Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-07 11:05:09 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for CRISPRseek on nebbiolo1


To the developers/maintainers of the CRISPRseek package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 432/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.39.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/CRISPRseek
git_branch: master
git_last_commit: 1ce9399
git_last_commit_date: 2022-11-01 11:09:00 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    TIMEOUT    OK  

Summary

Package: CRISPRseek
Version: 1.39.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CRISPRseek_1.39.0.tar.gz
StartedAt: 2023-02-06 19:59:25 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 20:34:25 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 2099.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CRISPRseek.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CRISPRseek_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRISPRseek’ version ‘1.39.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CRISPRseek’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.4Mb
  sub-directories of 1Mb or more:
    extdata  11.9Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
CRISPRseek-package               155.402 10.795 166.337
offTargetAnalysisWithoutBSgenome  34.401  0.476  34.879
offTargetAnalysis                 12.056  0.432  12.508
compare2Sequences                  6.373  0.059   6.585
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CRISPRseek.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.



Installation output

CRISPRseek.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CRISPRseek
###
##############################################################################
##############################################################################


* installing to library ‘/home/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)

Tests output

CRISPRseek.Rcheck/tests/runTests.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #BiocGenerics:::testPackage("CRISPRseek")
> 
> proc.time()
   user  system elapsed 
  0.163   0.025   0.176 

CRISPRseek.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
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  /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Feb-06-2023/ 
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory  /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Feb-06-2023/ 
[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  /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Feb-06-2023/ 
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory  /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Feb-06-2023/ 
[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  /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Feb-06-2023/ 
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory  /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Feb-06-2023/ 
[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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 
 /home/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 ...
>>> DONE searching
>>> Finding all hits in sequence chr19 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Done. Please check output files in directory 
 /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ 
Testing for target and offtarget not found when a gRNAsequence is from another species serving as a negative control…
Validating input ...
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
Testing for 5 prime PAM target and offtarget not found when qgRNA sequence is from another species serving as a negative control…
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
2nd testValidating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr12 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Done. Please check output files in directory 
 /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ]
> 
> proc.time()
    user   system  elapsed 
1347.161   39.569 1387.721 

Example timings

CRISPRseek.Rcheck/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package155.402 10.795166.337
annotateOffTargets2.7260.1322.858
buildFeatureVectorForScoring0.1260.0160.142
calculategRNAEfficiency0.0150.0000.032
compare2Sequences6.3730.0596.585
deepCpf10.0510.0040.055
filterOffTarget3.1040.1353.261
filtergRNAs0.5990.0720.671
findgRNAs0.2420.0160.259
getOfftargetScore0.0790.0000.078
isPatternUnique0.0130.0000.013
offTargetAnalysis12.056 0.43212.508
offTargetAnalysisWithoutBSgenome34.401 0.47634.879
predictRelativeFreqIndels000
searchHits0.1310.0160.147
searchHits23.1340.3433.478
translatePattern0.0010.0000.002
uniqueREs0.3200.0040.324
writeHits0.0000.0000.001
writeHits20.1310.0070.138