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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:crisprBowtie.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings crisprBowtie_1.13.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/crisprBowtie.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘crisprBowtie/DESCRIPTION’ ... OK
* this is package ‘crisprBowtie’ version ‘1.13.1’
* 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 ‘crisprBowtie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  runCrisprBowtie.Rd: BSgenome-class, CrisprNuclease-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/crisprBowtie.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL crisprBowtie
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘crisprBowtie’ ...
** this is package ‘crisprBowtie’ version ‘1.13.1’
** 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 (crisprBowtie)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> library(testthat)
> library(crisprBowtie)
> 
> test_check("crisprBowtie")
# reads processed: 3
# reads with at least one alignment: 1 (33.33%)
# reads that failed to align: 2 (66.67%)
Reported 1 alignments
# reads processed: 3
# reads with at least one alignment: 3 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 14 alignments
# reads processed: 3
# reads with at least one alignment: 3 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 118 alignments
# reads processed: 3
# reads with at least one alignment: 3 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 561 alignments
# reads processed: 1
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 28
# reads with at least one alignment: 3 (10.71%)
# reads that failed to align: 25 (89.29%)
Reported 3 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 28
# reads with at least one alignment: 13 (46.43%)
# reads that failed to align: 15 (53.57%)
Reported 13 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 28
# reads with at least one alignment: 18 (64.29%)
# reads that failed to align: 10 (35.71%)
Reported 18 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 28
# reads with at least one alignment: 25 (89.29%)
# reads that failed to align: 3 (10.71%)
Reported 25 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 84
# reads with at least one alignment: 4 (4.76%)
# reads that failed to align: 80 (95.24%)
Reported 4 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 84
# reads with at least one alignment: 23 (27.38%)
# reads that failed to align: 61 (72.62%)
Reported 23 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 84
# reads with at least one alignment: 47 (55.95%)
# reads that failed to align: 37 (44.05%)
Reported 47 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 84
# reads with at least one alignment: 61 (72.62%)
# reads that failed to align: 23 (27.38%)
Reported 61 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 84
# reads with at least one alignment: 72 (85.71%)
# reads that failed to align: 12 (14.29%)
Reported 72 alignments
[runCrisprBowtie] Searching for AsCas12a protospacers 
# reads processed: 18
# reads with at least one alignment: 3 (16.67%)
# reads that failed to align: 15 (83.33%)
Reported 3 alignments
[runCrisprBowtie] Searching for AsCas12a protospacers 
# reads processed: 18
# reads with at least one alignment: 10 (55.56%)
# reads that failed to align: 8 (44.44%)
Reported 10 alignments
[runCrisprBowtie] Searching for AsCas12a protospacers 
# reads processed: 18
# reads with at least one alignment: 13 (72.22%)
# reads that failed to align: 5 (27.78%)
Reported 13 alignments
[runCrisprBowtie] Searching for AsCas12a protospacers 
# reads processed: 18
# reads with at least one alignment: 16 (88.89%)
# reads that failed to align: 2 (11.11%)
Reported 16 alignments
[runCrisprBowtie] Searching for AsCas12a protospacers 
[runCrisprBowtie] Searching for AsCas12a protospacers 
# reads processed: 18
# reads with at least one alignment: 16 (88.89%)
# reads that failed to align: 2 (11.11%)
Reported 16 alignments
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
 13.151   1.131  14.279