Multiple platform build/check report for BioC 3.11 - CHECK report for snapcount on tokay2

Package: snapcount

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapcount.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings snapcount_1.0.0.tar.gz

StartedAt: 2020-10-17 08:27:58 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 08:37:20 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 561.7 seconds

RetCode: 0

Status: OK

CheckDir: snapcount.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapcount.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings snapcount_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/snapcount.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snapcount/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'snapcount' 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 'snapcount' 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
junction_intersection 9.77   1.47   13.84
junction_union        2.80   0.56    5.33
Compilation           2.88   0.28    6.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
junction_intersection 10.13   0.50   14.82
Compilation            3.30   0.14    6.22
junction_union         3.06   0.03    5.20
* 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 https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/snapcount_1.0.0.tar.gz && rm -rf snapcount.buildbin-libdir && mkdir snapcount.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapcount.buildbin-libdir snapcount_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL snapcount_1.0.0.zip && rm snapcount_1.0.0.tar.gz snapcount_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
100  265k  100  265k    0     0  4669k      0 --:--:-- --:--:-- --:--:-- 5301k

install for i386

* installing *source* package 'snapcount' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'snapcount'
    finding HTML links ... done
    Compilation                             html  
    Coordinates                             html  
    QueryBuilder                            html  
    from_url                                html  
    get_JunctionSeq_params                  html  
    get_column_filters                      html  
    get_compilation                         html  
    get_coordinate_modifier                 html  
    get_regions                             html  
    get_row_filters                         html  
    get_sids                                html  
    junction_inclusion_ratio                html  
    junction_intersection                   html  
    junction_union                          html  
    percent_spliced_in                      html  
    query_jx                                html  
    shared_sample_counts                    html  
    snapcount-package                       html  
    tissue_specificity                      html  
    uri_of_last_successful_request          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 'snapcount' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snapcount' as snapcount_1.0.0.zip
* DONE (snapcount)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'snapcount' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(snapcount)
> 
> test_check("snapcount")
Read 2 items
== testthat results  ===========================================================
[ OK: 84 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.82    1.42   86.34


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(snapcount)
> 
> test_check("snapcount")
Read 2 items
== testthat results  ===========================================================
[ OK: 84 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.51    0.84   89.40

name	user	system	elapsed
Compilation	2.88	0.28	6.14
Coordinates	0.01	0.00	0.02
QueryBuilder	0.14	0.03	0.18
from_url	0.02	0.00	1.54
get_JunctionSeq_params	0	0	0
get_column_filters	0.22	0.07	0.28
get_compilation	0	0	0
get_coordinate_modifier	0.02	0.00	0.02
get_regions	0.1	0.0	0.1
get_row_filters	0	0	0
get_sids	0	0	0
junction_inclusion_ratio	0.25	0.04	2.75
junction_intersection	9.77	1.47	13.84
junction_union	2.80	0.56	5.33
percent_spliced_in	0.08	0.00	3.54
query_jx	1.03	0.04	3.36
shared_sample_counts	0.15	0.00	2.05
tissue_specificity	0.07	0.01	1.92
uri_of_last_successful_request	1.31	0.38	3.32

name	user	system	elapsed
Compilation	3.30	0.14	6.22
Coordinates	0.03	0.00	0.03
QueryBuilder	0.12	0.01	0.14
from_url	0.02	0.00	1.50
get_JunctionSeq_params	0	0	0
get_column_filters	0.22	0.05	0.26
get_compilation	0	0	0
get_coordinate_modifier	0	0	0
get_regions	0.10	0.00	0.09
get_row_filters	0	0	0
get_sids	0	0	0
junction_inclusion_ratio	0.20	0.00	2.78
junction_intersection	10.13	0.50	14.82
junction_union	3.06	0.03	5.20
percent_spliced_in	0.06	0.00	3.52
query_jx	0.94	0.00	3.24
shared_sample_counts	0.12	0.00	2.07
tissue_specificity	0.10	0.00	1.75
uri_of_last_successful_request	1.47	0.03	3.11

CHECK report for snapcount on tokay2

Summary

Command output

Installation output

Tests output

Example timings