Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:39 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 452/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crisprBwa 1.9.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.9.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings crisprBwa_1.9.0.tar.gz |
StartedAt: 2024-08-26 21:53:49 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 21:58:06 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 256.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crisprBwa.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings crisprBwa_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/crisprBwa.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * 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 ‘1.9.0’ * 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 ... 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 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/crisprBwa.Rcheck/00check.log’ for details.
crisprBwa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL crisprBwa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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-3.20-bioc/R/site-library/Rbwa/bwa index -p /tmp/Rtmpd5HNPY/chr12 /home/biocbuild/bbs-3.20-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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308395b85c2bf [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308395b85c2bf.sai /tmp/Rtmpd5HNPY/file1308395b85c2bf [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308395f20579c [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308395f20579c.sai /tmp/Rtmpd5HNPY/file1308395f20579c [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308394f6a7faa [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308394f6a7faa.sai /tmp/Rtmpd5HNPY/file1308394f6a7faa [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083921dc54c3 [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] 3 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /home/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083921dc54c3.sai /tmp/Rtmpd5HNPY/file13083921dc54c3 [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] 1 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /home/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file130839787750aa [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] 1 sequences have been processed. [main] Version: 0.7.17-r1198-dirty [main] CMD: /home/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file130839787750aa.sai /tmp/Rtmpd5HNPY/file130839787750aa [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... 0.02 sec [main] Version: 0.7.17-r1198-dirty [main] CMD: /home/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa index -p /tmp/Rtmpd5HNPY/chr12 /home/biocbuild/bbs-3.20-bioc/R/site-library/crisprBwa/example/chr12.fa [main] Real time: 0.063 sec; CPU: 0.058 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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308394561fb25 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308394561fb25.sai /tmp/Rtmpd5HNPY/file1308394561fb25 [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308393878c7bf [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308393878c7bf.sai /tmp/Rtmpd5HNPY/file1308393878c7bf [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308392ccfe3e [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308392ccfe3e.sai /tmp/Rtmpd5HNPY/file1308392ccfe3e [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308396347dd53 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308396347dd53.sai /tmp/Rtmpd5HNPY/file1308396347dd53 [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083944be48c8 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083944be48c8.sai /tmp/Rtmpd5HNPY/file13083944be48c8 [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file130839744b32b5 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file130839744b32b5.sai /tmp/Rtmpd5HNPY/file130839744b32b5 [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308397240e55a [main] Real time: 0.003 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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308397240e55a.sai /tmp/Rtmpd5HNPY/file1308397240e55a [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308396554f5ff [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308396554f5ff.sai /tmp/Rtmpd5HNPY/file1308396554f5ff [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308392cc7739b [main] Real time: 0.003 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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file1308392cc7739b.sai /tmp/Rtmpd5HNPY/file1308392cc7739b [main] Real time: 0.002 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/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083919501cf4 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083919501cf4.sai /tmp/Rtmpd5HNPY/file13083919501cf4 [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083989db438 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083989db438.sai /tmp/Rtmpd5HNPY/file13083989db438 [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-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083972181183 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083972181183.sai /tmp/Rtmpd5HNPY/file13083972181183 [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/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083976c36204 [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-3.20-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/Rtmpd5HNPY/chr12 /tmp/Rtmpd5HNPY/file13083976c36204.sai /tmp/Rtmpd5HNPY/file13083976c36204 [main] Real time: 0.001 sec; CPU: 0.001 sec [ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ] > > proc.time() user system elapsed 17.049 1.545 18.538
crisprBwa.Rcheck/crisprBwa-Ex.timings
name | user | system | elapsed | |
runBwa | 0.302 | 0.047 | 0.372 | |
runCrisprBwa | 0.747 | 0.029 | 0.776 | |