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This page was generated on 2023-09-25 11:35:42 -0400 (Mon, 25 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 1329/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multicrispr 1.10.1  (landing page)
Aditya Bhagwat
Snapshot Date: 2023-09-24 14:00:11 -0400 (Sun, 24 Sep 2023)
git_url: https://git.bioconductor.org/packages/multicrispr
git_branch: RELEASE_3_17
git_last_commit: 192e6ab
git_last_commit_date: 2023-05-17 05:44:54 -0400 (Wed, 17 May 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for multicrispr on nebbiolo1


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: 1.10.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:multicrispr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings multicrispr_1.10.1.tar.gz
StartedAt: 2023-09-24 23:12:24 -0400 (Sun, 24 Sep 2023)
EndedAt: 2023-09-24 23:19:34 -0400 (Sun, 24 Sep 2023)
EllapsedTime: 429.8 seconds
RetCode: 0
Status:   OK  
CheckDir: multicrispr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:multicrispr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings multicrispr_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/multicrispr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘multicrispr/DESCRIPTION’ ... OK
* this is package ‘multicrispr’ version ‘1.10.1’
* 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
find_primespacers  15.225  1.767  17.130
score_ontargets    15.390  1.276  16.629
index_genome       16.291  0.240  16.529
find_spacers       10.334  1.606  12.010
up_flank           10.526  0.192  10.678
add_genome_matches  8.215  0.832   9.012
plot_intervals      8.162  0.728   8.913
add_target_matches  7.864  0.846   8.210
extend_for_pe       7.428  0.631   8.111
* 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

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL multicrispr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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 
 11.769   0.641  12.400 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches8.2150.8329.012
add_inverse_strand2.6240.1402.765
add_seq2.0230.1882.210
add_target_matches7.8640.8468.210
bed_to_granges1.6090.1801.790
char_to_granges0.7750.0000.775
double_flank2.3110.0682.369
extend_for_pe7.4280.6318.111
extend_pe_to_gg0.4780.0320.510
extract_matchranges2.6350.2922.894
extract_subranges0.5290.0480.577
find_gg1.0390.1001.139
find_primespacers15.225 1.76717.130
find_spacers10.334 1.60612.010
genes_to_granges2.9760.3043.280
gr2dt0.1540.0040.159
has_been_indexed000
index_genome16.291 0.24016.529
index_targets1.9830.3042.285
plot_intervals8.1620.7288.913
plot_karyogram1.0680.0441.112
score_ontargets15.390 1.27616.629
up_flank10.526 0.19210.678
write_ranges0.1400.0080.148