Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-03-18 11:07:17 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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

CHECK results for crisprBowtie on riesling1


To the developers/maintainers of the crisprBowtie package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crisprBowtie.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 420/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprBowtie 0.99.4  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/crisprBowtie
git_branch: master
git_last_commit: f8a0f33
git_last_commit_date: 2022-03-08 21:49:06 -0400 (Tue, 08 Mar 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package requires version >= 0.99.15 of 'crisprBase' but only version 0.99.8 is available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: crisprBowtie
Version: 0.99.4
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprBowtie.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings crisprBowtie_0.99.4.tar.gz
StartedAt: 2022-03-17 18:49:59 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 18:53:17 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 197.2 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprBowtie.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprBowtie.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings crisprBowtie_0.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/crisprBowtie.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'crisprBowtie/DESCRIPTION' ... OK
* this is package 'crisprBowtie' version '0.99.4'
* 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 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:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL crisprBowtie
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'crisprBowtie' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'crisprBowtie'
    finding HTML links ... done
    runBowtie                               html  
    runCrisprBowtie                         html  
    finding level-2 HTML links ... done

** 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)
Making 'packages.html' ... done

Tests output

crisprBowtie.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(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 
  10.87    1.34   15.62 

Example timings

crisprBowtie.Rcheck/crisprBowtie-Ex.timings

nameusersystemelapsed
runBowtie0.850.041.58
runCrisprBowtie0.100.070.84