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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings crisprBwa_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/crisprBwa.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘crisprBwa/DESCRIPTION’ ... OK
* this is package ‘crisprBwa’ version ‘1.14.0’
* 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 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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/crisprBwa.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL crisprBwa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘crisprBwa’ ...
** this is package ‘crisprBwa’ version ‘1.14.0’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(crisprBwa)
> 
> test_check("crisprBwa")
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.03 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-3.22-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpQMn8T2/chr12 /home/biocbuild/bbs-3.22-bioc/R/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.073 sec; CPU: 0.056 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7072e8d2d9
[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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7072e8d2d9.sai /tmp/RtmpQMn8T2/file6e7072e8d2d9
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7081b8987
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7081b8987.sai /tmp/RtmpQMn8T2/file6e7081b8987
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e701f6aa01d
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e701f6aa01d.sai /tmp/RtmpQMn8T2/file6e701f6aa01d
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70589d8b80
[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] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70589d8b80.sai /tmp/RtmpQMn8T2/file6e70589d8b80
[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] 1 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7013e7e002
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7013e7e002.sai /tmp/RtmpQMn8T2/file6e7013e7e002
[main] Real time: 0.001 sec; CPU: 0.001 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.03 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-3.22-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpQMn8T2/chr12 /home/biocbuild/bbs-3.22-bioc/R/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.065 sec; CPU: 0.056 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e707eff7921
[main] Real time: 0.002 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e707eff7921.sai /tmp/RtmpQMn8T2/file6e707eff7921
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7039e69d66
[main] Real time: 0.002 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7039e69d66.sai /tmp/RtmpQMn8T2/file6e7039e69d66
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e705e885527
[main] Real time: 0.002 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e705e885527.sai /tmp/RtmpQMn8T2/file6e705e885527
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7076a2e10
[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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7076a2e10.sai /tmp/RtmpQMn8T2/file6e7076a2e10
[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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7037048701
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7037048701.sai /tmp/RtmpQMn8T2/file6e7037048701
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70487ebd10
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70487ebd10.sai /tmp/RtmpQMn8T2/file6e70487ebd10
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70508738bb
[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] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70508738bb.sai /tmp/RtmpQMn8T2/file6e70508738bb
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7059c6bda6
[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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7059c6bda6.sai /tmp/RtmpQMn8T2/file6e7059c6bda6
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e707b4d0bd1
[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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e707b4d0bd1.sai /tmp/RtmpQMn8T2/file6e707b4d0bd1
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70741f8283
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e70741f8283.sai /tmp/RtmpQMn8T2/file6e70741f8283
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e702bc4062a
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e702bc4062a.sai /tmp/RtmpQMn8T2/file6e702bc4062a
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7064ac2d95
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e7064ac2d95.sai /tmp/RtmpQMn8T2/file6e7064ac2d95
[main] Real time: 0.001 sec; CPU: 0.001 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e704dcbcb06
[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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQMn8T2/chr12 /tmp/RtmpQMn8T2/file6e704dcbcb06.sai /tmp/RtmpQMn8T2/file6e704dcbcb06
[main] Real time: 0.001 sec; CPU: 0.001 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 16.197   1.393  17.626