Multiple platform build/check report for BioC 3.13 - CHECK results for multicrispr on tokay2

Package: multicrispr

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multicrispr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings multicrispr_1.2.0.tar.gz

StartedAt: 2021-10-15 02:26:57 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:38:11 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 674.9 seconds

RetCode: 0

Status: OK

CheckDir: multicrispr.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multicrispr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings multicrispr_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/multicrispr.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.2.0'
* 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  19.48   1.09   20.58
score_ontargets    17.83   0.70   18.54
add_genome_matches  9.56   1.90   11.50
find_spacers       10.31   0.44   10.75
extend_for_pe       9.28   0.67    9.95
up_flank            9.74   0.06    9.80
plot_intervals      9.07   0.38    9.44
add_target_matches  6.72   0.61   11.81
index_genome        1.32   0.09   16.90
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
find_primespacers  20.44   0.77   21.20
score_ontargets    17.37   0.68   18.06
find_spacers       12.83   0.45   13.30
add_genome_matches 10.91   1.24   12.14
up_flank           11.52   0.05   11.57
add_target_matches  9.86   0.51   72.08
extend_for_pe       9.44   0.53    9.97
plot_intervals      8.89   0.32    9.22
index_genome        0.71   0.03   16.92
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/multicrispr_1.2.0.tar.gz && rm -rf multicrispr.buildbin-libdir && mkdir multicrispr.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multicrispr.buildbin-libdir multicrispr_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL multicrispr_1.2.0.zip && rm multicrispr_1.2.0.tar.gz multicrispr_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 44 3817k   44 1696k    0     0  2677k      0  0:00:01 --:--:--  0:00:01 2675k
100 3817k  100 3817k    0     0  3393k      0  0:00:01  0:00:01 --:--:-- 3396k

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_1.2.0.zip
* DONE (multicrispr)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'multicrispr' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  15.40    2.79   18.23


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  13.09    1.21   14.45

name	user	system	elapsed
add_genome_matches	9.56	1.90	11.50
add_inverse_strand	1.74	0.08	1.82
add_seq	3.12	0.30	3.42
add_target_matches	6.72	0.61	11.81
bed_to_granges	0.75	0.03	0.78
char_to_granges	0.74	0.01	0.75
double_flank	2.64	0.02	2.65
extend_for_pe	9.28	0.67	9.95
extend_pe_to_gg	0.54	0.00	0.55
extract_matchranges	2.83	0.11	2.94
extract_subranges	0.64	0.00	0.64
find_gg	1.17	0.05	1.22
find_primespacers	19.48	1.09	20.58
find_spacers	10.31	0.44	10.75
genes_to_granges	3.24	0.22	3.45
gr2dt	0.18	0.00	0.19
has_been_indexed	0	0	0
index_genome	1.32	0.09	16.90
index_targets	2.07	0.08	3.08
plot_intervals	9.07	0.38	9.44
plot_karyogram	1.17	0.03	1.21
score_ontargets	17.83	0.70	18.54
up_flank	9.74	0.06	9.80
write_ranges	0.19	0.02	0.20

name	user	system	elapsed
add_genome_matches	10.91	1.24	12.14
add_inverse_strand	1.91	0.03	1.93
add_seq	2.53	0.05	2.58
add_target_matches	9.86	0.51	72.08
bed_to_granges	1.01	0.05	1.06
char_to_granges	0.91	0.02	0.93
double_flank	2.70	0.04	2.75
extend_for_pe	9.44	0.53	9.97
extend_pe_to_gg	0.62	0.00	0.62
extract_matchranges	3.43	0.10	3.52
extract_subranges	0.82	0.00	0.82
find_gg	1.36	0.01	1.38
find_primespacers	20.44	0.77	21.20
find_spacers	12.83	0.45	13.30
genes_to_granges	3.70	0.08	3.79
gr2dt	0.23	0.00	0.23
has_been_indexed	0	0	0
index_genome	0.71	0.03	16.92
index_targets	2.28	0.27	3.97
plot_intervals	8.89	0.32	9.22
plot_karyogram	1.27	0.04	1.29
score_ontargets	17.37	0.68	18.06
up_flank	11.52	0.05	11.57
write_ranges	0.2	0.0	0.2

CHECK results for multicrispr on tokay2

Summary

Command output

Installation output

Tests output

Example timings