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This page was generated on 2023-10-02 11:37:32 -0400 (Mon, 02 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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: 2023-10-01 14:00:12 -0400 (Sun, 01 Oct 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 merida1


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: /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_1.10.1.tar.gz
StartedAt: 2023-10-02 04:32:27 -0400 (Mon, 02 Oct 2023)
EndedAt: 2023-10-02 04:48:42 -0400 (Mon, 02 Oct 2023)
EllapsedTime: 975.1 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_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/multicrispr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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
score_ontargets     37.111  1.481  50.276
find_primespacers   36.391  1.730  52.982
index_genome        26.353  0.531  34.207
up_flank            25.085  0.212  32.680
find_spacers        23.707  1.138  33.749
add_genome_matches  20.142  2.247  29.376
add_target_matches  19.270  1.387  27.654
plot_intervals      18.840  0.773  24.573
extend_for_pe       18.319  1.096  26.968
genes_to_granges     6.256  0.298   8.808
add_seq              6.206  0.318   8.495
extract_matchranges  6.150  0.267   9.279
double_flank         5.575  0.064   7.565
index_targets        4.324  0.368   5.779
add_inverse_strand   4.176  0.103   5.633
* 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/4.3-x86_64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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(multicrispr)
> 
> test_check("multicrispr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 26.504   2.433  36.571 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches20.142 2.24729.376
add_inverse_strand4.1760.1035.633
add_seq6.2060.3188.495
add_target_matches19.270 1.38727.654
bed_to_granges1.4370.0611.982
char_to_granges1.9640.0392.696
double_flank5.5750.0647.565
extend_for_pe18.319 1.09626.968
extend_pe_to_gg1.0500.0151.502
extract_matchranges6.1500.2679.279
extract_subranges1.2120.0241.727
find_gg2.3870.1323.557
find_primespacers36.391 1.73052.982
find_spacers23.707 1.13833.749
genes_to_granges6.2560.2988.808
gr2dt0.3790.0060.489
has_been_indexed0.0000.0010.001
index_genome26.353 0.53134.207
index_targets4.3240.3685.779
plot_intervals18.840 0.77324.573
plot_karyogram2.4360.0873.183
score_ontargets37.111 1.48150.276
up_flank25.085 0.21232.680
write_ranges0.3500.0040.427