Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-26 12:04 -0400 (Tue, 26 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" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4610 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
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: 2025-08-25 20:00:48 -0400 (Mon, 25 Aug 2025) |
EndedAt: 2025-08-25 20:05:20 -0400 (Mon, 25 Aug 2025) |
EllapsedTime: 271.9 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/Rtmp6H6rf1/chr12 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/crisprBwa/example/chr12.fa [main] Real time: 0.055 sec; CPU: 0.061 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b5e9143d8 [main] Real time: 0.031 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b5e9143d8.sai /tmp/Rtmp6H6rf1/file670b5e9143d8 [main] Real time: 0.029 sec; CPU: 0.032 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b12fd4a69 [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b12fd4a69.sai /tmp/Rtmp6H6rf1/file670b12fd4a69 [main] Real time: 0.030 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b33203d3c [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] 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b33203d3c.sai /tmp/Rtmp6H6rf1/file670b33203d3c [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b994485d [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] 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b994485d.sai /tmp/Rtmp6H6rf1/file670b994485d [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b661ad694 [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] 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b661ad694.sai /tmp/Rtmp6H6rf1/file670b661ad694 [main] Real time: 0.033 sec; CPU: 0.036 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: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rbwa/bwa index -p /tmp/Rtmp6H6rf1/chr12 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/crisprBwa/example/chr12.fa [main] Real time: 0.056 sec; CPU: 0.062 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b21beadcf [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] 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b21beadcf.sai /tmp/Rtmp6H6rf1/file670b21beadcf [main] Real time: 0.033 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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b6d850257 [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b6d850257.sai /tmp/Rtmp6H6rf1/file670b6d850257 [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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b375cd5ed [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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b375cd5ed.sai /tmp/Rtmp6H6rf1/file670b375cd5ed [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 3 -l 60 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b2fe0d700 [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b2fe0d700.sai /tmp/Rtmp6H6rf1/file670b2fe0d700 [main] Real time: 0.030 sec; CPU: 0.032 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b7b37945a [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] 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b7b37945a.sai /tmp/Rtmp6H6rf1/file670b7b37945a [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b7decdfe8 [main] Real time: 0.030 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b7decdfe8.sai /tmp/Rtmp6H6rf1/file670b7decdfe8 [main] Real time: 0.029 sec; CPU: 0.032 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b4a6038ee [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b4a6038ee.sai /tmp/Rtmp6H6rf1/file670b4a6038ee [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 3 -l 60 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b7339b767 [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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b7339b767.sai /tmp/Rtmp6H6rf1/file670b7339b767 [main] Real time: 0.029 sec; CPU: 0.032 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b4d74bfa [main] Real time: 0.032 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b4d74bfa.sai /tmp/Rtmp6H6rf1/file670b4d74bfa [main] Real time: 0.033 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 0 -l 69 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b54e9ca3d [main] Real time: 0.034 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/4.5-x86_64/Resources/library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b54e9ca3d.sai /tmp/Rtmp6H6rf1/file670b54e9ca3d [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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b40dc9658 [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b40dc9658.sai /tmp/Rtmp6H6rf1/file670b40dc9658 [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/4.5-x86_64/Resources/library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b52128cac [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] 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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b52128cac.sai /tmp/Rtmp6H6rf1/file670b52128cac [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 3 -l 69 -o 0 /tmp/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b3fd19a4c [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/Rtmp6H6rf1/chr12 /tmp/Rtmp6H6rf1/file670b3fd19a4c.sai /tmp/Rtmp6H6rf1/file670b3fd19a4c [main] Real time: 0.031 sec; CPU: 0.034 sec [ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ] > > proc.time() user system elapsed 19.678 2.432 23.111
crisprBwa.Rcheck/crisprBwa-Ex.timings
name | user | system | elapsed | |
runBwa | 0.356 | 0.118 | 0.604 | |
runCrisprBwa | 1.147 | 0.208 | 1.412 | |