Multiple platform build/check report for BioC 3.12 - CHECK report for multicrispr on tokay1

Package: multicrispr

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multicrispr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings multicrispr_1.0.0.tar.gz

StartedAt: 2021-05-06 04:55:58 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:07:19 -0400 (Thu, 06 May 2021)

EllapsedTime: 681.0 seconds

RetCode: 0

Status: OK

CheckDir: multicrispr.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multicrispr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings multicrispr_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/multicrispr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.0.0'
* 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
score_ontargets    17.42   0.77   18.19
find_primespacers  17.20   0.72   17.92
add_genome_matches  9.94   2.08   15.05
up_flank           11.70   0.03   11.73
find_spacers       10.95   0.48   11.44
add_target_matches  8.81   0.55   13.61
extend_for_pe       8.75   0.61    9.36
plot_intervals      8.49   0.42    8.91
index_genome        0.64   0.08   23.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
find_primespacers  22.51   0.82   23.33
score_ontargets    21.22   0.67   21.89
add_genome_matches 13.16   1.44   16.19
find_spacers       12.78   0.48   13.28
add_target_matches 11.67   0.42   15.63
up_flank           11.14   0.04   11.19
plot_intervals     10.46   0.40   10.86
extend_for_pe       8.89   0.51    9.41
genes_to_granges    4.88   0.14    5.01
index_genome        0.84   0.08   24.44
* 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://172.29.0.3/BBS/3.12/bioc/src/contrib/multicrispr_1.0.0.tar.gz && rm -rf multicrispr.buildbin-libdir && mkdir multicrispr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multicrispr.buildbin-libdir multicrispr_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL multicrispr_1.0.0.zip && rm multicrispr_1.0.0.tar.gz multicrispr_1.0.0.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
 73 3832k   73 2799k    0     0  17.8M      0 --:--:-- --:--:-- --:--:-- 17.8M
100 3832k  100 3832k    0     0  23.0M      0 --:--:-- --:--:-- --:--:-- 23.1M

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_1.0.0.zip
* DONE (multicrispr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'multicrispr' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
  13.73    2.26   15.98


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
  13.50    1.17   14.65

name	user	system	elapsed
add_genome_matches	9.94	2.08	15.05
add_inverse_strand	2.92	0.06	2.99
add_seq	2.58	0.03	2.61
add_target_matches	8.81	0.55	13.61
bed_to_granges	0.72	0.06	0.78
char_to_granges	1.48	0.02	1.50
double_flank	2.36	0.01	2.38
extend_for_pe	8.75	0.61	9.36
extend_pe_to_gg	0.47	0.00	0.47
extract_matchranges	3.40	0.07	3.47
extract_subranges	0.55	0.00	0.54
find_gg	1.03	0.06	1.10
find_primespacers	17.20	0.72	17.92
find_spacers	10.95	0.48	11.44
genes_to_granges	4.56	0.28	4.85
gr2dt	0.16	0.00	0.15
has_been_indexed	0	0	0
index_genome	0.64	0.08	23.50
index_targets	2.59	0.05	3.47
plot_intervals	8.49	0.42	8.91
plot_karyogram	1.11	0.09	1.20
score_ontargets	17.42	0.77	18.19
up_flank	11.70	0.03	11.73
write_ranges	0.18	0.00	0.19

name	user	system	elapsed
add_genome_matches	13.16	1.44	16.19
add_inverse_strand	2.35	0.08	2.42
add_seq	2.74	0.18	2.92
add_target_matches	11.67	0.42	15.63
bed_to_granges	0.89	0.04	0.92
char_to_granges	0.94	0.00	0.94
double_flank	3.17	0.03	3.20
extend_for_pe	8.89	0.51	9.41
extend_pe_to_gg	0.53	0.00	0.53
extract_matchranges	3.55	0.10	3.62
extract_subranges	0.56	0.00	0.57
find_gg	1.55	0.07	1.62
find_primespacers	22.51	0.82	23.33
find_spacers	12.78	0.48	13.28
genes_to_granges	4.88	0.14	5.01
gr2dt	0.19	0.00	0.19
has_been_indexed	0	0	0
index_genome	0.84	0.08	24.44
index_targets	2.56	0.06	3.46
plot_intervals	10.46	0.40	10.86
plot_karyogram	1.68	0.02	1.71
score_ontargets	21.22	0.67	21.89
up_flank	11.14	0.04	11.19
write_ranges	0.21	0.00	0.20

CHECK report for multicrispr on tokay1

Summary

Command output

Installation output

Tests output

Example timings