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This page was generated on 2024-02-28 11:36:11 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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

Package 1358/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multicrispr 1.12.3  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-02-27 14:05:07 -0500 (Tue, 27 Feb 2024)
git_url: https://git.bioconductor.org/packages/multicrispr
git_branch: RELEASE_3_18
git_last_commit: fdead8c
git_last_commit_date: 2023-11-13 04:55:16 -0500 (Mon, 13 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for multicrispr on nebbiolo2


To the developers/maintainers of the multicrispr package:
- 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 Troubleshooting Build Report for more information.
- 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: multicrispr
Version: 1.12.3
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:multicrispr.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings multicrispr_1.12.3.tar.gz
StartedAt: 2024-02-28 00:22:49 -0500 (Wed, 28 Feb 2024)
EndedAt: 2024-02-28 00:30:07 -0500 (Wed, 28 Feb 2024)
EllapsedTime: 438.5 seconds
RetCode: 0
Status:   OK  
CheckDir: multicrispr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:multicrispr.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings multicrispr_1.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/multicrispr.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘multicrispr/DESCRIPTION’ ... OK
* this is package ‘multicrispr’ version ‘1.12.3’
* 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 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 ... 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       16.261  0.264  16.525
score_ontargets    14.995  0.704  15.613
find_primespacers  14.447  1.059  15.619
up_flank            9.905  0.653  10.414
find_spacers        9.340  0.716  10.112
add_target_matches  8.970  0.643   9.256
add_genome_matches  8.816  0.544   9.328
plot_intervals      7.454  0.270   7.732
extend_for_pe       7.003  0.314   7.354
* 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 ...
  ‘crispr_grna_design.Rmd’ using ‘UTF-8’... OK
  ‘genome_arithmetics.Rmd’ using ‘UTF-8’... OK
  ‘prime_editing.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

multicrispr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL multicrispr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 11.876   0.687  12.551 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches8.8160.5449.328
add_inverse_strand1.8060.0601.859
add_seq2.0340.1162.150
add_target_matches8.9700.6439.256
bed_to_granges0.5930.0230.617
char_to_granges0.7240.0280.746
double_flank2.0160.0522.052
extend_for_pe7.0030.3147.354
extend_pe_to_gg0.4680.0520.505
extract_matchranges2.5800.2322.774
extract_subranges0.5070.0440.545
find_gg0.9280.0670.990
find_primespacers14.447 1.05915.619
find_spacers 9.340 0.71610.112
genes_to_granges3.1230.1283.251
gr2dt0.1740.0000.173
has_been_indexed000
index_genome16.261 0.26416.525
index_targets1.9080.2142.120
plot_intervals7.4540.2707.732
plot_karyogram1.0320.0161.049
score_ontargets14.995 0.70415.613
up_flank 9.905 0.65310.414
write_ranges0.1590.0000.159