| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:35:52 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 455/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprBwa 1.6.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings crisprBwa_1.6.0.tar.gz |
| StartedAt: 2024-04-15 21:39:20 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 21:43:44 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 264.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprBwa.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings crisprBwa_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/crisprBwa.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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
OK
* 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/bbs-3.18-bioc/R/bin/R CMD INSTALL crisprBwa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmplaI7nT/chr12 /home/biocbuild/bbs-3.18-bioc/R/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.066 sec; CPU: 0.058 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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8612f165b3a
[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-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8612f165b3a.sai /tmp/RtmplaI7nT/file21d8612f165b3a
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8613d30250d
[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-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8613d30250d.sai /tmp/RtmplaI7nT/file21d8613d30250d
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d861533837c0
[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-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d861533837c0.sai /tmp/RtmplaI7nT/file21d861533837c0
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86110844980
[main] Real time: 0.003 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-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86110844980.sai /tmp/RtmplaI7nT/file21d86110844980
[main] Real time: 0.001 sec; CPU: 0.002 sec
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d861531168a
[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-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d861531168a.sai /tmp/RtmplaI7nT/file21d861531168a
[main] Real time: 0.001 sec; CPU: 0.002 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... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmplaI7nT/chr12 /home/biocbuild/bbs-3.18-bioc/R/site-library/crisprBwa/example/chr12.fa
[main] Real time: 0.064 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: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86117d3d758
[main] Real time: 0.001 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86117d3d758.sai /tmp/RtmplaI7nT/file21d86117d3d758
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86179ffad00
[main] Real time: 0.002 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86179ffad00.sai /tmp/RtmplaI7nT/file21d86179ffad00
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8614cdf5464
[main] Real time: 0.001 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8614cdf5464.sai /tmp/RtmplaI7nT/file21d8614cdf5464
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8615d90ba5a
[main] Real time: 0.002 sec; CPU: 0.002 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8615d90ba5a.sai /tmp/RtmplaI7nT/file21d8615d90ba5a
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86162b7d74
[main] Real time: 0.004 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-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86162b7d74.sai /tmp/RtmplaI7nT/file21d86162b7d74
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8617e4ceac3
[main] Real time: 0.001 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8617e4ceac3.sai /tmp/RtmplaI7nT/file21d8617e4ceac3
[main] Real time: 0.002 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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d861734477aa
[main] Real time: 0.001 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d861734477aa.sai /tmp/RtmplaI7nT/file21d861734477aa
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86170445809
[main] Real time: 0.002 sec; CPU: 0.002 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86170445809.sai /tmp/RtmplaI7nT/file21d86170445809
[main] Real time: 0.001 sec; CPU: 0.001 sec
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBwa] Searching for SpCas9 protospacers
[runCrisprBwa] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBwa] Searching for SpCas9 protospacers
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86159f66f3c
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86159f66f3c.sai /tmp/RtmplaI7nT/file21d86159f66f3c
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86111cd5876
[main] Real time: 0.002 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86111cd5876.sai /tmp/RtmplaI7nT/file21d86111cd5876
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86147e34173
[main] Real time: 0.002 sec; CPU: 0.002 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d86147e34173.sai /tmp/RtmplaI7nT/file21d86147e34173
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8617f540b50
[main] Real time: 0.001 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8617f540b50.sai /tmp/RtmplaI7nT/file21d8617f540b50
[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-3.18-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8613737cfff
[main] Real time: 0.002 sec; CPU: 0.001 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.18-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmplaI7nT/chr12 /tmp/RtmplaI7nT/file21d8613737cfff.sai /tmp/RtmplaI7nT/file21d8613737cfff
[main] Real time: 0.001 sec; CPU: 0.001 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
17.048 1.755 18.747
crisprBwa.Rcheck/crisprBwa-Ex.timings
| name | user | system | elapsed | |
| runBwa | 0.261 | 0.063 | 0.346 | |
| runCrisprBwa | 0.829 | 0.065 | 0.891 | |