##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.ranges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.ranges_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.ranges.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.ranges/DESCRIPTION’ ... OK
* this is package ‘alabaster.ranges’ version ‘1.7.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alabaster.ranges’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readAtomicVectorList.Rd: CompressedAtomicList-class, readObject,
    saveObject, readObjectFile, altReadObject
  readDataFrameList.Rd: CompressedSplitDataFrameList-class, readObject,
    saveObject, readObjectFile, altReadObject
  readGRanges.Rd: GRanges-class, readObject, stageObject,
    readObjectFile, altReadObject
  readGRangesList.Rd: GRangesList-class, saveObject, readObjectFile,
    altReadObject
  readSeqinfo.Rd: Seqinfo-class, readObject, saveObject, readObjectFile
  saveAtomicVectorList.Rd: CompressedAtomicList-class
  saveCompressedSplitDataFrameList.Rd:
    CompressedSplitDataFrameList-class
  saveGRanges.Rd: GRanges-class
  saveGRangesList.Rd: GRangesList-class
  saveSeqinfo.Rd: Seqinfo-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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:
  Backtrace:
      ▆
   1. └─alabaster.ranges:::.validatedStage(grl, tmp, "thing") at test-GRangesList.R:140:5
   2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
   3.   └─alabaster.ranges::stageObject(x, dir, ...)
   4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
   5.       └─alabaster.ranges:::.compressed_stager(...)
   6.         └─base::tryCatch(...)
   7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.               └─value[[3L]](cond)
  
  [ FAIL 13 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.ranges.Rcheck/00check.log’
for details.

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.ranges
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘alabaster.ranges’ ...
** 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 (alabaster.ranges)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(alabaster.ranges)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: alabaster.base
> test_check("alabaster.ranges")
[ FAIL 13 | WARN 0 | SKIP 0 | PASS 16 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-AtomicVectorList.R:9:5'): staging and loading of atomic vector lists work as expected ──
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedCharacterList>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(X, tmp, path = "test1") at test-AtomicVectorList.R:9:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-DataFrameList.R:10:5'): staging and loading of data frame lists work as expected ──
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedSplitDFrameList>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(X, tmp, path = "test1") at test-DataFrameList.R:10:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-GRanges.R:15:5'): stageObject works correctly ──────────────────
Error in `value[[3L]](cond)`: failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(gr, tmp, "thing") at test-GRanges.R:15:5
 2. └─alabaster.ranges::stageObject(gr, tmp, "thing")
 3.   └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-GRanges.R:45:5'): stageObject handles non-trivial seqinfo ──────
Error in `value[[3L]](cond)`: failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(gr, tmp, "thing") at test-GRanges.R:45:5
 2. └─alabaster.ranges::stageObject(gr, tmp, "thing")
 3.   └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-GRanges.R:67:5'): stageObject works without names ──────────────
Error in `value[[3L]](cond)`: failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(gr, tmp, "thing") at test-GRanges.R:67:5
 2. └─alabaster.ranges::stageObject(gr, tmp, "thing")
 3.   └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-GRanges.R:86:5'): stageObject works with extra mcols ───────────
Error in `value[[3L]](cond)`: failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(gr, tmp, "thing") at test-GRanges.R:86:5
 2. └─alabaster.ranges::stageObject(gr, tmp, "thing")
 3.   └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-GRanges.R:116:5'): stageObject works with extra metadata ───────
Error in `value[[3L]](cond)`: failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(gr, tmp, "thing") at test-GRanges.R:116:5
 2. └─alabaster.ranges::stageObject(gr, tmp, "thing")
 3.   └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-GRangesList.R:19:5'): stageObject works correctly ──────────────
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedGRangesList>)'
  - failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(grl, tmp, "grl") at test-GRangesList.R:19:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-GRangesList.R:50:5'): stageObject handles its own metadata ─────
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedGRangesList>)'
  - failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(grl, tmp, "grl") at test-GRangesList.R:50:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-GRangesList.R:77:5'): stageObject handles GRLs with internal metadata ──
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedGRangesList>)'
  - failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(grl, tmp, "grl") at test-GRangesList.R:77:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-GRangesList.R:102:5'): stageObject handles unnamed GRLs ────────
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedGRangesList>)'
  - failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(grl, tmp, "grl") at test-GRangesList.R:102:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-GRangesList.R:124:5'): stageObject handles empty GRLs ──────────
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedGRangesList>)'
  - failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(copy, tmp, "grl") at test-GRangesList.R:124:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-GRangesList.R:140:5'): stageObject works with extra metadata ───
Error in `value[[3L]](cond)`: failed to stage 'unlist(<CompressedGRangesList>)'
  - failed to stage 'seqinfo(<GRanges>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. └─alabaster.ranges:::.validatedStage(grl, tmp, "thing") at test-GRangesList.R:140:5
 2.   ├─alabaster.base::stageObject(x, dir, ...) at tests/testthat/setup.R:2:5
 3.   └─alabaster.ranges::stageObject(x, dir, ...)
 4.     └─alabaster.ranges (local) .local(x, dir, path, child, ...)
 5.       └─alabaster.ranges:::.compressed_stager(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)

[ FAIL 13 | WARN 0 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted