Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-08 23:55 -0400 (Sat, 08 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
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 21/33HostnameOS / ArchCHECK
EpiMix 1.6.1  (landing page)
Yuanning Zheng
Snapshot Date: 2024-06-08 09:55 -0400 (Sat, 08 Jun 2024)
git_url: https://git.bioconductor.org/packages/EpiMix
git_branch: RELEASE_3_19
git_last_commit: 0e85cbb
git_last_commit_date: 2024-05-01 12:48:30 -0400 (Wed, 01 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  


CHECK results for EpiMix on lconway

To the developers/maintainers of the EpiMix package:
- 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: EpiMix
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no EpiMix_1.6.1.tar.gz
StartedAt: 2024-06-08 16:10:12 -0400 (Sat, 08 Jun 2024)
EndedAt: 2024-06-08 16:13:14 -0400 (Sat, 08 Jun 2024)
EllapsedTime: 182.1 seconds
RetCode: 0
Status:   OK  
CheckDir: EpiMix.Rcheck
Warnings: 0

Tests output

EpiMix.Rcheck/tests/test_GEO_download.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.

> test_GEO_download <- function(){
+   METdirectories <- GEO_Download_DNAMethylation(AccessionID = 'GSE114134', targetDirectory = tempdir())
+   RUnit::checkTrue(length(METdirectories)>0)
+ }
> 
> 
> 
> 
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.123   0.042   0.161 

EpiMix.Rcheck/tests/test_TCGA_getData.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.

> test_TCGA_getData <- function(){
+   EpiMixResults <- TCGA_GetData(CancerSite = "OV",
+                                 mode = "Regular",
+                                 roadmap.epigenome.ids =  "E097", # only required for running the enhancer mode
+                                 outputDirectory = tempdir(),
+                                 cores = 10)
+ 
+   RUnit::checkEquals(nrow(EpiMixResults$FunctionalPairs), 789)
+ }
> 
> 
> 
> 
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.122   0.041   0.161 

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no EpiMix_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/EpiMix.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* this is package ‘EpiMix’ version ‘1.6.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EpiMix’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 ... 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 ... SKIPPED
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'TCGA_Load_MolecularData.Rd':
  ‘MissingValueThresholdGene’ ‘MissingValueThresholdSample’

Documented arguments not in \usage in Rd file 'get.prevalence.Rd':
  ‘MET_matrix’

Documented arguments not in \usage in Rd file 'test_gene_expr.Rd':
  ‘raw.pvalue.threshold’ ‘adjusted.pvalue.threshold’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘test_GEO_download.R’
  Running ‘test_TCGA_getData.R’
 OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/EpiMix.Rcheck/00check.log’
for details.


Installation output

EpiMix.Rcheck/00install.out

* installing *source* package ‘EpiMix’ ...
** using staged installation
** R
** 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 (EpiMix)