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This page was generated on 2021-11-26 15:05:26 -0500 (Fri, 26 Nov 2021).

CHECK results for multicrispr on tokay2

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? here for more information.
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raw results

Package 1241/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multicrispr 1.4.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/multicrispr
git_branch: RELEASE_3_14
git_last_commit: 8406aec
git_last_commit_date: 2021-10-26 13:00:15 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: multicrispr
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multicrispr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings multicrispr_1.4.0.tar.gz
StartedAt: 2021-11-26 02:02:41 -0500 (Fri, 26 Nov 2021)
EndedAt: 2021-11-26 02:13:34 -0500 (Fri, 26 Nov 2021)
EllapsedTime: 652.8 seconds
RetCode: 0
Status:   OK  
CheckDir: multicrispr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multicrispr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings multicrispr_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/multicrispr.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'multicrispr/DESCRIPTION' ... OK
* this is package 'multicrispr' version '1.4.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
find_primespacers  17.89   0.62   18.51
score_ontargets    17.00   0.58   17.58
add_genome_matches 10.24   2.33   12.64
find_spacers       11.09   0.52   11.61
up_flank           11.26   0.06   11.33
extend_for_pe      10.34   0.58   10.97
plot_intervals      9.41   0.53    9.93
add_target_matches  7.67   0.71   12.01
index_genome        1.00   0.08   18.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
find_primespacers  21.36   0.76   22.12
score_ontargets    18.24   0.91   19.14
find_spacers       12.55   0.58   13.14
up_flank           12.67   0.03   12.70
add_genome_matches 11.19   1.33   12.55
extend_for_pe      10.11   0.56   10.67
add_target_matches 10.03   0.50   13.68
plot_intervals      9.67   0.42   10.09
index_genome        0.66   0.05   15.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/multicrispr_1.4.0.tar.gz && rm -rf multicrispr.buildbin-libdir && mkdir multicrispr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multicrispr.buildbin-libdir multicrispr_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL multicrispr_1.4.0.zip && rm multicrispr_1.4.0.tar.gz multicrispr_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7 3842k    7  304k    0     0  1028k      0  0:00:03 --:--:--  0:00:03 1028k
100 3842k  100 3842k    0     0  3971k      0 --:--:-- --:--:-- --:--:-- 3973k

install for i386

* installing *source* package 'multicrispr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'multicrispr'
    finding HTML links ... done
    add_genome_matches                      html  
    add_inverse_strand                      html  
    add_seq                                 html  
    add_target_matches                      html  
    bed_to_granges                          html  
    char_to_granges                         html  
    double_flank                            html  
    extend_for_pe                           html  
    extend_pe_to_gg                         html  
    extract_matchranges                     html  
    finding level-2 HTML links ... done

    extract_subranges                       html  
    find_gg                                 html  
    find_primespacers                       html  
    find_spacers                            html  
    genes_to_granges                        html  
    gr2dt                                   html  
    has_been_indexed                        html  
    index_genome                            html  
    index_targets                           html  
    plot_intervals                          html  
    plot_karyogram                          html  
    score_ontargets                         html  
    up_flank                                html  
    write_ranges                            html  
** 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

install for x64

* installing *source* package 'multicrispr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multicrispr' as multicrispr_1.4.0.zip
* DONE (multicrispr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'multicrispr' successfully unpacked and MD5 sums checked

Tests output

multicrispr.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  12.54    2.06   14.57 

multicrispr.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 
  14.92    1.32   16.62 

Example timings

multicrispr.Rcheck/examples_i386/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches10.24 2.3312.64
add_inverse_strand1.720.031.75
add_seq3.370.183.56
add_target_matches 7.67 0.7112.01
bed_to_granges0.830.060.89
char_to_granges0.860.020.88
double_flank2.690.012.70
extend_for_pe10.34 0.5810.97
extend_pe_to_gg0.620.000.62
extract_matchranges3.040.123.16
extract_subranges0.560.040.60
find_gg2.100.092.19
find_primespacers17.89 0.6218.51
find_spacers11.09 0.5211.61
genes_to_granges3.740.223.95
gr2dt0.260.000.27
has_been_indexed000
index_genome 1.00 0.0818.73
index_targets2.140.113.21
plot_intervals9.410.539.93
plot_karyogram1.350.011.36
score_ontargets17.00 0.5817.58
up_flank11.26 0.0611.33
write_ranges0.240.000.23

multicrispr.Rcheck/examples_x64/multicrispr-Ex.timings

nameusersystemelapsed
add_genome_matches11.19 1.3312.55
add_inverse_strand2.170.042.22
add_seq2.450.282.74
add_target_matches10.03 0.5013.68
bed_to_granges1.100.021.11
char_to_granges0.930.000.94
double_flank2.750.012.76
extend_for_pe10.11 0.5610.67
extend_pe_to_gg0.590.000.59
extract_matchranges3.610.223.83
extract_subranges0.850.000.84
find_gg1.480.051.54
find_primespacers21.36 0.7622.12
find_spacers12.55 0.5813.14
genes_to_granges3.590.143.74
gr2dt0.230.000.23
has_been_indexed000
index_genome 0.66 0.0515.81
index_targets2.220.163.05
plot_intervals 9.67 0.4210.09
plot_karyogram1.490.011.50
score_ontargets18.24 0.9119.14
up_flank12.67 0.0312.70
write_ranges0.220.000.22