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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicScores.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicScores_2.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicScores.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 ‘GenomicScores/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicScores’ version ‘2.14.1’
* package encoding: UTF-8
* 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:
  inst/gscores-template/inst/extdata/.gitkeep
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 ‘GenomicScores’ can be installed ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘hdf5Backend’
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicScores-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gscores
> ### Title: Accessing genomic gscores
> ### Aliases: gscores,GScores,GenomicRanges-method
> ###   gscores,GScores,character-method gscores score,GScores-method
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## one genomic range of width 5
> gr1 <- GRanges(seqnames="chr7", IRanges(start=117232380, width=5))
> gr1
GRanges object with 1 range and 0 metadata columns:
      seqnames              ranges strand
         <Rle>           <IRanges>  <Rle>
  [1]     chr7 117232380-117232384      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## five genomic ranges of width 1
> gr2 <- GRanges(seqnames="chr7", IRanges(start=117232380:117232384, width=1))
> gr2
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr7 117232380      *
  [2]     chr7 117232381      *
  [3]     chr7 117232382      *
  [4]     chr7 117232383      *
  [5]     chr7 117232384      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## accessing genomic gscores from an annotation package
> if (require(phastCons100way.UCSC.hg19)) {
+   library(GenomicRanges)
+ 
+   gsco <- phastCons100way.UCSC.hg19
+   gsco
+   gscores(gsco, gr1)
+   score(gsco, gr1)
+   gscores(gsco, gr2)
+   populations(gsco)
+   gscores(gsco, gr2, pop="DP2")
+ }
Loading required package: phastCons100way.UCSC.hg19
GRanges object with 5 ranges and 1 metadata column:
      seqnames    ranges strand |       DP2
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]     chr7 117232380      * |      0.81
  [2]     chr7 117232381      * |      0.81
  [3]     chr7 117232382      * |      0.99
  [4]     chr7 117232383      * |      0.99
  [5]     chr7 117232384      * |      0.98
  -------
  seqinfo: 93 sequences (1 circular) from Genome Reference Consortium GRCh37 genome
> 
> if (require(MafDb.1Kgenomes.phase1.hs37d5)) {
+   mafdb <- MafDb.1Kgenomes.phase1.hs37d5
+   mafdb
+   populations(mafdb)
+ 
+   ## lookup allele frequencies for SNP rs1129038, located at 15:28356859, a
+   ## SNP associated to blue and brown eye colors as reported by Eiberg et al.
+   ## Blue eye color in humans may be caused by a perfectly associated founder
+   ## mutation in a regulatory element located within the HERC2 gene
+   ## inhibiting OCA2 expression. Human Genetics, 123(2):177-87, 2008
+   ## [http://www.ncbi.nlm.nih.gov/pubmed/18172690]
+   gscores(mafdb, GRanges("15:28356859"), pop=populations(mafdb))
+   gscores(mafdb, "rs1129038", pop=populations(mafdb))
+ }
Loading required package: MafDb.1Kgenomes.phase1.hs37d5
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase1.hs37d5’
Loading first time annotations of identifiers to genomic positions, produced by data provider.
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicScores.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GenomicScores
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘GenomicScores’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicScores)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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.

> BiocGenerics:::testPackage("GenomicScores")

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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


Attaching package: 'GenomicScores'

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

    citation

Loading required package: phastCons100way.UCSC.hg19


RUNIT TEST PROTOCOL -- Thu Nov  2 10:56:14 2023 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicScores RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
Warning message:
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'phastCons100way.UCSC.hg19' 
> 
> proc.time()
   user  system elapsed 
 23.082   2.111  27.219