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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CrispRVariants_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CrispRVariants.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 ‘CrispRVariants/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CrispRVariants’ version ‘1.30.0’
* 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 ‘CrispRVariants’ 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 ... WARNING
'::' or ':::' import not declared from: ‘SummarizedExperiment’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘indelLabels’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CrispRVariants-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CrisprSet-class
> ### Title: CrisprSet class
> ### Aliases: CrisprSet-class CrisprSet
> 
> ### ** Examples
> 
> # Load the metadata table
> md_fname <- system.file("extdata", "gol_F1_metadata_small.txt", package = "CrispRVariants")
> md <- read.table(md_fname, sep = "\t", stringsAsFactors = FALSE)
> 
> # Get bam filenames and their full paths
> bam_fnames <- sapply(md$bam.filename, function(fn){
+  system.file("extdata", fn, package = "CrispRVariants")})
> 
> reference <- Biostrings::DNAString("GGTCTCTCGCAGGATGTTGCTGG")
> gd <- GenomicRanges::GRanges("18", IRanges::IRanges(4647377, 4647399), strand = "+")
> 
> crispr_set <- readsToTarget(bam_fnames, target = gd, reference = reference,
+                            names = md$experiment.name, target.loc = 17)
Read 8 alignments, excluded 0

0 from 0 (NaN%) chimeras did not involve guide
0 from 0 (NaN%) remaining chimeric reads included
0 (NaN%) assigned to more than one target

Read 8 alignments, excluded 0

0 from 2 (0.00%) chimeras did not involve guide
2 from 2 (100.00%) remaining chimeric reads included
0 (0.00%) assigned to more than one target

Read 11 alignments, excluded 0

0 from 0 (NaN%) chimeras did not involve guide
0 from 0 (NaN%) remaining chimeric reads included
0 (NaN%) assigned to more than one target

Read 12 alignments, excluded 0

0 from 2 (0.00%) chimeras did not involve guide
0 from 2 (0.00%) remaining chimeric reads included
0 (0.00%) assigned to more than one target

* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 874680 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("CrispRVariants")
  Loading required package: CrispRVariants
  Loading required package: ggplot2
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘gdata’
'library' or 'require' call not declared from: ‘gdata’
* checking package vignettes in ‘inst/doc’ ... WARNING
Located more than one ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘user_guide’: ‘user_guide.html’ (3.82289e+06 bytes), ‘user_guide.pdf’ (496045 bytes)
Package vignette without corresponding single PDF/HTML:
  ‘user_guide.Rmd’
* 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 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL CrispRVariants
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘CrispRVariants’ ...
** using staged installation
** R
** data
** 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 (CrispRVariants)

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.

> library(testthat)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2