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This page was generated on 2025-09-08 12:03 -0400 (Mon, 08 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 462/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprBwa 1.13.1  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2025-09-07 13:45 -0400 (Sun, 07 Sep 2025)
git_url: https://git.bioconductor.org/packages/crisprBwa
git_branch: devel
git_last_commit: e36c347
git_last_commit_date: 2025-07-22 22:40:21 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for crisprBwa on nebbiolo2

To the developers/maintainers of the crisprBwa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crisprBwa.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: crisprBwa
Version: 1.13.1
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_1.13.1.tar.gz
StartedAt: 2025-09-07 22:22:34 -0400 (Sun, 07 Sep 2025)
EndedAt: 2025-09-07 22:29:16 -0400 (Sun, 07 Sep 2025)
EllapsedTime: 402.7 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprBwa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/crisprBwa.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.13.1’
* 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.


Installation output

crisprBwa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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 ‘1.13.1’
** 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)

Tests output

crisprBwa.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "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/RtmpBvSQmL/chr12 /home/biocbuild/bbs-3.22-bioc/R/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.062 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc213e3c173
[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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc213e3c173.sai /tmp/RtmpBvSQmL/file3a8cc213e3c173
[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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc229c95a41
[main] Real time: 0.009 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc229c95a41.sai /tmp/RtmpBvSQmL/file3a8cc229c95a41
[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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2301ea3e9
[main] Real time: 0.015 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2301ea3e9.sai /tmp/RtmpBvSQmL/file3a8cc2301ea3e9
[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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc26e64125
[main] Real time: 0.007 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-3.22-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc26e64125.sai /tmp/RtmpBvSQmL/file3a8cc26e64125
[main] Real time: 0.005 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc27c4a559
[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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc27c4a559.sai /tmp/RtmpBvSQmL/file3a8cc27c4a559
[main] Real time: 0.009 sec; CPU: 0.001 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.05 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/RtmpBvSQmL/chr12 /home/biocbuild/bbs-3.22-bioc/R/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.102 sec; CPU: 0.076 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc27dfd1510
[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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc27dfd1510.sai /tmp/RtmpBvSQmL/file3a8cc27dfd1510
[main] Real time: 0.002 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc256730835
[main] Real time: 0.006 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc256730835.sai /tmp/RtmpBvSQmL/file3a8cc256730835
[main] Real time: 0.008 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 2 -l 60 -o 0 /tmp/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2429e8c61
[main] Real time: 0.005 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2429e8c61.sai /tmp/RtmpBvSQmL/file3a8cc2429e8c61
[main] Real time: 0.008 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc260645e99
[main] Real time: 0.011 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc260645e99.sai /tmp/RtmpBvSQmL/file3a8cc260645e99
[main] Real time: 0.003 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 0 -l 60 -o 0 /tmp/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc264217730
[main] Real time: 0.008 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc264217730.sai /tmp/RtmpBvSQmL/file3a8cc264217730
[main] Real time: 0.008 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc24709eedf
[main] Real time: 0.003 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc24709eedf.sai /tmp/RtmpBvSQmL/file3a8cc24709eedf
[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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2964325c
[main] Real time: 0.005 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2964325c.sai /tmp/RtmpBvSQmL/file3a8cc2964325c
[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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc26d7ec4f6
[main] Real time: 0.016 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc26d7ec4f6.sai /tmp/RtmpBvSQmL/file3a8cc26d7ec4f6
[main] Real time: 0.002 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2446870a4
[main] Real time: 0.009 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2446870a4.sai /tmp/RtmpBvSQmL/file3a8cc2446870a4
[main] Real time: 0.005 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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc21aa66a51
[main] Real time: 0.005 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc21aa66a51.sai /tmp/RtmpBvSQmL/file3a8cc21aa66a51
[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-3.22-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc25272a69e
[main] Real time: 0.003 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc25272a69e.sai /tmp/RtmpBvSQmL/file3a8cc25272a69e
[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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc24bd236a3
[main] Real time: 0.005 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc24bd236a3.sai /tmp/RtmpBvSQmL/file3a8cc24bd236a3
[main] Real time: 0.008 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2e7ccfef
[main] Real time: 0.006 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/RtmpBvSQmL/chr12 /tmp/RtmpBvSQmL/file3a8cc2e7ccfef.sai /tmp/RtmpBvSQmL/file3a8cc2e7ccfef
[main] Real time: 0.009 sec; CPU: 0.002 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 20.755   1.857  34.497 

Example timings

crisprBwa.Rcheck/crisprBwa-Ex.timings

nameusersystemelapsed
runBwa1.3990.0641.657
runCrisprBwa1.2510.1201.547