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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings coMET_1.39.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data      7.7Mb
    extdata   6.1Mb
* 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 loading without being on the library search path ... 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 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.web
> ### Title: Visualize EWAS results in a genomic region of interest with
> ###   predefined annotation tracks
> ### Aliases: comet.web
> ### Keywords: hplot
> 
> ### ** Examples
> 
> extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
> configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver.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")
> 
> comet.web(config.file=configfile, mydata.file=myinfofile, cormatrix.file=mycorrelation,
+     mydata.large.file=myexpressfile, print.image=FALSE,verbose=FALSE)
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.web ... doTryCatch -> <Anonymous> -> handleResponse -> errorHandler
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
coMET-package 6.448  0.248  18.058
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘coMET.Rnw’ using knitr

Quitting from coMET.Rnw:336-345 [cometwebPlot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     x
  1. \-coMET::comet.web(...)
  2.   \-coMET:::create.tracks.web(config.var, gbl.var)
  3.     \-coMET::chromatinHMMAll_UCSC(...)
  4.       \-coMET::chromatinHMMOne_UCSC(...)
  5.         +-rtracklayer::getTable(ucscTableQuery(gen, range = mygrange, table = table.name))
  6.         \-rtracklayer::getTable(ucscTableQuery(gen, range = mygrange, table = table.name))
  7.           \-rtracklayer (local) .local(object, ...)
  8.             +-restfulr::read(url$getData$track, query)
  9.             \-restfulr::read(url$getData$track, query)
 10.               +-base::tryCatch(...)
 11.               | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.               |   \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.               |     \-base (local) doTryCatch(return(expr), name, parentenv, handler)
 14.               \-x@protocol$read(x, cacheInfo)
 15.                 \-restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 16.                   \-restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'coMET.Rnw' failed with diagnostics:
Internal Server Error

--- failed re-building ‘coMET.Rnw’

SUMMARY: processing the following file failed:
  ‘coMET.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL coMET
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> 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 -- Wed Mar 19 21:36:06 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 
 14.991   0.818  15.799