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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAprobR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAprobR_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/RNAprobR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAprobR/DESCRIPTION’ ... OK
* this is package ‘RNAprobR’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘RNAprobR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'RNAprobR' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/RNAprobR.Rcheck/00install.out’ for details.
* 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 ... OK
* checking R 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RNAprobR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bedgraph2norm
> ### Title: Import bedgraph to GRanges
> ### Aliases: bedgraph2norm
> 
> ### ** Examples
> 
> dummy_euc_GR_control <- GRanges(seqnames="DummyRNA",
+ IRanges(start=round(runif(100)*100), width=round(runif(100)*100+1)),
+         strand="+", EUC=round(runif(100)*100))
> dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
+                                 IRanges(start=round(runif(100)*100),
+                                         width=round(runif(100)*100+1)),
+                                 strand="+", EUC=round(runif(100)*100))
> dummy_comp_GR_control <- comp(dummy_euc_GR_control)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_norm <- dtcr(control_GR=dummy_comp_GR_control,
+                    treated_GR=dummy_comp_GR_treated)
> 
> write(paste(c("chr1", 134212702, 134229870, "DummyRNA", 0, "+", 134212806,
+             134228958, 0, 8, "347,121,24,152,66,120,133,1973,",
+             "0,8827,10080,11571,12005,13832,14433,15195,"), collapse = "\t"),
+       file="dummy.bed")
> norm2bedgraph(norm_GR = dummy_norm, bed_file = "dummy.bed")
Warning: normalization method to convert not specified. dtcr chosen.
> 
> write(c(">DummyRNA", paste(sample(c("A","C","G","T"), 100, replace=TRUE),
+                            collapse="")), file="dummy.fa")
> bedgraph2norm(bedgraph_file = "out_file.bedgraph", fasta_file = "dummy.fa",
+               bed_file = "dummy.bed")
Warning in asMethod(object) : NAs introduced by coercion
Error: 'GenomicRangesList' is defunct.
Use 'GRangesList(..., compress=FALSE)' instead.
See help("Defunct")
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/RNAprobR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RNAprobR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RNAprobR’ ...
** 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
Warning: Package 'RNAprobR' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'RNAprobR' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package keeps a record of temporary installation path
* DONE (RNAprobR)