Multiple platform build/check report for BioC 3.14 - CHECK results for multicrispr on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: multicrispr

Version: 1.4.3

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_1.4.3.tar.gz

StartedAt: 2022-04-12 23:26:21 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:37:43 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 682.2 seconds

RetCode: 0

Status: OK

CheckDir: multicrispr.Rcheck

Warnings: 0

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### 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_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/multicrispr.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.4.3'
* 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
* 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  18.67   0.69   19.36
score_ontargets    17.76   0.75   18.50
find_spacers       11.66   0.50   12.16
add_genome_matches  9.58   2.11   11.73
up_flank           10.86   0.09   10.95
extend_for_pe       9.92   0.59   10.58
plot_intervals      9.60   0.41   10.01
add_target_matches  8.88   0.73   13.56
index_genome        1.25   0.13   21.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
score_ontargets    19.39   0.91   20.30
find_primespacers  19.06   0.91   19.97
find_spacers       12.94   0.56   13.50
add_genome_matches 11.76   1.41   13.15
up_flank           11.44   0.05   11.49
plot_intervals     10.80   0.24   11.05
extend_for_pe      10.00   0.50   10.50
add_target_matches  8.88   0.50   13.33
index_genome        0.89   0.01   17.42
* 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://155.52.207.166/BBS/3.14/bioc/src/contrib/multicrispr_1.4.3.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_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL multicrispr_1.4.3.zip && rm multicrispr_1.4.3.tar.gz multicrispr_1.4.3.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
 11 3842k   11  450k    0     0   694k      0  0:00:05 --:--:--  0:00:05  694k
 36 3842k   36 1393k    0     0   845k      0  0:00:04  0:00:01  0:00:03  845k
 67 3842k   67 2579k    0     0   967k      0  0:00:03  0:00:02  0:00:01  966k
100 3842k  100 3842k    0     0  1080k      0  0:00:03  0:00:03 --:--:-- 1080k

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_1.4.3.zip
* DONE (multicrispr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'multicrispr' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  12.87    2.39   15.26


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  14.15    1.45   22.09

name	user	system	elapsed
add_genome_matches	9.58	2.11	11.73
add_inverse_strand	1.71	0.06	1.79
add_seq	4.02	0.19	4.20
add_target_matches	8.88	0.73	13.56
bed_to_granges	0.81	0.05	0.86
char_to_granges	1.03	0.02	1.05
double_flank	2.80	0.01	2.81
extend_for_pe	9.92	0.59	10.58
extend_pe_to_gg	0.57	0.00	0.57
extract_matchranges	3.01	0.11	3.14
extract_subranges	0.81	0.00	0.81
find_gg	2.18	0.05	2.22
find_primespacers	18.67	0.69	19.36
find_spacers	11.66	0.50	12.16
genes_to_granges	3.63	0.30	3.92
gr2dt	0.21	0.00	0.22
has_been_indexed	0	0	0
index_genome	1.25	0.13	21.31
index_targets	2.04	0.15	2.86
plot_intervals	9.60	0.41	10.01
plot_karyogram	1.46	0.03	1.49
score_ontargets	17.76	0.75	18.50
up_flank	10.86	0.09	10.95
write_ranges	0.26	0.00	0.26

name	user	system	elapsed
add_genome_matches	11.76	1.41	13.15
add_inverse_strand	2.13	0.06	2.19
add_seq	3.97	0.17	4.14
add_target_matches	8.88	0.50	13.33
bed_to_granges	0.81	0.03	0.84
char_to_granges	1.11	0.00	1.16
double_flank	3.86	0.05	3.90
extend_for_pe	10.0	0.5	10.5
extend_pe_to_gg	0.61	0.00	0.61
extract_matchranges	3.04	0.06	3.11
extract_subranges	0.66	0.00	0.66
find_gg	1.41	0.03	1.43
find_primespacers	19.06	0.91	19.97
find_spacers	12.94	0.56	13.50
genes_to_granges	4.75	0.18	4.92
gr2dt	0.27	0.00	0.27
has_been_indexed	0	0	0
index_genome	0.89	0.01	17.42
index_targets	2.42	0.17	3.56
plot_intervals	10.80	0.24	11.05
plot_karyogram	1.40	0.01	1.42
score_ontargets	19.39	0.91	20.30
up_flank	11.44	0.05	11.49
write_ranges	0.23	0.00	0.23

CHECK results for multicrispr on tokay2

Summary

Command output

Installation output

Tests output

Example timings