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###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings crisprDesign_1.1.24.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/crisprDesign.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'crisprDesign/DESCRIPTION' ... OK
* this is package 'crisprDesign' version '1.1.24'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'crisprBwa', 'Rbwa'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'crisprDesign' can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
addSNPAnnotation 11.36   0.20   11.56
addEditedAlleles 10.20   0.26   10.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/crisprDesign.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL crisprDesign
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'crisprDesign' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (crisprDesign)

R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

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

> library(testthat)
> library(crisprDesign)
Loading required package: crisprBase
> 
> test_check("crisprDesign")
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 7
# reads with at least one alignment: 6 (85.71%)
# reads that failed to align: 1 (14.29%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 7
# reads with at least one alignment: 6 (85.71%)
# reads that failed to align: 1 (14.29%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
Failed with error:  'there is no package called 'crisprBwa''
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1018 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (69)
• long run time (8)
• no del for guideSetExample (1)

[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1018 ]
> 
> proc.time()
   user  system elapsed 
 180.37    5.40  193.59