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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 658/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EpiMix 1.8.0  (landing page)
Yuanning Zheng
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/EpiMix
git_branch: RELEASE_3_20
git_last_commit: 5a1afba
git_last_commit_date: 2024-10-29 11:12:55 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for EpiMix on lconway

To the developers/maintainers of the EpiMix package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EpiMix.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: EpiMix
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiMix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiMix_1.8.0.tar.gz
StartedAt: 2024-11-19 21:49:33 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 22:00:36 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 663.1 seconds
RetCode: 0
Status:   OK  
CheckDir: EpiMix.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiMix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiMix_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EpiMix.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* this is package ‘EpiMix’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘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 ... 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 ... OK
* 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
Preprocess_DNAMethylation 10.869   0.91  12.338
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/EpiMix.Rcheck/00check.log’
for details.


Installation output

EpiMix.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* 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)

Tests output

EpiMix.Rcheck/tests/runTests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> BiocGenerics:::testPackage("EpiMix")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Running Enhancer mode...
Fetching probe annotation...
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
require("GenomicRanges")
Found 457 samples in group.1 and 32 samples in group.2
Fetching enhancer CpGs from Roadmap Epigenomics...
Downloading chromatin states from the Roadmap Epigenomics...
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

	Identifed 65057 enhancer CpGs from the epigenome E096 
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Returning distal probes: 160862
Found 3 CpGs associated with distal enhancers in the methylation dataset

Starting Beta mixture modeling.
Running Beta mixture model on 3 probes and on 457 samples.

  |                                                                            
  |                                                                      |   0%
Found 3 differentially methylated CpGs
Modeling the gene expression for enhancers...
Searching for the 20 near genes
Identifying gene position for each probe
Looking for differentially methylated enhancers associated with gene expression

  |                                                                            
  |                                                                      |   0%Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 805 random genes instead.

  |                                                                            
  |=======================                                               |  33%Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 793 random genes instead.

  |                                                                            
  |===============================================                       |  67%Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 798 random genes instead.

  |                                                                            
  |======================================================================| 100%
Found 7 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
Running lncRNA mode...
We recommend using the kallisto-sleuth pipline to process the RNA-seq data in order to detect more lncRNAs.
        Please see our publication for details: PMID: 31808800
Fetching probe annotation...
Found 457 samples in group.1 and 32 samples in group.2

Starting Beta mixture modeling.
Running Beta mixture model on 5 probes and on 457 samples.

  |                                                                            
  |                                                                      |   0%
Found 5 differentially methylated probes
Identifying functional CpG-gene pairs...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
Found 5 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
Running miRNA mode...
Please be mindful that the gene expression data are expected to be data obtained from microRNA-seq.
Fetching probe annotation...
Found 457 samples in group.1 and 32 samples in group.2

Starting Beta mixture modeling.
Running Beta mixture model on 6 probes and on 457 samples.

  |                                                                            
  |                                                                      |   0%
Found 6 differentially methylated probes
Identifying functional CpG-gene pairs...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%
Found 6 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
Running Regular mode...
Fetching probe annotation...
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Found 474 samples with both methylation and gene expression data.
Modeling gene expression...

  |                                                                            
  |                                                                      |   0%
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  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
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  |=====================                                                 |  30%
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  |============================                                          |  40%
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  |===================================                                   |  50%
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  |==========================================                            |  60%
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  |=================================================                     |  70%
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  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
Found 5 transcriptionally predictive probes.
Found 457 samples in group.1 and 32 samples in group.2

Starting Beta mixture modeling.
Running Beta mixture model on 5 probes and on 457 samples.

  |                                                                            
  |                                                                      |   0%
Found 5 differentially methylated CpGs
Identifying functional CpG-gene pairs...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |======================================================================| 100%
Found 5 functional probe-gene pairs.
Saving the EpiMix results to the output directory...


RUNIT TEST PROTOCOL -- Tue Nov 19 22:00:24 2024 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
EpiMix RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning message:
executing %dopar% sequentially: no parallel backend registered 
> 
> proc.time()
   user  system elapsed 
107.870   7.222 146.900 

Example timings

EpiMix.Rcheck/EpiMix-Ex.timings

nameusersystemelapsed
EpiMix000
EpiMix_PlotGene000
EpiMix_PlotModel0.5780.0400.630
EpiMix_PlotProbe000
EpiMix_PlotSurvival000
EpiMix_getInfiniumAnnotation000
GEO_Download_DNAMethylation000
GEO_Download_GeneExpression000
GetSurvivalProbe000
Preprocess_DNAMethylation10.869 0.91012.338
Preprocess_GeneExpression1.0520.0121.067
TCGA_Download_DNAmethylation0.0000.0000.001
TCGA_Download_GeneExpression0.0010.0010.000
TCGA_GetData000
TCGA_GetSampleInfo0.0110.0020.012
TCGA_Preprocess_DNAmethylation000
TCGA_Preprocess_GeneExpression000
find_miRNA_targets0.0010.0000.000
functionEnrich000
getFunctionalGenes000
getRoadMapEnhancerProbes0.0000.0000.001