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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1293/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMUPHin 1.20.0  (landing page)
Siyuan MA
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MMUPHin
git_branch: RELEASE_3_20
git_last_commit: 0f730a6
git_last_commit_date: 2024-10-29 10:41:21 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MMUPHin on kjohnson1

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: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MMUPHin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MMUPHin_1.20.0.tar.gz
StartedAt: 2024-12-21 01:46:34 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 01:48:15 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 100.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MMUPHin.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MMUPHin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MMUPHin_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MMUPHin.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMUPHin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMUPHin’ version ‘1.20.0’
* 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 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 ... 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 15.877  1.565  17.448
lm_meta             14.179  0.817  15.041
discrete_discover   10.318  0.609  10.968
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MMUPHin.Rcheck/00check.log’
for details.


Installation output

MMUPHin.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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(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 
  1.439   0.146   1.572 

Example timings

MMUPHin.Rcheck/MMUPHin-Ex.timings

nameusersystemelapsed
CRC_abd0.0600.0230.082
CRC_meta0.0070.0020.009
adjust_batch2.4070.1442.596
continuous_discover15.877 1.56517.448
discrete_discover10.318 0.60910.968
lm_meta14.179 0.81715.041
vaginal_abd0.0050.0070.011
vaginal_meta0.0020.0020.004