Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-05-15 13:46:30 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 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 448/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.45.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/CRISPRseek
git_branch: devel
git_last_commit: d63723f
git_last_commit_date: 2024-04-30 10:34:25 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for CRISPRseek on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CRISPRseek
Version: 1.44.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings CRISPRseek_1.44.0.tar.gz
StartedAt: 2024-05-09 06:17:27 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 06:51:48 -0000 (Thu, 09 May 2024)
EllapsedTime: 2060.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CRISPRseek.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings CRISPRseek_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRISPRseek’ version ‘1.44.0’
* 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 12.9Mb
  sub-directories of 1Mb or more:
    extdata  12.4Mb
* 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 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 ... 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
checkRd: (-1) annotateOffTargets.Rd:13-14: Lost braces
    13 | \item{strand} - {strand of the off target ((+) for plus and (-) for minus
       |                 ^
checkRd: (-1) annotateOffTargets.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{chrom} - {chromosome of the off target}
       |                ^
checkRd: (-1) annotateOffTargets.Rd:16-17: Lost braces
    16 | \item{chromStart} - {start position of
       |                     ^
checkRd: (-1) annotateOffTargets.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{chromEnd} - {end position of the off target}
       |                   ^
checkRd: (-1) annotateOffTargets.Rd:19-20: Lost braces
    19 | \item{name} - {gRNA
       |               ^
checkRd: (-1) annotateOffTargets.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated}
       |                      ^
checkRd: (-1) annotateOffTargets.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{OffTargetSequence} - {the genomic sequence of the off target}
       |                            ^
checkRd: (-1) annotateOffTargets.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA}
       |                     ^
checkRd: (-1) annotateOffTargets.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707}
       |                        ^
checkRd: (-1) annotateOffTargets.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{score} - {score of the off target}
       |                ^
checkRd: (-1) annotateOffTargets.Rd:26-28: Lost braces
    26 | \item{mismatch.distance2PAM} - {a comma separated
       |                                ^
checkRd: (-1) annotateOffTargets.Rd:29-31: Lost braces
    29 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means
       |                    ^
checkRd: (-1) annotateOffTargets.Rd:32-33: Lost braces
    32 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes
       |              ^
checkRd: (-1) annotateOffTargets.Rd:34-35: Lost braces
    34 | \item{mean.neighbor.distance.mismatch} - {mean distance between
       |                                          ^
checkRd: (-1) annotateOffTargets.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{TxDb.Rnorvegicus.UCSC.rn5.refGene} - {for rat}
       |                                            ^
checkRd: (-1) annotateOffTargets.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{TxDb.Mmusculus.UCSC.mm10.knownGene} - {for mouse}
       |                                             ^
checkRd: (-1) annotateOffTargets.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{TxDb.Hsapiens.UCSC.hg19.knownGene} - {for human}
       |                                            ^
checkRd: (-1) annotateOffTargets.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{TxDb.Dmelanogaster.UCSC.dm3.ensGene} - {for Drosophila}
       |                                              ^
checkRd: (-1) annotateOffTargets.Rd:49: Lost braces; missing escapes or markup?
    49 | \item{TxDb.Celegans.UCSC.ce6.ensGene} - {for C.elegans}
       |                                         ^
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
checkRd: (-1) buildFeatureVectorForScoring.Rd:19-21: Lost braces
    19 | \item{IsMismatch.posX} - {Indicator variable indicating whether this position X is
       |                          ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:22-23: Lost braces
    22 | \item{strand} - {strand of the
       |                 ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:24-25: Lost braces
    24 | \item{chrom} - {chromosome of the off
       |                ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{chromStart} - {start position of the off target}
       |                     ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:27-28: Lost braces
    27 | \item{chromEnd} - {end
       |                   ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{name} - {gRNA name}
       |               ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:30-31: Lost braces
    30 | \item{gRNAPlusPAM} - {gRNA sequence
       |                      ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:32-33: Lost braces
    32 | \item{OffTargetSequence} - {the genomic sequence of
       |                            ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:34-35: Lost braces
    34 | \item{n.mismatch} - {number of mismatches between the off target and
       |                     ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:36-37: Lost braces
    36 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g.,
       |                        ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:38-39: Lost braces
    38 | \item{score} - {Set to 100, and will be calculated in
       |                ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:59-61: Lost braces
    59 | \item{IsMismatch.posX} - {Indicator variable
       |                          ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:62: Lost braces; missing escapes or markup?
    62 | \item{strand} - {strand of the off target, + for plus and - for minus strand}
       |                 ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{chrom} - {chromosome of the off target}
       |                ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:64-65: Lost braces
    64 | \item{chromStart} - {start position of the off
       |                     ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{chromEnd} - {end position of the off target}
       |                   ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{name} - {gRNA name}
       |               ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:68: Lost braces; missing escapes or markup?
    68 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated}
       |                      ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:69: Lost braces; missing escapes or markup?
    69 | \item{OffTargetSequence} - {the genomic sequence of the off target}
       |                            ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:70: Lost braces; missing escapes or markup?
    70 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA}
       |                     ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:71: Lost braces; missing escapes or markup?
    71 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707}
       |                        ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:72: Lost braces; missing escapes or markup?
    72 | \item{score} - {score of the off target}
       |                ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:73-75: Lost braces
    73 | \item{mismatche.distance2PAM} - {a comma separated
       |                                 ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:76-77: Lost braces
    76 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means
       |                    ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:78: Lost braces; missing escapes or markup?
    78 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes and 0 for no}
       |              ^
checkRd: (-1) buildFeatureVectorForScoring.Rd:79-80: Lost braces
    79 | \item{mean.neighbor.distance.mismatch} - {mean distance between neighboring
       |                                          ^
checkRd: (-1) calculategRNAEfficiency.Rd:30-31: Lost braces
    30 | \item{GC_LOW} - {penalty for low
       |                 ^
checkRd: (-1) calculategRNAEfficiency.Rd:32-33: Lost braces
    32 | \item{GC_HIGH} - {penalty for high GC content in
       |                  ^
checkRd: (-1) calculategRNAEfficiency.Rd:34-35: Lost braces
    34 | \item{G02} - {means G at second position of the
       |              ^
checkRd: (-1) calculategRNAEfficiency.Rd:36-37: Lost braces
    36 | \item{GT02} - {means GT di-nucleotides starting at 2nd position of
       |               ^
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
checkRd: (-1) filterOffTarget.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{strand} - {strand of the off target, + for plus and - for minus strand}
       |                 ^
checkRd: (-1) filterOffTarget.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{chrom} - {chromosome of the off target}
       |                ^
checkRd: (-1) filterOffTarget.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{chromStart} - {start position of the offtarget}
       |                     ^
checkRd: (-1) filterOffTarget.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{chromEnd} - {end position of the offtarget}
       |                   ^
checkRd: (-1) filterOffTarget.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{name} - {gRNA name}
       |               ^
checkRd: (-1) filterOffTarget.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated}
       |                      ^
checkRd: (-1) filterOffTarget.Rd:43: Lost braces; missing escapes or markup?
    43 | \item{OffTargetSequence} - {the genomic sequence of the off target}
       |                            ^
checkRd: (-1) filterOffTarget.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA}
       |                     ^
checkRd: (-1) filterOffTarget.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707}
       |                        ^
checkRd: (-1) filterOffTarget.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{score} - {score of the off target}
       |                ^
checkRd: (-1) filterOffTarget.Rd:47-49: Lost braces
    47 | \item{mismatch.distance2PAM} - {a comma separated
       |                                ^
checkRd: (-1) filterOffTarget.Rd:50-52: Lost braces
    50 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means
       |                    ^
checkRd: (-1) filterOffTarget.Rd:53-54: Lost braces
    53 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes
       |              ^
checkRd: (-1) filterOffTarget.Rd:55-56: Lost braces
    55 | \item{mean.neighbor.distance.mismatch} - {mean distance between
       |                                          ^
checkRd: (-1) filterOffTarget.Rd:101: Lost braces; missing escapes or markup?
   101 | \item{BSgenome.Hsapiens.UCSC.hg19} - {for hg19}
       |                                      ^
checkRd: (-1) filterOffTarget.Rd:102: Lost braces; missing escapes or markup?
   102 | \item{BSgenome.Mmusculus.UCSC.mm10} - {for mm10}
       |                                       ^
checkRd: (-1) filterOffTarget.Rd:103: Lost braces; missing escapes or markup?
   103 | \item{BSgenome.Celegans.UCSC.ce6} - {for ce6}
       |                                     ^
checkRd: (-1) filterOffTarget.Rd:104: Lost braces; missing escapes or markup?
   104 | \item{BSgenome.Rnorvegicus.UCSC.rn5} - {for rn5}
       |                                        ^
checkRd: (-1) filterOffTarget.Rd:105: Lost braces; missing escapes or markup?
   105 | \item{BSgenome.Dmelanogaster.UCSC.dm3} - {for dm3}
       |                                          ^
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
checkRd: (-1) getOfftargetScore.Rd:17-19: Lost braces
    17 | \item{IsMismatch.posX} - {Indicator variable
       |                          ^
checkRd: (-1) getOfftargetScore.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{strand} - {strand of the off target, + for plus and - for minus strand}
       |                 ^
checkRd: (-1) getOfftargetScore.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{chrom} - {chromosome of the off target}
       |                ^
checkRd: (-1) getOfftargetScore.Rd:22-23: Lost braces
    22 | \item{chromStart} - {start position of the off
       |                     ^
checkRd: (-1) getOfftargetScore.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{chromEnd} - {end position of the off target}
       |                   ^
checkRd: (-1) getOfftargetScore.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{name} - {gRNA name}
       |               ^
checkRd: (-1) getOfftargetScore.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated}
       |                      ^
checkRd: (-1) getOfftargetScore.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{OffTargetSequence} - {the genomic sequence of the off target}
       |                            ^
checkRd: (-1) getOfftargetScore.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA}
       |                     ^
checkRd: (-1) getOfftargetScore.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707}
       |                        ^
checkRd: (-1) getOfftargetScore.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{score} - {score of the off target}
       |                ^
checkRd: (-1) getOfftargetScore.Rd:31-33: Lost braces
    31 | \item{mismatche.distance2PAM} - {a comma separated
       |                                 ^
checkRd: (-1) getOfftargetScore.Rd:34-35: Lost braces
    34 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means
       |                    ^
checkRd: (-1) getOfftargetScore.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes and 0 for no}
       |              ^
checkRd: (-1) getOfftargetScore.Rd:37-38: Lost braces
    37 | \item{mean.neighbor.distance.mismatch} - {mean distance between neighboring
       |                                          ^
checkRd: (-1) getOfftargetScore.Rd:49-50: Lost braces
    49 | {strand} - {strand of the match, + for plus and
       |            ^
checkRd: (-1) getOfftargetScore.Rd:51: Lost braces; missing escapes or markup?
    51 | \item{chrom} - {chromosome of the off target}
       |                ^
checkRd: (-1) getOfftargetScore.Rd:52-53: Lost braces
    52 | \item{chromStart} - {start
       |                     ^
checkRd: (-1) getOfftargetScore.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{chromEnd} - {end position of the off target}
       |                   ^
checkRd: (-1) getOfftargetScore.Rd:55: Lost braces; missing escapes or markup?
    55 | \item{name} - {gRNA name}
       |               ^
checkRd: (-1) getOfftargetScore.Rd:56: Lost braces; missing escapes or markup?
    56 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated}
       |                      ^
checkRd: (-1) getOfftargetScore.Rd:57: Lost braces; missing escapes or markup?
    57 | \item{OffTargetSequence} - {the genomic sequence of the off target}
       |                            ^
checkRd: (-1) getOfftargetScore.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA}
       |                     ^
checkRd: (-1) getOfftargetScore.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707}
       |                        ^
checkRd: (-1) getOfftargetScore.Rd:60: Lost braces; missing escapes or markup?
    60 | \item{score} - {score of the off target}
       |                ^
checkRd: (-1) getOfftargetScore.Rd:61-63: Lost braces
    61 | \item{mismatch.distance2PAM} - {a comma separated
       |                                ^
checkRd: (-1) getOfftargetScore.Rd:64-65: Lost braces
    64 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means
       |                    ^
checkRd: (-1) getOfftargetScore.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes and 0 for no}
       |              ^
checkRd: (-1) getOfftargetScore.Rd:67-68: Lost braces
    67 | \item{mean.neighbor.distance.mismatch} - {mean distance between neighboring
       |                                          ^
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
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:296: Lost braces; missing escapes or markup?
   296 | \item{TxDb.Rnorvegicus.UCSC.rn5.refGene} - {for rat}
       |                                            ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:297: Lost braces; missing escapes or markup?
   297 | \item{TxDb.Mmusculus.UCSC.mm10.knownGene} - {for mouse}
       |                                             ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:298: Lost braces; missing escapes or markup?
   298 | \item{TxDb.Hsapiens.UCSC.hg19.knownGene} - {for human}
       |                                            ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:299: Lost braces; missing escapes or markup?
   299 | \item{TxDb.Dmelanogaster.UCSC.dm3.ensGene} - {for Drosophila}
       |                                              ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:300: Lost braces; missing escapes or markup?
   300 | \item{TxDb.Celegans.UCSC.ce6.ensGene} - {for C.elegans}
       |                                         ^
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
checkRd: (-1) searchHits.Rd:74-75: Lost braces
    74 | \item{IsMismatch.posX} - {indicator variable indicating
       |                          ^
checkRd: (-1) searchHits.Rd:76-77: Lost braces
    76 | \item{strand} - {strand of
       |                 ^
checkRd: (-1) searchHits.Rd:78-79: Lost braces
    78 | \item{chrom} - {chromosome of the off
       |                ^
checkRd: (-1) searchHits.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{chromStart} - {start position of the off target}
       |                     ^
checkRd: (-1) searchHits.Rd:81-82: Lost braces
    81 | \item{chromEnd} - {end
       |                   ^
checkRd: (-1) searchHits.Rd:83: Lost braces; missing escapes or markup?
    83 | \item{name} - {gRNA name}
       |               ^
checkRd: (-1) searchHits.Rd:84-85: Lost braces
    84 | \item{gRNAPlusPAM} - {gRNA sequence
       |                      ^
checkRd: (-1) searchHits.Rd:86-87: Lost braces
    86 | \item{OffTargetSequence} - {the genomic sequence of
       |                            ^
checkRd: (-1) searchHits.Rd:88-89: Lost braces
    88 | \item{n.mismatch} - {number of mismatches between the off target and
       |                     ^
checkRd: (-1) searchHits.Rd:90-91: Lost braces
    90 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g.,
       |                        ^
checkRd: (-1) searchHits.Rd:92-93: Lost braces
    92 | \item{score} - {set to 100, and will be updated in
       |                ^
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
checkRd: (-1) searchHits2.Rd:90-92: Lost braces
    90 | \item{IsMismatch.posX} - {indicator variable indicating
       |                          ^
checkRd: (-1) searchHits2.Rd:93-94: Lost braces
    93 | \item{strand} - {strand of
       |                 ^
checkRd: (-1) searchHits2.Rd:95-96: Lost braces
    95 | \item{chrom} - {chromosome of the off
       |                ^
checkRd: (-1) searchHits2.Rd:97: Lost braces; missing escapes or markup?
    97 | \item{chromStart} - {start position of the off target}
       |                     ^
checkRd: (-1) searchHits2.Rd:98-99: Lost braces
    98 | \item{chromEnd} - {end
       |                   ^
checkRd: (-1) searchHits2.Rd:100: Lost braces; missing escapes or markup?
   100 | \item{name} - {gRNA name}
       |               ^
checkRd: (-1) searchHits2.Rd:101-102: Lost braces
   101 | \item{gRNAPlusPAM} - {gRNA sequence
       |                      ^
checkRd: (-1) searchHits2.Rd:103-104: Lost braces
   103 | \item{OffTargetSequence} - {the genomic sequence of
       |                            ^
checkRd: (-1) searchHits2.Rd:105-106: Lost braces
   105 | \item{n.mismatch} - {number of mismatches between the off target and
       |                     ^
checkRd: (-1) searchHits2.Rd:107-108: Lost braces
   107 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g.,
       |                        ^
checkRd: (-1) searchHits2.Rd:109-110: Lost braces
   109 | \item{score} - {set to 100, and will be updated in
       |                ^
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
checkRd: (-1) uniqueREs.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{BSgenome.Hsapiens.UCSC.hg19} - {for hg19}
       |                                      ^
checkRd: (-1) uniqueREs.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{BSgenome.Mmusculus.UCSC.mm10} - {for mm10}
       |                                       ^
checkRd: (-1) uniqueREs.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{BSgenome.Celegans.UCSC.ce6} - {for ce6}
       |                                     ^
checkRd: (-1) uniqueREs.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{BSgenome.Rnorvegicus.UCSC.rn5} - {for rn5}
       |                                        ^
checkRd: (-1) uniqueREs.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{BSgenome.Drerio.UCSC.danRer7} - {for Zv9}
       |                                       ^
checkRd: (-1) uniqueREs.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{BSgenome.Dmelanogaster.UCSC.dm3} - {for dm3}
       |                                          ^
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
checkRd: (-1) writeHits2.Rd:68: Lost braces; missing escapes or markup?
    68 | \item{BSgenome.Hsapiens.UCSC.hg19} - {for hg19}
       |                                      ^
checkRd: (-1) writeHits2.Rd:69: Lost braces; missing escapes or markup?
    69 | \item{BSgenome.Mmusculus.UCSC.mm10} - {for mm10}
       |                                       ^
checkRd: (-1) writeHits2.Rd:70: Lost braces; missing escapes or markup?
    70 | \item{BSgenome.Celegans.UCSC.ce6} - {for ce6}
       |                                     ^
checkRd: (-1) writeHits2.Rd:71: Lost braces; missing escapes or markup?
    71 | \item{BSgenome.Rnorvegicus.UCSC.rn5} - {for rn5}
       |                                        ^
checkRd: (-1) writeHits2.Rd:72: Lost braces; missing escapes or markup?
    72 | \item{BSgenome.Drerio.UCSC.danRer7} - {for Zv9}
       |                                       ^
checkRd: (-1) writeHits2.Rd:73: Lost braces; missing escapes or markup?
    73 | \item{BSgenome.Dmelanogaster.UCSC.dm3} - {for dm3}
       |                                          ^
* 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               201.439  4.726 207.719
offTargetAnalysisWithoutBSgenome  53.161  0.835  54.111
offTargetAnalysis                 15.895  0.353  16.283
compare2Sequences                 11.212  0.599  11.825
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.


Installation output

CRISPRseek.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CRISPRseek
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> #BiocGenerics:::testPackage("CRISPRseek")
> 
> proc.time()
   user  system elapsed 
  0.204   0.024   0.211 

CRISPRseek.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> 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, 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
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: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat

[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-3.19-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-May-09-2024/ 
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory  /home/biocbuild/bbs-3.19-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-May-09-2024/ 
[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-3.19-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-May-09-2024/ 
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory  /home/biocbuild/bbs-3.19-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-May-09-2024/ 
[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-3.19-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-May-09-2024/ 
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory  /home/biocbuild/bbs-3.19-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-May-09-2024/ 
[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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ]
> 
> proc.time()
    user   system  elapsed 
1419.876   13.745 1439.908 

Example timings

CRISPRseek.Rcheck/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package201.439 4.726207.719
annotateOffTargets3.9970.0604.066
buildFeatureVectorForScoring0.1060.0040.110
calculategRNAEfficiency0.0200.0020.021
compare2Sequences11.212 0.59911.825
deepCpf10.0640.0160.080
filterOffTarget4.4780.1644.650
filtergRNAs0.8680.0560.926
findgRNAs0.4570.0510.509
getOfftargetScore0.1160.0080.124
isPatternUnique0.0200.0000.021
offTargetAnalysis15.895 0.35316.283
offTargetAnalysisWithoutBSgenome53.161 0.83554.111
predictRelativeFreqIndels0.0000.0000.001
searchHits0.1990.0120.213
searchHits24.3870.0764.472
translatePattern000
uniqueREs0.4580.0030.463
writeHits0.0010.0000.000
writeHits20.1940.0080.202