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This page was generated on 2024-03-28 11:39:39 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1357/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multicrispr 1.13.12  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/multicrispr
git_branch: devel
git_last_commit: 5aadbd3
git_last_commit_date: 2024-03-27 05:52:56 -0400 (Wed, 27 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for multicrispr on lconway


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: 1.13.12
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_1.13.12.tar.gz
StartedAt: 2024-03-27 22:41:05 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 22:48:50 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 464.9 seconds
RetCode: 0
Status:   OK  
CheckDir: multicrispr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.13.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/multicrispr.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multicrispr/DESCRIPTION’ ... OK
* this is package ‘multicrispr’ version ‘1.13.12’
* 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 code 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       21.332  0.439  21.982
score_ontargets    18.322  1.114  19.656
find_primespacers  18.035  1.132  19.401
add_genome_matches 12.450  1.779  14.601
find_spacers       12.726  0.802  13.688
add_target_matches 12.489  0.900  13.670
up_flank           11.924  0.210  12.231
extend_for_pe       9.444  0.706  10.260
plot_intervals      9.492  0.564  10.189
genes_to_granges    4.968  0.180   5.213
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 17.409   1.737  19.295 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches12.450 1.77914.601
add_inverse_strand2.5490.0842.655
add_seq3.0140.2563.308
add_target_matches12.489 0.90013.670
bed_to_granges2.0660.0822.159
char_to_granges0.8950.0190.920
double_flank2.7230.0592.796
extend_for_pe 9.444 0.70610.260
extend_pe_to_gg0.5700.0090.584
extract_matchranges3.2950.1673.491
extract_subranges0.5890.0070.600
find_gg1.1650.0731.250
find_primespacers18.035 1.13219.401
find_spacers12.726 0.80213.688
genes_to_granges4.9680.1805.213
gr2dt0.1910.0040.195
has_been_indexed000
index_genome21.332 0.43921.982
index_targets2.5730.2502.885
plot_intervals 9.492 0.56410.189
plot_karyogram1.4400.0851.547
score_ontargets18.322 1.11419.656
up_flank11.924 0.21012.231
write_ranges0.1890.0030.193