##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings crisprBwa_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/crisprBwa.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprBwa/DESCRIPTION’ ... OK
* this is package ‘crisprBwa’ version ‘1.0.0’
* 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 ... 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/crisprBwa.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL crisprBwa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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)
> library(crisprBwa)
> 
> test_check("crisprBwa")
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.04 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa index -p /tmp/RtmpffIl0l/chr12 /home/biocbuild/bbs-3.15-bioc/R/library/crisprBwa/example/chr12.fa
[main] Real time: 0.076 sec; CPU: 0.071 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 0 -k 0 -l 12 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb7e3dd2fa
[main] Real time: 0.001 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb7e3dd2fa.sai /tmp/RtmpffIl0l/file2c03fb7e3dd2fa
[main] Real time: 0.001 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 1 -k 1 -l 12 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb3f491c30
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb3f491c30.sai /tmp/RtmpffIl0l/file2c03fb3f491c30
[main] Real time: 0.002 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 2 -k 2 -l 12 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb2fc3a164
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb2fc3a164.sai /tmp/RtmpffIl0l/file2c03fb2fc3a164
[main] Real time: 0.001 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 3 -k 3 -l 12 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb3a2625f9
[main] Real time: 0.005 sec; CPU: 0.006 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb3a2625f9.sai /tmp/RtmpffIl0l/file2c03fb3a2625f9
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 0 -k 0 -l 48 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb4a2f86f6
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb4a2f86f6.sai /tmp/RtmpffIl0l/file2c03fb4a2f86f6
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.04 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa index -p /tmp/RtmpffIl0l/chr12 /home/biocbuild/bbs-3.15-bioc/R/library/crisprBwa/example/chr12.fa
[main] Real time: 0.078 sec; CPU: 0.073 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 0 -k 0 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb72fb3b54
[main] Real time: 0.003 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb72fb3b54.sai /tmp/RtmpffIl0l/file2c03fb72fb3b54
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 1 -k 1 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb9051490
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb9051490.sai /tmp/RtmpffIl0l/file2c03fb9051490
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 2 -k 2 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fbb2dc84e
[main] Real time: 0.002 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fbb2dc84e.sai /tmp/RtmpffIl0l/file2c03fbb2dc84e
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 3 -k 3 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb7520cde7
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb7520cde7.sai /tmp/RtmpffIl0l/file2c03fb7520cde7
[main] Real time: 0.001 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 0 -k 0 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb424a46f2
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb424a46f2.sai /tmp/RtmpffIl0l/file2c03fb424a46f2
[main] Real time: 0.001 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 1 -k 1 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb3b284d3b
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb3b284d3b.sai /tmp/RtmpffIl0l/file2c03fb3b284d3b
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 2 -k 2 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb73f1bf8f
[main] Real time: 0.003 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb73f1bf8f.sai /tmp/RtmpffIl0l/file2c03fb73f1bf8f
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 3 -k 3 -l 20 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb1c4f0374
[main] Real time: 0.004 sec; CPU: 0.005 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb1c4f0374.sai /tmp/RtmpffIl0l/file2c03fb1c4f0374
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 3 -k 3 -l 17 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb75103cdb
[main] Real time: 0.005 sec; CPU: 0.006 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb75103cdb.sai /tmp/RtmpffIl0l/file2c03fb75103cdb
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 0 -k 0 -l 23 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb1467bb44
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb1467bb44.sai /tmp/RtmpffIl0l/file2c03fb1467bb44
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 1 -k 1 -l 23 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb45935f3d
[main] Real time: 0.002 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb45935f3d.sai /tmp/RtmpffIl0l/file2c03fb45935f3d
[main] Real time: 0.001 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 2 -k 2 -l 23 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb1377911b
[main] Real time: 0.002 sec; CPU: 0.002 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb1377911b.sai /tmp/RtmpffIl0l/file2c03fb1377911b
[main] Real time: 0.002 sec; CPU: 0.003 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa aln -N -n 3 -k 3 -l 23 -o 0 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb5b4c4776
[main] Real time: 0.003 sec; CPU: 0.004 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: /home/biocbuild/bbs-3.15-bioc/R/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpffIl0l/chr12 /tmp/RtmpffIl0l/file2c03fb5b4c4776.sai /tmp/RtmpffIl0l/file2c03fb5b4c4776
[main] Real time: 0.001 sec; CPU: 0.001 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 16.109   2.024  18.032