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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 450/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprBowtie 1.4.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/crisprBowtie
git_branch: RELEASE_3_17
git_last_commit: 64a92ed
git_last_commit_date: 2023-04-25 11:36:03 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for crisprBowtie on kjohnson2


To the developers/maintainers of the crisprBowtie package:
- 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.

raw results


Summary

Package: crisprBowtie
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crisprBowtie.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crisprBowtie_1.4.0.tar.gz
StartedAt: 2023-10-17 12:38:57 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 12:45:23 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 385.6 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprBowtie.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crisprBowtie.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crisprBowtie_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/crisprBowtie.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprBowtie/DESCRIPTION’ ... OK
* this is package ‘crisprBowtie’ version ‘1.4.0’
* 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 ‘crisprBowtie’ 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 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 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: OK


Installation output

crisprBowtie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crisprBowtie
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘crisprBowtie’ ...
** 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)

Tests output

crisprBowtie.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(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 
 13.622   0.932  22.546 

Example timings

crisprBowtie.Rcheck/crisprBowtie-Ex.timings

nameusersystemelapsed
runBowtie0.3470.0990.886
runCrisprBowtie0.2060.0650.446