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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings plyranges_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/plyranges.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘plyranges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plyranges’ version ‘1.21.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘plyranges’ 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
group_split:
  function(.tbl, ..., .keep)
group_split.GroupedGenomicRanges:
  function(.data, ..., keep)

group_split:
  function(.tbl, ..., .keep)
group_split.GroupedIntegerRanges:
  function(.data, ..., keep)

group_split:
  function(.tbl, ..., .keep)
group_split.Ranges:
  function(.data, ..., keep)

group_keys:
  function(.tbl, ...)
group_keys.Ranges:
  function(.data, ...)

group_keys:
  function(.tbl, ...)
group_keys.GroupedGenomicRanges:
  function(.data, ...)

group_keys:
  function(.tbl, ...)
group_keys.GroupedIntegerRanges:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Missing link or links in documentation object 'ranges-info.Rd':
  ‘[GenomeInfoDb:fetchExtendedChromInfoFromUCSC]{GenomeInfoDb::fetchExtendedChromInfoFromUCSC()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
io-bed-read 2.978  0.184  10.947
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─plyranges (local) createCorrectGR(hg19_seqinfo) at test-io-wig.R:35:2
    2. │ ├─base::factor(c(rep("chr19", 9), rep("chr18", 10)), seqlevels(seqinfo)) at test-io-wig.R:9:2
    3. │ ├─GenomeInfoDb::seqlevels(seqinfo) at test-io-wig.R:9:2
    4. │ └─GenomeInfoDb::seqlevels(seqinfo)
    5. │   ├─GenomeInfoDb::seqlevels(seqinfo(x))
    6. │   └─GenomeInfoDb::seqinfo(x)
    7. │     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
    8. │       └─base::stop(...)
    9. └─base::.handleSimpleError(...)
   10.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 5 | WARN 6 | SKIP 0 | PASS 373 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘an-introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/plyranges.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL plyranges
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘plyranges’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (plyranges)

R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(plyranges)
Loading required package: BiocGenerics

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

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'plyranges'

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

    slice

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

    filter

> 
> test_check("plyranges")
[ FAIL 5 | WARN 6 | SKIP 0 | PASS 373 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-io-bed.R:72:3'): read_bed returns correct GRanges ──────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'seqlevels': unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Backtrace:
     ▆
  1. ├─plyranges (local) createCorrectGR(hg19_seqinfo) at test-io-bed.R:72:2
  2. │ ├─base::factor(rep(c("chr7", "chr9"), c(3, 2)), seqlevels(seqinfo)) at test-io-bed.R:6:2
  3. │ ├─GenomeInfoDb::seqlevels(seqinfo) at test-io-bed.R:6:2
  4. │ └─GenomeInfoDb::seqlevels(seqinfo)
  5. │   ├─GenomeInfoDb::seqlevels(seqinfo(x))
  6. │   └─GenomeInfoDb::seqinfo(x)
  7. │     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  8. │       └─base::stop(...)
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))
── Error ('test-io-bedGraph.R:45:3'): read_bed_graph returns correct GRanges ───
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'seqlevels': unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Backtrace:
     ▆
  1. ├─plyranges (local) createCorrectGR(hg19_seqinfo) at test-io-bedGraph.R:45:2
  2. │ ├─base::factor(c(rep("chr19", 6), "chr17", rep("chr18", 2)), seqlevels(seqinfo)) at test-io-bedGraph.R:7:2
  3. │ ├─GenomeInfoDb::seqlevels(seqinfo) at test-io-bedGraph.R:7:2
  4. │ └─GenomeInfoDb::seqlevels(seqinfo)
  5. │   ├─GenomeInfoDb::seqlevels(seqinfo(x))
  6. │   └─GenomeInfoDb::seqinfo(x)
  7. │     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  8. │       └─base::stop(...)
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))
── Error ('test-io-bw.R:19:3'): reading/ writing bigwig files returns correct GRanges ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Backtrace:
    ▆
 1. ├─plyranges (local) createCorrectGR() at test-io-bw.R:19:2
 2. │ ├─GenomeInfoDb::seqlengths(si) at test-io-bw.R:10:2
 3. │ └─GenomeInfoDb::seqlengths(si)
 4. │   ├─GenomeInfoDb::seqlengths(seqinfo(x))
 5. │   └─GenomeInfoDb::seqinfo(x)
 6. │     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
 7. │       └─base::stop(...)
 8. └─base::.handleSimpleError(...)
 9.   └─base (local) h(simpleError(msg, call))
── Error ('test-io-gff.R:87:3'): reading GFF files returns correct GRanges ─────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'seqlevels': unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Backtrace:
    ▆
 1. ├─GenomeInfoDb::seqlevels(si_hg19) at test-io-gff.R:87:2
 2. ├─GenomeInfoDb::seqlevels(si_hg19)
 3. │ ├─GenomeInfoDb::seqlevels(seqinfo(x))
 4. │ └─GenomeInfoDb::seqinfo(x)
 5. │   └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
 6. │     └─base::stop(...)
 7. └─base::.handleSimpleError(...)
 8.   └─base (local) h(simpleError(msg, call))
── Error ('test-io-wig.R:35:3'): reading WIG files ─────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'seqlevels': unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Backtrace:
     ▆
  1. ├─plyranges (local) createCorrectGR(hg19_seqinfo) at test-io-wig.R:35:2
  2. │ ├─base::factor(c(rep("chr19", 9), rep("chr18", 10)), seqlevels(seqinfo)) at test-io-wig.R:9:2
  3. │ ├─GenomeInfoDb::seqlevels(seqinfo) at test-io-wig.R:9:2
  4. │ └─GenomeInfoDb::seqlevels(seqinfo)
  5. │   ├─GenomeInfoDb::seqlevels(seqinfo(x))
  6. │   └─GenomeInfoDb::seqinfo(x)
  7. │     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  8. │       └─base::stop(...)
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))

[ FAIL 5 | WARN 6 | SKIP 0 | PASS 373 ]
Error: Test failures
Execution halted