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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crisprBwa_1.8.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/crisprBwa.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprBwa/DESCRIPTION’ ... OK
* this is package ‘crisprBwa’ version ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘crisprBwa’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/crisprBwa.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crisprBwa
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘crisprBwa’ ...
** 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 (crisprBwa)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> library(testthat)
> library(crisprBwa)
> 
> test_check("crisprBwa")
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.06 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa index -p /tmp/RtmpGONlXn/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/crisprBwa/example/chr12.fa
[main] Real time: 0.109 sec; CPU: 0.103 sec
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2029cbebb3
[main] Real time: 0.031 sec; CPU: 0.023 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2029cbebb3.sai /tmp/RtmpGONlXn/file1a2029cbebb3
[main] Real time: 0.018 sec; CPU: 0.020 sec
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20adf4a35
[main] Real time: 0.027 sec; CPU: 0.017 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20adf4a35.sai /tmp/RtmpGONlXn/file1a20adf4a35
[main] Real time: 0.017 sec; CPU: 0.022 sec
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204980e326
[main] Real time: 0.036 sec; CPU: 0.024 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204980e326.sai /tmp/RtmpGONlXn/file1a204980e326
[main] Real time: 0.055 sec; CPU: 0.019 sec
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a202cc0f97d
[main] Real time: 0.025 sec; CPU: 0.024 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a202cc0f97d.sai /tmp/RtmpGONlXn/file1a202cc0f97d
[main] Real time: 0.031 sec; CPU: 0.023 sec
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20313b947f
[main] Real time: 0.160 sec; CPU: 0.023 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20313b947f.sai /tmp/RtmpGONlXn/file1a20313b947f
[main] Real time: 0.060 sec; CPU: 0.015 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.06 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa index -p /tmp/RtmpGONlXn/chr12 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/crisprBwa/example/chr12.fa
[main] Real time: 0.093 sec; CPU: 0.100 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2059f1f7c5
[main] Real time: 0.106 sec; CPU: 0.024 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2059f1f7c5.sai /tmp/RtmpGONlXn/file1a2059f1f7c5
[main] Real time: 0.066 sec; CPU: 0.022 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a201cc1d4a5
[main] Real time: 0.052 sec; CPU: 0.022 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a201cc1d4a5.sai /tmp/RtmpGONlXn/file1a201cc1d4a5
[main] Real time: 0.060 sec; CPU: 0.019 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20796fab62
[main] Real time: 0.025 sec; CPU: 0.025 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20796fab62.sai /tmp/RtmpGONlXn/file1a20796fab62
[main] Real time: 0.029 sec; CPU: 0.018 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20125ced37
[main] Real time: 0.015 sec; CPU: 0.017 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20125ced37.sai /tmp/RtmpGONlXn/file1a20125ced37
[main] Real time: 0.016 sec; CPU: 0.015 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204057132f
[main] Real time: 0.028 sec; CPU: 0.020 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204057132f.sai /tmp/RtmpGONlXn/file1a204057132f
[main] Real time: 0.051 sec; CPU: 0.022 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2014ac93a9
[main] Real time: 0.132 sec; CPU: 0.023 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2014ac93a9.sai /tmp/RtmpGONlXn/file1a2014ac93a9
[main] Real time: 0.029 sec; CPU: 0.011 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204e1246d9
[main] Real time: 0.030 sec; CPU: 0.022 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204e1246d9.sai /tmp/RtmpGONlXn/file1a204e1246d9
[main] Real time: 0.017 sec; CPU: 0.022 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2011e9789a
[main] Real time: 0.072 sec; CPU: 0.021 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2011e9789a.sai /tmp/RtmpGONlXn/file1a2011e9789a
[main] Real time: 0.030 sec; CPU: 0.022 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for SpCas9 protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20f8d80f8
[main] Real time: 0.098 sec; CPU: 0.019 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a20f8d80f8.sai /tmp/RtmpGONlXn/file1a20f8d80f8
[main] Real time: 0.032 sec; CPU: 0.020 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for AsCas12a protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a207ea16440
[main] Real time: 0.052 sec; CPU: 0.023 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a207ea16440.sai /tmp/RtmpGONlXn/file1a207ea16440
[main] Real time: 0.018 sec; CPU: 0.021 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for AsCas12a protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2015bce6b3
[main] Real time: 0.036 sec; CPU: 0.022 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2015bce6b3.sai /tmp/RtmpGONlXn/file1a2015bce6b3
[main] Real time: 0.021 sec; CPU: 0.023 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for AsCas12a protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2024cdfceb
[main] Real time: 0.025 sec; CPU: 0.022 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a2024cdfceb.sai /tmp/RtmpGONlXn/file1a2024cdfceb
[main] Real time: 0.042 sec; CPU: 0.023 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBwa] Searching for AsCas12a protospacers 
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204f97bb2d
[main] Real time: 0.064 sec; CPU: 0.023 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpGONlXn/chr12 /tmp/RtmpGONlXn/file1a204f97bb2d.sai /tmp/RtmpGONlXn/file1a204f97bb2d
[main] Real time: 0.039 sec; CPU: 0.024 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 20.861   2.698  30.174