000862,PW_C000148,PW_C000164
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C00084,C00249,C00507,C00879,C06187,C05378
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0000128,HMDB0002065,HMDB0002111,HMDB0000002,HMDB0001341,HMDB0002111
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> 
> proc.time()
   user  system elapsed 
   8.28    0.64    8.95 

Example timings

MicrobiomeProfiler.Rcheck/MicrobiomeProfiler-Ex.timings

nameusersystemelapsed
Psoriasis_data000
Rat_data0.010.000.01
bitr_smpdb0.070.010.08
enrichCOG0.040.020.06
enrichHMDB0.060.020.08
enrichKO0.270.000.27
enrichMBKEGG0.130.000.12
enrichMDA0.090.010.13
enrichSMPDB0.090.000.09
microbiota_taxlist000
run_MicrobiomeProfiler000