##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:G4SNVHunter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings G4SNVHunter_1.1.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/G4SNVHunter.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘G4SNVHunter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘G4SNVHunter’ version ‘1.1.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘G4SNVHunter’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in checkSNV(gr1, mode = "w") : checkSNV is deprecated.
  Warning in checkSNV(gr3, mode = "w") : checkSNV is deprecated.
  Warning in plotSNVImpact(res_snp) : 'plotSNVImpact' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
G4VarImpact     392.243  3.990 399.799
plotVarImpact   121.678  1.121 123.741
plotImpactedG4  121.009  1.201 123.024
filterVarImpact 118.067  1.132 120.001
SNVImpactG4      83.445  0.759  84.773
plotSNVImpact    16.825  0.432  17.392
filterSNVImpact  16.495  0.631  17.266
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/G4SNVHunter.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL G4SNVHunter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘G4SNVHunter’ ...
** this is package ‘G4SNVHunter’ version ‘1.1.4’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c G4HTranslate.cpp -o G4HTranslate.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o G4SNVHunter.so G4HTranslate.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-G4SNVHunter/00new/G4SNVHunter/libs
** 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
** 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 (G4SNVHunter)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(G4SNVHunter)
> 
> test_check("G4SNVHunter")
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: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer
Start processing...
Now process: seq1.
Now process: seq2.
Merging predicted G4s...
Done!
Start processing...
Now process: seq1.
Now process: seq2.
Merging predicted G4s...
Done!
Start processing...
Now process: seq1.
Now process: seq2.
Merging predicted G4s...
Done!
Start processing...
Now process: seq1.
Now process: seq2.
Merging predicted G4s...
Done!
Start processing...
The sequence length of seq2 is less than the window size. Skipping this sequence.
The sequence length of seq8 is less than the window size. Skipping this sequence.
Merging predicted G4s...
Done!
Start processing...
The sequence length of seq1 is less than the window size. Skipping this sequence.
The sequence length of seq2 is less than the window size. Skipping this sequence.
The sequence length of seq3 is less than the window size. Skipping this sequence.
No G4 sequences were found.
Done!
Start processing...
Now process: CHR.
Merging predicted G4s...
Done!
Start processing...
Processing finished!
Start processing...
No overlaps found between variants and G4 regions
Start processing...
Processing finished!
Start processing...
Processing finished!
Start processing...
Processing finished!
Start processing...
Processing finished!
Start processing...
Processing finished!
Start processing...
Merging predicted G4s...
Done!
Start processing...
Processing finished!
Start processing...
Processing finished!
Some SNVs do not have a width of 1.
Invalid nucleotides found in ref column. Only (A, T, C, G) are supported.
Invalid nucleotides found in alt column. Only (A, T, C, G) are supported.
Start processing...
Merging predicted G4s...
Done!
Start processing...
Merging predicted G4s...
Done!
Start processing...
Processing finished!
All G4s are on the positive strand; reverse complementation for G4 sequences was not applied.
All G4s are on the positive strand; reverse complementation for G4 sequences was not applied.
All G4s are on the positive strand; reverse complementation for mutated G4 sequences was not applied.
All G4s are on the positive strand; reverse complementation for G4 sequences was not applied.
All G4s are on the positive strand; reverse complementation for mutated G4 sequences was not applied.
All G4s are on the positive strand; reverse complementation for mutated G4 sequences was not applied.
Start processing...
Now process: chr21.
Merging predicted G4s...
Done!
Start processing...
Processing finished!
Start processing...
Merging predicted G4s...
Done!
Start processing...
Processing finished!
VCF loading summary:
    - Initial variants: 5000
    - Filtered out by type: 0
    - Final variants retained: 5000
VCF loading summary:
    - Initial variants: 5000
    - Filtered out by type: 0
    - Final variants retained: 5000
MAF loading summary:
    - Initial variants: 13
    - Filtered out by type: 0
    - Final variants retained: 13
[ FAIL 0 | WARN 45 | SKIP 0 | PASS 165 ]

[ FAIL 0 | WARN 45 | SKIP 0 | PASS 165 ]
> 
> proc.time()
   user  system elapsed 
 48.184   1.835  50.543