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This page was generated on 2024-02-21 11:37:41 -0500 (Wed, 21 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 455/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprBwa 1.6.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2024-02-20 14:05:06 -0500 (Tue, 20 Feb 2024)
git_url: https://git.bioconductor.org/packages/crisprBwa
git_branch: RELEASE_3_18
git_last_commit: e4775a7
git_last_commit_date: 2023-10-24 11:41:41 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for crisprBwa on lconway


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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2024-02-20 19:42:48 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 19:47:19 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 270.8 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprBwa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/crisprBwa.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprBwa/DESCRIPTION’ ... OK
* this is package ‘crisprBwa’ version ‘1.6.0’
* 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/crisprBwa.Rcheck/00check.log’
for details.



Installation output

crisprBwa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crisprBwa
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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)

Tests output

crisprBwa.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpbofoIw/chr12 /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/crisprBwa/example/chr12.fa
[main] Real time: 0.065 sec; CPU: 0.069 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba864d287a5
[main] Real time: 0.035 sec; CPU: 0.038 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba864d287a5.sai /tmp/RtmpbofoIw/file11ba864d287a5
[main] Real time: 0.033 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba839c79559
[main] Real time: 0.029 sec; CPU: 0.032 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba839c79559.sai /tmp/RtmpbofoIw/file11ba839c79559
[main] Real time: 0.032 sec; CPU: 0.035 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba85e1e23b1
[main] Real time: 0.033 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba85e1e23b1.sai /tmp/RtmpbofoIw/file11ba85e1e23b1
[main] Real time: 0.032 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba8cb969bd
[main] Real time: 0.032 sec; CPU: 0.035 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba8cb969bd.sai /tmp/RtmpbofoIw/file11ba8cb969bd
[main] Real time: 0.034 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba860ccfdd1
[main] Real time: 0.031 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba860ccfdd1.sai /tmp/RtmpbofoIw/file11ba860ccfdd1
[main] Real time: 0.035 sec; CPU: 0.038 sec
[bwa_index] Pack FASTA... 0.01 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpbofoIw/chr12 /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/crisprBwa/example/chr12.fa
[main] Real time: 0.065 sec; CPU: 0.069 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba87e1ccb39
[main] Real time: 0.034 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba87e1ccb39.sai /tmp/RtmpbofoIw/file11ba87e1ccb39
[main] Real time: 0.035 sec; CPU: 0.039 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba814624bde
[main] Real time: 0.035 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba814624bde.sai /tmp/RtmpbofoIw/file11ba814624bde
[main] Real time: 0.033 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba84162e646
[main] Real time: 0.037 sec; CPU: 0.038 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba84162e646.sai /tmp/RtmpbofoIw/file11ba84162e646
[main] Real time: 0.036 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba843fc1f33
[main] Real time: 0.033 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba843fc1f33.sai /tmp/RtmpbofoIw/file11ba843fc1f33
[main] Real time: 0.034 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba826805be4
[main] Real time: 0.033 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba826805be4.sai /tmp/RtmpbofoIw/file11ba826805be4
[main] Real time: 0.031 sec; CPU: 0.033 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba83510e97b
[main] Real time: 0.033 sec; CPU: 0.034 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba83510e97b.sai /tmp/RtmpbofoIw/file11ba83510e97b
[main] Real time: 0.034 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba86950a574
[main] Real time: 0.035 sec; CPU: 0.039 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba86950a574.sai /tmp/RtmpbofoIw/file11ba86950a574
[main] Real time: 0.037 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba82d9e98b0
[main] Real time: 0.036 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba82d9e98b0.sai /tmp/RtmpbofoIw/file11ba82d9e98b0
[main] Real time: 0.032 sec; CPU: 0.035 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba824e160d
[main] Real time: 0.029 sec; CPU: 0.034 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba824e160d.sai /tmp/RtmpbofoIw/file11ba824e160d
[main] Real time: 0.034 sec; CPU: 0.032 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba8100a4c4f
[main] Real time: 0.033 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba8100a4c4f.sai /tmp/RtmpbofoIw/file11ba8100a4c4f
[main] Real time: 0.032 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba81417dec3
[main] Real time: 0.032 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba81417dec3.sai /tmp/RtmpbofoIw/file11ba81417dec3
[main] Real time: 0.032 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba82b21de83
[main] Real time: 0.041 sec; CPU: 0.038 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba82b21de83.sai /tmp/RtmpbofoIw/file11ba82b21de83
[main] Real time: 0.035 sec; CPU: 0.037 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/4.3-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba83c978094
[main] Real time: 0.035 sec; CPU: 0.036 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/4.3-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpbofoIw/chr12 /tmp/RtmpbofoIw/file11ba83c978094.sai /tmp/RtmpbofoIw/file11ba83c978094
[main] Real time: 0.035 sec; CPU: 0.037 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 19.933   2.638  23.605 

Example timings

crisprBwa.Rcheck/crisprBwa-Ex.timings

nameusersystemelapsed
runBwa0.3850.1480.656
runCrisprBwa1.0360.1791.281