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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.string.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.string_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.string.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.string/DESCRIPTION’ ... OK
* this is package ‘alabaster.string’ 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.string’ 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:
  readXStringSet.Rd: XStringSet-class, readObject, saveObject,
    readObjectFile, altReadObject, QualityScaledDNAStringSet-class
  saveXStringSet.Rd: XStringSet-class, QualityScaledXStringSet-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:
       ▆
    1. ├─alabaster.base::stageObject(astuff, tmp, path = "sequence_thing") at test-XStringSet.R:114:5
    2. ├─alabaster.string::stageObject(astuff, tmp, path = "sequence_thing")
    3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
    4. │   └─alabaster.base::writeMetadata(...)
    5. │     └─jsonvalidate::json_validate(...)
    6. │       └─jsonvalidate::json_validator(...)
    7. │         └─jsonvalidate:::jsonvalidate_js()
    8. └─base::loadNamespace(x)
    9.   └─base::library.dynam(lib, package, package.lib)
   10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 1 ]
  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.string.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.string
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘alabaster.string’ ...
** using staged installation
** R
** 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.string)

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.string)
Loading required package: Biostrings
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
Loading required package: stats4

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: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: alabaster.base
> test_check("alabaster.string")
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-QualityScaledXStringSet.R:13:5'): saving and loading works for quality scaled DNAStringSets ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(qstuff, tmp, path = "dna_thing") at test-QualityScaledXStringSet.R:13:5
  2. ├─alabaster.string::stageObject(qstuff, tmp, path = "dna_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-QualityScaledXStringSet.R:36:5'): saving and loading acknowledges the quality encoding type ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(qstuff, tmp, path = "dna_thing") at test-QualityScaledXStringSet.R:36:5
  2. ├─alabaster.string::stageObject(qstuff, tmp, path = "dna_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-XStringSet.R:11:5'): saving and loading works without names ────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(stuff, tmp, path = "sequence_thing") at test-XStringSet.R:11:5
  2. ├─alabaster.string::stageObject(stuff, tmp, path = "sequence_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-XStringSet.R:35:5'): saving and loading works with names ───────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(stuff, tmp, path = "sequence_thing") at test-XStringSet.R:35:5
  2. ├─alabaster.string::stageObject(stuff, tmp, path = "sequence_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-XStringSet.R:54:5'): saving and loading works with mcols ───────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(stuff, tmp, path = "sequence_thing") at test-XStringSet.R:54:5
  2. ├─alabaster.string::stageObject(stuff, tmp, path = "sequence_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-XStringSet.R:72:5'): saving and loading works with metadata ────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(stuff, tmp, path = "sequence_thing") at test-XStringSet.R:72:5
  2. ├─alabaster.string::stageObject(stuff, tmp, path = "sequence_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-XStringSet.R:91:5'): saving and loading works with RNA ─────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(rstuff, tmp, path = "sequence_thing") at test-XStringSet.R:91:5
  2. ├─alabaster.string::stageObject(rstuff, tmp, path = "sequence_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-XStringSet.R:114:5'): saving and loading works with proteins ───
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: 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(astuff, tmp, path = "sequence_thing") at test-XStringSet.R:114:5
  2. ├─alabaster.string::stageObject(astuff, tmp, path = "sequence_thing")
  3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
  4. │   └─alabaster.base::writeMetadata(...)
  5. │     └─jsonvalidate::json_validate(...)
  6. │       └─jsonvalidate::json_validator(...)
  7. │         └─jsonvalidate:::jsonvalidate_js()
  8. └─base::loadNamespace(x)
  9.   └─base::library.dynam(lib, package, package.lib)
 10.     └─base::dyn.load(file, DLLpath = DLLpath, ...)

[ FAIL 8 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted