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This page was generated on 2023-03-22 11:06:52 -0400 (Wed, 22 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4508
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4293
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4290
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 merida1


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 1307/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multicrispr 1.9.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2023-03-21 14:00:22 -0400 (Tue, 21 Mar 2023)
git_url: https://git.bioconductor.org/packages/multicrispr
git_branch: master
git_last_commit: d19c1d3
git_last_commit_date: 2022-11-01 11:22:14 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'CRISPRseek' which is not available

Summary

Package: multicrispr
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2023-03-22 04:11:54 -0400 (Wed, 22 Mar 2023)
EndedAt: 2023-03-22 04:28:11 -0400 (Wed, 22 Mar 2023)
EllapsedTime: 976.9 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/multicrispr.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multicrispr/DESCRIPTION’ ... OK
* this is package ‘multicrispr’ version ‘1.9.0’
* 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
score_ontargets     36.715  0.943  49.265
find_primespacers   34.919  0.959  48.029
index_genome        27.783  0.597  37.242
up_flank            25.136  0.150  33.255
find_spacers        22.928  0.635  31.089
add_genome_matches  20.773  1.417  31.739
add_target_matches  19.477  1.166  28.292
plot_intervals      18.525  0.479  24.893
extend_for_pe       17.418  0.591  24.726
genes_to_granges     6.425  0.196   8.687
extract_matchranges  5.872  0.138   8.183
double_flank         5.403  0.059   7.606
add_seq              4.845  0.191   6.849
index_targets        4.243  0.501   5.917
add_inverse_strand   3.979  0.087   5.548
* 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/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
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 
 25.819   1.629  36.773 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches20.773 1.41731.739
add_inverse_strand3.9790.0875.548
add_seq4.8450.1916.849
add_target_matches19.477 1.16628.292
bed_to_granges1.3560.0361.945
char_to_granges1.8660.0142.695
double_flank5.4030.0597.606
extend_for_pe17.418 0.59124.726
extend_pe_to_gg1.0190.0041.368
extract_matchranges5.8720.1388.183
extract_subranges1.1850.0041.634
find_gg2.2760.0613.120
find_primespacers34.919 0.95948.029
find_spacers22.928 0.63531.089
genes_to_granges6.4250.1968.687
gr2dt0.3590.0010.477
has_been_indexed0.0000.0010.004
index_genome27.783 0.59737.242
index_targets4.2430.5015.917
plot_intervals18.525 0.47924.893
plot_karyogram2.4980.0583.340
score_ontargets36.715 0.94349.265
up_flank25.136 0.15033.255
write_ranges0.3320.0020.436