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### Running command:
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###   /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_1.39.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.39.0’
* 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 ... 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 18.9Mb
  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 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: imprintedGenes_GTEx
> ### Title: Creates a imprinted genes track from GTEx
> ### Aliases: imprintedGenes_GTEx
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library("Gviz")
> gen<-"hg19"
> chr<- "chr6"
> start <- 144251437
> end <- 144330541
> 
> if(interactive()){
+    allIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="all", classification="imprinted",showId=TRUE)
+    allimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="all", classification="imprinted",showId=TRUE)
+    StomachIGtrack <-imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="Stomach", classification="all",showId=TRUE)
+    PancreasIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="Pancreas", classification="all",showId=TRUE)
+    PancreasimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="Pancreas", classification="biallelic",showId=TRUE)
+ 
+    imprintinglist <- list(allIGtrack,allimprintedIGtrack,
+    StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)
+ 
+   plotTracks(imprintinglist, from = start, to = end,
+                                    fontfamily="sans",fontfamily.title="sans")
+ 
+ } else {
+ 
+   data(allIGtrack)
+   data(allimprintedIGtrack)
+   data(StomachIGtrack)
+   data(PancreasIGtrack)
+   data(PancreasimprintedIGtrack)
+ 
+    imprintinglist <- list(allIGtrack,allimprintedIGtrack,
+    StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)
+ 
+   plotTracks(imprintinglist, from = start, to = end,
+                                    fontfamily="sans",fontfamily.title="sans")
+ }
Error in do.call(c, obj@http_config) : 
  no slot of name "http_config" for this object of class "Mart"
Calls: plotTracks ... list2 -> martHTTPConfig -> martHTTPConfig -> do.call
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
coMET-package 5.887  0.213  19.494
comet.web     4.902  0.215  22.152
* 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.