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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CoverageView.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CoverageView_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CoverageView.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoverageView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoverageView’ version ‘1.40.0’
* 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:
  .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 ‘CoverageView’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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 ... WARNING
Undocumented S4 classes:
  ‘BiocFile’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 ‘CoverageView-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cov.matrix
> ### Title: Compute a coverage matrix
> ### Aliases: cov.matrix cov.matrix,ANY,missing-method
> ###   cov.matrix,ANY,ANY-method
> 
> ### ** Examples
> 
> ###########
> ##BAM files
> ###########
>   
> ## Generating a coverage matrix with a single BAM file
>   
> #get a BAM test file
> aBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
>   
> #get a BED file with the TSS (transcription start site) coordinates of some genes
> bedfile<-system.file("extdata","testTSS.bed",package="CoverageView")
>   
> #create the CoverageBamFile object
> trm<-CoverageBamFile(aBAMfile,reads_mapped=28564510)
>   
> #generate the coverage matrix extending 100 nts on each side of the provided TSS
> #in the bedfile
> DF1=cov.matrix(tr=trm,coordfile=bedfile,extend=100,num_cores=2)
[INFO] A coverage matrix composed of average coverages will be generated.
[INFO] processing coords:chrI 200 +
[INFO] processing coords:chrI 400 -
>   
> #generate the coverage matrix extending 100 nts on each side of the TSS provided
> #in the bedfile and normalize the resulting coverages
> DF2=cov.matrix(tr=trm,coordfile=bedfile,extend=100,normalization="rpm",num_cores=2)
[INFO] A coverage matrix composed of average coverages will be generated.
[INFO] processing coords:chrI 200 +
[INFO] processing coords:chrI 400 -
>   
> #generate the coverage matrix extending 100 nts on each side of the TSS provided
> #in the bedfile and normalize the resulting coverages. This time we calculate the average
> #coverage in bins of 2 nucleotides
> DF3=cov.matrix(tr=trm,coordfile=bedfile,extend=100,normalization="rpm",bin_width=2,num_cores=2)
[INFO] A coverage matrix composed of average coverages will be generated.
[INFO] processing coords:chrI 200 +
[INFO] processing coords:chrI 400 -
>   
> ## Generating a coverage matrix with 2 BAM files
>   
> #get 2 BAM test files
> treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
> ctrlBAMfile<-system.file("extdata","ctrl.bam",package="CoverageView")
>   
> #get a BED file with the TSS (transcription start site) coordinates of some genes
> bedfile<-system.file("extdata","testTSS.bed",package="CoverageView")
>   
> #create 2 CoverageBamFile objects
> trm<-CoverageBamFile(treatBAMfile,reads_mapped=28564510)
> ctl<-CoverageBamFile(ctrlBAMfile,reads_mapped=26713667)
>   
> #generate the coverage matrix extending 100 nts on each side of the TSS provided
> #in the bedfile and normalize the resulting coverages.The matrix elements are obtained
> #by computing the ratio of the coverages of the trm against the ctl objects and then
> #calculating the log2 of the ratios
> DF4=cov.matrix(tr=trm,ctl=ctl,coordfile=bedfile,extend=100,normalization="rpm",do="log2ratio",num_cores=2)
[INFO] A coverage matrix will be generated by calculating the 'log2ratio' of the coverages.
[INFO] processing:/home/biocbuild/R/R-4.3.1/site-library/CoverageView/extdata/treat.bam
[INFO] processing coords:chrI 200 +
[INFO] processing coords:chrI 400 -
[INFO] processing:/home/biocbuild/R/R-4.3.1/site-library/CoverageView/extdata/ctrl.bam
[INFO] processing coords:chrI 200 +
Warning in mclapply(1:nrow(grDF), loopfun, mc.cores = num_cores, obj = ctl) :
  scheduled core 2 did not deliver a result, all values of the job will be affected
Error in m/readcount : non-numeric argument to binary operator
Calls: cov.matrix -> cov.matrix -> .do.normalization
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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CoverageView.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL CoverageView
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘CoverageView’ ...
** using staged installation
** R
** data
** 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 (CoverageView)