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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SingleMoleculeFootprinting_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SingleMoleculeFootprinting.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK
* this is package ‘SingleMoleculeFootprinting’ version ‘1.11.0’
* 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 ‘SingleMoleculeFootprinting’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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
PlotAvgSMF: no visible global function definition for ‘points’
PlotAvgSMF: no visible global function definition for ‘abline’
PlotAvgSMF: no visible global function definition for ‘rect’
PlotAvgSMF: no visible global function definition for ‘text’
PlotSingleMoleculeStack: no visible global function definition for
  ‘points’
SampleCorrelation: no visible global function definition for ‘pairs’
SampleCorrelation: no visible binding for global variable ‘panel.cor’
SampleCorrelation: no visible binding for global variable ‘panel.hist’
SampleCorrelation: no visible binding for global variable ‘panel.jet’
SingleTFStateQuantificationPlot: no visible global function definition
  for ‘points’
SingleTFStateQuantificationPlot: no visible global function definition
  for ‘text’
TFPairStateQuantificationPlot: no visible global function definition
  for ‘points’
TFPairStateQuantificationPlot: no visible global function definition
  for ‘text’
Undefined global functions or variables:
  abline pairs panel.cor panel.hist panel.jet points rect text
Consider adding
  importFrom("graphics", "abline", "pairs", "points", "rect", "text")
to your NAMESPACE file.
* 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 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:
  ── Error ('test_single_molecule_manipulation_functions.R:7:1'): (code run outside of `test_that()`) ──
  Error: '/home/biocbuild/.cache/R/ExperimentHub/NRF1Pair_Qinput.txt' does not exist.
  Backtrace:
      ▆
   1. ├─base::suppressMessages(readr::read_delim(Qinput, delim = "\t")[[2]]) at test_single_molecule_manipulation_functions.R:7:1
   2. │ └─base::withCallingHandlers(...)
   3. ├─readr::read_delim(Qinput, delim = "\t")
   4. │ └─vroom::vroom(...)
   5. │   └─vroom:::vroom_(...)
   6. └─vroom (local) `<fn>`("/home/biocbuild/.cache/R/ExperimentHub/NRF1Pair_Qinput.txt")
   7.   └─vroom:::check_path(path)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  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-3.19-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SingleMoleculeFootprinting
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘SingleMoleculeFootprinting’ ...
** 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 (SingleMoleculeFootprinting)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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(SingleMoleculeFootprinting)
> 
> test_check("SingleMoleculeFootprinting")
Loading required package: BSgenome
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, table, tapply,
    union, 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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_context_methylation_function.R:7:1'): (code run outside of `test_that()`) ──
Error: '/home/biocbuild/.cache/R/ExperimentHub/NRF1Pair_Qinput.txt' does not exist.
Backtrace:
    ▆
 1. ├─base::suppressMessages(readr::read_delim(Qinput, delim = "\t")[[2]]) at test_context_methylation_function.R:7:1
 2. │ └─base::withCallingHandlers(...)
 3. ├─readr::read_delim(Qinput, delim = "\t")
 4. │ └─vroom::vroom(...)
 5. │   └─vroom:::vroom_(...)
 6. └─vroom (local) `<fn>`("/home/biocbuild/.cache/R/ExperimentHub/NRF1Pair_Qinput.txt")
 7.   └─vroom:::check_path(path)
── Error ('test_sequencing_QCs.R:9:3'): BaitCapture returns a numeric ──────────
Error: Cannot open /home/biocbuild/.cache/R/ExperimentHub/NRF1Pair_Qinput.txt
Backtrace:
    ▆
 1. ├─testthat::expect_true(...) at test_sequencing_QCs.R:9:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─SingleMoleculeFootprinting::BaitCapture(...)
 5.   └─SingleMoleculeFootprinting::GetQuasRprj(sampleSheet, genome)
 6.     └─QuasR::qAlign(...)
 7.       └─QuasR:::createQProject(...)
── Error ('test_single_molecule_manipulation_functions.R:7:1'): (code run outside of `test_that()`) ──
Error: '/home/biocbuild/.cache/R/ExperimentHub/NRF1Pair_Qinput.txt' does not exist.
Backtrace:
    ▆
 1. ├─base::suppressMessages(readr::read_delim(Qinput, delim = "\t")[[2]]) at test_single_molecule_manipulation_functions.R:7:1
 2. │ └─base::withCallingHandlers(...)
 3. ├─readr::read_delim(Qinput, delim = "\t")
 4. │ └─vroom::vroom(...)
 5. │   └─vroom:::vroom_(...)
 6. └─vroom (local) `<fn>`("/home/biocbuild/.cache/R/ExperimentHub/NRF1Pair_Qinput.txt")
 7.   └─vroom:::check_path(path)

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