Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
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 460/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crisprBwa 1.8.0 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.8.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings crisprBwa_1.8.0.tar.gz |
StartedAt: 2024-10-16 23:12:19 -0400 (Wed, 16 Oct 2024) |
EndedAt: 2024-10-16 23:16:53 -0400 (Wed, 16 Oct 2024) |
EllapsedTime: 274.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crisprBwa.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:crisprBwa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings crisprBwa_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-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 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘crisprBwa/DESCRIPTION’ ... OK * this is package ‘crisprBwa’ version ‘1.8.0’ * 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-3.19-bioc/meat/crisprBwa.Rcheck/00check.log’ for details.
crisprBwa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL crisprBwa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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-3.19-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpSehoiM/chr12 /home/biocbuild/bbs-3.19-bioc/R/site-library/crisprBwa/example/chr12.fa [main] Real time: 0.064 sec; CPU: 0.059 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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 36 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c12b714cb2 [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/bbs-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c12b714cb2.sai /tmp/RtmpSehoiM/file3044c12b714cb2 [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 36 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c12abc90be [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c12abc90be.sai /tmp/RtmpSehoiM/file3044c12abc90be [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 36 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16b8dc54f [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16b8dc54f.sai /tmp/RtmpSehoiM/file3044c16b8dc54f [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 36 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1196b6e5e [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1196b6e5e.sai /tmp/RtmpSehoiM/file3044c1196b6e5e [main] Real time: 0.002 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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 144 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1174057af [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1174057af.sai /tmp/RtmpSehoiM/file3044c1174057af [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-3.19-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpSehoiM/chr12 /home/biocbuild/bbs-3.19-bioc/R/site-library/crisprBwa/example/chr12.fa [main] Real time: 0.064 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/bbs-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c14ff85da3 [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/bbs-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c14ff85da3.sai /tmp/RtmpSehoiM/file3044c14ff85da3 [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/bbs-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c173ee471c [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c173ee471c.sai /tmp/RtmpSehoiM/file3044c173ee471c [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/bbs-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16639a4cc [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16639a4cc.sai /tmp/RtmpSehoiM/file3044c16639a4cc [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c11d6f5a6c [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c11d6f5a6c.sai /tmp/RtmpSehoiM/file3044c11d6f5a6c [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16c2a4baf [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16c2a4baf.sai /tmp/RtmpSehoiM/file3044c16c2a4baf [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1d3cae79 [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1d3cae79.sai /tmp/RtmpSehoiM/file3044c1d3cae79 [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c15a8f9676 [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c15a8f9676.sai /tmp/RtmpSehoiM/file3044c15a8f9676 [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 60 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c165cc25b6 [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c165cc25b6.sai /tmp/RtmpSehoiM/file3044c165cc25b6 [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 51 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c152c35c9 [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c152c35c9.sai /tmp/RtmpSehoiM/file3044c152c35c9 [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 0 -l 69 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c114e1d806 [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c114e1d806.sai /tmp/RtmpSehoiM/file3044c114e1d806 [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 1 -l 69 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1714c3e85 [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c1714c3e85.sai /tmp/RtmpSehoiM/file3044c1714c3e85 [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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 2 -l 69 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16616c049 [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-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c16616c049.sai /tmp/RtmpSehoiM/file3044c16616c049 [main] Real time: 0.002 sec; CPU: 0.003 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-3.19-bioc/R/site-library/Rbwa/bwa aln -N -n 3 -l 69 -o 0 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c15e719211 [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/bbs-3.19-bioc/R/site-library/Rbwa/bwa samse -n 1000000000 /tmp/RtmpSehoiM/chr12 /tmp/RtmpSehoiM/file3044c15e719211.sai /tmp/RtmpSehoiM/file3044c15e719211 [main] Real time: 0.001 sec; CPU: 0.001 sec [ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ] > > proc.time() user system elapsed 19.344 1.664 20.941
crisprBwa.Rcheck/crisprBwa-Ex.timings
name | user | system | elapsed | |
runBwa | 0.328 | 0.050 | 0.400 | |
runCrisprBwa | 0.849 | 0.102 | 0.948 | |