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This page was generated on 2024-02-27 11:36:53 -0500 (Tue, 27 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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: 2024-02-26 14:53:20 -0500 (Mon, 26 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 palomino4


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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multicrispr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings multicrispr_1.12.3.tar.gz
StartedAt: 2024-02-27 06:22:45 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 06:30:05 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 440.1 seconds
RetCode: 0
Status:   OK  
CheckDir: multicrispr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multicrispr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings multicrispr_1.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/multicrispr.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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    15.40   1.42   17.02
find_primespacers  14.94   1.28   16.22
add_genome_matches 12.46   2.63   49.34
find_spacers       12.53   2.50   15.12
up_flank           10.70   1.39   12.25
plot_intervals      8.81   1.82   10.66
extend_for_pe       7.17   0.92    8.50
add_target_matches  6.87   0.72   22.42
index_targets       3.64   1.69    6.10
index_genome        0.91   0.08   15.25
* 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:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL multicrispr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  14.76    1.95   16.67 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches12.46 2.6349.34
add_inverse_strand1.860.062.08
add_seq2.500.484.55
add_target_matches 6.87 0.7222.42
bed_to_granges0.810.131.04
char_to_granges0.750.030.78
double_flank2.290.032.31
extend_for_pe7.170.928.50
extend_pe_to_gg0.450.000.46
extract_matchranges2.770.243.12
extract_subranges0.470.010.48
find_gg0.850.110.97
find_primespacers14.94 1.2816.22
find_spacers12.53 2.5015.12
genes_to_granges2.590.193.14
gr2dt0.170.000.18
has_been_indexed000
index_genome 0.91 0.0815.25
index_targets3.641.696.10
plot_intervals 8.81 1.8210.66
plot_karyogram1.190.191.58
score_ontargets15.40 1.4217.02
up_flank10.70 1.3912.25
write_ranges0.190.000.20