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This page was generated on 2023-04-12 11:06:16 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 multicrispr on lconway


To the developers/maintainers of the multicrispr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multicrispr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1298/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multicrispr 1.8.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/multicrispr
git_branch: RELEASE_3_16
git_last_commit: 1f27204
git_last_commit_date: 2022-11-01 11:22:14 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: multicrispr
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multicrispr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multicrispr_1.8.0.tar.gz
StartedAt: 2023-04-10 21:26:31 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:32:19 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 348.4 seconds
RetCode: 0
Status:   OK  
CheckDir: multicrispr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multicrispr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multicrispr_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/multicrispr.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multicrispr/DESCRIPTION’ ... OK
* this is package ‘multicrispr’ version ‘1.8.0’
* 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 ‘multicrispr’ 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
index_genome       15.598  0.240  15.909
find_primespacers  14.762  0.853  15.735
score_ontargets    12.932  0.708  13.698
add_genome_matches  9.956  1.174  11.173
find_spacers       10.187  0.592  10.848
add_target_matches  9.493  0.657  10.217
up_flank            9.738  0.125   9.920
extend_for_pe       7.447  0.512   8.020
plot_intervals      7.380  0.429   7.875
* 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

multicrispr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘multicrispr’ ...
** 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 (multicrispr)

Tests output

multicrispr.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(multicrispr)
> 
> test_check("multicrispr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 12.464   1.199  13.711 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches 9.956 1.17411.173
add_inverse_strand1.6870.0451.736
add_seq2.2620.1692.440
add_target_matches 9.493 0.65710.217
bed_to_granges1.5660.0541.624
char_to_granges0.7150.0160.732
double_flank2.2580.0652.327
extend_for_pe7.4470.5128.020
extend_pe_to_gg0.3530.0030.355
extract_matchranges2.4130.1072.524
extract_subranges0.4580.0020.461
find_gg1.0090.0571.068
find_primespacers14.762 0.85315.735
find_spacers10.187 0.59210.848
genes_to_granges3.9280.1614.102
gr2dt0.1450.0010.147
has_been_indexed000
index_genome15.598 0.24015.909
index_targets1.8940.1702.081
plot_intervals7.3800.4297.875
plot_karyogram1.0400.0461.088
score_ontargets12.932 0.70813.698
up_flank9.7380.1259.920
write_ranges0.1470.0030.151