| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:02 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 454/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CRISPRseek 1.40.0 (landing page) Lihua Julie Zhu
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the CRISPRseek package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRISPRseek.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: CRISPRseek |
| Version: 1.40.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CRISPRseek.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CRISPRseek_1.40.0.tar.gz |
| StartedAt: 2023-10-16 01:03:41 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 01:43:41 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 2400.2 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: CRISPRseek.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CRISPRseek.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CRISPRseek_1.40.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CRISPRseek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRISPRseek' version '1.40.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'CRISPRseek' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.6Mb
sub-directories of 1Mb or more:
extdata 12.2Mb
* 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 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 ... NOTE
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
'seqlevels<-'
annotateOffTargets: no visible global function definition for 'genes'
getOfftargetScore2: no visible binding for global variable 'subPAM'
getOfftargetScoreBulge: no visible global function definition for
'import'
predictRelativeFreqIndels : <anonymous>: no visible global function
definition for 'predIndelFreq'
Undefined global functions or variables:
exons genes import predIndelFreq seqlevels<- subPAM
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:64-66: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:67-69: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:86-88: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:89-91: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:99-101: Dropping empty section \references
prepare_Rd: compare2Sequences.Rd:263-265: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:266-268: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:151-153: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:154-156: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:48-50: Dropping empty section \details
prepare_Rd: filtergRNAs.Rd:51-53: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:70-72: Dropping empty section \references
prepare_Rd: findgRNAs.Rd:307-309: Dropping empty section \references
prepare_Rd: getOfftargetScore.Rd:79-81: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:23-25: Dropping empty section \details
prepare_Rd: isPatternUnique.Rd:26-28: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:37-39: Dropping empty section \references
prepare_Rd: isPatternUnique.Rd:40-42: Dropping empty section \seealso
prepare_Rd: offTargetAnalysis.Rd:438-440: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:441-443: Dropping empty section \note
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:440-442: Dropping empty section \details
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:443-445: Dropping empty section \note
prepare_Rd: searchHits.Rd:99-101: Dropping empty section \details
prepare_Rd: searchHits.Rd:102-104: Dropping empty section \note
prepare_Rd: searchHits.Rd:130-132: Dropping empty section \references
prepare_Rd: searchHits2.Rd:116-118: Dropping empty section \details
prepare_Rd: searchHits2.Rd:119-121: Dropping empty section \note
prepare_Rd: searchHits2.Rd:152-154: Dropping empty section \references
prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details
prepare_Rd: translatePattern.Rd:25-27: Dropping empty section \note
prepare_Rd: translatePattern.Rd:33-35: Dropping empty section \references
prepare_Rd: translatePattern.Rd:36-38: Dropping empty section \seealso
prepare_Rd: uniqueREs.Rd:46-48: Dropping empty section \details
prepare_Rd: uniqueREs.Rd:49-51: Dropping empty section \note
prepare_Rd: uniqueREs.Rd:61-63: Dropping empty section \references
prepare_Rd: uniqueREs.Rd:64-66: Dropping empty section \seealso
prepare_Rd: writeHits.Rd:89-91: Dropping empty section \details
prepare_Rd: writeHits.Rd:92-94: Dropping empty section \note
prepare_Rd: writeHits2.Rd:99-101: Dropping empty section \details
prepare_Rd: writeHits2.Rd:102-104: Dropping empty section \note
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CRISPRseek-package 292.39 6.66 311.16
offTargetAnalysisWithoutBSgenome 40.70 0.42 41.22
offTargetAnalysis 16.94 0.27 17.25
searchHits2 9.05 0.22 9.28
compare2Sequences 7.23 0.16 7.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
Running 'testthat.R'
CRISPRseek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL CRISPRseek ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'CRISPRseek' ... ** 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 (CRISPRseek)
CRISPRseek.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> #BiocGenerics:::testPackage("CRISPRseek")
>
> proc.time()
user system elapsed
0.21 0.06 0.21
CRISPRseek.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> Sys.setenv(R_TESTS="")
> require("CRISPRseek") || stop("unable to load Package:CRISPRseek")
Loading required package: CRISPRseek
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") ||
+ stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: rtracklayer
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg19.knownGene") ||
+ stop("unable to load TxDb.Hsapiens.UCSC.hg19.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
[1] TRUE
> require("BSgenome.Mmusculus.UCSC.mm10") ||
+ stop("unable to load Package: BSgenome.Mmusculus.UCSC.mm10")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") ||
+ stop("unable to load Package:TxDb.Mmusculus.UCSC.mm10.knownGene")
Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
[1] TRUE
> require("org.Mm.eg.db") ||
+ stop("unable to load Package:org.Mm.eg.db")
Loading required package: org.Mm.eg.db
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("CRISPRseek")
testing compare2Sequences
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Oct-16-2023/
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Oct-16-2023/
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331T ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Oct-16-2023/
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Oct-16-2023/
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331T ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Oct-16-2023/
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Oct-16-2023/
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331T ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
[1] "Scoring ..."
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
testing gRNAs provided and filter gRNAs with RE for offTargetAnalysis
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
testing gRNAs provided without filtering gRNAs with RE for offTargetAnalysis
checking N in PAM...Testing for mouse with orgAnn...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for mouse without orgAnn...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for mouse without orgAnn...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for findgRNAs = FALSE...
Validating input ...
>>> Finding all hits in sequence chr3 ...
>>> DONE searching
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr6 ...
>>> DONE searching
>>> Finding all hits in sequence chr8 ...
>>> DONE searching
>>> Finding all hits in sequence chr11 ...
>>> DONE searching
>>> Finding all hits in sequence chr15 ...
>>> DONE searching
>>> Finding all hits in sequence chrX ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr2 ...
>>> DONE searching
>>> Finding all hits in sequence chr3 ...
>>> DONE searching
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr6 ...
>>> DONE searching
>>> Finding all hits in sequence chr7 ...
>>> DONE searching
>>> Finding all hits in sequence chr8 ...
>>> DONE searching
>>> Finding all hits in sequence chr9 ...
>>> DONE searching
>>> Finding all hits in sequence chr10 ...
>>> DONE searching
>>> Finding all hits in sequence chr11 ...
>>> DONE searching
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
>>> Finding all hits in sequence chr14 ...
>>> DONE searching
>>> Finding all hits in sequence chr15 ...
>>> DONE searching
>>> Finding all hits in sequence chr16 ...
>>> DONE searching
>>> Finding all hits in sequence chr17 ...
>>> DONE searching
>>> Finding all hits in sequence chr18 ...
>>> DONE searching
>>> Finding all hits in sequence chr19 ...
>>> DONE searching
>>> Finding all hits in sequence chr20 ...
>>> DONE searching
>>> Finding all hits in sequence chr22 ...
>>> DONE searching
>>> Finding all hits in sequence chrX ...
>>> DONE searching
>>> Finding all hits in sequence chrY ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for paired with RE sites...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr2 ...
>>> DONE searching
>>> Finding all hits in sequence chr3 ...
>>> DONE searching
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr6 ...
>>> DONE searching
>>> Finding all hits in sequence chr7 ...
>>> DONE searching
>>> Finding all hits in sequence chr8 ...
>>> DONE searching
>>> Finding all hits in sequence chr9 ...
>>> DONE searching
>>> Finding all hits in sequence chr10 ...
>>> DONE searching
>>> Finding all hits in sequence chr11 ...
>>> DONE searching
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
>>> Finding all hits in sequence chr14 ...
>>> DONE searching
>>> Finding all hits in sequence chr15 ...
>>> DONE searching
>>> Finding all hits in sequence chr16 ...
>>> DONE searching
>>> Finding all hits in sequence chr17 ...
>>> DONE searching
>>> Finding all hits in sequence chr18 ...
>>> DONE searching
>>> Finding all hits in sequence chr19 ...
>>> DONE searching
>>> Finding all hits in sequence chr20 ...
>>> DONE searching
>>> Finding all hits in sequence chr22 ...
>>> DONE searching
>>> Finding all hits in sequence chrX ...
>>> DONE searching
>>> Finding all hits in sequence chrY ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for paired with or without RE sites...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr2 ...
>>> DONE searching
>>> Finding all hits in sequence chr3 ...
>>> DONE searching
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr6 ...
>>> DONE searching
>>> Finding all hits in sequence chr7 ...
>>> DONE searching
>>> Finding all hits in sequence chr8 ...
>>> DONE searching
>>> Finding all hits in sequence chr9 ...
>>> DONE searching
>>> Finding all hits in sequence chr10 ...
>>> DONE searching
>>> Finding all hits in sequence chr11 ...
>>> DONE searching
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
>>> Finding all hits in sequence chr14 ...
>>> DONE searching
>>> Finding all hits in sequence chr15 ...
>>> DONE searching
>>> Finding all hits in sequence chr16 ...
>>> DONE searching
>>> Finding all hits in sequence chr17 ...
>>> DONE searching
>>> Finding all hits in sequence chr18 ...
>>> DONE searching
>>> Finding all hits in sequence chr19 ...
>>> DONE searching
>>> Finding all hits in sequence chr20 ...
>>> DONE searching
>>> Finding all hits in sequence chr22 ...
>>> DONE searching
>>> Finding all hits in sequence chrX ...
>>> DONE searching
>>> Finding all hits in sequence chrY ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for unPaired with RE sites...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr2 ...
>>> DONE searching
>>> Finding all hits in sequence chr3 ...
>>> DONE searching
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr6 ...
>>> DONE searching
>>> Finding all hits in sequence chr7 ...
>>> DONE searching
>>> Finding all hits in sequence chr8 ...
>>> DONE searching
>>> Finding all hits in sequence chr9 ...
>>> DONE searching
>>> Finding all hits in sequence chr10 ...
>>> DONE searching
>>> Finding all hits in sequence chr11 ...
>>> DONE searching
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
>>> Finding all hits in sequence chr14 ...
>>> DONE searching
>>> Finding all hits in sequence chr15 ...
>>> DONE searching
>>> Finding all hits in sequence chr16 ...
>>> DONE searching
>>> Finding all hits in sequence chr17 ...
>>> DONE searching
>>> Finding all hits in sequence chr18 ...
>>> DONE searching
>>> Finding all hits in sequence chr19 ...
>>> DONE searching
>>> Finding all hits in sequence chr20 ...
>>> DONE searching
>>> Finding all hits in sequence chr22 ...
>>> DONE searching
>>> Finding all hits in sequence chrX ...
>>> DONE searching
>>> Finding all hits in sequence chrY ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
F:/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for unPaired with or without RE sites...
Testing for target not found when a gRNA sequence is from another species serving as a negative control…
Validating input ...
>>> Finding all hits in sequence chr11 ...
>>> DONE searching
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
>>> Finding all hits in sequence chr18 ...
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 292.39 | 6.66 | 311.16 | |
| annotateOffTargets | 2.80 | 0.11 | 2.93 | |
| buildFeatureVectorForScoring | 0.11 | 0.02 | 0.14 | |
| calculategRNAEfficiency | 0.02 | 0.00 | 0.01 | |
| compare2Sequences | 7.23 | 0.16 | 7.53 | |
| deepCpf1 | 0.05 | 0.01 | 0.08 | |
| filterOffTarget | 3.25 | 0.16 | 3.42 | |
| filtergRNAs | 0.81 | 0.03 | 0.86 | |
| findgRNAs | 0.25 | 0.01 | 0.30 | |
| getOfftargetScore | 0.08 | 0.00 | 0.08 | |
| isPatternUnique | 0.01 | 0.00 | 0.01 | |
| offTargetAnalysis | 16.94 | 0.27 | 17.25 | |
| offTargetAnalysisWithoutBSgenome | 40.70 | 0.42 | 41.22 | |
| predictRelativeFreqIndels | 0 | 0 | 0 | |
| searchHits | 0.13 | 0.00 | 0.19 | |
| searchHits2 | 9.05 | 0.22 | 9.28 | |
| translatePattern | 0 | 0 | 0 | |
| uniqueREs | 0.36 | 0.02 | 0.38 | |
| writeHits | 0 | 0 | 0 | |
| writeHits2 | 0.14 | 0.01 | 0.15 | |