Jean-Philippe Fortin
| Snapshot Date: 2025-08-26 13:45 -0400 (Tue, 26 Aug 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-27 12:04 -0400 (Wed, 27 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4612 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
| 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 462/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprBwa 1.13.1 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: crisprBwa |
| Version: 1.13.1 |
| 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_1.13.1.tar.gz |
| StartedAt: 2025-08-26 20:03:34 -0400 (Tue, 26 Aug 2025) |
| EndedAt: 2025-08-26 20:08:08 -0400 (Tue, 26 Aug 2025) |
| EllapsedTime: 274.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprBwa.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.13.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/crisprBwa.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/crisprBwa.Rcheck/00check.log’
for details.
crisprBwa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crisprBwa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)
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-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(crisprBwa)
>
> test_check("crisprBwa")
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.03 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/4.5-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpQbmEa0/chr12 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/crisprBwa/example/chr12.fa
[main] Real time: 0.054 sec; CPU: 0.060 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef7175ffb4
[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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef7175ffb4.sai /tmp/RtmpQbmEa0/fileeef7175ffb4
[main] Real time: 0.030 sec; CPU: 0.033 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef769e6832b
[main] Real time: 0.030 sec; CPU: 0.033 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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef769e6832b.sai /tmp/RtmpQbmEa0/fileeef769e6832b
[main] Real time: 0.031 sec; CPU: 0.034 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef71cadb25e
[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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef71cadb25e.sai /tmp/RtmpQbmEa0/fileeef71cadb25e
[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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef74f994807
[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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef74f994807.sai /tmp/RtmpQbmEa0/fileeef74f994807
[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] 1 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef75847ec64
[main] Real time: 0.031 sec; CPU: 0.033 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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef75847ec64.sai /tmp/RtmpQbmEa0/fileeef75847ec64
[main] Real time: 0.032 sec; CPU: 0.036 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa index -p /tmp/RtmpQbmEa0/chr12 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/crisprBwa/example/chr12.fa
[main] Real time: 0.053 sec; CPU: 0.059 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef73cae0676
[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] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef73cae0676.sai /tmp/RtmpQbmEa0/fileeef73cae0676
[main] Real time: 0.032 sec; CPU: 0.035 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef7452a4c19
[main] Real time: 0.029 sec; CPU: 0.033 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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef7452a4c19.sai /tmp/RtmpQbmEa0/fileeef7452a4c19
[main] Real time: 0.031 sec; CPU: 0.034 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef75bea20c8
[main] Real time: 0.033 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] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef75bea20c8.sai /tmp/RtmpQbmEa0/fileeef75bea20c8
[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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef7680e599c
[main] Real time: 0.031 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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef7680e599c.sai /tmp/RtmpQbmEa0/fileeef7680e599c
[main] Real time: 0.030 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef73582d979
[main] Real time: 0.032 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] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef73582d979.sai /tmp/RtmpQbmEa0/fileeef73582d979
[main] Real time: 0.032 sec; CPU: 0.035 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef72193b261
[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] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef72193b261.sai /tmp/RtmpQbmEa0/fileeef72193b261
[main] Real time: 0.031 sec; CPU: 0.034 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef767a40f7f
[main] Real time: 0.030 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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef767a40f7f.sai /tmp/RtmpQbmEa0/fileeef767a40f7f
[main] Real time: 0.030 sec; CPU: 0.034 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef743f59001
[main] Real time: 0.030 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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef743f59001.sai /tmp/RtmpQbmEa0/fileeef743f59001
[main] Real time: 0.035 sec; CPU: 0.037 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef71bf86db3
[main] Real time: 0.035 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] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef71bf86db3.sai /tmp/RtmpQbmEa0/fileeef71bf86db3
[main] Real time: 0.031 sec; CPU: 0.033 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef73f60b5f3
[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] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef73f60b5f3.sai /tmp/RtmpQbmEa0/fileeef73f60b5f3
[main] Real time: 0.030 sec; CPU: 0.033 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef766498506
[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] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef766498506.sai /tmp/RtmpQbmEa0/fileeef766498506
[main] Real time: 0.031 sec; CPU: 0.035 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef764bc8160
[main] Real time: 0.031 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] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef764bc8160.sai /tmp/RtmpQbmEa0/fileeef764bc8160
[main] Real time: 0.035 sec; CPU: 0.039 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef713d1f94b
[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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpQbmEa0/chr12 /tmp/RtmpQbmEa0/fileeef713d1f94b.sai /tmp/RtmpQbmEa0/fileeef713d1f94b
[main] Real time: 0.030 sec; CPU: 0.033 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
20.210 2.509 23.704
crisprBwa.Rcheck/crisprBwa-Ex.timings
| name | user | system | elapsed | |
| runBwa | 0.398 | 0.136 | 0.616 | |
| runCrisprBwa | 1.204 | 0.196 | 1.507 | |