| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:29 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 442/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprBwa 1.5.0 (landing page) Jean-Philippe Fortin
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: crisprBwa |
| Version: 1.5.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings crisprBwa_1.5.0.tar.gz |
| StartedAt: 2023-06-05 20:20:29 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 20:25:53 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 324.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprBwa.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings crisprBwa_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/crisprBwa.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘crisprBwa/DESCRIPTION’ ... OK
* this is package ‘crisprBwa’ version ‘1.5.0’
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘crisprBwa.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/crisprBwa.Rcheck/00check.log’
for details.
crisprBwa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL crisprBwa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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)
crisprBwa.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(crisprBwa)
>
> test_check("crisprBwa")
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.04 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.3.0/site-library/Rbwa/bwa index -p /tmp/RtmphgDA0V/chr12 /home/biocbuild/R/R-4.3.0/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.057 sec; CPU: 0.057 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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d75e9557a3
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d75e9557a3.sai /tmp/RtmphgDA0V/file30e8d75e9557a3
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d764f30819
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d764f30819.sai /tmp/RtmphgDA0V/file30e8d764f30819
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77afebcd3
[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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77afebcd3.sai /tmp/RtmphgDA0V/file30e8d77afebcd3
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d773c2b8f5
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 3 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d773c2b8f5.sai /tmp/RtmphgDA0V/file30e8d773c2b8f5
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d715586745
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d715586745.sai /tmp/RtmphgDA0V/file30e8d715586745
[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] 0.04 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: /home/biocbuild/R/R-4.3.0/site-library/Rbwa/bwa index -p /tmp/RtmphgDA0V/chr12 /home/biocbuild/R/R-4.3.0/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.061 sec; CPU: 0.060 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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d76e4f0bf3
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d76e4f0bf3.sai /tmp/RtmphgDA0V/file30e8d76e4f0bf3
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77180466e
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77180466e.sai /tmp/RtmphgDA0V/file30e8d77180466e
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d74c130263
[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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d74c130263.sai /tmp/RtmphgDA0V/file30e8d74c130263
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77046d612
[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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77046d612.sai /tmp/RtmphgDA0V/file30e8d77046d612
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d71faefc71
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d71faefc71.sai /tmp/RtmphgDA0V/file30e8d71faefc71
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d757e50ad8
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d757e50ad8.sai /tmp/RtmphgDA0V/file30e8d757e50ad8
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d75d049e70
[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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d75d049e70.sai /tmp/RtmphgDA0V/file30e8d75d049e70
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77f2104c6
[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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d77f2104c6.sai /tmp/RtmphgDA0V/file30e8d77f2104c6
[main] Real time: 0.001 sec; CPU: 0.002 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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d74aa777a5
[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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d74aa777a5.sai /tmp/RtmphgDA0V/file30e8d74aa777a5
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d7684b80d0
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d7684b80d0.sai /tmp/RtmphgDA0V/file30e8d7684b80d0
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d73f2adc0c
[main] Real time: 0.000 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/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d73f2adc0c.sai /tmp/RtmphgDA0V/file30e8d73f2adc0c
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d76adfd0bc
[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] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d76adfd0bc.sai /tmp/RtmphgDA0V/file30e8d76adfd0bc
[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/R/R-4.3.0/site-library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d757439218
[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] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.3.0/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmphgDA0V/chr12 /tmp/RtmphgDA0V/file30e8d757439218.sai /tmp/RtmphgDA0V/file30e8d757439218
[main] Real time: 0.001 sec; CPU: 0.001 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
21.999 1.553 23.502
crisprBwa.Rcheck/crisprBwa-Ex.timings
| name | user | system | elapsed | |
| runBwa | 0.356 | 0.035 | 0.392 | |
| runCrisprBwa | 1.161 | 0.067 | 1.230 | |