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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.39.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.39.1’
* 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 ‘coMET’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 19.0Mb
  sub-directories of 1Mb or more:
    data      7.6Mb
    extdata  10.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 whether startup messages can be suppressed ... 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
draw.plot.annotation : <anonymous>: no visible global function
  definition for 'ggplotGrob'
draw.plot.annotation: no visible global function definition for
  'viewTracks'
draw.plot.annotation: no visible global function definition for
  'trackList'
eQTL: no visible binding for global variable 'chromosome_stop'
eQTL: no visible binding for global variable 'chromosome_start'
eQTL: no visible binding for global variable 'chromosome_name'
eQTL_GTEx: no visible binding for global variable 'snp_pos'
eQTL_GTEx: no visible binding for global variable 'snp_chrom'
eQTL_GTEx: no visible binding for global variable 'gene_start'
eQTL_GTEx: no visible binding for global variable 'gene_stop'
eQTL_GTEx: no visible binding for global variable 'gene_chr'
geneExpression_GTEx: no visible global function definition for 'as'
metQTL: no visible binding for global variable 'chromosome_stop'
metQTL: no visible binding for global variable 'chromosome_start'
metQTL: no visible binding for global variable 'chromosome_name'
pizza: no visible global function definition for 'par'
pizza: no visible global function definition for 'plot.new'
pizza: no visible global function definition for 'plot.window'
pizza: no visible global function definition for 'polygon'
pizza: no visible global function definition for 'lines'
pizza: no visible global function definition for 'text'
psiQTL_GTEx: no visible binding for global variable 'pos_snp'
psiQTL_GTEx: no visible binding for global variable 'chr_snp'
psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon'
psiQTL_GTEx: no visible binding for global variable 'chr_exon'
Undefined global functions or variables:
  as chr_exon chr_snp chromosome_name chromosome_start chromosome_stop
  gene_chr gene_start gene_stop ggplotGrob lines par plot.new
  plot.window polygon pos_middle_exon pos_snp snp_chrom snp_pos text
  trackList viewTracks
Consider adding
  importFrom("graphics", "lines", "par", "plot.new", "plot.window",
             "polygon", "text")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) ChIPTF_ENCODE.Rd:36: Escaped LaTeX specials: \#
* 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
Objects in \usage without \alias in Rd file 'check.configVar.cometlist.Rd':
  ‘check.configVar.cometlist’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘coMET-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coMET-package
> ### Title: visualisation of regional epigenome-wide association scan (EWAS)
> ###   results and DNA co-methylation patterns (and also for other omic-WAS)
> ### Aliases: coMET-package coMET
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
> configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
> myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
> myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
> mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
> 
> chrom <- "chr2"
> start <- 38290160
> end <- 38303219
> gen <- "hg38"
> 
> if(interactive()){
+     genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE)
+     snptrack <- snpBiomart_ENSEMBL(gen, chrom, start, end,
+                 dataset="hsapiens_snp_som",showId=FALSE)
+     strutrack <- structureBiomart_ENSEMBL(gen, chrom, start, end,
+                 strand, dataset="hsapiens_structvar_som")
+     clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
+     clinCNV<-ClinVarCnv_UCSC(gen,chrom,start,end)
+     gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end)
+     geneRtrack <-GeneReviews_UCSC(gen,chrom,start,end)
+     listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
+                  clinCNV,gwastrack,geneRtrack)
+     comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
+       cormatrix.file=mycorrelation, cormatrix.type="listfile",
+       mydata.large.file=myexpressfile, mydata.large.type="listfile",
+       tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)
+ } else {
+     data(geneENSEMBLtrack)
+     data(snpBiomarttrack)
+     data(ISCAtrack)
+     data(strucBiomarttrack)
+     data(ClinVarCnvTrack)
+     data(clinVarMaintrack)
+     data(GWASTrack)
+     data(GeneReviewTrack)
+ 
+     listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
+                     clinCNV,gwastrack,geneRtrack)
+     comet(config.file=configfile, mydata.file=myinfofile, mydata.type="listfile",
+         cormatrix.file=mycorrelation, cormatrix.type="listfile",
+         mydata.large.file=myexpressfile, mydata.large.type="listfile",
+         tracks.gviz=listgviz,
+         verbose=FALSE, print.image=FALSE,disp.pvalueplot=TRUE)
+ }
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Error in errorHandler(responseError) : Internal Server Error
Calls: comet ... doTryCatch -> <Anonymous> -> handleResponse -> errorHandler
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
chromatinHMMAll_UCSC 5.359  0.029   5.409
* 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: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘coMET’ ...
** this is package ‘coMET’ version ‘1.39.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
Warning in fun(libname, pkgname) :
  Package 'coMET' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package can be loaded from final location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
Warning in fun(libname, pkgname) :
  Package 'coMET' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (coMET)

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> require("coMET") || stop("unable to load Package:coMET")
Loading required package: coMET
Loading required package: grid
Loading required package: biomaRt
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

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


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: psych

Attaching package: 'psych'

The following object is masked from 'package:GenomicRanges':

    distance

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

    distance, reflect

[1] TRUE
Warning messages:
1: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' 
2: In fun(libname, pkgname) :
  Package 'coMET' is deprecated and will be removed from Bioconductor
  version 3.22
> BiocGenerics:::testPackage("coMET")


RUNIT TEST PROTOCOL -- Mon Mar 17 20:07:07 2025 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
coMET RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 18.197   1.008  19.333