##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:amplican.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings amplican_1.33.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/amplican.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.33.7’
* 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 ‘amplican’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 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 ... NOTE
amplicanConsensus: no visible binding for global variable ‘seqnames’
getHits: no visible binding for global variable ‘seqnames’
getHits: no visible binding for global variable ‘fwd_idx’
getHits: no visible binding for global variable ‘rve_idx’
is_hdr_strict: no visible binding for global variable ‘..join_cols’
is_hdr_strict: no visible binding for global variable ‘..needed’
is_hdr_strict: no visible binding for global variable ‘seqnames’
is_hdr_strict: no visible binding for global variable ‘N’
is_hdr_strict: no visible binding for global variable ‘n_expected’
Undefined global functions or variables:
  ..join_cols ..needed N fwd_idx n_expected rve_idx seqnames
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘amplican-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: amplicanAlign
> ### Title: Align reads to amplicons.
> ### Aliases: amplicanAlign
> 
> ### ** Examples
> 
> # path to example config file
> config <- system.file("extdata", "config.csv", package = "amplican")
> # path to example fastq files
> fastq_folder <- system.file("extdata", package = "amplican")
> aln <- amplicanAlign(config, fastq_folder)
Checking configuration file...
Making alignments...
Aligning reads for barcode_1
Error: BiocParallel errors
  1 remote errors, element index: 1
  1 unevaluated and other errors
  first remote error:
Error: class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
Execution halted
* 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:
  Error: class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_filters_helpers.R:5:1
   2.   ├─base::namespaceImport(...)
   3.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   4.     ├─base::namespaceImport(...)
   5.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   6.       └─base::namespaceImportClasses(...)
   7.         └─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   8.           └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 95 ]
  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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/amplican.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL amplican
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘amplican’ ...
** this is package ‘amplican’ version ‘1.33.7’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c bezier.cpp -o bezier.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o amplican.so RcppExports.o bezier.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-amplican/00new/amplican/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (amplican)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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(amplican)
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: Biostrings
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: Seqinfo

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: pwalign
version: 1.33.7
Please consider supporting this software by citing:

Labun et al. 2019
Accurate analysis of genuine CRISPR editing events with ampliCan.
Genome Res. 2019 Mar 8
doi: 10.1101/gr.244293.118

> 
> test_check("amplican")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 95 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_AlignmentsExperimentSet.R:11:1'): (code run outside of `test_that()`) ──
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  1 unevaluated and other errors
  first remote error:
Error: class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'

Backtrace:
    ▆
 1. ├─base::suppressWarnings(...) at test_AlignmentsExperimentSet.R:11:1
 2. │ └─base::withCallingHandlers(...)
 3. └─amplican::amplicanAlign(...)
 4.   ├─BiocParallel::bplapply(...)
 5.   └─BiocParallel::bplapply(...)
 6.     └─BiocParallel:::.bpinit(...)
── Error ('test_amplican.R:25:3'): amplican runs through example files without any issues ──
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  1 unevaluated and other errors
  first remote error:
Error: class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'

Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test_amplican.R:25:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─amplican::amplicanPipeline(...)
  7.   └─amplican::amplicanAlign(...)
  8.     ├─BiocParallel::bplapply(...)
  9.     └─BiocParallel::bplapply(...)
 10.       └─BiocParallel:::.bpinit(...)
── Error ('test_filters_helpers.R:5:1'): (code run outside of `test_that()`) ───
Error: class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
Backtrace:
    ▆
 1. └─base::loadNamespace(x) at test_filters_helpers.R:5:1
 2.   ├─base::namespaceImport(...)
 3.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 4.     ├─base::namespaceImport(...)
 5.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 6.       └─base::namespaceImportClasses(...)
 7.         └─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
 8.           └─base::importIntoEnv(impenv, impnames, ns, impvars)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 95 ]
Error: Test failures
Execution halted