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This page was generated on 2023-03-20 11:05:56 -0400 (Mon, 20 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4297
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4286
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4150
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 palomino3


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: 2023-03-19 14:00:12 -0400 (Sun, 19 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: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multicrispr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings multicrispr_1.9.0.tar.gz
StartedAt: 2023-03-20 04:06:31 -0400 (Mon, 20 Mar 2023)
EndedAt: 2023-03-20 04:13:18 -0400 (Mon, 20 Mar 2023)
EllapsedTime: 407.1 seconds
RetCode: 0
Status:   OK  
CheckDir: multicrispr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multicrispr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings multicrispr_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/multicrispr.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* 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 '1.9.0'
* 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 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
find_primespacers  16.05   1.67   17.72
score_ontargets    15.37   1.27   16.66
add_genome_matches 10.96   2.08   21.36
find_spacers       10.42   1.23   11.73
up_flank           10.55   0.19   10.73
extend_for_pe       8.05   0.91    9.25
plot_intervals      8.25   0.57    8.85
add_target_matches  6.89   0.80   10.14
index_genome        0.86   0.04   16.78
* 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-3.17-bioc\R\bin\R.exe CMD INSTALL multicrispr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"
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 
  13.40    2.28   35.76 

Example timings

multicrispr.Rcheck/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches10.96 2.0821.36
add_inverse_strand1.790.162.14
add_seq2.280.344.22
add_target_matches 6.89 0.8010.14
bed_to_granges0.560.110.67
char_to_granges0.830.010.85
double_flank2.420.032.45
extend_for_pe8.050.919.25
extend_pe_to_gg0.50.00.5
extract_matchranges2.700.282.98
extract_subranges0.50.00.5
find_gg1.170.131.30
find_primespacers16.05 1.6717.72
find_spacers10.42 1.2311.73
genes_to_granges3.500.144.11
gr2dt0.170.000.17
has_been_indexed000
index_genome 0.86 0.0416.78
index_targets1.700.252.64
plot_intervals8.250.578.85
plot_karyogram1.100.111.20
score_ontargets15.37 1.2716.66
up_flank10.55 0.1910.73
write_ranges0.120.010.14