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This page was generated on 2024-04-17 11:36:08 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1290/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMUPHin 1.16.0  (landing page)
Siyuan MA
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/MMUPHin
git_branch: RELEASE_3_18
git_last_commit: 61bc5dc
git_last_commit_date: 2023-10-24 11:17:37 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MMUPHin on nebbiolo2


To the developers/maintainers of the MMUPHin package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MMUPHin.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: MMUPHin
Version: 1.16.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MMUPHin.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MMUPHin_1.16.0.tar.gz
StartedAt: 2024-04-16 01:02:15 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 01:04:40 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 144.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MMUPHin.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MMUPHin.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MMUPHin_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MMUPHin.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MMUPHin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMUPHin’ version ‘1.16.0’
* 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 ‘MMUPHin’ 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 ... NOTE
Maaslin2_wrapper: no visible binding for global variable
  ‘feature_rename’
Maaslin2_wrapper: no visible binding for global variable ‘name’
check_exposure: no visible binding for global variable ‘lvl_batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘Adjustment’
diagnostic_adjust_batch: no visible binding for global variable ‘batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘mean_overall’
diagnostic_adjust_batch: no visible binding for global variable
  ‘mean_batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘Feature’
diagnostic_continuous_discover: no visible binding for global variable
  ‘community’
diagnostic_continuous_discover: no visible binding for global variable
  ‘correlation’
diagnostic_continuous_discover: no visible binding for global variable
  ‘batch’
diagnostic_discrete_discover: no visible binding for global variable
  ‘k’
Undefined global functions or variables:
  Adjustment Feature batch community correlation feature_rename k
  lvl_batch mean_batch mean_overall name
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
continuous_discover 27.097  2.848  29.947
lm_meta             13.738  0.203  13.943
discrete_discover   10.914  0.228  11.143
* 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 ...
  ‘MMUPHin.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘MMUPHin.Rmd’
  ...
       YuJ_2015.metaphlan_bugs_list.stool 
                                      128 
   ZellerG_2014.metaphlan_bugs_list.stool 
                                      157 

> knitr::include_graphics("../man/figures/adj_batch_example.png")

  When sourcing ‘MMUPHin.R’:
Error: Cannot find the file(s): "../man/figures/adj_batch_example.png"
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MMUPHin.Rcheck/00check.log’
for details.


Installation output

MMUPHin.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MMUPHin
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MMUPHin’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (MMUPHin)

Tests output

MMUPHin.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(MMUPHin)
> 
> test_check("MMUPHin")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 41 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
  1.174   0.098   1.259 

Example timings

MMUPHin.Rcheck/MMUPHin-Ex.timings

nameusersystemelapsed
CRC_abd0.0440.0080.052
CRC_meta0.0060.0000.006
adjust_batch2.3570.0882.445
continuous_discover27.097 2.84829.947
discrete_discover10.914 0.22811.143
lm_meta13.738 0.20313.943
vaginal_abd0.0000.0040.004
vaginal_meta0.0000.0020.002