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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CRISPRseek_1.49.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK
* this is package ‘CRISPRseek’ version ‘1.49.1’
* 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 ... INFO
  installed size is 13.2Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
offTargetAnalysis  39.651  1.426  41.104
annotateOffTargets  4.910  0.177   5.197
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Component "OffTargetSequence": 210 string mismatches
  Component "inExon": Lengths (232, 239) differ (comparison on first 232 components)
  Component "inExon": 'is.NA' value mismatch: 195 in current 208 in target
  Component "inIntron": Lengths (232, 239) differ (comparison on first 232 components)
  Component "inIntron": 'is.NA' value mismatch: 125 in current 138 in target
  ...
  ── Failure ('test-offTargetAnalysis.R:185:3'): test_offTargetAnalysis ──────────
  `offtarget.gRNAProvided` not equal to offtarget[names(offtarget.gRNAProvided)].
  Component "inIntron": 'is.NA' value mismatch: 12 in current 11 in target
  Component "entrez_id": 'is.NA' value mismatch: 11 in current 10 in target
  Component "symbol": 2 string mismatches
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CRISPRseek
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘CRISPRseek’ ...
** this is package ‘CRISPRseek’ version ‘1.49.1’
** 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)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> dependencies <- c("CRISPRseek", 
+                   "BSgenome.Hsapiens.UCSC.hg19", 
+                   "org.Hs.eg.db",
+                   "TxDb.Hsapiens.UCSC.hg19.knownGene",
+                   "BSgenome.Mmusculus.UCSC.mm10",
+                   "org.Mm.eg.db",
+                   "TxDb.Mmusculus.UCSC.mm10.knownGene",
+                   "testthat")
> sapply(dependencies, function(x) ifelse(do.call(require, list(x)), "okay", abort(x, "is not loaded for unit testing!")))
Loading required package: CRISPRseek
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: GenomicFeatures
Loading required package: GenomicRanges
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")'.

Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer
Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: BSgenome.Mmusculus.UCSC.mm10
Loading required package: org.Mm.eg.db

Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
Loading required package: testthat
                        CRISPRseek        BSgenome.Hsapiens.UCSC.hg19 
                            "okay"                             "okay" 
                      org.Hs.eg.db  TxDb.Hsapiens.UCSC.hg19.knownGene 
                            "okay"                             "okay" 
      BSgenome.Mmusculus.UCSC.mm10                       org.Mm.eg.db 
                            "okay"                             "okay" 
TxDb.Mmusculus.UCSC.mm10.knownGene                           testthat 
                            "okay"                             "okay" 
> if (Sys.info()["sysname"] == "Windows") {
+   message("Skipping test_check() on Windows as it takes too long ...")
+ } else {
+   test_check("CRISPRseek")
+ }
search for gRNAs for input file1...
search for gRNAs for input file2...
[1] "Scoring ..."
finish off-target search in sequence 2
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
search for gRNAs for input file2...
[1] "Scoring ..."
finish off-target search in sequence 2
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
search for gRNAs for input file2...
[1] "Scoring ..."
finish off-target search in sequence 2
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
[1] "Scoring ..."
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
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
testing gRNAs provided without filtering gRNAs with RE for offTargetAnalysis
checking N in PAM...[ FAIL 5 | WARN 0 | SKIP 0 | PASS 60 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-offTargetAnalysis.R:107:3'): test_offTargetAnalysis ──────────
`offtarget.pairedSearchRE` not equal to offtarget[names(offtarget.pairedSearchRE)].
Attributes: < Component "row.names": Numeric: lengths (131, 135) differ >
Component "name": Lengths (131, 135) differ (string compare on first 131)
Component "name": 5 string mismatches
Component "OffTargetSequence": Lengths (131, 135) differ (string compare on first 131)
Component "OffTargetSequence": 103 string mismatches
Component "inExon": Lengths (131, 135) differ (comparison on first 131 components)
Component "inExon": 'is.NA' value mismatch: 107 in current 118 in target
Component "inIntron": Lengths (131, 135) differ (comparison on first 131 components)
Component "inIntron": 'is.NA' value mismatch: 75 in current 80 in target
...
── Failure ('test-offTargetAnalysis.R:121:3'): test_offTargetAnalysis ──────────
`offtarget.pairedSearchNoRE` not equal to offtarget[names(offtarget.pairedSearchNoRE)].
Attributes: < Component "row.names": Numeric: lengths (131, 135) differ >
Component "name": Lengths (131, 135) differ (string compare on first 131)
Component "name": 5 string mismatches
Component "OffTargetSequence": Lengths (131, 135) differ (string compare on first 131)
Component "OffTargetSequence": 103 string mismatches
Component "inExon": Lengths (131, 135) differ (comparison on first 131 components)
Component "inExon": 'is.NA' value mismatch: 107 in current 118 in target
Component "inIntron": Lengths (131, 135) differ (comparison on first 131 components)
Component "inIntron": 'is.NA' value mismatch: 75 in current 80 in target
...
── Failure ('test-offTargetAnalysis.R:135:3'): test_offTargetAnalysis ──────────
`offtarget.unPairedSearchRE` not equal to offtarget[names(offtarget.unPairedSearchRE)].
Attributes: < Component "row.names": Numeric: lengths (206, 212) differ >
Component "name": Lengths (206, 212) differ (string compare on first 206)
Component "name": 11 string mismatches
Component "OffTargetSequence": Lengths (206, 212) differ (string compare on first 206)
Component "OffTargetSequence": 198 string mismatches
Component "inExon": Lengths (206, 212) differ (comparison on first 206 components)
Component "inExon": 'is.NA' value mismatch: 170 in current 183 in target
Component "inIntron": Lengths (206, 212) differ (comparison on first 206 components)
Component "inIntron": 'is.NA' value mismatch: 114 in current 126 in target
...
── Failure ('test-offTargetAnalysis.R:149:3'): test_offTargetAnalysis ──────────
`offtarget.unPairedSearchNoRE` not equal to offtarget[names(offtarget.unPairedSearchNoRE)].
Attributes: < Component "row.names": Numeric: lengths (232, 239) differ >
Component "name": Lengths (232, 239) differ (string compare on first 232)
Component "name": 15 string mismatches
Component "OffTargetSequence": Lengths (232, 239) differ (string compare on first 232)
Component "OffTargetSequence": 210 string mismatches
Component "inExon": Lengths (232, 239) differ (comparison on first 232 components)
Component "inExon": 'is.NA' value mismatch: 195 in current 208 in target
Component "inIntron": Lengths (232, 239) differ (comparison on first 232 components)
Component "inIntron": 'is.NA' value mismatch: 125 in current 138 in target
...
── Failure ('test-offTargetAnalysis.R:185:3'): test_offTargetAnalysis ──────────
`offtarget.gRNAProvided` not equal to offtarget[names(offtarget.gRNAProvided)].
Component "inIntron": 'is.NA' value mismatch: 12 in current 11 in target
Component "entrez_id": 'is.NA' value mismatch: 11 in current 10 in target
Component "symbol": 2 string mismatches

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 60 ]
Error: Test failures
Execution halted