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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:EpiMix.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings EpiMix_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiMix.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* this is package ‘EpiMix’ version ‘1.9.0’
* 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'
 INFO
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 ... 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 10.516  0.985  11.876
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiMix.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL EpiMix
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Running Enhancer mode...
Fetching probe annotation...
sesameData not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
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 
sesameData not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
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...
sesameData not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Found 474 samples with both methylation and gene expression data.
Modeling gene expression...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  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 -- Thu Nov 21 23:59:13 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 
109.435   4.333 118.077